Annotation of imach/src/imach.c, revision 1.230
1.230 ! brouard 1: /* $Id: imach.c,v 1.229 2016/07/23 09:45:53 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.230 ! brouard 4: Revision 1.229 2016/07/23 09:45:53 brouard
! 5: Summary: Completing for func too
! 6:
1.229 brouard 7: Revision 1.228 2016/07/22 17:45:30 brouard
8: Summary: Fixing some arrays, still debugging
9:
1.227 brouard 10: Revision 1.226 2016/07/12 18:42:34 brouard
11: Summary: temp
12:
1.226 brouard 13: Revision 1.225 2016/07/12 08:40:03 brouard
14: Summary: saving but not running
15:
1.225 brouard 16: Revision 1.224 2016/07/01 13:16:01 brouard
17: Summary: Fixes
18:
1.224 brouard 19: Revision 1.223 2016/02/19 09:23:35 brouard
20: Summary: temporary
21:
1.223 brouard 22: Revision 1.222 2016/02/17 08:14:50 brouard
23: Summary: Probably last 0.98 stable version 0.98r6
24:
1.222 brouard 25: Revision 1.221 2016/02/15 23:35:36 brouard
26: Summary: minor bug
27:
1.220 brouard 28: Revision 1.219 2016/02/15 00:48:12 brouard
29: *** empty log message ***
30:
1.219 brouard 31: Revision 1.218 2016/02/12 11:29:23 brouard
32: Summary: 0.99 Back projections
33:
1.218 brouard 34: Revision 1.217 2015/12/23 17:18:31 brouard
35: Summary: Experimental backcast
36:
1.217 brouard 37: Revision 1.216 2015/12/18 17:32:11 brouard
38: Summary: 0.98r4 Warning and status=-2
39:
40: Version 0.98r4 is now:
41: - displaying an error when status is -1, date of interview unknown and date of death known;
42: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
43: Older changes concerning s=-2, dating from 2005 have been supersed.
44:
1.216 brouard 45: Revision 1.215 2015/12/16 08:52:24 brouard
46: Summary: 0.98r4 working
47:
1.215 brouard 48: Revision 1.214 2015/12/16 06:57:54 brouard
49: Summary: temporary not working
50:
1.214 brouard 51: Revision 1.213 2015/12/11 18:22:17 brouard
52: Summary: 0.98r4
53:
1.213 brouard 54: Revision 1.212 2015/11/21 12:47:24 brouard
55: Summary: minor typo
56:
1.212 brouard 57: Revision 1.211 2015/11/21 12:41:11 brouard
58: Summary: 0.98r3 with some graph of projected cross-sectional
59:
60: Author: Nicolas Brouard
61:
1.211 brouard 62: Revision 1.210 2015/11/18 17:41:20 brouard
63: Summary: Start working on projected prevalences
64:
1.210 brouard 65: Revision 1.209 2015/11/17 22:12:03 brouard
66: Summary: Adding ftolpl parameter
67: Author: N Brouard
68:
69: We had difficulties to get smoothed confidence intervals. It was due
70: to the period prevalence which wasn't computed accurately. The inner
71: parameter ftolpl is now an outer parameter of the .imach parameter
72: file after estepm. If ftolpl is small 1.e-4 and estepm too,
73: computation are long.
74:
1.209 brouard 75: Revision 1.208 2015/11/17 14:31:57 brouard
76: Summary: temporary
77:
1.208 brouard 78: Revision 1.207 2015/10/27 17:36:57 brouard
79: *** empty log message ***
80:
1.207 brouard 81: Revision 1.206 2015/10/24 07:14:11 brouard
82: *** empty log message ***
83:
1.206 brouard 84: Revision 1.205 2015/10/23 15:50:53 brouard
85: Summary: 0.98r3 some clarification for graphs on likelihood contributions
86:
1.205 brouard 87: Revision 1.204 2015/10/01 16:20:26 brouard
88: Summary: Some new graphs of contribution to likelihood
89:
1.204 brouard 90: Revision 1.203 2015/09/30 17:45:14 brouard
91: Summary: looking at better estimation of the hessian
92:
93: Also a better criteria for convergence to the period prevalence And
94: therefore adding the number of years needed to converge. (The
95: prevalence in any alive state shold sum to one
96:
1.203 brouard 97: Revision 1.202 2015/09/22 19:45:16 brouard
98: Summary: Adding some overall graph on contribution to likelihood. Might change
99:
1.202 brouard 100: Revision 1.201 2015/09/15 17:34:58 brouard
101: Summary: 0.98r0
102:
103: - Some new graphs like suvival functions
104: - Some bugs fixed like model=1+age+V2.
105:
1.201 brouard 106: Revision 1.200 2015/09/09 16:53:55 brouard
107: Summary: Big bug thanks to Flavia
108:
109: Even model=1+age+V2. did not work anymore
110:
1.200 brouard 111: Revision 1.199 2015/09/07 14:09:23 brouard
112: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
113:
1.199 brouard 114: Revision 1.198 2015/09/03 07:14:39 brouard
115: Summary: 0.98q5 Flavia
116:
1.198 brouard 117: Revision 1.197 2015/09/01 18:24:39 brouard
118: *** empty log message ***
119:
1.197 brouard 120: Revision 1.196 2015/08/18 23:17:52 brouard
121: Summary: 0.98q5
122:
1.196 brouard 123: Revision 1.195 2015/08/18 16:28:39 brouard
124: Summary: Adding a hack for testing purpose
125:
126: After reading the title, ftol and model lines, if the comment line has
127: a q, starting with #q, the answer at the end of the run is quit. It
128: permits to run test files in batch with ctest. The former workaround was
129: $ echo q | imach foo.imach
130:
1.195 brouard 131: Revision 1.194 2015/08/18 13:32:00 brouard
132: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
133:
1.194 brouard 134: Revision 1.193 2015/08/04 07:17:42 brouard
135: Summary: 0.98q4
136:
1.193 brouard 137: Revision 1.192 2015/07/16 16:49:02 brouard
138: Summary: Fixing some outputs
139:
1.192 brouard 140: Revision 1.191 2015/07/14 10:00:33 brouard
141: Summary: Some fixes
142:
1.191 brouard 143: Revision 1.190 2015/05/05 08:51:13 brouard
144: Summary: Adding digits in output parameters (7 digits instead of 6)
145:
146: Fix 1+age+.
147:
1.190 brouard 148: Revision 1.189 2015/04/30 14:45:16 brouard
149: Summary: 0.98q2
150:
1.189 brouard 151: Revision 1.188 2015/04/30 08:27:53 brouard
152: *** empty log message ***
153:
1.188 brouard 154: Revision 1.187 2015/04/29 09:11:15 brouard
155: *** empty log message ***
156:
1.187 brouard 157: Revision 1.186 2015/04/23 12:01:52 brouard
158: Summary: V1*age is working now, version 0.98q1
159:
160: Some codes had been disabled in order to simplify and Vn*age was
161: working in the optimization phase, ie, giving correct MLE parameters,
162: but, as usual, outputs were not correct and program core dumped.
163:
1.186 brouard 164: Revision 1.185 2015/03/11 13:26:42 brouard
165: Summary: Inclusion of compile and links command line for Intel Compiler
166:
1.185 brouard 167: Revision 1.184 2015/03/11 11:52:39 brouard
168: Summary: Back from Windows 8. Intel Compiler
169:
1.184 brouard 170: Revision 1.183 2015/03/10 20:34:32 brouard
171: Summary: 0.98q0, trying with directest, mnbrak fixed
172:
173: We use directest instead of original Powell test; probably no
174: incidence on the results, but better justifications;
175: We fixed Numerical Recipes mnbrak routine which was wrong and gave
176: wrong results.
177:
1.183 brouard 178: Revision 1.182 2015/02/12 08:19:57 brouard
179: Summary: Trying to keep directest which seems simpler and more general
180: Author: Nicolas Brouard
181:
1.182 brouard 182: Revision 1.181 2015/02/11 23:22:24 brouard
183: Summary: Comments on Powell added
184:
185: Author:
186:
1.181 brouard 187: Revision 1.180 2015/02/11 17:33:45 brouard
188: Summary: Finishing move from main to function (hpijx and prevalence_limit)
189:
1.180 brouard 190: Revision 1.179 2015/01/04 09:57:06 brouard
191: Summary: back to OS/X
192:
1.179 brouard 193: Revision 1.178 2015/01/04 09:35:48 brouard
194: *** empty log message ***
195:
1.178 brouard 196: Revision 1.177 2015/01/03 18:40:56 brouard
197: Summary: Still testing ilc32 on OSX
198:
1.177 brouard 199: Revision 1.176 2015/01/03 16:45:04 brouard
200: *** empty log message ***
201:
1.176 brouard 202: Revision 1.175 2015/01/03 16:33:42 brouard
203: *** empty log message ***
204:
1.175 brouard 205: Revision 1.174 2015/01/03 16:15:49 brouard
206: Summary: Still in cross-compilation
207:
1.174 brouard 208: Revision 1.173 2015/01/03 12:06:26 brouard
209: Summary: trying to detect cross-compilation
210:
1.173 brouard 211: Revision 1.172 2014/12/27 12:07:47 brouard
212: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
213:
1.172 brouard 214: Revision 1.171 2014/12/23 13:26:59 brouard
215: Summary: Back from Visual C
216:
217: Still problem with utsname.h on Windows
218:
1.171 brouard 219: Revision 1.170 2014/12/23 11:17:12 brouard
220: Summary: Cleaning some \%% back to %%
221:
222: The escape was mandatory for a specific compiler (which one?), but too many warnings.
223:
1.170 brouard 224: Revision 1.169 2014/12/22 23:08:31 brouard
225: Summary: 0.98p
226:
227: Outputs some informations on compiler used, OS etc. Testing on different platforms.
228:
1.169 brouard 229: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 230: Summary: update
1.169 brouard 231:
1.168 brouard 232: Revision 1.167 2014/12/22 13:50:56 brouard
233: Summary: Testing uname and compiler version and if compiled 32 or 64
234:
235: Testing on Linux 64
236:
1.167 brouard 237: Revision 1.166 2014/12/22 11:40:47 brouard
238: *** empty log message ***
239:
1.166 brouard 240: Revision 1.165 2014/12/16 11:20:36 brouard
241: Summary: After compiling on Visual C
242:
243: * imach.c (Module): Merging 1.61 to 1.162
244:
1.165 brouard 245: Revision 1.164 2014/12/16 10:52:11 brouard
246: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
247:
248: * imach.c (Module): Merging 1.61 to 1.162
249:
1.164 brouard 250: Revision 1.163 2014/12/16 10:30:11 brouard
251: * imach.c (Module): Merging 1.61 to 1.162
252:
1.163 brouard 253: Revision 1.162 2014/09/25 11:43:39 brouard
254: Summary: temporary backup 0.99!
255:
1.162 brouard 256: Revision 1.1 2014/09/16 11:06:58 brouard
257: Summary: With some code (wrong) for nlopt
258:
259: Author:
260:
261: Revision 1.161 2014/09/15 20:41:41 brouard
262: Summary: Problem with macro SQR on Intel compiler
263:
1.161 brouard 264: Revision 1.160 2014/09/02 09:24:05 brouard
265: *** empty log message ***
266:
1.160 brouard 267: Revision 1.159 2014/09/01 10:34:10 brouard
268: Summary: WIN32
269: Author: Brouard
270:
1.159 brouard 271: Revision 1.158 2014/08/27 17:11:51 brouard
272: *** empty log message ***
273:
1.158 brouard 274: Revision 1.157 2014/08/27 16:26:55 brouard
275: Summary: Preparing windows Visual studio version
276: Author: Brouard
277:
278: In order to compile on Visual studio, time.h is now correct and time_t
279: and tm struct should be used. difftime should be used but sometimes I
280: just make the differences in raw time format (time(&now).
281: Trying to suppress #ifdef LINUX
282: Add xdg-open for __linux in order to open default browser.
283:
1.157 brouard 284: Revision 1.156 2014/08/25 20:10:10 brouard
285: *** empty log message ***
286:
1.156 brouard 287: Revision 1.155 2014/08/25 18:32:34 brouard
288: Summary: New compile, minor changes
289: Author: Brouard
290:
1.155 brouard 291: Revision 1.154 2014/06/20 17:32:08 brouard
292: Summary: Outputs now all graphs of convergence to period prevalence
293:
1.154 brouard 294: Revision 1.153 2014/06/20 16:45:46 brouard
295: Summary: If 3 live state, convergence to period prevalence on same graph
296: Author: Brouard
297:
1.153 brouard 298: Revision 1.152 2014/06/18 17:54:09 brouard
299: Summary: open browser, use gnuplot on same dir than imach if not found in the path
300:
1.152 brouard 301: Revision 1.151 2014/06/18 16:43:30 brouard
302: *** empty log message ***
303:
1.151 brouard 304: Revision 1.150 2014/06/18 16:42:35 brouard
305: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
306: Author: brouard
307:
1.150 brouard 308: Revision 1.149 2014/06/18 15:51:14 brouard
309: Summary: Some fixes in parameter files errors
310: Author: Nicolas Brouard
311:
1.149 brouard 312: Revision 1.148 2014/06/17 17:38:48 brouard
313: Summary: Nothing new
314: Author: Brouard
315:
316: Just a new packaging for OS/X version 0.98nS
317:
1.148 brouard 318: Revision 1.147 2014/06/16 10:33:11 brouard
319: *** empty log message ***
320:
1.147 brouard 321: Revision 1.146 2014/06/16 10:20:28 brouard
322: Summary: Merge
323: Author: Brouard
324:
325: Merge, before building revised version.
326:
1.146 brouard 327: Revision 1.145 2014/06/10 21:23:15 brouard
328: Summary: Debugging with valgrind
329: Author: Nicolas Brouard
330:
331: Lot of changes in order to output the results with some covariates
332: After the Edimburgh REVES conference 2014, it seems mandatory to
333: improve the code.
334: No more memory valgrind error but a lot has to be done in order to
335: continue the work of splitting the code into subroutines.
336: Also, decodemodel has been improved. Tricode is still not
337: optimal. nbcode should be improved. Documentation has been added in
338: the source code.
339:
1.144 brouard 340: Revision 1.143 2014/01/26 09:45:38 brouard
341: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
342:
343: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
344: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
345:
1.143 brouard 346: Revision 1.142 2014/01/26 03:57:36 brouard
347: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
348:
349: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
350:
1.142 brouard 351: Revision 1.141 2014/01/26 02:42:01 brouard
352: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
353:
1.141 brouard 354: Revision 1.140 2011/09/02 10:37:54 brouard
355: Summary: times.h is ok with mingw32 now.
356:
1.140 brouard 357: Revision 1.139 2010/06/14 07:50:17 brouard
358: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
359: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
360:
1.139 brouard 361: Revision 1.138 2010/04/30 18:19:40 brouard
362: *** empty log message ***
363:
1.138 brouard 364: Revision 1.137 2010/04/29 18:11:38 brouard
365: (Module): Checking covariates for more complex models
366: than V1+V2. A lot of change to be done. Unstable.
367:
1.137 brouard 368: Revision 1.136 2010/04/26 20:30:53 brouard
369: (Module): merging some libgsl code. Fixing computation
370: of likelione (using inter/intrapolation if mle = 0) in order to
371: get same likelihood as if mle=1.
372: Some cleaning of code and comments added.
373:
1.136 brouard 374: Revision 1.135 2009/10/29 15:33:14 brouard
375: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
376:
1.135 brouard 377: Revision 1.134 2009/10/29 13:18:53 brouard
378: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
379:
1.134 brouard 380: Revision 1.133 2009/07/06 10:21:25 brouard
381: just nforces
382:
1.133 brouard 383: Revision 1.132 2009/07/06 08:22:05 brouard
384: Many tings
385:
1.132 brouard 386: Revision 1.131 2009/06/20 16:22:47 brouard
387: Some dimensions resccaled
388:
1.131 brouard 389: Revision 1.130 2009/05/26 06:44:34 brouard
390: (Module): Max Covariate is now set to 20 instead of 8. A
391: lot of cleaning with variables initialized to 0. Trying to make
392: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
393:
1.130 brouard 394: Revision 1.129 2007/08/31 13:49:27 lievre
395: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
396:
1.129 lievre 397: Revision 1.128 2006/06/30 13:02:05 brouard
398: (Module): Clarifications on computing e.j
399:
1.128 brouard 400: Revision 1.127 2006/04/28 18:11:50 brouard
401: (Module): Yes the sum of survivors was wrong since
402: imach-114 because nhstepm was no more computed in the age
403: loop. Now we define nhstepma in the age loop.
404: (Module): In order to speed up (in case of numerous covariates) we
405: compute health expectancies (without variances) in a first step
406: and then all the health expectancies with variances or standard
407: deviation (needs data from the Hessian matrices) which slows the
408: computation.
409: In the future we should be able to stop the program is only health
410: expectancies and graph are needed without standard deviations.
411:
1.127 brouard 412: Revision 1.126 2006/04/28 17:23:28 brouard
413: (Module): Yes the sum of survivors was wrong since
414: imach-114 because nhstepm was no more computed in the age
415: loop. Now we define nhstepma in the age loop.
416: Version 0.98h
417:
1.126 brouard 418: Revision 1.125 2006/04/04 15:20:31 lievre
419: Errors in calculation of health expectancies. Age was not initialized.
420: Forecasting file added.
421:
422: Revision 1.124 2006/03/22 17:13:53 lievre
423: Parameters are printed with %lf instead of %f (more numbers after the comma).
424: The log-likelihood is printed in the log file
425:
426: Revision 1.123 2006/03/20 10:52:43 brouard
427: * imach.c (Module): <title> changed, corresponds to .htm file
428: name. <head> headers where missing.
429:
430: * imach.c (Module): Weights can have a decimal point as for
431: English (a comma might work with a correct LC_NUMERIC environment,
432: otherwise the weight is truncated).
433: Modification of warning when the covariates values are not 0 or
434: 1.
435: Version 0.98g
436:
437: Revision 1.122 2006/03/20 09:45:41 brouard
438: (Module): Weights can have a decimal point as for
439: English (a comma might work with a correct LC_NUMERIC environment,
440: otherwise the weight is truncated).
441: Modification of warning when the covariates values are not 0 or
442: 1.
443: Version 0.98g
444:
445: Revision 1.121 2006/03/16 17:45:01 lievre
446: * imach.c (Module): Comments concerning covariates added
447:
448: * imach.c (Module): refinements in the computation of lli if
449: status=-2 in order to have more reliable computation if stepm is
450: not 1 month. Version 0.98f
451:
452: Revision 1.120 2006/03/16 15:10:38 lievre
453: (Module): refinements in the computation of lli if
454: status=-2 in order to have more reliable computation if stepm is
455: not 1 month. Version 0.98f
456:
457: Revision 1.119 2006/03/15 17:42:26 brouard
458: (Module): Bug if status = -2, the loglikelihood was
459: computed as likelihood omitting the logarithm. Version O.98e
460:
461: Revision 1.118 2006/03/14 18:20:07 brouard
462: (Module): varevsij Comments added explaining the second
463: table of variances if popbased=1 .
464: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
465: (Module): Function pstamp added
466: (Module): Version 0.98d
467:
468: Revision 1.117 2006/03/14 17:16:22 brouard
469: (Module): varevsij Comments added explaining the second
470: table of variances if popbased=1 .
471: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
472: (Module): Function pstamp added
473: (Module): Version 0.98d
474:
475: Revision 1.116 2006/03/06 10:29:27 brouard
476: (Module): Variance-covariance wrong links and
477: varian-covariance of ej. is needed (Saito).
478:
479: Revision 1.115 2006/02/27 12:17:45 brouard
480: (Module): One freematrix added in mlikeli! 0.98c
481:
482: Revision 1.114 2006/02/26 12:57:58 brouard
483: (Module): Some improvements in processing parameter
484: filename with strsep.
485:
486: Revision 1.113 2006/02/24 14:20:24 brouard
487: (Module): Memory leaks checks with valgrind and:
488: datafile was not closed, some imatrix were not freed and on matrix
489: allocation too.
490:
491: Revision 1.112 2006/01/30 09:55:26 brouard
492: (Module): Back to gnuplot.exe instead of wgnuplot.exe
493:
494: Revision 1.111 2006/01/25 20:38:18 brouard
495: (Module): Lots of cleaning and bugs added (Gompertz)
496: (Module): Comments can be added in data file. Missing date values
497: can be a simple dot '.'.
498:
499: Revision 1.110 2006/01/25 00:51:50 brouard
500: (Module): Lots of cleaning and bugs added (Gompertz)
501:
502: Revision 1.109 2006/01/24 19:37:15 brouard
503: (Module): Comments (lines starting with a #) are allowed in data.
504:
505: Revision 1.108 2006/01/19 18:05:42 lievre
506: Gnuplot problem appeared...
507: To be fixed
508:
509: Revision 1.107 2006/01/19 16:20:37 brouard
510: Test existence of gnuplot in imach path
511:
512: Revision 1.106 2006/01/19 13:24:36 brouard
513: Some cleaning and links added in html output
514:
515: Revision 1.105 2006/01/05 20:23:19 lievre
516: *** empty log message ***
517:
518: Revision 1.104 2005/09/30 16:11:43 lievre
519: (Module): sump fixed, loop imx fixed, and simplifications.
520: (Module): If the status is missing at the last wave but we know
521: that the person is alive, then we can code his/her status as -2
522: (instead of missing=-1 in earlier versions) and his/her
523: contributions to the likelihood is 1 - Prob of dying from last
524: health status (= 1-p13= p11+p12 in the easiest case of somebody in
525: the healthy state at last known wave). Version is 0.98
526:
527: Revision 1.103 2005/09/30 15:54:49 lievre
528: (Module): sump fixed, loop imx fixed, and simplifications.
529:
530: Revision 1.102 2004/09/15 17:31:30 brouard
531: Add the possibility to read data file including tab characters.
532:
533: Revision 1.101 2004/09/15 10:38:38 brouard
534: Fix on curr_time
535:
536: Revision 1.100 2004/07/12 18:29:06 brouard
537: Add version for Mac OS X. Just define UNIX in Makefile
538:
539: Revision 1.99 2004/06/05 08:57:40 brouard
540: *** empty log message ***
541:
542: Revision 1.98 2004/05/16 15:05:56 brouard
543: New version 0.97 . First attempt to estimate force of mortality
544: directly from the data i.e. without the need of knowing the health
545: state at each age, but using a Gompertz model: log u =a + b*age .
546: This is the basic analysis of mortality and should be done before any
547: other analysis, in order to test if the mortality estimated from the
548: cross-longitudinal survey is different from the mortality estimated
549: from other sources like vital statistic data.
550:
551: The same imach parameter file can be used but the option for mle should be -3.
552:
1.133 brouard 553: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 554: former routines in order to include the new code within the former code.
555:
556: The output is very simple: only an estimate of the intercept and of
557: the slope with 95% confident intervals.
558:
559: Current limitations:
560: A) Even if you enter covariates, i.e. with the
561: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
562: B) There is no computation of Life Expectancy nor Life Table.
563:
564: Revision 1.97 2004/02/20 13:25:42 lievre
565: Version 0.96d. Population forecasting command line is (temporarily)
566: suppressed.
567:
568: Revision 1.96 2003/07/15 15:38:55 brouard
569: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
570: rewritten within the same printf. Workaround: many printfs.
571:
572: Revision 1.95 2003/07/08 07:54:34 brouard
573: * imach.c (Repository):
574: (Repository): Using imachwizard code to output a more meaningful covariance
575: matrix (cov(a12,c31) instead of numbers.
576:
577: Revision 1.94 2003/06/27 13:00:02 brouard
578: Just cleaning
579:
580: Revision 1.93 2003/06/25 16:33:55 brouard
581: (Module): On windows (cygwin) function asctime_r doesn't
582: exist so I changed back to asctime which exists.
583: (Module): Version 0.96b
584:
585: Revision 1.92 2003/06/25 16:30:45 brouard
586: (Module): On windows (cygwin) function asctime_r doesn't
587: exist so I changed back to asctime which exists.
588:
589: Revision 1.91 2003/06/25 15:30:29 brouard
590: * imach.c (Repository): Duplicated warning errors corrected.
591: (Repository): Elapsed time after each iteration is now output. It
592: helps to forecast when convergence will be reached. Elapsed time
593: is stamped in powell. We created a new html file for the graphs
594: concerning matrix of covariance. It has extension -cov.htm.
595:
596: Revision 1.90 2003/06/24 12:34:15 brouard
597: (Module): Some bugs corrected for windows. Also, when
598: mle=-1 a template is output in file "or"mypar.txt with the design
599: of the covariance matrix to be input.
600:
601: Revision 1.89 2003/06/24 12:30:52 brouard
602: (Module): Some bugs corrected for windows. Also, when
603: mle=-1 a template is output in file "or"mypar.txt with the design
604: of the covariance matrix to be input.
605:
606: Revision 1.88 2003/06/23 17:54:56 brouard
607: * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
608:
609: Revision 1.87 2003/06/18 12:26:01 brouard
610: Version 0.96
611:
612: Revision 1.86 2003/06/17 20:04:08 brouard
613: (Module): Change position of html and gnuplot routines and added
614: routine fileappend.
615:
616: Revision 1.85 2003/06/17 13:12:43 brouard
617: * imach.c (Repository): Check when date of death was earlier that
618: current date of interview. It may happen when the death was just
619: prior to the death. In this case, dh was negative and likelihood
620: was wrong (infinity). We still send an "Error" but patch by
621: assuming that the date of death was just one stepm after the
622: interview.
623: (Repository): Because some people have very long ID (first column)
624: we changed int to long in num[] and we added a new lvector for
625: memory allocation. But we also truncated to 8 characters (left
626: truncation)
627: (Repository): No more line truncation errors.
628:
629: Revision 1.84 2003/06/13 21:44:43 brouard
630: * imach.c (Repository): Replace "freqsummary" at a correct
631: place. It differs from routine "prevalence" which may be called
632: many times. Probs is memory consuming and must be used with
633: parcimony.
634: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
635:
636: Revision 1.83 2003/06/10 13:39:11 lievre
637: *** empty log message ***
638:
639: Revision 1.82 2003/06/05 15:57:20 brouard
640: Add log in imach.c and fullversion number is now printed.
641:
642: */
643: /*
644: Interpolated Markov Chain
645:
646: Short summary of the programme:
647:
1.227 brouard 648: This program computes Healthy Life Expectancies or State-specific
649: (if states aren't health statuses) Expectancies from
650: cross-longitudinal data. Cross-longitudinal data consist in:
651:
652: -1- a first survey ("cross") where individuals from different ages
653: are interviewed on their health status or degree of disability (in
654: the case of a health survey which is our main interest)
655:
656: -2- at least a second wave of interviews ("longitudinal") which
657: measure each change (if any) in individual health status. Health
658: expectancies are computed from the time spent in each health state
659: according to a model. More health states you consider, more time is
660: necessary to reach the Maximum Likelihood of the parameters involved
661: in the model. The simplest model is the multinomial logistic model
662: where pij is the probability to be observed in state j at the second
663: wave conditional to be observed in state i at the first
664: wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
665: etc , where 'age' is age and 'sex' is a covariate. If you want to
666: have a more complex model than "constant and age", you should modify
667: the program where the markup *Covariates have to be included here
668: again* invites you to do it. More covariates you add, slower the
1.126 brouard 669: convergence.
670:
671: The advantage of this computer programme, compared to a simple
672: multinomial logistic model, is clear when the delay between waves is not
673: identical for each individual. Also, if a individual missed an
674: intermediate interview, the information is lost, but taken into
675: account using an interpolation or extrapolation.
676:
677: hPijx is the probability to be observed in state i at age x+h
678: conditional to the observed state i at age x. The delay 'h' can be
679: split into an exact number (nh*stepm) of unobserved intermediate
680: states. This elementary transition (by month, quarter,
681: semester or year) is modelled as a multinomial logistic. The hPx
682: matrix is simply the matrix product of nh*stepm elementary matrices
683: and the contribution of each individual to the likelihood is simply
684: hPijx.
685:
686: Also this programme outputs the covariance matrix of the parameters but also
1.218 brouard 687: of the life expectancies. It also computes the period (stable) prevalence.
688:
689: Back prevalence and projections:
1.227 brouard 690:
691: - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
692: double agemaxpar, double ftolpl, int *ncvyearp, double
693: dateprev1,double dateprev2, int firstpass, int lastpass, int
694: mobilavproj)
695:
696: Computes the back prevalence limit for any combination of
697: covariate values k at any age between ageminpar and agemaxpar and
698: returns it in **bprlim. In the loops,
699:
700: - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
701: **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
702:
703: - hBijx Back Probability to be in state i at age x-h being in j at x
1.218 brouard 704: Computes for any combination of covariates k and any age between bage and fage
705: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
706: oldm=oldms;savm=savms;
1.227 brouard 707:
708: - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.218 brouard 709: Computes the transition matrix starting at age 'age' over
710: 'nhstepm*hstepm*stepm' months (i.e. until
711: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1.227 brouard 712: nhstepm*hstepm matrices.
713:
714: Returns p3mat[i][j][h] after calling
715: p3mat[i][j][h]=matprod2(newm,
716: bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
717: dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
718: oldm);
1.226 brouard 719:
720: Important routines
721:
722: - func (or funcone), computes logit (pij) distinguishing
723: o fixed variables (single or product dummies or quantitative);
724: o varying variables by:
725: (1) wave (single, product dummies, quantitative),
726: (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
727: % fixed dummy (treated) or quantitative (not done because time-consuming);
728: % varying dummy (not done) or quantitative (not done);
729: - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
730: and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
731: - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
732: o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
733: race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
1.218 brouard 734:
1.226 brouard 735:
736:
1.133 brouard 737: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
738: Institut national d'études démographiques, Paris.
1.126 brouard 739: This software have been partly granted by Euro-REVES, a concerted action
740: from the European Union.
741: It is copyrighted identically to a GNU software product, ie programme and
742: software can be distributed freely for non commercial use. Latest version
743: can be accessed at http://euroreves.ined.fr/imach .
744:
745: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
746: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
747:
748: **********************************************************************/
749: /*
750: main
751: read parameterfile
752: read datafile
753: concatwav
754: freqsummary
755: if (mle >= 1)
756: mlikeli
757: print results files
758: if mle==1
759: computes hessian
760: read end of parameter file: agemin, agemax, bage, fage, estepm
761: begin-prev-date,...
762: open gnuplot file
763: open html file
1.145 brouard 764: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
765: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
766: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
767: freexexit2 possible for memory heap.
768:
769: h Pij x | pij_nom ficrestpij
770: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
771: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
772: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
773:
774: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
775: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
776: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
777: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
778: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
779:
1.126 brouard 780: forecasting if prevfcast==1 prevforecast call prevalence()
781: health expectancies
782: Variance-covariance of DFLE
783: prevalence()
784: movingaverage()
785: varevsij()
786: if popbased==1 varevsij(,popbased)
787: total life expectancies
788: Variance of period (stable) prevalence
789: end
790: */
791:
1.187 brouard 792: /* #define DEBUG */
793: /* #define DEBUGBRENT */
1.203 brouard 794: /* #define DEBUGLINMIN */
795: /* #define DEBUGHESS */
796: #define DEBUGHESSIJ
1.224 brouard 797: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan) *\/ */
1.165 brouard 798: #define POWELL /* Instead of NLOPT */
1.224 brouard 799: #define POWELLNOF3INFF1TEST /* Skip test */
1.186 brouard 800: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
801: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 802:
803: #include <math.h>
804: #include <stdio.h>
805: #include <stdlib.h>
806: #include <string.h>
1.226 brouard 807: #include <ctype.h>
1.159 brouard 808:
809: #ifdef _WIN32
810: #include <io.h>
1.172 brouard 811: #include <windows.h>
812: #include <tchar.h>
1.159 brouard 813: #else
1.126 brouard 814: #include <unistd.h>
1.159 brouard 815: #endif
1.126 brouard 816:
817: #include <limits.h>
818: #include <sys/types.h>
1.171 brouard 819:
820: #if defined(__GNUC__)
821: #include <sys/utsname.h> /* Doesn't work on Windows */
822: #endif
823:
1.126 brouard 824: #include <sys/stat.h>
825: #include <errno.h>
1.159 brouard 826: /* extern int errno; */
1.126 brouard 827:
1.157 brouard 828: /* #ifdef LINUX */
829: /* #include <time.h> */
830: /* #include "timeval.h" */
831: /* #else */
832: /* #include <sys/time.h> */
833: /* #endif */
834:
1.126 brouard 835: #include <time.h>
836:
1.136 brouard 837: #ifdef GSL
838: #include <gsl/gsl_errno.h>
839: #include <gsl/gsl_multimin.h>
840: #endif
841:
1.167 brouard 842:
1.162 brouard 843: #ifdef NLOPT
844: #include <nlopt.h>
845: typedef struct {
846: double (* function)(double [] );
847: } myfunc_data ;
848: #endif
849:
1.126 brouard 850: /* #include <libintl.h> */
851: /* #define _(String) gettext (String) */
852:
1.141 brouard 853: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 854:
855: #define GNUPLOTPROGRAM "gnuplot"
856: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
857: #define FILENAMELENGTH 132
858:
859: #define GLOCK_ERROR_NOPATH -1 /* empty path */
860: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
861:
1.144 brouard 862: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
863: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 864:
865: #define NINTERVMAX 8
1.144 brouard 866: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
867: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
868: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 869: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 870: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
871: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.126 brouard 872: #define MAXN 20000
1.144 brouard 873: #define YEARM 12. /**< Number of months per year */
1.218 brouard 874: /* #define AGESUP 130 */
875: #define AGESUP 150
876: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126 brouard 877: #define AGEBASE 40
1.194 brouard 878: #define AGEOVERFLOW 1.e20
1.164 brouard 879: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 880: #ifdef _WIN32
881: #define DIRSEPARATOR '\\'
882: #define CHARSEPARATOR "\\"
883: #define ODIRSEPARATOR '/'
884: #else
1.126 brouard 885: #define DIRSEPARATOR '/'
886: #define CHARSEPARATOR "/"
887: #define ODIRSEPARATOR '\\'
888: #endif
889:
1.230 ! brouard 890: /* $Id: imach.c,v 1.229 2016/07/23 09:45:53 brouard Exp $ */
1.126 brouard 891: /* $State: Exp $ */
1.196 brouard 892: #include "version.h"
893: char version[]=__IMACH_VERSION__;
1.224 brouard 894: char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";
1.230 ! brouard 895: char fullversion[]="$Revision: 1.229 $ $Date: 2016/07/23 09:45:53 $";
1.126 brouard 896: char strstart[80];
897: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 898: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 899: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 900: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
901: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
902: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
1.225 brouard 903: int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
904: int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
1.145 brouard 905: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
906: int cptcovprodnoage=0; /**< Number of covariate products without age */
907: int cptcoveff=0; /* Total number of covariates to vary for printing results */
1.224 brouard 908: int ncoveff=0; /* Total number of effective covariates in the model */
1.225 brouard 909: int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
1.224 brouard 910: int ntveff=0; /**< ntveff number of effective time varying variables */
911: int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
1.145 brouard 912: int cptcov=0; /* Working variable */
1.218 brouard 913: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.126 brouard 914: int npar=NPARMAX;
915: int nlstate=2; /* Number of live states */
916: int ndeath=1; /* Number of dead states */
1.130 brouard 917: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.223 brouard 918: int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
1.126 brouard 919: int popbased=0;
920:
921: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 922: int maxwav=0; /* Maxim number of waves */
923: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
924: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
925: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 926: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 927: int mle=1, weightopt=0;
1.126 brouard 928: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
929: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
930: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
931: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 932: int countcallfunc=0; /* Count the number of calls to func */
1.230 ! brouard 933: int selected(int kvar); /* Is covariate kvar selected for printing results */
! 934:
1.130 brouard 935: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 936: double **matprod2(); /* test */
1.126 brouard 937: double **oldm, **newm, **savm; /* Working pointers to matrices */
938: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218 brouard 939: double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
940:
1.136 brouard 941: /*FILE *fic ; */ /* Used in readdata only */
1.217 brouard 942: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 943: FILE *ficlog, *ficrespow;
1.130 brouard 944: int globpr=0; /* Global variable for printing or not */
1.126 brouard 945: double fretone; /* Only one call to likelihood */
1.130 brouard 946: long ipmx=0; /* Number of contributions */
1.126 brouard 947: double sw; /* Sum of weights */
948: char filerespow[FILENAMELENGTH];
949: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
950: FILE *ficresilk;
951: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
952: FILE *ficresprobmorprev;
953: FILE *fichtm, *fichtmcov; /* Html File */
954: FILE *ficreseij;
955: char filerese[FILENAMELENGTH];
956: FILE *ficresstdeij;
957: char fileresstde[FILENAMELENGTH];
958: FILE *ficrescveij;
959: char filerescve[FILENAMELENGTH];
960: FILE *ficresvij;
961: char fileresv[FILENAMELENGTH];
962: FILE *ficresvpl;
963: char fileresvpl[FILENAMELENGTH];
964: char title[MAXLINE];
1.217 brouard 965: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 966: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
967: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
968: char command[FILENAMELENGTH];
969: int outcmd=0;
970:
1.217 brouard 971: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 972: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 973: char filelog[FILENAMELENGTH]; /* Log file */
974: char filerest[FILENAMELENGTH];
975: char fileregp[FILENAMELENGTH];
976: char popfile[FILENAMELENGTH];
977:
978: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
979:
1.157 brouard 980: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
981: /* struct timezone tzp; */
982: /* extern int gettimeofday(); */
983: struct tm tml, *gmtime(), *localtime();
984:
985: extern time_t time();
986:
987: struct tm start_time, end_time, curr_time, last_time, forecast_time;
988: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
989: struct tm tm;
990:
1.126 brouard 991: char strcurr[80], strfor[80];
992:
993: char *endptr;
994: long lval;
995: double dval;
996:
997: #define NR_END 1
998: #define FREE_ARG char*
999: #define FTOL 1.0e-10
1000:
1001: #define NRANSI
1002: #define ITMAX 200
1003:
1004: #define TOL 2.0e-4
1005:
1006: #define CGOLD 0.3819660
1007: #define ZEPS 1.0e-10
1008: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
1009:
1010: #define GOLD 1.618034
1011: #define GLIMIT 100.0
1012: #define TINY 1.0e-20
1013:
1014: static double maxarg1,maxarg2;
1015: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
1016: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
1017:
1018: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
1019: #define rint(a) floor(a+0.5)
1.166 brouard 1020: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 1021: #define mytinydouble 1.0e-16
1.166 brouard 1022: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
1023: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
1024: /* static double dsqrarg; */
1025: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 1026: static double sqrarg;
1027: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
1028: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1029: int agegomp= AGEGOMP;
1030:
1031: int imx;
1032: int stepm=1;
1033: /* Stepm, step in month: minimum step interpolation*/
1034:
1035: int estepm;
1036: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
1037:
1038: int m,nb;
1039: long *num;
1.197 brouard 1040: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 1041: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
1042: covariate for which somebody answered excluding
1043: undefined. Usually 2: 0 and 1. */
1044: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
1045: covariate for which somebody answered including
1046: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 1047: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218 brouard 1048: double **pmmij, ***probs; /* Global pointer */
1.219 brouard 1049: double ***mobaverage, ***mobaverages; /* New global variable */
1.126 brouard 1050: double *ageexmed,*agecens;
1051: double dateintmean=0;
1052:
1053: double *weight;
1054: int **s; /* Status */
1.141 brouard 1055: double *agedc;
1.145 brouard 1056: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 1057: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 1058: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.225 brouard 1059: double **coqvar; /* Fixed quantitative covariate iqv */
1060: double ***cotvar; /* Time varying covariate itv */
1061: double ***cotqvar; /* Time varying quantitative covariate itqv */
1.141 brouard 1062: double idx;
1063: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.230 ! brouard 1064: int *Tvarsel; /**< Selected covariates for output */
! 1065: double *Tvalsel; /**< Selected modality value of covariate for output */
1.226 brouard 1066: int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
1.227 brouard 1067: int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
1068: int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */
1.197 brouard 1069: int *Tage;
1.227 brouard 1070: int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
1.228 brouard 1071: int *Tmodelind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.230 ! brouard 1072: int *TmodelInvind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
! 1073: int *TmodelInvQind; /** Tmodelqind[1]=1 for V5(quantitative varying) position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.145 brouard 1074: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 1075: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.227 brouard 1076: int **Tvard;
1077: int *Tprod;/**< Gives the k position of the k1 product */
1078: int *Tposprod; /**< Gives the k1 product from the k position */
1079: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
1080: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
1081: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
1082: */
1083: int cptcovprod, *Tvaraff, *invalidvarcomb;
1.126 brouard 1084: double *lsurv, *lpop, *tpop;
1085:
1.143 brouard 1086: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
1087: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 1088:
1089: /**************** split *************************/
1090: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1091: {
1092: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1093: the name of the file (name), its extension only (ext) and its first part of the name (finame)
1094: */
1095: char *ss; /* pointer */
1.186 brouard 1096: int l1=0, l2=0; /* length counters */
1.126 brouard 1097:
1098: l1 = strlen(path ); /* length of path */
1099: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1100: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1101: if ( ss == NULL ) { /* no directory, so determine current directory */
1102: strcpy( name, path ); /* we got the fullname name because no directory */
1103: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
1104: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1105: /* get current working directory */
1106: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 1107: #ifdef WIN32
1108: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
1109: #else
1110: if (getcwd(dirc, FILENAME_MAX) == NULL) {
1111: #endif
1.126 brouard 1112: return( GLOCK_ERROR_GETCWD );
1113: }
1114: /* got dirc from getcwd*/
1115: printf(" DIRC = %s \n",dirc);
1.205 brouard 1116: } else { /* strip directory from path */
1.126 brouard 1117: ss++; /* after this, the filename */
1118: l2 = strlen( ss ); /* length of filename */
1119: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1120: strcpy( name, ss ); /* save file name */
1121: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1122: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1123: printf(" DIRC2 = %s \n",dirc);
1124: }
1125: /* We add a separator at the end of dirc if not exists */
1126: l1 = strlen( dirc ); /* length of directory */
1127: if( dirc[l1-1] != DIRSEPARATOR ){
1128: dirc[l1] = DIRSEPARATOR;
1129: dirc[l1+1] = 0;
1130: printf(" DIRC3 = %s \n",dirc);
1131: }
1132: ss = strrchr( name, '.' ); /* find last / */
1133: if (ss >0){
1134: ss++;
1135: strcpy(ext,ss); /* save extension */
1136: l1= strlen( name);
1137: l2= strlen(ss)+1;
1138: strncpy( finame, name, l1-l2);
1139: finame[l1-l2]= 0;
1140: }
1141:
1142: return( 0 ); /* we're done */
1143: }
1144:
1145:
1146: /******************************************/
1147:
1148: void replace_back_to_slash(char *s, char*t)
1149: {
1150: int i;
1151: int lg=0;
1152: i=0;
1153: lg=strlen(t);
1154: for(i=0; i<= lg; i++) {
1155: (s[i] = t[i]);
1156: if (t[i]== '\\') s[i]='/';
1157: }
1158: }
1159:
1.132 brouard 1160: char *trimbb(char *out, char *in)
1.137 brouard 1161: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1162: char *s;
1163: s=out;
1164: while (*in != '\0'){
1.137 brouard 1165: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1166: in++;
1167: }
1168: *out++ = *in++;
1169: }
1170: *out='\0';
1171: return s;
1172: }
1173:
1.187 brouard 1174: /* char *substrchaine(char *out, char *in, char *chain) */
1175: /* { */
1176: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1177: /* char *s, *t; */
1178: /* t=in;s=out; */
1179: /* while ((*in != *chain) && (*in != '\0')){ */
1180: /* *out++ = *in++; */
1181: /* } */
1182:
1183: /* /\* *in matches *chain *\/ */
1184: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1185: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1186: /* } */
1187: /* in--; chain--; */
1188: /* while ( (*in != '\0')){ */
1189: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1190: /* *out++ = *in++; */
1191: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1192: /* } */
1193: /* *out='\0'; */
1194: /* out=s; */
1195: /* return out; */
1196: /* } */
1197: char *substrchaine(char *out, char *in, char *chain)
1198: {
1199: /* Substract chain 'chain' from 'in', return and output 'out' */
1200: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1201:
1202: char *strloc;
1203:
1204: strcpy (out, in);
1205: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1206: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1207: if(strloc != NULL){
1208: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1209: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1210: /* strcpy (strloc, strloc +strlen(chain));*/
1211: }
1212: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1213: return out;
1214: }
1215:
1216:
1.145 brouard 1217: char *cutl(char *blocc, char *alocc, char *in, char occ)
1218: {
1.187 brouard 1219: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1220: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1221: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1222: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1223: */
1.160 brouard 1224: char *s, *t;
1.145 brouard 1225: t=in;s=in;
1226: while ((*in != occ) && (*in != '\0')){
1227: *alocc++ = *in++;
1228: }
1229: if( *in == occ){
1230: *(alocc)='\0';
1231: s=++in;
1232: }
1233:
1234: if (s == t) {/* occ not found */
1235: *(alocc-(in-s))='\0';
1236: in=s;
1237: }
1238: while ( *in != '\0'){
1239: *blocc++ = *in++;
1240: }
1241:
1242: *blocc='\0';
1243: return t;
1244: }
1.137 brouard 1245: char *cutv(char *blocc, char *alocc, char *in, char occ)
1246: {
1.187 brouard 1247: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1248: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1249: gives blocc="abcdef2ghi" and alocc="j".
1250: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1251: */
1252: char *s, *t;
1253: t=in;s=in;
1254: while (*in != '\0'){
1255: while( *in == occ){
1256: *blocc++ = *in++;
1257: s=in;
1258: }
1259: *blocc++ = *in++;
1260: }
1261: if (s == t) /* occ not found */
1262: *(blocc-(in-s))='\0';
1263: else
1264: *(blocc-(in-s)-1)='\0';
1265: in=s;
1266: while ( *in != '\0'){
1267: *alocc++ = *in++;
1268: }
1269:
1270: *alocc='\0';
1271: return s;
1272: }
1273:
1.126 brouard 1274: int nbocc(char *s, char occ)
1275: {
1276: int i,j=0;
1277: int lg=20;
1278: i=0;
1279: lg=strlen(s);
1280: for(i=0; i<= lg; i++) {
1281: if (s[i] == occ ) j++;
1282: }
1283: return j;
1284: }
1285:
1.137 brouard 1286: /* void cutv(char *u,char *v, char*t, char occ) */
1287: /* { */
1288: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1289: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1290: /* gives u="abcdef2ghi" and v="j" *\/ */
1291: /* int i,lg,j,p=0; */
1292: /* i=0; */
1293: /* lg=strlen(t); */
1294: /* for(j=0; j<=lg-1; j++) { */
1295: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1296: /* } */
1.126 brouard 1297:
1.137 brouard 1298: /* for(j=0; j<p; j++) { */
1299: /* (u[j] = t[j]); */
1300: /* } */
1301: /* u[p]='\0'; */
1.126 brouard 1302:
1.137 brouard 1303: /* for(j=0; j<= lg; j++) { */
1304: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1305: /* } */
1306: /* } */
1.126 brouard 1307:
1.160 brouard 1308: #ifdef _WIN32
1309: char * strsep(char **pp, const char *delim)
1310: {
1311: char *p, *q;
1312:
1313: if ((p = *pp) == NULL)
1314: return 0;
1315: if ((q = strpbrk (p, delim)) != NULL)
1316: {
1317: *pp = q + 1;
1318: *q = '\0';
1319: }
1320: else
1321: *pp = 0;
1322: return p;
1323: }
1324: #endif
1325:
1.126 brouard 1326: /********************** nrerror ********************/
1327:
1328: void nrerror(char error_text[])
1329: {
1330: fprintf(stderr,"ERREUR ...\n");
1331: fprintf(stderr,"%s\n",error_text);
1332: exit(EXIT_FAILURE);
1333: }
1334: /*********************** vector *******************/
1335: double *vector(int nl, int nh)
1336: {
1337: double *v;
1338: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1339: if (!v) nrerror("allocation failure in vector");
1340: return v-nl+NR_END;
1341: }
1342:
1343: /************************ free vector ******************/
1344: void free_vector(double*v, int nl, int nh)
1345: {
1346: free((FREE_ARG)(v+nl-NR_END));
1347: }
1348:
1349: /************************ivector *******************************/
1350: int *ivector(long nl,long nh)
1351: {
1352: int *v;
1353: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1354: if (!v) nrerror("allocation failure in ivector");
1355: return v-nl+NR_END;
1356: }
1357:
1358: /******************free ivector **************************/
1359: void free_ivector(int *v, long nl, long nh)
1360: {
1361: free((FREE_ARG)(v+nl-NR_END));
1362: }
1363:
1364: /************************lvector *******************************/
1365: long *lvector(long nl,long nh)
1366: {
1367: long *v;
1368: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1369: if (!v) nrerror("allocation failure in ivector");
1370: return v-nl+NR_END;
1371: }
1372:
1373: /******************free lvector **************************/
1374: void free_lvector(long *v, long nl, long nh)
1375: {
1376: free((FREE_ARG)(v+nl-NR_END));
1377: }
1378:
1379: /******************* imatrix *******************************/
1380: int **imatrix(long nrl, long nrh, long ncl, long nch)
1381: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1382: {
1383: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1384: int **m;
1385:
1386: /* allocate pointers to rows */
1387: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1388: if (!m) nrerror("allocation failure 1 in matrix()");
1389: m += NR_END;
1390: m -= nrl;
1391:
1392:
1393: /* allocate rows and set pointers to them */
1394: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1395: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1396: m[nrl] += NR_END;
1397: m[nrl] -= ncl;
1398:
1399: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1400:
1401: /* return pointer to array of pointers to rows */
1402: return m;
1403: }
1404:
1405: /****************** free_imatrix *************************/
1406: void free_imatrix(m,nrl,nrh,ncl,nch)
1407: int **m;
1408: long nch,ncl,nrh,nrl;
1409: /* free an int matrix allocated by imatrix() */
1410: {
1411: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1412: free((FREE_ARG) (m+nrl-NR_END));
1413: }
1414:
1415: /******************* matrix *******************************/
1416: double **matrix(long nrl, long nrh, long ncl, long nch)
1417: {
1418: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1419: double **m;
1420:
1421: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1422: if (!m) nrerror("allocation failure 1 in matrix()");
1423: m += NR_END;
1424: m -= nrl;
1425:
1426: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1427: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1428: m[nrl] += NR_END;
1429: m[nrl] -= ncl;
1430:
1431: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1432: return m;
1.145 brouard 1433: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1434: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1435: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1436: */
1437: }
1438:
1439: /*************************free matrix ************************/
1440: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1441: {
1442: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1443: free((FREE_ARG)(m+nrl-NR_END));
1444: }
1445:
1446: /******************* ma3x *******************************/
1447: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1448: {
1449: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1450: double ***m;
1451:
1452: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1453: if (!m) nrerror("allocation failure 1 in matrix()");
1454: m += NR_END;
1455: m -= nrl;
1456:
1457: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1458: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1459: m[nrl] += NR_END;
1460: m[nrl] -= ncl;
1461:
1462: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1463:
1464: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1465: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1466: m[nrl][ncl] += NR_END;
1467: m[nrl][ncl] -= nll;
1468: for (j=ncl+1; j<=nch; j++)
1469: m[nrl][j]=m[nrl][j-1]+nlay;
1470:
1471: for (i=nrl+1; i<=nrh; i++) {
1472: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1473: for (j=ncl+1; j<=nch; j++)
1474: m[i][j]=m[i][j-1]+nlay;
1475: }
1476: return m;
1477: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1478: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1479: */
1480: }
1481:
1482: /*************************free ma3x ************************/
1483: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1484: {
1485: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1486: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1487: free((FREE_ARG)(m+nrl-NR_END));
1488: }
1489:
1490: /*************** function subdirf ***********/
1491: char *subdirf(char fileres[])
1492: {
1493: /* Caution optionfilefiname is hidden */
1494: strcpy(tmpout,optionfilefiname);
1495: strcat(tmpout,"/"); /* Add to the right */
1496: strcat(tmpout,fileres);
1497: return tmpout;
1498: }
1499:
1500: /*************** function subdirf2 ***********/
1501: char *subdirf2(char fileres[], char *preop)
1502: {
1503:
1504: /* Caution optionfilefiname is hidden */
1505: strcpy(tmpout,optionfilefiname);
1506: strcat(tmpout,"/");
1507: strcat(tmpout,preop);
1508: strcat(tmpout,fileres);
1509: return tmpout;
1510: }
1511:
1512: /*************** function subdirf3 ***********/
1513: char *subdirf3(char fileres[], char *preop, char *preop2)
1514: {
1515:
1516: /* Caution optionfilefiname is hidden */
1517: strcpy(tmpout,optionfilefiname);
1518: strcat(tmpout,"/");
1519: strcat(tmpout,preop);
1520: strcat(tmpout,preop2);
1521: strcat(tmpout,fileres);
1522: return tmpout;
1523: }
1.213 brouard 1524:
1525: /*************** function subdirfext ***********/
1526: char *subdirfext(char fileres[], char *preop, char *postop)
1527: {
1528:
1529: strcpy(tmpout,preop);
1530: strcat(tmpout,fileres);
1531: strcat(tmpout,postop);
1532: return tmpout;
1533: }
1.126 brouard 1534:
1.213 brouard 1535: /*************** function subdirfext3 ***********/
1536: char *subdirfext3(char fileres[], char *preop, char *postop)
1537: {
1538:
1539: /* Caution optionfilefiname is hidden */
1540: strcpy(tmpout,optionfilefiname);
1541: strcat(tmpout,"/");
1542: strcat(tmpout,preop);
1543: strcat(tmpout,fileres);
1544: strcat(tmpout,postop);
1545: return tmpout;
1546: }
1547:
1.162 brouard 1548: char *asc_diff_time(long time_sec, char ascdiff[])
1549: {
1550: long sec_left, days, hours, minutes;
1551: days = (time_sec) / (60*60*24);
1552: sec_left = (time_sec) % (60*60*24);
1553: hours = (sec_left) / (60*60) ;
1554: sec_left = (sec_left) %(60*60);
1555: minutes = (sec_left) /60;
1556: sec_left = (sec_left) % (60);
1557: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1558: return ascdiff;
1559: }
1560:
1.126 brouard 1561: /***************** f1dim *************************/
1562: extern int ncom;
1563: extern double *pcom,*xicom;
1564: extern double (*nrfunc)(double []);
1565:
1566: double f1dim(double x)
1567: {
1568: int j;
1569: double f;
1570: double *xt;
1571:
1572: xt=vector(1,ncom);
1573: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1574: f=(*nrfunc)(xt);
1575: free_vector(xt,1,ncom);
1576: return f;
1577: }
1578:
1579: /*****************brent *************************/
1580: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1581: {
1582: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1583: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1584: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1585: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1586: * returned function value.
1587: */
1.126 brouard 1588: int iter;
1589: double a,b,d,etemp;
1.159 brouard 1590: double fu=0,fv,fw,fx;
1.164 brouard 1591: double ftemp=0.;
1.126 brouard 1592: double p,q,r,tol1,tol2,u,v,w,x,xm;
1593: double e=0.0;
1594:
1595: a=(ax < cx ? ax : cx);
1596: b=(ax > cx ? ax : cx);
1597: x=w=v=bx;
1598: fw=fv=fx=(*f)(x);
1599: for (iter=1;iter<=ITMAX;iter++) {
1600: xm=0.5*(a+b);
1601: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1602: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1603: printf(".");fflush(stdout);
1604: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1605: #ifdef DEBUGBRENT
1.126 brouard 1606: printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
1607: fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
1608: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1609: #endif
1610: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1611: *xmin=x;
1612: return fx;
1613: }
1614: ftemp=fu;
1615: if (fabs(e) > tol1) {
1616: r=(x-w)*(fx-fv);
1617: q=(x-v)*(fx-fw);
1618: p=(x-v)*q-(x-w)*r;
1619: q=2.0*(q-r);
1620: if (q > 0.0) p = -p;
1621: q=fabs(q);
1622: etemp=e;
1623: e=d;
1624: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1.224 brouard 1625: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1.126 brouard 1626: else {
1.224 brouard 1627: d=p/q;
1628: u=x+d;
1629: if (u-a < tol2 || b-u < tol2)
1630: d=SIGN(tol1,xm-x);
1.126 brouard 1631: }
1632: } else {
1633: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1634: }
1635: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1636: fu=(*f)(u);
1637: if (fu <= fx) {
1638: if (u >= x) a=x; else b=x;
1639: SHFT(v,w,x,u)
1.183 brouard 1640: SHFT(fv,fw,fx,fu)
1641: } else {
1642: if (u < x) a=u; else b=u;
1643: if (fu <= fw || w == x) {
1.224 brouard 1644: v=w;
1645: w=u;
1646: fv=fw;
1647: fw=fu;
1.183 brouard 1648: } else if (fu <= fv || v == x || v == w) {
1.224 brouard 1649: v=u;
1650: fv=fu;
1.183 brouard 1651: }
1652: }
1.126 brouard 1653: }
1654: nrerror("Too many iterations in brent");
1655: *xmin=x;
1656: return fx;
1657: }
1658:
1659: /****************** mnbrak ***********************/
1660:
1661: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1662: double (*func)(double))
1.183 brouard 1663: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1664: the downhill direction (defined by the function as evaluated at the initial points) and returns
1665: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1666: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1667: */
1.126 brouard 1668: double ulim,u,r,q, dum;
1669: double fu;
1.187 brouard 1670:
1671: double scale=10.;
1672: int iterscale=0;
1673:
1674: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1675: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1676:
1677:
1678: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1679: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1680: /* *bx = *ax - (*ax - *bx)/scale; */
1681: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1682: /* } */
1683:
1.126 brouard 1684: if (*fb > *fa) {
1685: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1686: SHFT(dum,*fb,*fa,dum)
1687: }
1.126 brouard 1688: *cx=(*bx)+GOLD*(*bx-*ax);
1689: *fc=(*func)(*cx);
1.183 brouard 1690: #ifdef DEBUG
1.224 brouard 1691: printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
1692: fprintf(ficlog,"mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
1.183 brouard 1693: #endif
1.224 brouard 1694: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc. If fc=inf it exits and if flat fb=fc it exits too.*/
1.126 brouard 1695: r=(*bx-*ax)*(*fb-*fc);
1.224 brouard 1696: q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
1.126 brouard 1697: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1698: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1699: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1700: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1701: fu=(*func)(u);
1.163 brouard 1702: #ifdef DEBUG
1703: /* f(x)=A(x-u)**2+f(u) */
1704: double A, fparabu;
1705: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1706: fparabu= *fa - A*(*ax-u)*(*ax-u);
1.224 brouard 1707: printf("\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
1708: fprintf(ficlog,"\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
1.183 brouard 1709: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1710: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1711: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1712: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1713: #endif
1.184 brouard 1714: #ifdef MNBRAKORIGINAL
1.183 brouard 1715: #else
1.191 brouard 1716: /* if (fu > *fc) { */
1717: /* #ifdef DEBUG */
1718: /* printf("mnbrak4 fu > fc \n"); */
1719: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1720: /* #endif */
1721: /* /\* SHFT(u,*cx,*cx,u) /\\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\\/ *\/ */
1722: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1723: /* dum=u; /\* Shifting c and u *\/ */
1724: /* u = *cx; */
1725: /* *cx = dum; */
1726: /* dum = fu; */
1727: /* fu = *fc; */
1728: /* *fc =dum; */
1729: /* } else { /\* end *\/ */
1730: /* #ifdef DEBUG */
1731: /* printf("mnbrak3 fu < fc \n"); */
1732: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1733: /* #endif */
1734: /* dum=u; /\* Shifting c and u *\/ */
1735: /* u = *cx; */
1736: /* *cx = dum; */
1737: /* dum = fu; */
1738: /* fu = *fc; */
1739: /* *fc =dum; */
1740: /* } */
1.224 brouard 1741: #ifdef DEBUGMNBRAK
1742: double A, fparabu;
1743: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1744: fparabu= *fa - A*(*ax-u)*(*ax-u);
1745: printf("\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
1746: fprintf(ficlog,"\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
1.183 brouard 1747: #endif
1.191 brouard 1748: dum=u; /* Shifting c and u */
1749: u = *cx;
1750: *cx = dum;
1751: dum = fu;
1752: fu = *fc;
1753: *fc =dum;
1.183 brouard 1754: #endif
1.162 brouard 1755: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1756: #ifdef DEBUG
1.224 brouard 1757: printf("\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1758: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1.183 brouard 1759: #endif
1.126 brouard 1760: fu=(*func)(u);
1761: if (fu < *fc) {
1.183 brouard 1762: #ifdef DEBUG
1.224 brouard 1763: printf("\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
1764: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
1765: #endif
1766: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1767: SHFT(*fb,*fc,fu,(*func)(u))
1768: #ifdef DEBUG
1769: printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
1.183 brouard 1770: #endif
1771: }
1.162 brouard 1772: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1773: #ifdef DEBUG
1.224 brouard 1774: printf("\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1775: fprintf(ficlog,"\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1.183 brouard 1776: #endif
1.126 brouard 1777: u=ulim;
1778: fu=(*func)(u);
1.183 brouard 1779: } else { /* u could be left to b (if r > q parabola has a maximum) */
1780: #ifdef DEBUG
1.224 brouard 1781: printf("\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
1782: fprintf(ficlog,"\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
1.183 brouard 1783: #endif
1.126 brouard 1784: u=(*cx)+GOLD*(*cx-*bx);
1785: fu=(*func)(u);
1.224 brouard 1786: #ifdef DEBUG
1787: printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
1788: fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
1789: #endif
1.183 brouard 1790: } /* end tests */
1.126 brouard 1791: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1792: SHFT(*fa,*fb,*fc,fu)
1793: #ifdef DEBUG
1.224 brouard 1794: printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
1795: fprintf(ficlog, "\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
1.183 brouard 1796: #endif
1797: } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
1.126 brouard 1798: }
1799:
1800: /*************** linmin ************************/
1.162 brouard 1801: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1802: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1803: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1804: the value of func at the returned location p . This is actually all accomplished by calling the
1805: routines mnbrak and brent .*/
1.126 brouard 1806: int ncom;
1807: double *pcom,*xicom;
1808: double (*nrfunc)(double []);
1809:
1.224 brouard 1810: #ifdef LINMINORIGINAL
1.126 brouard 1811: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1.224 brouard 1812: #else
1813: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat)
1814: #endif
1.126 brouard 1815: {
1816: double brent(double ax, double bx, double cx,
1817: double (*f)(double), double tol, double *xmin);
1818: double f1dim(double x);
1819: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1820: double *fc, double (*func)(double));
1821: int j;
1822: double xx,xmin,bx,ax;
1823: double fx,fb,fa;
1.187 brouard 1824:
1.203 brouard 1825: #ifdef LINMINORIGINAL
1826: #else
1827: double scale=10., axs, xxs; /* Scale added for infinity */
1828: #endif
1829:
1.126 brouard 1830: ncom=n;
1831: pcom=vector(1,n);
1832: xicom=vector(1,n);
1833: nrfunc=func;
1834: for (j=1;j<=n;j++) {
1835: pcom[j]=p[j];
1.202 brouard 1836: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1837: }
1.187 brouard 1838:
1.203 brouard 1839: #ifdef LINMINORIGINAL
1840: xx=1.;
1841: #else
1842: axs=0.0;
1843: xxs=1.;
1844: do{
1845: xx= xxs;
1846: #endif
1.187 brouard 1847: ax=0.;
1848: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1849: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1850: /* xt[x,j]=pcom[j]+x*xicom[j] f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j)) */
1851: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1852: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1853: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1854: /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus [0:xi[j]]*/
1.203 brouard 1855: #ifdef LINMINORIGINAL
1856: #else
1857: if (fx != fx){
1.224 brouard 1858: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1859: printf("|");
1860: fprintf(ficlog,"|");
1.203 brouard 1861: #ifdef DEBUGLINMIN
1.224 brouard 1862: printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n", axs, xxs, fx,fb, fa, xx, ax, bx);
1.203 brouard 1863: #endif
1864: }
1.224 brouard 1865: }while(fx != fx && xxs > 1.e-5);
1.203 brouard 1866: #endif
1867:
1.191 brouard 1868: #ifdef DEBUGLINMIN
1869: printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb);
1.202 brouard 1870: fprintf(ficlog,"\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb);
1.191 brouard 1871: #endif
1.224 brouard 1872: #ifdef LINMINORIGINAL
1873: #else
1874: if(fb == fx){ /* Flat function in the direction */
1875: xmin=xx;
1876: *flat=1;
1877: }else{
1878: *flat=0;
1879: #endif
1880: /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
1.187 brouard 1881: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1882: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1883: /* fmin = f(p[j] + xmin * xi[j]) */
1884: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1885: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1886: #ifdef DEBUG
1.224 brouard 1887: printf("retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
1888: fprintf(ficlog,"retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
1889: #endif
1890: #ifdef LINMINORIGINAL
1891: #else
1892: }
1.126 brouard 1893: #endif
1.191 brouard 1894: #ifdef DEBUGLINMIN
1895: printf("linmin end ");
1.202 brouard 1896: fprintf(ficlog,"linmin end ");
1.191 brouard 1897: #endif
1.126 brouard 1898: for (j=1;j<=n;j++) {
1.203 brouard 1899: #ifdef LINMINORIGINAL
1900: xi[j] *= xmin;
1901: #else
1902: #ifdef DEBUGLINMIN
1903: if(xxs <1.0)
1904: printf(" before xi[%d]=%12.8f", j,xi[j]);
1905: #endif
1906: xi[j] *= xmin*xxs; /* xi rescaled by xmin and number of loops: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
1907: #ifdef DEBUGLINMIN
1908: if(xxs <1.0)
1909: printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs );
1910: #endif
1911: #endif
1.187 brouard 1912: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1913: }
1.191 brouard 1914: #ifdef DEBUGLINMIN
1.203 brouard 1915: printf("\n");
1.191 brouard 1916: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 1917: fprintf(ficlog,"Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.191 brouard 1918: for (j=1;j<=n;j++) {
1.202 brouard 1919: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1920: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1921: if(j % ncovmodel == 0){
1.191 brouard 1922: printf("\n");
1.202 brouard 1923: fprintf(ficlog,"\n");
1924: }
1.191 brouard 1925: }
1.203 brouard 1926: #else
1.191 brouard 1927: #endif
1.126 brouard 1928: free_vector(xicom,1,n);
1929: free_vector(pcom,1,n);
1930: }
1931:
1932:
1933: /*************** powell ************************/
1.162 brouard 1934: /*
1935: Minimization of a function func of n variables. Input consists of an initial starting point
1936: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1937: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1938: such that failure to decrease by more than this amount on one iteration signals doneness. On
1939: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1940: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1941: */
1.224 brouard 1942: #ifdef LINMINORIGINAL
1943: #else
1944: int *flatdir; /* Function is vanishing in that direction */
1.225 brouard 1945: int flat=0, flatd=0; /* Function is vanishing in that direction */
1.224 brouard 1946: #endif
1.126 brouard 1947: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1948: double (*func)(double []))
1949: {
1.224 brouard 1950: #ifdef LINMINORIGINAL
1951: void linmin(double p[], double xi[], int n, double *fret,
1.126 brouard 1952: double (*func)(double []));
1.224 brouard 1953: #else
1954: void linmin(double p[], double xi[], int n, double *fret,
1955: double (*func)(double []),int *flat);
1956: #endif
1.126 brouard 1957: int i,ibig,j;
1958: double del,t,*pt,*ptt,*xit;
1.181 brouard 1959: double directest;
1.126 brouard 1960: double fp,fptt;
1961: double *xits;
1962: int niterf, itmp;
1.224 brouard 1963: #ifdef LINMINORIGINAL
1964: #else
1965:
1966: flatdir=ivector(1,n);
1967: for (j=1;j<=n;j++) flatdir[j]=0;
1968: #endif
1.126 brouard 1969:
1970: pt=vector(1,n);
1971: ptt=vector(1,n);
1972: xit=vector(1,n);
1973: xits=vector(1,n);
1974: *fret=(*func)(p);
1975: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 1976: rcurr_time = time(NULL);
1.126 brouard 1977: for (*iter=1;;++(*iter)) {
1.187 brouard 1978: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1979: ibig=0;
1980: del=0.0;
1.157 brouard 1981: rlast_time=rcurr_time;
1982: /* (void) gettimeofday(&curr_time,&tzp); */
1983: rcurr_time = time(NULL);
1984: curr_time = *localtime(&rcurr_time);
1985: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1986: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1987: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1988: for (i=1;i<=n;i++) {
1.126 brouard 1989: printf(" %d %.12f",i, p[i]);
1990: fprintf(ficlog," %d %.12lf",i, p[i]);
1991: fprintf(ficrespow," %.12lf", p[i]);
1992: }
1993: printf("\n");
1994: fprintf(ficlog,"\n");
1995: fprintf(ficrespow,"\n");fflush(ficrespow);
1996: if(*iter <=3){
1.157 brouard 1997: tml = *localtime(&rcurr_time);
1998: strcpy(strcurr,asctime(&tml));
1999: rforecast_time=rcurr_time;
1.126 brouard 2000: itmp = strlen(strcurr);
2001: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.224 brouard 2002: strcurr[itmp-1]='\0';
1.162 brouard 2003: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 2004: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 2005: for(niterf=10;niterf<=30;niterf+=10){
1.224 brouard 2006: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
2007: forecast_time = *localtime(&rforecast_time);
2008: strcpy(strfor,asctime(&forecast_time));
2009: itmp = strlen(strfor);
2010: if(strfor[itmp-1]=='\n')
2011: strfor[itmp-1]='\0';
2012: printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
2013: fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
1.126 brouard 2014: }
2015: }
1.187 brouard 2016: for (i=1;i<=n;i++) { /* For each direction i */
2017: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 2018: fptt=(*fret);
2019: #ifdef DEBUG
1.203 brouard 2020: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
2021: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 2022: #endif
1.203 brouard 2023: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 2024: fprintf(ficlog,"%d",i);fflush(ficlog);
1.224 brouard 2025: #ifdef LINMINORIGINAL
1.188 brouard 2026: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1.224 brouard 2027: #else
2028: linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
2029: flatdir[i]=flat; /* Function is vanishing in that direction i */
2030: #endif
2031: /* Outputs are fret(new point p) p is updated and xit rescaled */
1.188 brouard 2032: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1.224 brouard 2033: /* because that direction will be replaced unless the gain del is small */
2034: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
2035: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
2036: /* with the new direction. */
2037: del=fabs(fptt-(*fret));
2038: ibig=i;
1.126 brouard 2039: }
2040: #ifdef DEBUG
2041: printf("%d %.12e",i,(*fret));
2042: fprintf(ficlog,"%d %.12e",i,(*fret));
2043: for (j=1;j<=n;j++) {
1.224 brouard 2044: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
2045: printf(" x(%d)=%.12e",j,xit[j]);
2046: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1.126 brouard 2047: }
2048: for(j=1;j<=n;j++) {
1.225 brouard 2049: printf(" p(%d)=%.12e",j,p[j]);
2050: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 2051: }
2052: printf("\n");
2053: fprintf(ficlog,"\n");
2054: #endif
1.187 brouard 2055: } /* end loop on each direction i */
2056: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 2057: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 2058: /* New value of last point Pn is not computed, P(n-1) */
1.224 brouard 2059: for(j=1;j<=n;j++) {
1.225 brouard 2060: if(flatdir[j] >0){
2061: printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2062: fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2063: }
2064: /* printf("\n"); */
2065: /* fprintf(ficlog,"\n"); */
2066: }
1.182 brouard 2067: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 2068: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
2069: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
2070: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
2071: /* decreased of more than 3.84 */
2072: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
2073: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
2074: /* By adding 10 parameters more the gain should be 18.31 */
1.224 brouard 2075:
1.188 brouard 2076: /* Starting the program with initial values given by a former maximization will simply change */
2077: /* the scales of the directions and the directions, because the are reset to canonical directions */
2078: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
2079: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 2080: #ifdef DEBUG
2081: int k[2],l;
2082: k[0]=1;
2083: k[1]=-1;
2084: printf("Max: %.12e",(*func)(p));
2085: fprintf(ficlog,"Max: %.12e",(*func)(p));
2086: for (j=1;j<=n;j++) {
2087: printf(" %.12e",p[j]);
2088: fprintf(ficlog," %.12e",p[j]);
2089: }
2090: printf("\n");
2091: fprintf(ficlog,"\n");
2092: for(l=0;l<=1;l++) {
2093: for (j=1;j<=n;j++) {
2094: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
2095: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2096: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2097: }
2098: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2099: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2100: }
2101: #endif
2102:
1.224 brouard 2103: #ifdef LINMINORIGINAL
2104: #else
2105: free_ivector(flatdir,1,n);
2106: #endif
1.126 brouard 2107: free_vector(xit,1,n);
2108: free_vector(xits,1,n);
2109: free_vector(ptt,1,n);
2110: free_vector(pt,1,n);
2111: return;
1.192 brouard 2112: } /* enough precision */
1.126 brouard 2113: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 2114: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 2115: ptt[j]=2.0*p[j]-pt[j];
2116: xit[j]=p[j]-pt[j];
2117: pt[j]=p[j];
2118: }
1.181 brouard 2119: fptt=(*func)(ptt); /* f_3 */
1.224 brouard 2120: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
2121: if (*iter <=4) {
1.225 brouard 2122: #else
2123: #endif
1.224 brouard 2124: #ifdef POWELLNOF3INFF1TEST /* skips test F3 <F1 */
1.192 brouard 2125: #else
1.161 brouard 2126: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 2127: #endif
1.162 brouard 2128: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 2129: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 2130: /* Let f"(x2) be the 2nd derivative equal everywhere. */
2131: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
2132: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.224 brouard 2133: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
2134: /* also lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
2135: /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
1.161 brouard 2136: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.224 brouard 2137: /* Even if f3 <f1, directest can be negative and t >0 */
2138: /* mu² and del² are equal when f3=f1 */
2139: /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
2140: /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
2141: /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0 */
2142: /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0 */
1.183 brouard 2143: #ifdef NRCORIGINAL
2144: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
2145: #else
2146: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
1.161 brouard 2147: t= t- del*SQR(fp-fptt);
1.183 brouard 2148: #endif
1.202 brouard 2149: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 2150: #ifdef DEBUG
1.181 brouard 2151: printf("t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
2152: fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
1.161 brouard 2153: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2154: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2155: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2156: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2157: printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
2158: fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
2159: #endif
1.183 brouard 2160: #ifdef POWELLORIGINAL
2161: if (t < 0.0) { /* Then we use it for new direction */
2162: #else
1.182 brouard 2163: if (directest*t < 0.0) { /* Contradiction between both tests */
1.224 brouard 2164: printf("directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
1.192 brouard 2165: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1.224 brouard 2166: fprintf(ficlog,"directest= %.12lf (if directest<0 or t<0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1.192 brouard 2167: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
2168: }
1.181 brouard 2169: if (directest < 0.0) { /* Then we use it for new direction */
2170: #endif
1.191 brouard 2171: #ifdef DEBUGLINMIN
1.224 brouard 2172: printf("Before linmin in direction P%d-P0\n",n);
2173: for (j=1;j<=n;j++) {
2174: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2175: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2176: if(j % ncovmodel == 0){
2177: printf("\n");
2178: fprintf(ficlog,"\n");
2179: }
2180: }
2181: #endif
2182: #ifdef LINMINORIGINAL
2183: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
2184: #else
2185: linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
2186: flatdir[i]=flat; /* Function is vanishing in that direction i */
1.191 brouard 2187: #endif
1.224 brouard 2188:
1.191 brouard 2189: #ifdef DEBUGLINMIN
1.224 brouard 2190: for (j=1;j<=n;j++) {
2191: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2192: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2193: if(j % ncovmodel == 0){
2194: printf("\n");
2195: fprintf(ficlog,"\n");
2196: }
2197: }
2198: #endif
2199: for (j=1;j<=n;j++) {
2200: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
2201: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
2202: }
2203: #ifdef LINMINORIGINAL
2204: #else
1.225 brouard 2205: for (j=1, flatd=0;j<=n;j++) {
2206: if(flatdir[j]>0)
2207: flatd++;
2208: }
2209: if(flatd >0){
2210: printf("%d flat directions\n",flatd);
2211: fprintf(ficlog,"%d flat directions\n",flatd);
2212: for (j=1;j<=n;j++) {
2213: if(flatdir[j]>0){
2214: printf("%d ",j);
2215: fprintf(ficlog,"%d ",j);
2216: }
2217: }
2218: printf("\n");
2219: fprintf(ficlog,"\n");
2220: }
1.191 brouard 2221: #endif
1.224 brouard 2222: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2223: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2224:
1.126 brouard 2225: #ifdef DEBUG
1.224 brouard 2226: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2227: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2228: for(j=1;j<=n;j++){
2229: printf(" %lf",xit[j]);
2230: fprintf(ficlog," %lf",xit[j]);
2231: }
2232: printf("\n");
2233: fprintf(ficlog,"\n");
1.126 brouard 2234: #endif
1.192 brouard 2235: } /* end of t or directest negative */
1.224 brouard 2236: #ifdef POWELLNOF3INFF1TEST
1.192 brouard 2237: #else
1.162 brouard 2238: } /* end if (fptt < fp) */
1.192 brouard 2239: #endif
1.225 brouard 2240: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
1.224 brouard 2241: } /*NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done */
1.225 brouard 2242: #else
1.224 brouard 2243: #endif
1.192 brouard 2244: } /* loop iteration */
1.126 brouard 2245: }
2246:
2247: /**** Prevalence limit (stable or period prevalence) ****************/
2248:
1.203 brouard 2249: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
1.126 brouard 2250: {
1.218 brouard 2251: /* Computes the prevalence limit in each live state at age x and for covariate ij by left multiplying the unit
1.203 brouard 2252: matrix by transitions matrix until convergence is reached with precision ftolpl */
1.206 brouard 2253: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2254: /* Wx is row vector: population in state 1, population in state 2, population dead */
2255: /* or prevalence in state 1, prevalence in state 2, 0 */
2256: /* newm is the matrix after multiplications, its rows are identical at a factor */
2257: /* Initial matrix pimij */
2258: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2259: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2260: /* 0, 0 , 1} */
2261: /*
2262: * and after some iteration: */
2263: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2264: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2265: /* 0, 0 , 1} */
2266: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2267: /* {0.51571254859325999, 0.4842874514067399, */
2268: /* 0.51326036147820708, 0.48673963852179264} */
2269: /* If we start from prlim again, prlim tends to a constant matrix */
2270:
1.126 brouard 2271: int i, ii,j,k;
1.209 brouard 2272: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2273: /* double **matprod2(); */ /* test */
1.218 brouard 2274: double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126 brouard 2275: double **newm;
1.209 brouard 2276: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2277: int ncvloop=0;
1.169 brouard 2278:
1.209 brouard 2279: min=vector(1,nlstate);
2280: max=vector(1,nlstate);
2281: meandiff=vector(1,nlstate);
2282:
1.218 brouard 2283: /* Starting with matrix unity */
1.126 brouard 2284: for (ii=1;ii<=nlstate+ndeath;ii++)
2285: for (j=1;j<=nlstate+ndeath;j++){
2286: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2287: }
1.169 brouard 2288:
2289: cov[1]=1.;
2290:
2291: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2292: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2293: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2294: ncvloop++;
1.126 brouard 2295: newm=savm;
2296: /* Covariates have to be included here again */
1.138 brouard 2297: cov[2]=agefin;
1.187 brouard 2298: if(nagesqr==1)
2299: cov[3]= agefin*agefin;;
1.138 brouard 2300: for (k=1; k<=cptcovn;k++) {
1.200 brouard 2301: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.218 brouard 2302: /* Here comes the value of the covariate 'ij' */
1.200 brouard 2303: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
1.198 brouard 2304: /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */
1.138 brouard 2305: }
1.186 brouard 2306: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2307: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2308: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
1.186 brouard 2309: for (k=1; k<=cptcovprod;k++) /* Useless */
1.200 brouard 2310: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2311: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.138 brouard 2312:
2313: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2314: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2315: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2316: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2317: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2318: /* age and covariate values of ij are in 'cov' */
1.142 brouard 2319: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2320:
1.126 brouard 2321: savm=oldm;
2322: oldm=newm;
1.209 brouard 2323:
2324: for(j=1; j<=nlstate; j++){
2325: max[j]=0.;
2326: min[j]=1.;
2327: }
2328: for(i=1;i<=nlstate;i++){
2329: sumnew=0;
2330: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2331: for(j=1; j<=nlstate; j++){
2332: prlim[i][j]= newm[i][j]/(1-sumnew);
2333: max[j]=FMAX(max[j],prlim[i][j]);
2334: min[j]=FMIN(min[j],prlim[i][j]);
2335: }
2336: }
2337:
1.126 brouard 2338: maxmax=0.;
1.209 brouard 2339: for(j=1; j<=nlstate; j++){
2340: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2341: maxmax=FMAX(maxmax,meandiff[j]);
2342: /* printf(" age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, j, meandiff[j],(int)agefin, j, max[j], j, min[j],maxmax); */
1.169 brouard 2343: } /* j loop */
1.203 brouard 2344: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2345: /* printf("maxmax=%lf maxmin=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.126 brouard 2346: if(maxmax < ftolpl){
1.209 brouard 2347: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2348: free_vector(min,1,nlstate);
2349: free_vector(max,1,nlstate);
2350: free_vector(meandiff,1,nlstate);
1.126 brouard 2351: return prlim;
2352: }
1.169 brouard 2353: } /* age loop */
1.208 brouard 2354: /* After some age loop it doesn't converge */
1.209 brouard 2355: printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
1.208 brouard 2356: Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
1.209 brouard 2357: /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
2358: free_vector(min,1,nlstate);
2359: free_vector(max,1,nlstate);
2360: free_vector(meandiff,1,nlstate);
1.208 brouard 2361:
1.169 brouard 2362: return prlim; /* should not reach here */
1.126 brouard 2363: }
2364:
1.217 brouard 2365:
2366: /**** Back Prevalence limit (stable or period prevalence) ****************/
2367:
1.218 brouard 2368: /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ageminpar, double agemaxpar, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
2369: /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
2370: double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij)
1.217 brouard 2371: {
1.218 brouard 2372: /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit
1.217 brouard 2373: matrix by transitions matrix until convergence is reached with precision ftolpl */
2374: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2375: /* Wx is row vector: population in state 1, population in state 2, population dead */
2376: /* or prevalence in state 1, prevalence in state 2, 0 */
2377: /* newm is the matrix after multiplications, its rows are identical at a factor */
2378: /* Initial matrix pimij */
2379: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2380: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2381: /* 0, 0 , 1} */
2382: /*
2383: * and after some iteration: */
2384: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2385: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2386: /* 0, 0 , 1} */
2387: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2388: /* {0.51571254859325999, 0.4842874514067399, */
2389: /* 0.51326036147820708, 0.48673963852179264} */
2390: /* If we start from prlim again, prlim tends to a constant matrix */
2391:
2392: int i, ii,j,k;
2393: double *min, *max, *meandiff, maxmax,sumnew=0.;
2394: /* double **matprod2(); */ /* test */
2395: double **out, cov[NCOVMAX+1], **bmij();
2396: double **newm;
1.218 brouard 2397: double **dnewm, **doldm, **dsavm; /* for use */
2398: double **oldm, **savm; /* for use */
2399:
1.217 brouard 2400: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
2401: int ncvloop=0;
2402:
2403: min=vector(1,nlstate);
2404: max=vector(1,nlstate);
2405: meandiff=vector(1,nlstate);
2406:
1.218 brouard 2407: dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
2408: oldm=oldms; savm=savms;
2409:
2410: /* Starting with matrix unity */
2411: for (ii=1;ii<=nlstate+ndeath;ii++)
2412: for (j=1;j<=nlstate+ndeath;j++){
1.217 brouard 2413: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2414: }
2415:
2416: cov[1]=1.;
2417:
2418: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2419: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218 brouard 2420: /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
2421: for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217 brouard 2422: ncvloop++;
1.218 brouard 2423: newm=savm; /* oldm should be kept from previous iteration or unity at start */
2424: /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217 brouard 2425: /* Covariates have to be included here again */
2426: cov[2]=agefin;
2427: if(nagesqr==1)
2428: cov[3]= agefin*agefin;;
2429: for (k=1; k<=cptcovn;k++) {
2430: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
2431: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2432: /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */
2433: }
2434: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2435: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2436: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
2437: for (k=1; k<=cptcovprod;k++) /* Useless */
2438: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2439: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2440:
2441: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2442: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2443: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
2444: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2445: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2446: /* ij should be linked to the correct index of cov */
2447: /* age and covariate values ij are in 'cov', but we need to pass
2448: * ij for the observed prevalence at age and status and covariate
2449: * number: prevacurrent[(int)agefin][ii][ij]
2450: */
2451: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
2452: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
2453: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
1.217 brouard 2454: savm=oldm;
2455: oldm=newm;
2456: for(j=1; j<=nlstate; j++){
2457: max[j]=0.;
2458: min[j]=1.;
2459: }
2460: for(j=1; j<=nlstate; j++){
2461: for(i=1;i<=nlstate;i++){
1.218 brouard 2462: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
2463: bprlim[i][j]= newm[i][j];
2464: max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
2465: min[i]=FMIN(min[i],bprlim[i][j]);
1.217 brouard 2466: }
2467: }
1.218 brouard 2468:
1.217 brouard 2469: maxmax=0.;
2470: for(i=1; i<=nlstate; i++){
2471: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
2472: maxmax=FMAX(maxmax,meandiff[i]);
2473: /* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */
2474: } /* j loop */
2475: *ncvyear= -( (int)age- (int)agefin);
1.218 brouard 2476: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/
1.217 brouard 2477: if(maxmax < ftolpl){
1.220 brouard 2478: /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2479: free_vector(min,1,nlstate);
2480: free_vector(max,1,nlstate);
2481: free_vector(meandiff,1,nlstate);
2482: return bprlim;
2483: }
2484: } /* age loop */
2485: /* After some age loop it doesn't converge */
2486: printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
2487: Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
2488: /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
2489: free_vector(min,1,nlstate);
2490: free_vector(max,1,nlstate);
2491: free_vector(meandiff,1,nlstate);
2492:
2493: return bprlim; /* should not reach here */
2494: }
2495:
1.126 brouard 2496: /*************** transition probabilities ***************/
2497:
2498: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2499: {
1.138 brouard 2500: /* According to parameters values stored in x and the covariate's values stored in cov,
2501: computes the probability to be observed in state j being in state i by appying the
2502: model to the ncovmodel covariates (including constant and age).
2503: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2504: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2505: ncth covariate in the global vector x is given by the formula:
2506: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2507: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2508: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2509: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2510: Outputs ps[i][j] the probability to be observed in j being in j according to
2511: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2512: */
2513: double s1, lnpijopii;
1.126 brouard 2514: /*double t34;*/
1.164 brouard 2515: int i,j, nc, ii, jj;
1.126 brouard 2516:
1.223 brouard 2517: for(i=1; i<= nlstate; i++){
2518: for(j=1; j<i;j++){
2519: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2520: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2521: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2522: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2523: }
2524: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2525: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2526: }
2527: for(j=i+1; j<=nlstate+ndeath;j++){
2528: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2529: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2530: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2531: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2532: }
2533: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2534: }
2535: }
1.218 brouard 2536:
1.223 brouard 2537: for(i=1; i<= nlstate; i++){
2538: s1=0;
2539: for(j=1; j<i; j++){
2540: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2541: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2542: }
2543: for(j=i+1; j<=nlstate+ndeath; j++){
2544: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2545: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2546: }
2547: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2548: ps[i][i]=1./(s1+1.);
2549: /* Computing other pijs */
2550: for(j=1; j<i; j++)
2551: ps[i][j]= exp(ps[i][j])*ps[i][i];
2552: for(j=i+1; j<=nlstate+ndeath; j++)
2553: ps[i][j]= exp(ps[i][j])*ps[i][i];
2554: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2555: } /* end i */
1.218 brouard 2556:
1.223 brouard 2557: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2558: for(jj=1; jj<= nlstate+ndeath; jj++){
2559: ps[ii][jj]=0;
2560: ps[ii][ii]=1;
2561: }
2562: }
1.218 brouard 2563:
2564:
1.223 brouard 2565: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2566: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2567: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2568: /* } */
2569: /* printf("\n "); */
2570: /* } */
2571: /* printf("\n ");printf("%lf ",cov[2]);*/
2572: /*
2573: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1.218 brouard 2574: goto end;*/
1.223 brouard 2575: return ps;
1.126 brouard 2576: }
2577:
1.218 brouard 2578: /*************** backward transition probabilities ***************/
2579:
2580: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ageminpar, double agemaxpar, double ***dnewm, double **doldm, double **dsavm, int ij ) */
2581: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
2582: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij )
2583: {
1.222 brouard 2584: /* Computes the backward probability at age agefin and covariate ij
2585: * and returns in **ps as well as **bmij.
2586: */
1.218 brouard 2587: int i, ii, j,k;
1.222 brouard 2588:
2589: double **out, **pmij();
2590: double sumnew=0.;
1.218 brouard 2591: double agefin;
1.222 brouard 2592:
2593: double **dnewm, **dsavm, **doldm;
2594: double **bbmij;
2595:
1.218 brouard 2596: doldm=ddoldms; /* global pointers */
1.222 brouard 2597: dnewm=ddnewms;
2598: dsavm=ddsavms;
2599:
2600: agefin=cov[2];
2601: /* bmij *//* age is cov[2], ij is included in cov, but we need for
2602: the observed prevalence (with this covariate ij) */
2603: dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
2604: /* We do have the matrix Px in savm and we need pij */
2605: for (j=1;j<=nlstate+ndeath;j++){
2606: sumnew=0.; /* w1 p11 + w2 p21 only on live states */
2607: for (ii=1;ii<=nlstate;ii++){
2608: sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
2609: } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
2610: for (ii=1;ii<=nlstate+ndeath;ii++){
2611: if(sumnew >= 1.e-10){
2612: /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
2613: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
2614: /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
2615: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
2616: /* }else */
2617: doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
2618: }else{
2619: printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin);
2620: }
2621: } /*End ii */
2622: } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
2623: /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
2624: bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
2625: /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
2626: /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
2627: /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
2628: /* left Product of this matrix by diag matrix of prevalences (savm) */
2629: for (j=1;j<=nlstate+ndeath;j++){
2630: for (ii=1;ii<=nlstate+ndeath;ii++){
2631: dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
2632: }
2633: } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
2634: ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
2635: /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
2636: /* end bmij */
2637: return ps;
1.218 brouard 2638: }
1.217 brouard 2639: /*************** transition probabilities ***************/
2640:
1.218 brouard 2641: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217 brouard 2642: {
2643: /* According to parameters values stored in x and the covariate's values stored in cov,
2644: computes the probability to be observed in state j being in state i by appying the
2645: model to the ncovmodel covariates (including constant and age).
2646: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2647: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2648: ncth covariate in the global vector x is given by the formula:
2649: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2650: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2651: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2652: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2653: Outputs ps[i][j] the probability to be observed in j being in j according to
2654: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2655: */
2656: double s1, lnpijopii;
2657: /*double t34;*/
2658: int i,j, nc, ii, jj;
2659:
1.218 brouard 2660: for(i=1; i<= nlstate; i++){
2661: for(j=1; j<i;j++){
2662: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2663: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2664: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2665: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2666: }
2667: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2668: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2669: }
2670: for(j=i+1; j<=nlstate+ndeath;j++){
2671: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2672: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2673: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2674: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2675: }
2676: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2677: }
2678: }
2679:
2680: for(i=1; i<= nlstate; i++){
2681: s1=0;
2682: for(j=1; j<i; j++){
2683: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2684: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2685: }
2686: for(j=i+1; j<=nlstate+ndeath; j++){
2687: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2688: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2689: }
2690: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2691: ps[i][i]=1./(s1+1.);
2692: /* Computing other pijs */
2693: for(j=1; j<i; j++)
2694: ps[i][j]= exp(ps[i][j])*ps[i][i];
2695: for(j=i+1; j<=nlstate+ndeath; j++)
2696: ps[i][j]= exp(ps[i][j])*ps[i][i];
2697: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2698: } /* end i */
2699:
2700: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2701: for(jj=1; jj<= nlstate+ndeath; jj++){
2702: ps[ii][jj]=0;
2703: ps[ii][ii]=1;
2704: }
2705: }
2706: /* Added for backcast */ /* Transposed matrix too */
2707: for(jj=1; jj<= nlstate+ndeath; jj++){
2708: s1=0.;
2709: for(ii=1; ii<= nlstate+ndeath; ii++){
2710: s1+=ps[ii][jj];
2711: }
2712: for(ii=1; ii<= nlstate; ii++){
2713: ps[ii][jj]=ps[ii][jj]/s1;
2714: }
2715: }
2716: /* Transposition */
2717: for(jj=1; jj<= nlstate+ndeath; jj++){
2718: for(ii=jj; ii<= nlstate+ndeath; ii++){
2719: s1=ps[ii][jj];
2720: ps[ii][jj]=ps[jj][ii];
2721: ps[jj][ii]=s1;
2722: }
2723: }
2724: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2725: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2726: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2727: /* } */
2728: /* printf("\n "); */
2729: /* } */
2730: /* printf("\n ");printf("%lf ",cov[2]);*/
2731: /*
2732: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2733: goto end;*/
2734: return ps;
1.217 brouard 2735: }
2736:
2737:
1.126 brouard 2738: /**************** Product of 2 matrices ******************/
2739:
1.145 brouard 2740: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2741: {
2742: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2743: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2744: /* in, b, out are matrice of pointers which should have been initialized
2745: before: only the contents of out is modified. The function returns
2746: a pointer to pointers identical to out */
1.145 brouard 2747: int i, j, k;
1.126 brouard 2748: for(i=nrl; i<= nrh; i++)
1.145 brouard 2749: for(k=ncolol; k<=ncoloh; k++){
2750: out[i][k]=0.;
2751: for(j=ncl; j<=nch; j++)
2752: out[i][k] +=in[i][j]*b[j][k];
2753: }
1.126 brouard 2754: return out;
2755: }
2756:
2757:
2758: /************* Higher Matrix Product ***************/
2759:
2760: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2761: {
1.218 brouard 2762: /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
1.126 brouard 2763: 'nhstepm*hstepm*stepm' months (i.e. until
2764: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2765: nhstepm*hstepm matrices.
2766: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2767: (typically every 2 years instead of every month which is too big
2768: for the memory).
2769: Model is determined by parameters x and covariates have to be
2770: included manually here.
2771:
2772: */
2773:
2774: int i, j, d, h, k;
1.131 brouard 2775: double **out, cov[NCOVMAX+1];
1.126 brouard 2776: double **newm;
1.187 brouard 2777: double agexact;
1.214 brouard 2778: double agebegin, ageend;
1.126 brouard 2779:
2780: /* Hstepm could be zero and should return the unit matrix */
2781: for (i=1;i<=nlstate+ndeath;i++)
2782: for (j=1;j<=nlstate+ndeath;j++){
2783: oldm[i][j]=(i==j ? 1.0 : 0.0);
2784: po[i][j][0]=(i==j ? 1.0 : 0.0);
2785: }
2786: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2787: for(h=1; h <=nhstepm; h++){
2788: for(d=1; d <=hstepm; d++){
2789: newm=savm;
2790: /* Covariates have to be included here again */
2791: cov[1]=1.;
1.214 brouard 2792: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 2793: cov[2]=agexact;
2794: if(nagesqr==1)
1.227 brouard 2795: cov[3]= agexact*agexact;
1.131 brouard 2796: for (k=1; k<=cptcovn;k++)
1.227 brouard 2797: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2798: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.186 brouard 2799: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1.227 brouard 2800: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2801: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2802: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.145 brouard 2803: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.227 brouard 2804: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2805: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2806:
2807:
1.126 brouard 2808: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2809: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 2810: /* right multiplication of oldm by the current matrix */
1.126 brouard 2811: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2812: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 brouard 2813: /* if((int)age == 70){ */
2814: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
2815: /* for(i=1; i<=nlstate+ndeath; i++) { */
2816: /* printf("%d pmmij ",i); */
2817: /* for(j=1;j<=nlstate+ndeath;j++) { */
2818: /* printf("%f ",pmmij[i][j]); */
2819: /* } */
2820: /* printf(" oldm "); */
2821: /* for(j=1;j<=nlstate+ndeath;j++) { */
2822: /* printf("%f ",oldm[i][j]); */
2823: /* } */
2824: /* printf("\n"); */
2825: /* } */
2826: /* } */
1.126 brouard 2827: savm=oldm;
2828: oldm=newm;
2829: }
2830: for(i=1; i<=nlstate+ndeath; i++)
2831: for(j=1;j<=nlstate+ndeath;j++) {
1.218 brouard 2832: po[i][j][h]=newm[i][j];
2833: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2834: }
1.128 brouard 2835: /*printf("h=%d ",h);*/
1.126 brouard 2836: } /* end h */
1.218 brouard 2837: /* printf("\n H=%d \n",h); */
1.126 brouard 2838: return po;
2839: }
2840:
1.217 brouard 2841: /************* Higher Back Matrix Product ***************/
1.218 brouard 2842: /* double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */
1.222 brouard 2843: double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )
1.217 brouard 2844: {
1.218 brouard 2845: /* Computes the transition matrix starting at age 'age' over
1.217 brouard 2846: 'nhstepm*hstepm*stepm' months (i.e. until
1.218 brouard 2847: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2848: nhstepm*hstepm matrices.
2849: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2850: (typically every 2 years instead of every month which is too big
1.217 brouard 2851: for the memory).
1.218 brouard 2852: Model is determined by parameters x and covariates have to be
2853: included manually here.
1.217 brouard 2854:
1.222 brouard 2855: */
1.217 brouard 2856:
2857: int i, j, d, h, k;
2858: double **out, cov[NCOVMAX+1];
2859: double **newm;
2860: double agexact;
2861: double agebegin, ageend;
1.222 brouard 2862: double **oldm, **savm;
1.217 brouard 2863:
1.222 brouard 2864: oldm=oldms;savm=savms;
1.217 brouard 2865: /* Hstepm could be zero and should return the unit matrix */
2866: for (i=1;i<=nlstate+ndeath;i++)
2867: for (j=1;j<=nlstate+ndeath;j++){
2868: oldm[i][j]=(i==j ? 1.0 : 0.0);
2869: po[i][j][0]=(i==j ? 1.0 : 0.0);
2870: }
2871: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2872: for(h=1; h <=nhstepm; h++){
2873: for(d=1; d <=hstepm; d++){
2874: newm=savm;
2875: /* Covariates have to be included here again */
2876: cov[1]=1.;
2877: agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
2878: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
2879: cov[2]=agexact;
2880: if(nagesqr==1)
1.222 brouard 2881: cov[3]= agexact*agexact;
1.218 brouard 2882: for (k=1; k<=cptcovn;k++)
1.222 brouard 2883: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2884: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.217 brouard 2885: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1.222 brouard 2886: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2887: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2888: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.217 brouard 2889: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.222 brouard 2890: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2891: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
1.218 brouard 2892:
2893:
1.217 brouard 2894: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2895: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 2896: /* Careful transposed matrix */
1.222 brouard 2897: /* age is in cov[2] */
1.218 brouard 2898: /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
1.222 brouard 2899: /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
1.218 brouard 2900: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1.222 brouard 2901: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217 brouard 2902: /* if((int)age == 70){ */
2903: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
2904: /* for(i=1; i<=nlstate+ndeath; i++) { */
2905: /* printf("%d pmmij ",i); */
2906: /* for(j=1;j<=nlstate+ndeath;j++) { */
2907: /* printf("%f ",pmmij[i][j]); */
2908: /* } */
2909: /* printf(" oldm "); */
2910: /* for(j=1;j<=nlstate+ndeath;j++) { */
2911: /* printf("%f ",oldm[i][j]); */
2912: /* } */
2913: /* printf("\n"); */
2914: /* } */
2915: /* } */
2916: savm=oldm;
2917: oldm=newm;
2918: }
2919: for(i=1; i<=nlstate+ndeath; i++)
2920: for(j=1;j<=nlstate+ndeath;j++) {
1.222 brouard 2921: po[i][j][h]=newm[i][j];
2922: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.217 brouard 2923: }
2924: /*printf("h=%d ",h);*/
2925: } /* end h */
1.222 brouard 2926: /* printf("\n H=%d \n",h); */
1.217 brouard 2927: return po;
2928: }
2929:
2930:
1.162 brouard 2931: #ifdef NLOPT
2932: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2933: double fret;
2934: double *xt;
2935: int j;
2936: myfunc_data *d2 = (myfunc_data *) pd;
2937: /* xt = (p1-1); */
2938: xt=vector(1,n);
2939: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2940:
2941: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2942: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2943: printf("Function = %.12lf ",fret);
2944: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2945: printf("\n");
2946: free_vector(xt,1,n);
2947: return fret;
2948: }
2949: #endif
1.126 brouard 2950:
2951: /*************** log-likelihood *************/
2952: double func( double *x)
2953: {
1.226 brouard 2954: int i, ii, j, k, mi, d, kk;
2955: int ioffset=0;
2956: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
2957: double **out;
2958: double lli; /* Individual log likelihood */
2959: int s1, s2;
1.228 brouard 2960: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
1.226 brouard 2961: double bbh, survp;
2962: long ipmx;
2963: double agexact;
2964: /*extern weight */
2965: /* We are differentiating ll according to initial status */
2966: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2967: /*for(i=1;i<imx;i++)
2968: printf(" %d\n",s[4][i]);
2969: */
1.162 brouard 2970:
1.226 brouard 2971: ++countcallfunc;
1.162 brouard 2972:
1.226 brouard 2973: cov[1]=1.;
1.126 brouard 2974:
1.226 brouard 2975: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 2976: ioffset=0;
1.226 brouard 2977: if(mle==1){
2978: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2979: /* Computes the values of the ncovmodel covariates of the model
2980: depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
2981: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2982: to be observed in j being in i according to the model.
2983: */
2984: ioffset=2+nagesqr+cptcovage;
2985: /* for (k=1; k<=cptcovn;k++){ /\* Simple and product covariates without age* products *\/ */
2986: for (k=1; k<=ncoveff;k++){ /* Simple and product covariates without age* products */
2987: cov[++ioffset]=covar[Tvar[k]][i];
2988: }
2989: for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitatives and Fixed covariates */
1.228 brouard 2990: cov[++ioffset]=coqvar[Tvar[iqv]][i];
1.226 brouard 2991: }
2992:
2993: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
2994: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
2995: has been calculated etc */
2996: /* For an individual i, wav[i] gives the number of effective waves */
2997: /* We compute the contribution to Likelihood of each effective transition
2998: mw[mi][i] is real wave of the mi th effectve wave */
2999: /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
3000: s2=s[mw[mi+1][i]][i];
3001: And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
3002: But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
3003: meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
3004: */
3005: for(mi=1; mi<= wav[i]-1; mi++){
3006: for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
1.229 brouard 3007: /* cov[ioffset+itv]=cotvar[mw[mi][i]][Tvar[itv]][i]; /\* Not sure, Tvar V4+V3+V5 Tvaraff ? *\/ */
3008: cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i];
1.226 brouard 3009: }
3010: for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
3011: if(cotqvar[mw[mi][i]][iqtv][i] == -1){
3012: printf("i=%d, mi=%d, iqtv=%d, cotqvar[mw[mi][i]][iqtv][i]=%f",i,mi,iqtv,cotqvar[mw[mi][i]][iqtv][i]);
3013: }
1.229 brouard 3014: cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i];
3015: /* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i]; */
1.226 brouard 3016: }
3017: /* ioffset=2+nagesqr+cptcovn+nqv+ntv+nqtv; */
3018: for (ii=1;ii<=nlstate+ndeath;ii++)
3019: for (j=1;j<=nlstate+ndeath;j++){
3020: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3021: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3022: }
3023: for(d=0; d<dh[mi][i]; d++){
3024: newm=savm;
3025: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3026: cov[2]=agexact;
3027: if(nagesqr==1)
3028: cov[3]= agexact*agexact; /* Should be changed here */
3029: for (kk=1; kk<=cptcovage;kk++) {
3030: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
3031: }
3032: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3033: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3034: savm=oldm;
3035: oldm=newm;
3036: } /* end mult */
1.224 brouard 3037:
1.226 brouard 3038: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
3039: /* But now since version 0.9 we anticipate for bias at large stepm.
3040: * If stepm is larger than one month (smallest stepm) and if the exact delay
3041: * (in months) between two waves is not a multiple of stepm, we rounded to
3042: * the nearest (and in case of equal distance, to the lowest) interval but now
3043: * we keep into memory the bias bh[mi][i] and also the previous matrix product
3044: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
3045: * probability in order to take into account the bias as a fraction of the way
3046: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
3047: * -stepm/2 to stepm/2 .
3048: * For stepm=1 the results are the same as for previous versions of Imach.
3049: * For stepm > 1 the results are less biased than in previous versions.
3050: */
3051: s1=s[mw[mi][i]][i];
3052: s2=s[mw[mi+1][i]][i];
3053: bbh=(double)bh[mi][i]/(double)stepm;
3054: /* bias bh is positive if real duration
3055: * is higher than the multiple of stepm and negative otherwise.
3056: */
3057: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
3058: if( s2 > nlstate){
3059: /* i.e. if s2 is a death state and if the date of death is known
3060: then the contribution to the likelihood is the probability to
3061: die between last step unit time and current step unit time,
3062: which is also equal to probability to die before dh
3063: minus probability to die before dh-stepm .
3064: In version up to 0.92 likelihood was computed
3065: as if date of death was unknown. Death was treated as any other
3066: health state: the date of the interview describes the actual state
3067: and not the date of a change in health state. The former idea was
3068: to consider that at each interview the state was recorded
3069: (healthy, disable or death) and IMaCh was corrected; but when we
3070: introduced the exact date of death then we should have modified
3071: the contribution of an exact death to the likelihood. This new
3072: contribution is smaller and very dependent of the step unit
3073: stepm. It is no more the probability to die between last interview
3074: and month of death but the probability to survive from last
3075: interview up to one month before death multiplied by the
3076: probability to die within a month. Thanks to Chris
3077: Jackson for correcting this bug. Former versions increased
3078: mortality artificially. The bad side is that we add another loop
3079: which slows down the processing. The difference can be up to 10%
3080: lower mortality.
3081: */
3082: /* If, at the beginning of the maximization mostly, the
3083: cumulative probability or probability to be dead is
3084: constant (ie = 1) over time d, the difference is equal to
3085: 0. out[s1][3] = savm[s1][3]: probability, being at state
3086: s1 at precedent wave, to be dead a month before current
3087: wave is equal to probability, being at state s1 at
3088: precedent wave, to be dead at mont of the current
3089: wave. Then the observed probability (that this person died)
3090: is null according to current estimated parameter. In fact,
3091: it should be very low but not zero otherwise the log go to
3092: infinity.
3093: */
1.183 brouard 3094: /* #ifdef INFINITYORIGINAL */
3095: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3096: /* #else */
3097: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
3098: /* lli=log(mytinydouble); */
3099: /* else */
3100: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3101: /* #endif */
1.226 brouard 3102: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3103:
1.226 brouard 3104: } else if ( s2==-1 ) { /* alive */
3105: for (j=1,survp=0. ; j<=nlstate; j++)
3106: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3107: /*survp += out[s1][j]; */
3108: lli= log(survp);
3109: }
3110: else if (s2==-4) {
3111: for (j=3,survp=0. ; j<=nlstate; j++)
3112: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3113: lli= log(survp);
3114: }
3115: else if (s2==-5) {
3116: for (j=1,survp=0. ; j<=2; j++)
3117: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3118: lli= log(survp);
3119: }
3120: else{
3121: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3122: /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
3123: }
3124: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
3125: /*if(lli ==000.0)*/
3126: /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
3127: ipmx +=1;
3128: sw += weight[i];
3129: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3130: /* if (lli < log(mytinydouble)){ */
3131: /* printf("Close to inf lli = %.10lf < %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
3132: /* fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
3133: /* } */
3134: } /* end of wave */
3135: } /* end of individual */
3136: } else if(mle==2){
3137: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3138: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3139: for(mi=1; mi<= wav[i]-1; mi++){
3140: for (ii=1;ii<=nlstate+ndeath;ii++)
3141: for (j=1;j<=nlstate+ndeath;j++){
3142: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3143: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3144: }
3145: for(d=0; d<=dh[mi][i]; d++){
3146: newm=savm;
3147: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3148: cov[2]=agexact;
3149: if(nagesqr==1)
3150: cov[3]= agexact*agexact;
3151: for (kk=1; kk<=cptcovage;kk++) {
3152: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3153: }
3154: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3155: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3156: savm=oldm;
3157: oldm=newm;
3158: } /* end mult */
3159:
3160: s1=s[mw[mi][i]][i];
3161: s2=s[mw[mi+1][i]][i];
3162: bbh=(double)bh[mi][i]/(double)stepm;
3163: lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
3164: ipmx +=1;
3165: sw += weight[i];
3166: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3167: } /* end of wave */
3168: } /* end of individual */
3169: } else if(mle==3){ /* exponential inter-extrapolation */
3170: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3171: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3172: for(mi=1; mi<= wav[i]-1; mi++){
3173: for (ii=1;ii<=nlstate+ndeath;ii++)
3174: for (j=1;j<=nlstate+ndeath;j++){
3175: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3176: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3177: }
3178: for(d=0; d<dh[mi][i]; d++){
3179: newm=savm;
3180: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3181: cov[2]=agexact;
3182: if(nagesqr==1)
3183: cov[3]= agexact*agexact;
3184: for (kk=1; kk<=cptcovage;kk++) {
3185: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3186: }
3187: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3188: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3189: savm=oldm;
3190: oldm=newm;
3191: } /* end mult */
3192:
3193: s1=s[mw[mi][i]][i];
3194: s2=s[mw[mi+1][i]][i];
3195: bbh=(double)bh[mi][i]/(double)stepm;
3196: lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
3197: ipmx +=1;
3198: sw += weight[i];
3199: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3200: } /* end of wave */
3201: } /* end of individual */
3202: }else if (mle==4){ /* ml=4 no inter-extrapolation */
3203: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3204: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3205: for(mi=1; mi<= wav[i]-1; mi++){
3206: for (ii=1;ii<=nlstate+ndeath;ii++)
3207: for (j=1;j<=nlstate+ndeath;j++){
3208: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3209: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3210: }
3211: for(d=0; d<dh[mi][i]; d++){
3212: newm=savm;
3213: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3214: cov[2]=agexact;
3215: if(nagesqr==1)
3216: cov[3]= agexact*agexact;
3217: for (kk=1; kk<=cptcovage;kk++) {
3218: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3219: }
1.126 brouard 3220:
1.226 brouard 3221: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3222: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3223: savm=oldm;
3224: oldm=newm;
3225: } /* end mult */
3226:
3227: s1=s[mw[mi][i]][i];
3228: s2=s[mw[mi+1][i]][i];
3229: if( s2 > nlstate){
3230: lli=log(out[s1][s2] - savm[s1][s2]);
3231: } else if ( s2==-1 ) { /* alive */
3232: for (j=1,survp=0. ; j<=nlstate; j++)
3233: survp += out[s1][j];
3234: lli= log(survp);
3235: }else{
3236: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3237: }
3238: ipmx +=1;
3239: sw += weight[i];
3240: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.126 brouard 3241: /* printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
1.226 brouard 3242: } /* end of wave */
3243: } /* end of individual */
3244: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
3245: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3246: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3247: for(mi=1; mi<= wav[i]-1; mi++){
3248: for (ii=1;ii<=nlstate+ndeath;ii++)
3249: for (j=1;j<=nlstate+ndeath;j++){
3250: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3251: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3252: }
3253: for(d=0; d<dh[mi][i]; d++){
3254: newm=savm;
3255: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3256: cov[2]=agexact;
3257: if(nagesqr==1)
3258: cov[3]= agexact*agexact;
3259: for (kk=1; kk<=cptcovage;kk++) {
3260: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3261: }
1.126 brouard 3262:
1.226 brouard 3263: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3264: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3265: savm=oldm;
3266: oldm=newm;
3267: } /* end mult */
3268:
3269: s1=s[mw[mi][i]][i];
3270: s2=s[mw[mi+1][i]][i];
3271: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3272: ipmx +=1;
3273: sw += weight[i];
3274: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3275: /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
3276: } /* end of wave */
3277: } /* end of individual */
3278: } /* End of if */
3279: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3280: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3281: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3282: return -l;
1.126 brouard 3283: }
3284:
3285: /*************** log-likelihood *************/
3286: double funcone( double *x)
3287: {
1.228 brouard 3288: /* Same as func but slower because of a lot of printf and if */
1.126 brouard 3289: int i, ii, j, k, mi, d, kk;
1.228 brouard 3290: int ioffset=0;
1.131 brouard 3291: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 3292: double **out;
3293: double lli; /* Individual log likelihood */
3294: double llt;
3295: int s1, s2;
1.228 brouard 3296: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
3297:
1.126 brouard 3298: double bbh, survp;
1.187 brouard 3299: double agexact;
1.214 brouard 3300: double agebegin, ageend;
1.126 brouard 3301: /*extern weight */
3302: /* We are differentiating ll according to initial status */
3303: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3304: /*for(i=1;i<imx;i++)
3305: printf(" %d\n",s[4][i]);
3306: */
3307: cov[1]=1.;
3308:
3309: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3310: ioffset=0;
3311: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.225 brouard 3312: ioffset=2+nagesqr+cptcovage;
1.224 brouard 3313: /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
1.230 ! brouard 3314: for (k=1; k<=ncoveff+nqfveff;k++){ /* Simple and product fixed Dummy covariates without age* products */
! 3315: cov[++ioffset]=covar[TvarFD[k]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
1.225 brouard 3316: }
1.226 brouard 3317: for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitative fixed covariates */
1.230 ! brouard 3318: cov[++ioffset]=coqvar[Tvar[iqv]][i]; /* Only V1 k=9 */
1.225 brouard 3319: }
3320:
1.226 brouard 3321: for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */
1.225 brouard 3322: for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
1.228 brouard 3323: /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3324: /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
3325: k=ioffset-2-nagesqr-cptcovage+itv; /* position in simple model */
3326: cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i];
1.229 brouard 3327: /* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */
1.225 brouard 3328: }
3329: for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
1.228 brouard 3330: iv=TmodelInvQind[iqtv]; /* Counting the # varying covariate from 1 to ntveff */
1.229 brouard 3331: /* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); */
1.228 brouard 3332: cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i];
1.225 brouard 3333: }
1.126 brouard 3334: for (ii=1;ii<=nlstate+ndeath;ii++)
1.225 brouard 3335: for (j=1;j<=nlstate+ndeath;j++){
3336: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3337: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3338: }
1.214 brouard 3339:
3340: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
3341: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
3342: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
1.225 brouard 3343: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3344: and mw[mi+1][i]. dh depends on stepm.*/
3345: newm=savm;
3346: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3347: cov[2]=agexact;
3348: if(nagesqr==1)
3349: cov[3]= agexact*agexact;
3350: for (kk=1; kk<=cptcovage;kk++) {
3351: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3352: }
3353: /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
3354: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
3355: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3356: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3357: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
3358: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
3359: savm=oldm;
3360: oldm=newm;
1.126 brouard 3361: } /* end mult */
3362:
3363: s1=s[mw[mi][i]][i];
3364: s2=s[mw[mi+1][i]][i];
1.217 brouard 3365: /* if(s2==-1){ */
3366: /* printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */
3367: /* /\* exit(1); *\/ */
3368: /* } */
1.126 brouard 3369: bbh=(double)bh[mi][i]/(double)stepm;
3370: /* bias is positive if real duration
3371: * is higher than the multiple of stepm and negative otherwise.
3372: */
3373: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1.225 brouard 3374: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3375: } else if ( s2==-1 ) { /* alive */
1.225 brouard 3376: for (j=1,survp=0. ; j<=nlstate; j++)
3377: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3378: lli= log(survp);
1.126 brouard 3379: }else if (mle==1){
1.225 brouard 3380: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1.126 brouard 3381: } else if(mle==2){
1.225 brouard 3382: lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
1.126 brouard 3383: } else if(mle==3){ /* exponential inter-extrapolation */
1.225 brouard 3384: lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
1.126 brouard 3385: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1.225 brouard 3386: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 3387: } else{ /* mle=0 back to 1 */
1.225 brouard 3388: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3389: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 3390: } /* End of if */
3391: ipmx +=1;
3392: sw += weight[i];
3393: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 3394: /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
1.126 brouard 3395: if(globpr){
1.225 brouard 3396: fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
1.126 brouard 3397: %11.6f %11.6f %11.6f ", \
1.225 brouard 3398: num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
3399: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
3400: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
3401: llt +=ll[k]*gipmx/gsw;
3402: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
3403: }
3404: fprintf(ficresilk," %10.6f\n", -llt);
1.126 brouard 3405: }
3406: } /* end of wave */
3407: } /* end of individual */
3408: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3409: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3410: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3411: if(globpr==0){ /* First time we count the contributions and weights */
3412: gipmx=ipmx;
3413: gsw=sw;
3414: }
3415: return -l;
3416: }
3417:
3418:
3419: /*************** function likelione ***********/
3420: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
3421: {
3422: /* This routine should help understanding what is done with
3423: the selection of individuals/waves and
3424: to check the exact contribution to the likelihood.
3425: Plotting could be done.
3426: */
3427: int k;
3428:
3429: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 3430: strcpy(fileresilk,"ILK_");
1.202 brouard 3431: strcat(fileresilk,fileresu);
1.126 brouard 3432: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
3433: printf("Problem with resultfile: %s\n", fileresilk);
3434: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
3435: }
1.214 brouard 3436: fprintf(ficresilk, "#individual(line's_record) count ageb ageend s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
3437: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 3438: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
3439: for(k=1; k<=nlstate; k++)
3440: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
3441: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
3442: }
3443:
3444: *fretone=(*funcone)(p);
3445: if(*globpri !=0){
3446: fclose(ficresilk);
1.205 brouard 3447: if (mle ==0)
3448: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
3449: else if(mle >=1)
3450: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
3451: fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1.207 brouard 3452:
1.208 brouard 3453:
3454: for (k=1; k<= nlstate ; k++) {
1.211 brouard 3455: fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
1.208 brouard 3456: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
3457: }
1.207 brouard 3458: fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \
1.204 brouard 3459: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3460: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 3461: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3462: fflush(fichtm);
1.205 brouard 3463: }
1.126 brouard 3464: return;
3465: }
3466:
3467:
3468: /*********** Maximum Likelihood Estimation ***************/
3469:
3470: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
3471: {
1.165 brouard 3472: int i,j, iter=0;
1.126 brouard 3473: double **xi;
3474: double fret;
3475: double fretone; /* Only one call to likelihood */
3476: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 3477:
3478: #ifdef NLOPT
3479: int creturn;
3480: nlopt_opt opt;
3481: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
3482: double *lb;
3483: double minf; /* the minimum objective value, upon return */
3484: double * p1; /* Shifted parameters from 0 instead of 1 */
3485: myfunc_data dinst, *d = &dinst;
3486: #endif
3487:
3488:
1.126 brouard 3489: xi=matrix(1,npar,1,npar);
3490: for (i=1;i<=npar;i++)
3491: for (j=1;j<=npar;j++)
3492: xi[i][j]=(i==j ? 1.0 : 0.0);
3493: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 3494: strcpy(filerespow,"POW_");
1.126 brouard 3495: strcat(filerespow,fileres);
3496: if((ficrespow=fopen(filerespow,"w"))==NULL) {
3497: printf("Problem with resultfile: %s\n", filerespow);
3498: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
3499: }
3500: fprintf(ficrespow,"# Powell\n# iter -2*LL");
3501: for (i=1;i<=nlstate;i++)
3502: for(j=1;j<=nlstate+ndeath;j++)
3503: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
3504: fprintf(ficrespow,"\n");
1.162 brouard 3505: #ifdef POWELL
1.126 brouard 3506: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 3507: #endif
1.126 brouard 3508:
1.162 brouard 3509: #ifdef NLOPT
3510: #ifdef NEWUOA
3511: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
3512: #else
3513: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
3514: #endif
3515: lb=vector(0,npar-1);
3516: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
3517: nlopt_set_lower_bounds(opt, lb);
3518: nlopt_set_initial_step1(opt, 0.1);
3519:
3520: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
3521: d->function = func;
3522: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
3523: nlopt_set_min_objective(opt, myfunc, d);
3524: nlopt_set_xtol_rel(opt, ftol);
3525: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
3526: printf("nlopt failed! %d\n",creturn);
3527: }
3528: else {
3529: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
3530: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
3531: iter=1; /* not equal */
3532: }
3533: nlopt_destroy(opt);
3534: #endif
1.126 brouard 3535: free_matrix(xi,1,npar,1,npar);
3536: fclose(ficrespow);
1.203 brouard 3537: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
3538: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 3539: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 3540:
3541: }
3542:
3543: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 3544: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 3545: {
3546: double **a,**y,*x,pd;
1.203 brouard 3547: /* double **hess; */
1.164 brouard 3548: int i, j;
1.126 brouard 3549: int *indx;
3550:
3551: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 3552: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 3553: void lubksb(double **a, int npar, int *indx, double b[]) ;
3554: void ludcmp(double **a, int npar, int *indx, double *d) ;
3555: double gompertz(double p[]);
1.203 brouard 3556: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 3557:
3558: printf("\nCalculation of the hessian matrix. Wait...\n");
3559: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
3560: for (i=1;i<=npar;i++){
1.203 brouard 3561: printf("%d-",i);fflush(stdout);
3562: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 3563:
3564: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
3565:
3566: /* printf(" %f ",p[i]);
3567: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
3568: }
3569:
3570: for (i=1;i<=npar;i++) {
3571: for (j=1;j<=npar;j++) {
3572: if (j>i) {
1.203 brouard 3573: printf(".%d-%d",i,j);fflush(stdout);
3574: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
3575: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 3576:
3577: hess[j][i]=hess[i][j];
3578: /*printf(" %lf ",hess[i][j]);*/
3579: }
3580: }
3581: }
3582: printf("\n");
3583: fprintf(ficlog,"\n");
3584:
3585: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
3586: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
3587:
3588: a=matrix(1,npar,1,npar);
3589: y=matrix(1,npar,1,npar);
3590: x=vector(1,npar);
3591: indx=ivector(1,npar);
3592: for (i=1;i<=npar;i++)
3593: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
3594: ludcmp(a,npar,indx,&pd);
3595:
3596: for (j=1;j<=npar;j++) {
3597: for (i=1;i<=npar;i++) x[i]=0;
3598: x[j]=1;
3599: lubksb(a,npar,indx,x);
3600: for (i=1;i<=npar;i++){
3601: matcov[i][j]=x[i];
3602: }
3603: }
3604:
3605: printf("\n#Hessian matrix#\n");
3606: fprintf(ficlog,"\n#Hessian matrix#\n");
3607: for (i=1;i<=npar;i++) {
3608: for (j=1;j<=npar;j++) {
1.203 brouard 3609: printf("%.6e ",hess[i][j]);
3610: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 3611: }
3612: printf("\n");
3613: fprintf(ficlog,"\n");
3614: }
3615:
1.203 brouard 3616: /* printf("\n#Covariance matrix#\n"); */
3617: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
3618: /* for (i=1;i<=npar;i++) { */
3619: /* for (j=1;j<=npar;j++) { */
3620: /* printf("%.6e ",matcov[i][j]); */
3621: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
3622: /* } */
3623: /* printf("\n"); */
3624: /* fprintf(ficlog,"\n"); */
3625: /* } */
3626:
1.126 brouard 3627: /* Recompute Inverse */
1.203 brouard 3628: /* for (i=1;i<=npar;i++) */
3629: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
3630: /* ludcmp(a,npar,indx,&pd); */
3631:
3632: /* printf("\n#Hessian matrix recomputed#\n"); */
3633:
3634: /* for (j=1;j<=npar;j++) { */
3635: /* for (i=1;i<=npar;i++) x[i]=0; */
3636: /* x[j]=1; */
3637: /* lubksb(a,npar,indx,x); */
3638: /* for (i=1;i<=npar;i++){ */
3639: /* y[i][j]=x[i]; */
3640: /* printf("%.3e ",y[i][j]); */
3641: /* fprintf(ficlog,"%.3e ",y[i][j]); */
3642: /* } */
3643: /* printf("\n"); */
3644: /* fprintf(ficlog,"\n"); */
3645: /* } */
3646:
3647: /* Verifying the inverse matrix */
3648: #ifdef DEBUGHESS
3649: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 3650:
1.203 brouard 3651: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
3652: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 3653:
3654: for (j=1;j<=npar;j++) {
3655: for (i=1;i<=npar;i++){
1.203 brouard 3656: printf("%.2f ",y[i][j]);
3657: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 3658: }
3659: printf("\n");
3660: fprintf(ficlog,"\n");
3661: }
1.203 brouard 3662: #endif
1.126 brouard 3663:
3664: free_matrix(a,1,npar,1,npar);
3665: free_matrix(y,1,npar,1,npar);
3666: free_vector(x,1,npar);
3667: free_ivector(indx,1,npar);
1.203 brouard 3668: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 3669:
3670:
3671: }
3672:
3673: /*************** hessian matrix ****************/
3674: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 3675: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 3676: int i;
3677: int l=1, lmax=20;
1.203 brouard 3678: double k1,k2, res, fx;
1.132 brouard 3679: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 3680: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
3681: int k=0,kmax=10;
3682: double l1;
3683:
3684: fx=func(x);
3685: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 3686: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 3687: l1=pow(10,l);
3688: delts=delt;
3689: for(k=1 ; k <kmax; k=k+1){
3690: delt = delta*(l1*k);
3691: p2[theta]=x[theta] +delt;
1.145 brouard 3692: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 3693: p2[theta]=x[theta]-delt;
3694: k2=func(p2)-fx;
3695: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 3696: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 3697:
1.203 brouard 3698: #ifdef DEBUGHESSII
1.126 brouard 3699: printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
3700: fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
3701: #endif
3702: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
3703: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
3704: k=kmax;
3705: }
3706: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 3707: k=kmax; l=lmax*10;
1.126 brouard 3708: }
3709: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
3710: delts=delt;
3711: }
1.203 brouard 3712: } /* End loop k */
1.126 brouard 3713: }
3714: delti[theta]=delts;
3715: return res;
3716:
3717: }
3718:
1.203 brouard 3719: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 3720: {
3721: int i;
1.164 brouard 3722: int l=1, lmax=20;
1.126 brouard 3723: double k1,k2,k3,k4,res,fx;
1.132 brouard 3724: double p2[MAXPARM+1];
1.203 brouard 3725: int k, kmax=1;
3726: double v1, v2, cv12, lc1, lc2;
1.208 brouard 3727:
3728: int firstime=0;
1.203 brouard 3729:
1.126 brouard 3730: fx=func(x);
1.203 brouard 3731: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 3732: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 3733: p2[thetai]=x[thetai]+delti[thetai]*k;
3734: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3735: k1=func(p2)-fx;
3736:
1.203 brouard 3737: p2[thetai]=x[thetai]+delti[thetai]*k;
3738: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3739: k2=func(p2)-fx;
3740:
1.203 brouard 3741: p2[thetai]=x[thetai]-delti[thetai]*k;
3742: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3743: k3=func(p2)-fx;
3744:
1.203 brouard 3745: p2[thetai]=x[thetai]-delti[thetai]*k;
3746: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3747: k4=func(p2)-fx;
1.203 brouard 3748: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
3749: if(k1*k2*k3*k4 <0.){
1.208 brouard 3750: firstime=1;
1.203 brouard 3751: kmax=kmax+10;
1.208 brouard 3752: }
3753: if(kmax >=10 || firstime ==1){
1.218 brouard 3754: printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);
3755: fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);
1.203 brouard 3756: printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
3757: fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
3758: }
3759: #ifdef DEBUGHESSIJ
3760: v1=hess[thetai][thetai];
3761: v2=hess[thetaj][thetaj];
3762: cv12=res;
3763: /* Computing eigen value of Hessian matrix */
3764: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3765: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3766: if ((lc2 <0) || (lc1 <0) ){
3767: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3768: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3769: printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
3770: fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
3771: }
1.126 brouard 3772: #endif
3773: }
3774: return res;
3775: }
3776:
1.203 brouard 3777: /* Not done yet: Was supposed to fix if not exactly at the maximum */
3778: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
3779: /* { */
3780: /* int i; */
3781: /* int l=1, lmax=20; */
3782: /* double k1,k2,k3,k4,res,fx; */
3783: /* double p2[MAXPARM+1]; */
3784: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
3785: /* int k=0,kmax=10; */
3786: /* double l1; */
3787:
3788: /* fx=func(x); */
3789: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
3790: /* l1=pow(10,l); */
3791: /* delts=delt; */
3792: /* for(k=1 ; k <kmax; k=k+1){ */
3793: /* delt = delti*(l1*k); */
3794: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
3795: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3796: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3797: /* k1=func(p2)-fx; */
3798:
3799: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3800: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3801: /* k2=func(p2)-fx; */
3802:
3803: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3804: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3805: /* k3=func(p2)-fx; */
3806:
3807: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3808: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3809: /* k4=func(p2)-fx; */
3810: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
3811: /* #ifdef DEBUGHESSIJ */
3812: /* printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */
3813: /* fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */
3814: /* #endif */
3815: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
3816: /* k=kmax; */
3817: /* } */
3818: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
3819: /* k=kmax; l=lmax*10; */
3820: /* } */
3821: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
3822: /* delts=delt; */
3823: /* } */
3824: /* } /\* End loop k *\/ */
3825: /* } */
3826: /* delti[theta]=delts; */
3827: /* return res; */
3828: /* } */
3829:
3830:
1.126 brouard 3831: /************** Inverse of matrix **************/
3832: void ludcmp(double **a, int n, int *indx, double *d)
3833: {
3834: int i,imax,j,k;
3835: double big,dum,sum,temp;
3836: double *vv;
3837:
3838: vv=vector(1,n);
3839: *d=1.0;
3840: for (i=1;i<=n;i++) {
3841: big=0.0;
3842: for (j=1;j<=n;j++)
3843: if ((temp=fabs(a[i][j])) > big) big=temp;
3844: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
3845: vv[i]=1.0/big;
3846: }
3847: for (j=1;j<=n;j++) {
3848: for (i=1;i<j;i++) {
3849: sum=a[i][j];
3850: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
3851: a[i][j]=sum;
3852: }
3853: big=0.0;
3854: for (i=j;i<=n;i++) {
3855: sum=a[i][j];
3856: for (k=1;k<j;k++)
3857: sum -= a[i][k]*a[k][j];
3858: a[i][j]=sum;
3859: if ( (dum=vv[i]*fabs(sum)) >= big) {
3860: big=dum;
3861: imax=i;
3862: }
3863: }
3864: if (j != imax) {
3865: for (k=1;k<=n;k++) {
3866: dum=a[imax][k];
3867: a[imax][k]=a[j][k];
3868: a[j][k]=dum;
3869: }
3870: *d = -(*d);
3871: vv[imax]=vv[j];
3872: }
3873: indx[j]=imax;
3874: if (a[j][j] == 0.0) a[j][j]=TINY;
3875: if (j != n) {
3876: dum=1.0/(a[j][j]);
3877: for (i=j+1;i<=n;i++) a[i][j] *= dum;
3878: }
3879: }
3880: free_vector(vv,1,n); /* Doesn't work */
3881: ;
3882: }
3883:
3884: void lubksb(double **a, int n, int *indx, double b[])
3885: {
3886: int i,ii=0,ip,j;
3887: double sum;
3888:
3889: for (i=1;i<=n;i++) {
3890: ip=indx[i];
3891: sum=b[ip];
3892: b[ip]=b[i];
3893: if (ii)
3894: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
3895: else if (sum) ii=i;
3896: b[i]=sum;
3897: }
3898: for (i=n;i>=1;i--) {
3899: sum=b[i];
3900: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
3901: b[i]=sum/a[i][i];
3902: }
3903: }
3904:
3905: void pstamp(FILE *fichier)
3906: {
1.196 brouard 3907: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 3908: }
3909:
3910: /************ Frequencies ********************/
1.226 brouard 3911: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
3912: int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
3913: int firstpass, int lastpass, int stepm, int weightopt, char model[])
3914: { /* Some frequencies */
3915:
1.227 brouard 3916: int i, m, jk, j1, bool, z1,j, k, iv;
1.226 brouard 3917: int iind=0, iage=0;
3918: int mi; /* Effective wave */
3919: int first;
3920: double ***freq; /* Frequencies */
3921: double *meanq;
3922: double **meanqt;
3923: double *pp, **prop, *posprop, *pospropt;
3924: double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
3925: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
3926: double agebegin, ageend;
3927:
3928: pp=vector(1,nlstate);
3929: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
3930: posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
3931: pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
3932: /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
3933: meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
3934: meanqt=matrix(1,lastpass,1,nqtveff);
3935: strcpy(fileresp,"P_");
3936: strcat(fileresp,fileresu);
3937: /*strcat(fileresphtm,fileresu);*/
3938: if((ficresp=fopen(fileresp,"w"))==NULL) {
3939: printf("Problem with prevalence resultfile: %s\n", fileresp);
3940: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
3941: exit(0);
3942: }
1.214 brouard 3943:
1.226 brouard 3944: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
3945: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
3946: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3947: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3948: fflush(ficlog);
3949: exit(70);
3950: }
3951: else{
3952: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.214 brouard 3953: <hr size=\"2\" color=\"#EC5E5E\"> \n\
3954: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 3955: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
3956: }
3957: fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition</h4>\n",fileresphtm, fileresphtm);
1.214 brouard 3958:
1.226 brouard 3959: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
3960: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
3961: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
3962: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
3963: fflush(ficlog);
3964: exit(70);
3965: }
3966: else{
3967: fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.214 brouard 3968: <hr size=\"2\" color=\"#EC5E5E\"> \n\
3969: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 3970: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
3971: }
3972: fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions by age at begin of transition </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);
1.214 brouard 3973:
1.226 brouard 3974: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
3975: j1=0;
1.126 brouard 3976:
1.227 brouard 3977: /* j=ncoveff; /\* Only fixed dummy covariates *\/ */
3978: j=cptcoveff; /* Only dummy covariates of the model */
1.226 brouard 3979: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.220 brouard 3980:
1.226 brouard 3981: first=1;
1.220 brouard 3982:
1.226 brouard 3983: /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
3984: reference=low_education V1=0,V2=0
3985: med_educ V1=1 V2=0,
3986: high_educ V1=0 V2=1
3987: Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
3988: */
1.126 brouard 3989:
1.227 brouard 3990: for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives V4=0, V3=0 for example, fixed or varying covariates */
1.226 brouard 3991: posproptt=0.;
3992: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
3993: scanf("%d", i);*/
3994: for (i=-5; i<=nlstate+ndeath; i++)
3995: for (jk=-5; jk<=nlstate+ndeath; jk++)
3996: for(m=iagemin; m <= iagemax+3; m++)
3997: freq[i][jk][m]=0;
3998:
3999: for (i=1; i<=nlstate; i++) {
4000: for(m=iagemin; m <= iagemax+3; m++)
4001: prop[i][m]=0;
4002: posprop[i]=0;
4003: pospropt[i]=0;
4004: }
1.227 brouard 4005: /* for (z1=1; z1<= nqfveff; z1++) { */
4006: /* meanq[z1]+=0.; */
4007: /* for(m=1;m<=lastpass;m++){ */
4008: /* meanqt[m][z1]=0.; */
4009: /* } */
4010: /* } */
1.220 brouard 4011:
1.226 brouard 4012: dateintsum=0;
4013: k2cpt=0;
1.227 brouard 4014: /* For that combination of covariate j1, we count and print the frequencies in one pass */
1.226 brouard 4015: for (iind=1; iind<=imx; iind++) { /* For each individual iind */
4016: bool=1;
1.227 brouard 4017: if(anyvaryingduminmodel==0){ /* If All fixed covariates */
4018: if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
4019: /* for (z1=1; z1<= nqfveff; z1++) { */
4020: /* meanq[z1]+=coqvar[Tvar[z1]][iind]; /\* Computes mean of quantitative with selected filter *\/ */
4021: /* } */
4022: for (z1=1; z1<=cptcoveff; z1++) {
4023: /* if(Tvaraff[z1] ==-20){ */
4024: /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
4025: /* }else if(Tvaraff[z1] ==-10){ */
4026: /* /\* sumnew+=coqvar[z1][iind]; *\/ */
4027: /* }else */
4028: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
4029: /* Tests if this individual iind responded to j1 (V4=1 V3=0) */
4030: bool=0;
4031: /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",
4032: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
4033: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
4034: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
4035: } /* Onlyf fixed */
4036: } /* end z1 */
4037: } /* cptcovn > 0 */
4038: } /* end any */
4039: if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */
1.226 brouard 4040: /* for(m=firstpass; m<=lastpass; m++){ */
1.227 brouard 4041: for(mi=1; mi<wav[iind];mi++){ /* For that wave */
1.226 brouard 4042: m=mw[mi][iind];
1.227 brouard 4043: if(anyvaryingduminmodel==1){ /* Some are varying covariates */
4044: for (z1=1; z1<=cptcoveff; z1++) {
4045: if( Fixed[Tmodelind[z1]]==1){
4046: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4047: if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
4048: bool=0;
4049: }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
4050: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4051: bool=0;
4052: }
4053: }
4054: }
4055: }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */
4056: /* bool =0 we keep that guy which corresponds to the combination of dummy values */
4057: if(bool==1){
4058: /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
4059: and mw[mi+1][iind]. dh depends on stepm. */
4060: agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
4061: ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
4062: if(m >=firstpass && m <=lastpass){
4063: k2=anint[m][iind]+(mint[m][iind]/12.);
4064: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
4065: if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
4066: if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
4067: if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
4068: prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4069: if (m<lastpass) {
4070: /* if(s[m][iind]==4 && s[m+1][iind]==4) */
4071: /* printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */
4072: if(s[m][iind]==-1)
4073: printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
4074: freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4075: /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
4076: freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
4077: }
4078: } /* end if between passes */
4079: if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
4080: dateintsum=dateintsum+k2;
4081: k2cpt++;
4082: /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
1.226 brouard 4083: }
1.227 brouard 4084: } /* end bool 2 */
1.226 brouard 4085: } /* end m */
4086: } /* end bool */
4087: } /* end iind = 1 to imx */
4088: /* prop[s][age] is feeded for any initial and valid live state as well as
4089: freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
4090:
4091:
4092: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
4093: pstamp(ficresp);
1.227 brouard 4094: /* if (ncoveff>0) { */
4095: if (cptcoveff>0) {
1.226 brouard 4096: fprintf(ficresp, "\n#********** Variable ");
4097: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
4098: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
1.227 brouard 4099: for (z1=1; z1<=cptcoveff; z1++){
1.226 brouard 4100: fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4101: fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4102: fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4103: }
4104: fprintf(ficresp, "**********\n#");
4105: fprintf(ficresphtm, "**********</h3>\n");
4106: fprintf(ficresphtmfr, "**********</h3>\n");
4107: fprintf(ficlog, "\n#********** Variable ");
1.227 brouard 4108: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.226 brouard 4109: fprintf(ficlog, "**********\n");
4110: }
4111: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
4112: for(i=1; i<=nlstate;i++) {
4113: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
4114: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
4115: }
4116: fprintf(ficresp, "\n");
4117: fprintf(ficresphtm, "\n");
4118:
4119: /* Header of frequency table by age */
4120: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
4121: fprintf(ficresphtmfr,"<th>Age</th> ");
4122: for(jk=-1; jk <=nlstate+ndeath; jk++){
4123: for(m=-1; m <=nlstate+ndeath; m++){
4124: if(jk!=0 && m!=0)
4125: fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
4126: }
4127: }
4128: fprintf(ficresphtmfr, "\n");
4129:
4130: /* For each age */
4131: for(iage=iagemin; iage <= iagemax+3; iage++){
4132: fprintf(ficresphtm,"<tr>");
4133: if(iage==iagemax+1){
4134: fprintf(ficlog,"1");
4135: fprintf(ficresphtmfr,"<tr><th>0</th> ");
4136: }else if(iage==iagemax+2){
4137: fprintf(ficlog,"0");
4138: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
4139: }else if(iage==iagemax+3){
4140: fprintf(ficlog,"Total");
4141: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
4142: }else{
4143: if(first==1){
4144: first=0;
4145: printf("See log file for details...\n");
4146: }
4147: fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
4148: fprintf(ficlog,"Age %d", iage);
4149: }
4150: for(jk=1; jk <=nlstate ; jk++){
4151: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
4152: pp[jk] += freq[jk][m][iage];
4153: }
4154: for(jk=1; jk <=nlstate ; jk++){
4155: for(m=-1, pos=0; m <=0 ; m++)
4156: pos += freq[jk][m][iage];
4157: if(pp[jk]>=1.e-10){
4158: if(first==1){
4159: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
4160: }
4161: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
4162: }else{
4163: if(first==1)
4164: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
4165: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
4166: }
4167: }
4168:
4169: for(jk=1; jk <=nlstate ; jk++){
4170: /* posprop[jk]=0; */
4171: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
4172: pp[jk] += freq[jk][m][iage];
4173: } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
4174:
4175: for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
4176: pos += pp[jk]; /* pos is the total number of transitions until this age */
4177: posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
4178: from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4179: pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
4180: from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4181: }
4182: for(jk=1; jk <=nlstate ; jk++){
4183: if(pos>=1.e-5){
4184: if(first==1)
4185: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
4186: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
4187: }else{
4188: if(first==1)
4189: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
4190: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
4191: }
4192: if( iage <= iagemax){
4193: if(pos>=1.e-5){
4194: fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
4195: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
4196: /*probs[iage][jk][j1]= pp[jk]/pos;*/
4197: /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
4198: }
4199: else{
4200: fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
4201: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
4202: }
4203: }
4204: pospropt[jk] +=posprop[jk];
4205: } /* end loop jk */
4206: /* pospropt=0.; */
4207: for(jk=-1; jk <=nlstate+ndeath; jk++){
4208: for(m=-1; m <=nlstate+ndeath; m++){
4209: if(freq[jk][m][iage] !=0 ) { /* minimizing output */
4210: if(first==1){
4211: printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
4212: }
4213: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
4214: }
4215: if(jk!=0 && m!=0)
4216: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
4217: }
4218: } /* end loop jk */
4219: posproptt=0.;
4220: for(jk=1; jk <=nlstate; jk++){
4221: posproptt += pospropt[jk];
4222: }
4223: fprintf(ficresphtmfr,"</tr>\n ");
4224: if(iage <= iagemax){
4225: fprintf(ficresp,"\n");
4226: fprintf(ficresphtm,"</tr>\n");
4227: }
4228: if(first==1)
4229: printf("Others in log...\n");
4230: fprintf(ficlog,"\n");
4231: } /* end loop age iage */
4232: fprintf(ficresphtm,"<tr><th>Tot</th>");
4233: for(jk=1; jk <=nlstate ; jk++){
4234: if(posproptt < 1.e-5){
4235: fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);
4236: }else{
4237: fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);
4238: }
4239: }
4240: fprintf(ficresphtm,"</tr>\n");
4241: fprintf(ficresphtm,"</table>\n");
4242: fprintf(ficresphtmfr,"</table>\n");
4243: if(posproptt < 1.e-5){
4244: fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4245: fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4246: fprintf(ficres,"\n This combination (%d) is not valid and no result will be produced\n\n",j1);
4247: invalidvarcomb[j1]=1;
4248: }else{
4249: fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
4250: invalidvarcomb[j1]=0;
4251: }
4252: fprintf(ficresphtmfr,"</table>\n");
4253: } /* end selected combination of covariate j1 */
4254: dateintmean=dateintsum/k2cpt;
1.220 brouard 4255:
1.226 brouard 4256: fclose(ficresp);
4257: fclose(ficresphtm);
4258: fclose(ficresphtmfr);
4259: free_vector(meanq,1,nqfveff);
4260: free_matrix(meanqt,1,lastpass,1,nqtveff);
4261: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
4262: free_vector(pospropt,1,nlstate);
4263: free_vector(posprop,1,nlstate);
4264: free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
4265: free_vector(pp,1,nlstate);
4266: /* End of freqsummary */
4267: }
1.126 brouard 4268:
4269: /************ Prevalence ********************/
1.227 brouard 4270: void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
4271: {
4272: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
4273: in each health status at the date of interview (if between dateprev1 and dateprev2).
4274: We still use firstpass and lastpass as another selection.
4275: */
1.126 brouard 4276:
1.227 brouard 4277: int i, m, jk, j1, bool, z1,j, iv;
4278: int mi; /* Effective wave */
4279: int iage;
4280: double agebegin, ageend;
4281:
4282: double **prop;
4283: double posprop;
4284: double y2; /* in fractional years */
4285: int iagemin, iagemax;
4286: int first; /** to stop verbosity which is redirected to log file */
4287:
4288: iagemin= (int) agemin;
4289: iagemax= (int) agemax;
4290: /*pp=vector(1,nlstate);*/
4291: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
4292: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
4293: j1=0;
1.222 brouard 4294:
1.227 brouard 4295: /*j=cptcoveff;*/
4296: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.222 brouard 4297:
1.227 brouard 4298: first=1;
4299: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
4300: for (i=1; i<=nlstate; i++)
4301: for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
4302: prop[i][iage]=0.0;
4303: printf("Prevalence combination of varying and fixed dummies %d\n",j1);
4304: /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
4305: fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
4306:
4307: for (i=1; i<=imx; i++) { /* Each individual */
4308: bool=1;
4309: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
4310: for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
4311: m=mw[mi][i];
4312: /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
4313: /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
4314: for (z1=1; z1<=cptcoveff; z1++){
4315: if( Fixed[Tmodelind[z1]]==1){
4316: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4317: if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
4318: bool=0;
4319: }else if( Fixed[Tmodelind[z1]]== 0) /* fixed */
4320: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4321: bool=0;
4322: }
4323: }
4324: if(bool==1){ /* Otherwise we skip that wave/person */
4325: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
4326: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
4327: if(m >=firstpass && m <=lastpass){
4328: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
4329: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
4330: if(agev[m][i]==0) agev[m][i]=iagemax+1;
4331: if(agev[m][i]==1) agev[m][i]=iagemax+2;
4332: if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
4333: printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m);
4334: exit(1);
4335: }
4336: if (s[m][i]>0 && s[m][i]<=nlstate) {
4337: /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
4338: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
4339: prop[s[m][i]][iagemax+3] += weight[i];
4340: } /* end valid statuses */
4341: } /* end selection of dates */
4342: } /* end selection of waves */
4343: } /* end bool */
4344: } /* end wave */
4345: } /* end individual */
4346: for(i=iagemin; i <= iagemax+3; i++){
4347: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
4348: posprop += prop[jk][i];
4349: }
4350:
4351: for(jk=1; jk <=nlstate ; jk++){
4352: if( i <= iagemax){
4353: if(posprop>=1.e-5){
4354: probs[i][jk][j1]= prop[jk][i]/posprop;
4355: } else{
4356: if(first==1){
4357: first=0;
4358: printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,j1,probs[i][jk][j1]);
4359: }
4360: }
4361: }
4362: }/* end jk */
4363: }/* end i */
1.222 brouard 4364: /*} *//* end i1 */
1.227 brouard 4365: } /* end j1 */
1.222 brouard 4366:
1.227 brouard 4367: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
4368: /*free_vector(pp,1,nlstate);*/
4369: free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
4370: } /* End of prevalence */
1.126 brouard 4371:
4372: /************* Waves Concatenation ***************/
4373:
4374: void concatwav(int wav[], int **dh, int **bh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
4375: {
4376: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
4377: Death is a valid wave (if date is known).
4378: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
4379: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
4380: and mw[mi+1][i]. dh depends on stepm.
1.227 brouard 4381: */
1.126 brouard 4382:
1.224 brouard 4383: int i=0, mi=0, m=0, mli=0;
1.126 brouard 4384: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
4385: double sum=0., jmean=0.;*/
1.224 brouard 4386: int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
1.126 brouard 4387: int j, k=0,jk, ju, jl;
4388: double sum=0.;
4389: first=0;
1.214 brouard 4390: firstwo=0;
1.217 brouard 4391: firsthree=0;
1.218 brouard 4392: firstfour=0;
1.164 brouard 4393: jmin=100000;
1.126 brouard 4394: jmax=-1;
4395: jmean=0.;
1.224 brouard 4396:
4397: /* Treating live states */
1.214 brouard 4398: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.224 brouard 4399: mi=0; /* First valid wave */
1.227 brouard 4400: mli=0; /* Last valid wave */
1.126 brouard 4401: m=firstpass;
1.214 brouard 4402: while(s[m][i] <= nlstate){ /* a live state */
1.227 brouard 4403: if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */
4404: mli=m-1;/* mw[++mi][i]=m-1; */
4405: }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
4406: mw[++mi][i]=m;
4407: mli=m;
1.224 brouard 4408: } /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
4409: if(m < lastpass){ /* m < lastpass, standard case */
1.227 brouard 4410: m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
1.216 brouard 4411: }
1.227 brouard 4412: else{ /* m >= lastpass, eventual special issue with warning */
1.224 brouard 4413: #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
1.227 brouard 4414: break;
1.224 brouard 4415: #else
1.227 brouard 4416: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
4417: if(firsthree == 0){
4418: printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
4419: firsthree=1;
4420: }
4421: fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
4422: mw[++mi][i]=m;
4423: mli=m;
4424: }
4425: if(s[m][i]==-2){ /* Vital status is really unknown */
4426: nbwarn++;
4427: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */
4428: printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
4429: fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
4430: }
4431: break;
4432: }
4433: break;
1.224 brouard 4434: #endif
1.227 brouard 4435: }/* End m >= lastpass */
1.126 brouard 4436: }/* end while */
1.224 brouard 4437:
1.227 brouard 4438: /* mi is the last effective wave, m is lastpass, mw[j][i] gives the # of j-th effective wave for individual i */
1.216 brouard 4439: /* After last pass */
1.224 brouard 4440: /* Treating death states */
1.214 brouard 4441: if (s[m][i] > nlstate){ /* In a death state */
1.227 brouard 4442: /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
4443: /* } */
1.126 brouard 4444: mi++; /* Death is another wave */
4445: /* if(mi==0) never been interviewed correctly before death */
1.227 brouard 4446: /* Only death is a correct wave */
1.126 brouard 4447: mw[mi][i]=m;
1.224 brouard 4448: }
4449: #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
1.227 brouard 4450: else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */
1.216 brouard 4451: /* m++; */
4452: /* mi++; */
4453: /* s[m][i]=nlstate+1; /\* We are setting the status to the last of non live state *\/ */
4454: /* mw[mi][i]=m; */
1.218 brouard 4455: if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
1.227 brouard 4456: if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */
4457: nbwarn++;
4458: if(firstfiv==0){
4459: printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
4460: firstfiv=1;
4461: }else{
4462: fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
4463: }
4464: }else{ /* Death occured afer last wave potential bias */
4465: nberr++;
4466: if(firstwo==0){
4467: printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
4468: firstwo=1;
4469: }
4470: fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
4471: }
1.218 brouard 4472: }else{ /* end date of interview is known */
1.227 brouard 4473: /* death is known but not confirmed by death status at any wave */
4474: if(firstfour==0){
4475: printf("Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
4476: firstfour=1;
4477: }
4478: fprintf(ficlog,"Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
1.214 brouard 4479: }
1.224 brouard 4480: } /* end if date of death is known */
4481: #endif
4482: wav[i]=mi; /* mi should be the last effective wave (or mli) */
4483: /* wav[i]=mw[mi][i]; */
1.126 brouard 4484: if(mi==0){
4485: nbwarn++;
4486: if(first==0){
1.227 brouard 4487: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
4488: first=1;
1.126 brouard 4489: }
4490: if(first==1){
1.227 brouard 4491: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.126 brouard 4492: }
4493: } /* end mi==0 */
4494: } /* End individuals */
1.214 brouard 4495: /* wav and mw are no more changed */
1.223 brouard 4496:
1.214 brouard 4497:
1.126 brouard 4498: for(i=1; i<=imx; i++){
4499: for(mi=1; mi<wav[i];mi++){
4500: if (stepm <=0)
1.227 brouard 4501: dh[mi][i]=1;
1.126 brouard 4502: else{
1.227 brouard 4503: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
4504: if (agedc[i] < 2*AGESUP) {
4505: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
4506: if(j==0) j=1; /* Survives at least one month after exam */
4507: else if(j<0){
4508: nberr++;
4509: printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
4510: j=1; /* Temporary Dangerous patch */
4511: printf(" We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
4512: fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
4513: fprintf(ficlog," We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
4514: }
4515: k=k+1;
4516: if (j >= jmax){
4517: jmax=j;
4518: ijmax=i;
4519: }
4520: if (j <= jmin){
4521: jmin=j;
4522: ijmin=i;
4523: }
4524: sum=sum+j;
4525: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
4526: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
4527: }
4528: }
4529: else{
4530: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.126 brouard 4531: /* if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
1.223 brouard 4532:
1.227 brouard 4533: k=k+1;
4534: if (j >= jmax) {
4535: jmax=j;
4536: ijmax=i;
4537: }
4538: else if (j <= jmin){
4539: jmin=j;
4540: ijmin=i;
4541: }
4542: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
4543: /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
4544: if(j<0){
4545: nberr++;
4546: printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
4547: fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
4548: }
4549: sum=sum+j;
4550: }
4551: jk= j/stepm;
4552: jl= j -jk*stepm;
4553: ju= j -(jk+1)*stepm;
4554: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
4555: if(jl==0){
4556: dh[mi][i]=jk;
4557: bh[mi][i]=0;
4558: }else{ /* We want a negative bias in order to only have interpolation ie
4559: * to avoid the price of an extra matrix product in likelihood */
4560: dh[mi][i]=jk+1;
4561: bh[mi][i]=ju;
4562: }
4563: }else{
4564: if(jl <= -ju){
4565: dh[mi][i]=jk;
4566: bh[mi][i]=jl; /* bias is positive if real duration
4567: * is higher than the multiple of stepm and negative otherwise.
4568: */
4569: }
4570: else{
4571: dh[mi][i]=jk+1;
4572: bh[mi][i]=ju;
4573: }
4574: if(dh[mi][i]==0){
4575: dh[mi][i]=1; /* At least one step */
4576: bh[mi][i]=ju; /* At least one step */
4577: /* printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
4578: }
4579: } /* end if mle */
1.126 brouard 4580: }
4581: } /* end wave */
4582: }
4583: jmean=sum/k;
4584: printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
1.141 brouard 4585: fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
1.227 brouard 4586: }
1.126 brouard 4587:
4588: /*********** Tricode ****************************/
1.220 brouard 4589: void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 4590: {
1.144 brouard 4591: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
4592: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
1.169 brouard 4593: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.224 brouard 4594: * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
4595: * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
1.144 brouard 4596: */
1.130 brouard 4597:
1.145 brouard 4598: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 4599: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 4600: int cptcode=0; /* Modality max of covariates j */
4601: int modmincovj=0; /* Modality min of covariates j */
4602:
4603:
1.220 brouard 4604: /* cptcoveff=0; */
1.224 brouard 4605: /* *cptcov=0; */
1.126 brouard 4606:
1.144 brouard 4607: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 4608:
1.224 brouard 4609: /* Loop on covariates without age and products and no quantitative variable */
4610: /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
1.227 brouard 4611: for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
4612: for (j=-1; (j < maxncov); j++) Ndum[j]=0;
4613: if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
4614: switch(Fixed[k]) {
4615: case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
4616: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the modality of this covariate Vj*/
4617: ij=(int)(covar[Tvar[k]][i]);
4618: /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
4619: * If product of Vn*Vm, still boolean *:
4620: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
4621: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
4622: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
4623: modality of the nth covariate of individual i. */
4624: if (ij > modmaxcovj)
4625: modmaxcovj=ij;
4626: else if (ij < modmincovj)
4627: modmincovj=ij;
4628: if ((ij < -1) && (ij > NCOVMAX)){
4629: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
4630: exit(1);
4631: }else
4632: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
4633: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
4634: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
4635: /* getting the maximum value of the modality of the covariate
4636: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
4637: female ies 1, then modmaxcovj=1.
4638: */
4639: } /* end for loop on individuals i */
4640: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
4641: fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
4642: cptcode=modmaxcovj;
4643: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
4644: /*for (i=0; i<=cptcode; i++) {*/
4645: for (j=modmincovj; j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
4646: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
4647: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
4648: if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
4649: if( j != -1){
4650: ncodemax[k]++; /* ncodemax[k]= Number of modalities of the k th
4651: covariate for which somebody answered excluding
4652: undefined. Usually 2: 0 and 1. */
4653: }
4654: ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
4655: covariate for which somebody answered including
4656: undefined. Usually 3: -1, 0 and 1. */
4657: }
4658: /* In fact ncodemax[k]=2 (dichotom. variables only) but it could be more for
4659: * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
4660: } /* Ndum[-1] number of undefined modalities */
4661:
4662: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
4663: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
4664: If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
4665: modmincovj=3; modmaxcovj = 7;
4666: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
4667: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
4668: defining two dummy variables: variables V1_1 and V1_2.
4669: nbcode[Tvar[j]][ij]=k;
4670: nbcode[Tvar[j]][1]=0;
4671: nbcode[Tvar[j]][2]=1;
4672: nbcode[Tvar[j]][3]=2;
4673: To be continued (not working yet).
4674: */
4675: ij=0; /* ij is similar to i but can jump over null modalities */
4676: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
4677: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
4678: break;
4679: }
4680: ij++;
4681: nbcode[Tvar[k]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1*/
4682: cptcode = ij; /* New max modality for covar j */
4683: } /* end of loop on modality i=-1 to 1 or more */
4684: break;
4685: case 1: /* Testing on varying covariate, could be simple and
4686: * should look at waves or product of fixed *
4687: * varying. No time to test -1, assuming 0 and 1 only */
4688: ij=0;
4689: for(i=0; i<=1;i++){
4690: nbcode[Tvar[k]][++ij]=i;
4691: }
1.225 brouard 4692: break;
1.227 brouard 4693: default:
1.225 brouard 4694: break;
1.227 brouard 4695: } /* end switch */
4696: } /* end dummy test */
1.225 brouard 4697:
1.192 brouard 4698: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
4699: /* /\*recode from 0 *\/ */
4700: /* k is a modality. If we have model=V1+V1*sex */
4701: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
4702: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
4703: /* } */
4704: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
4705: /* if (ij > ncodemax[j]) { */
4706: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4707: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4708: /* break; */
4709: /* } */
4710: /* } /\* end of loop on modality k *\/ */
1.137 brouard 4711: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
4712:
1.225 brouard 4713: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.227 brouard 4714: /* Look at fixed dummy (single or product) covariates to check empty modalities */
1.187 brouard 4715: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.225 brouard 4716: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
1.227 brouard 4717: ij=Tvar[i]; /* Tvar 5,4,3,6,5,7,1,4 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V4*age */
4718: Ndum[ij]++; /* Count the # of 1, 2 etc: {1,1,1,2,2,1,1} because V1 once, V2 once, two V4 and V5 in above */
4719: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, {2, 1, 1, 1, 2, 1, 1, 0, 0} */
1.225 brouard 4720: } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
4721:
4722: ij=0;
1.227 brouard 4723: /* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
4724: for (k=1; k<= cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
1.225 brouard 4725: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.227 brouard 4726: /* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? *\/ */
4727: if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */
4728: /* If product not in single variable we don't print results */
1.225 brouard 4729: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
1.230 ! brouard 4730: ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
! 4731: Tvaraff[ij]=Tvar[k]; /* For printing combination *//* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/
! 4732: Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
! 4733: TmodelInvind[k]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */
1.227 brouard 4734: if(Fixed[k]!=0)
4735: anyvaryingduminmodel=1;
1.230 ! brouard 4736: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
! 4737: /* Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
! 4738: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
! 4739: /* Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
! 4740: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
! 4741: /* Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
1.227 brouard 4742: }
1.225 brouard 4743: } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
4744: /* ij--; */
4745: /* cptcoveff=ij; /\*Number of total covariates*\/ */
4746: *cptcov=ij; /*Number of total real effective covariates: effective
4747: * because they can be excluded from the model and real
1.227 brouard 4748: * if in the model but excluded because missing values, but how to get k from ij?*/
4749: for(j=ij+1; j<= cptcovt; j++){
4750: Tvaraff[j]=0;
4751: Tmodelind[j]=0;
4752: }
1.228 brouard 4753: for(j=ntveff+1; j<= cptcovt; j++){
4754: TmodelInvind[j]=0;
4755: }
1.227 brouard 4756: /* To be sorted */
4757: ;
1.126 brouard 4758: }
4759:
1.145 brouard 4760:
1.126 brouard 4761: /*********** Health Expectancies ****************/
4762:
1.127 brouard 4763: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
1.126 brouard 4764:
4765: {
4766: /* Health expectancies, no variances */
1.164 brouard 4767: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 4768: int nhstepma, nstepma; /* Decreasing with age */
4769: double age, agelim, hf;
4770: double ***p3mat;
4771: double eip;
4772:
4773: pstamp(ficreseij);
4774: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
4775: fprintf(ficreseij,"# Age");
4776: for(i=1; i<=nlstate;i++){
4777: for(j=1; j<=nlstate;j++){
4778: fprintf(ficreseij," e%1d%1d ",i,j);
4779: }
4780: fprintf(ficreseij," e%1d. ",i);
4781: }
4782: fprintf(ficreseij,"\n");
4783:
4784:
4785: if(estepm < stepm){
4786: printf ("Problem %d lower than %d\n",estepm, stepm);
4787: }
4788: else hstepm=estepm;
4789: /* We compute the life expectancy from trapezoids spaced every estepm months
4790: * This is mainly to measure the difference between two models: for example
4791: * if stepm=24 months pijx are given only every 2 years and by summing them
4792: * we are calculating an estimate of the Life Expectancy assuming a linear
4793: * progression in between and thus overestimating or underestimating according
4794: * to the curvature of the survival function. If, for the same date, we
4795: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4796: * to compare the new estimate of Life expectancy with the same linear
4797: * hypothesis. A more precise result, taking into account a more precise
4798: * curvature will be obtained if estepm is as small as stepm. */
4799:
4800: /* For example we decided to compute the life expectancy with the smallest unit */
4801: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4802: nhstepm is the number of hstepm from age to agelim
4803: nstepm is the number of stepm from age to agelin.
4804: Look at hpijx to understand the reason of that which relies in memory size
4805: and note for a fixed period like estepm months */
4806: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4807: survival function given by stepm (the optimization length). Unfortunately it
4808: means that if the survival funtion is printed only each two years of age and if
4809: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4810: results. So we changed our mind and took the option of the best precision.
4811: */
4812: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4813:
4814: agelim=AGESUP;
4815: /* If stepm=6 months */
4816: /* Computed by stepm unit matrices, product of hstepm matrices, stored
4817: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
4818:
4819: /* nhstepm age range expressed in number of stepm */
4820: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4821: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4822: /* if (stepm >= YEARM) hstepm=1;*/
4823: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4824: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4825:
4826: for (age=bage; age<=fage; age ++){
4827: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4828: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4829: /* if (stepm >= YEARM) hstepm=1;*/
4830: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
4831:
4832: /* If stepm=6 months */
4833: /* Computed by stepm unit matrices, product of hstepma matrices, stored
4834: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
4835:
4836: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
4837:
4838: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4839:
4840: printf("%d|",(int)age);fflush(stdout);
4841: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
4842:
4843: /* Computing expectancies */
4844: for(i=1; i<=nlstate;i++)
4845: for(j=1; j<=nlstate;j++)
4846: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
4847: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
4848:
4849: /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
4850:
4851: }
4852:
4853: fprintf(ficreseij,"%3.0f",age );
4854: for(i=1; i<=nlstate;i++){
4855: eip=0;
4856: for(j=1; j<=nlstate;j++){
4857: eip +=eij[i][j][(int)age];
4858: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
4859: }
4860: fprintf(ficreseij,"%9.4f", eip );
4861: }
4862: fprintf(ficreseij,"\n");
4863:
4864: }
4865: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4866: printf("\n");
4867: fprintf(ficlog,"\n");
4868:
4869: }
4870:
1.127 brouard 4871: void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
1.126 brouard 4872:
4873: {
4874: /* Covariances of health expectancies eij and of total life expectancies according
1.222 brouard 4875: to initial status i, ei. .
1.126 brouard 4876: */
4877: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
4878: int nhstepma, nstepma; /* Decreasing with age */
4879: double age, agelim, hf;
4880: double ***p3matp, ***p3matm, ***varhe;
4881: double **dnewm,**doldm;
4882: double *xp, *xm;
4883: double **gp, **gm;
4884: double ***gradg, ***trgradg;
4885: int theta;
4886:
4887: double eip, vip;
4888:
4889: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
4890: xp=vector(1,npar);
4891: xm=vector(1,npar);
4892: dnewm=matrix(1,nlstate*nlstate,1,npar);
4893: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
4894:
4895: pstamp(ficresstdeij);
4896: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
4897: fprintf(ficresstdeij,"# Age");
4898: for(i=1; i<=nlstate;i++){
4899: for(j=1; j<=nlstate;j++)
4900: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
4901: fprintf(ficresstdeij," e%1d. ",i);
4902: }
4903: fprintf(ficresstdeij,"\n");
4904:
4905: pstamp(ficrescveij);
4906: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
4907: fprintf(ficrescveij,"# Age");
4908: for(i=1; i<=nlstate;i++)
4909: for(j=1; j<=nlstate;j++){
4910: cptj= (j-1)*nlstate+i;
4911: for(i2=1; i2<=nlstate;i2++)
4912: for(j2=1; j2<=nlstate;j2++){
4913: cptj2= (j2-1)*nlstate+i2;
4914: if(cptj2 <= cptj)
4915: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
4916: }
4917: }
4918: fprintf(ficrescveij,"\n");
4919:
4920: if(estepm < stepm){
4921: printf ("Problem %d lower than %d\n",estepm, stepm);
4922: }
4923: else hstepm=estepm;
4924: /* We compute the life expectancy from trapezoids spaced every estepm months
4925: * This is mainly to measure the difference between two models: for example
4926: * if stepm=24 months pijx are given only every 2 years and by summing them
4927: * we are calculating an estimate of the Life Expectancy assuming a linear
4928: * progression in between and thus overestimating or underestimating according
4929: * to the curvature of the survival function. If, for the same date, we
4930: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4931: * to compare the new estimate of Life expectancy with the same linear
4932: * hypothesis. A more precise result, taking into account a more precise
4933: * curvature will be obtained if estepm is as small as stepm. */
4934:
4935: /* For example we decided to compute the life expectancy with the smallest unit */
4936: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4937: nhstepm is the number of hstepm from age to agelim
4938: nstepm is the number of stepm from age to agelin.
4939: Look at hpijx to understand the reason of that which relies in memory size
4940: and note for a fixed period like estepm months */
4941: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4942: survival function given by stepm (the optimization length). Unfortunately it
4943: means that if the survival funtion is printed only each two years of age and if
4944: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4945: results. So we changed our mind and took the option of the best precision.
4946: */
4947: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4948:
4949: /* If stepm=6 months */
4950: /* nhstepm age range expressed in number of stepm */
4951: agelim=AGESUP;
4952: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
4953: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4954: /* if (stepm >= YEARM) hstepm=1;*/
4955: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4956:
4957: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4958: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4959: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
4960: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
4961: gp=matrix(0,nhstepm,1,nlstate*nlstate);
4962: gm=matrix(0,nhstepm,1,nlstate*nlstate);
4963:
4964: for (age=bage; age<=fage; age ++){
4965: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4966: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4967: /* if (stepm >= YEARM) hstepm=1;*/
4968: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218 brouard 4969:
1.126 brouard 4970: /* If stepm=6 months */
4971: /* Computed by stepm unit matrices, product of hstepma matrices, stored
4972: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
4973:
4974: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.218 brouard 4975:
1.126 brouard 4976: /* Computing Variances of health expectancies */
4977: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
4978: decrease memory allocation */
4979: for(theta=1; theta <=npar; theta++){
4980: for(i=1; i<=npar; i++){
1.222 brouard 4981: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4982: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126 brouard 4983: }
4984: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
4985: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
1.218 brouard 4986:
1.126 brouard 4987: for(j=1; j<= nlstate; j++){
1.222 brouard 4988: for(i=1; i<=nlstate; i++){
4989: for(h=0; h<=nhstepm-1; h++){
4990: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
4991: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
4992: }
4993: }
1.126 brouard 4994: }
1.218 brouard 4995:
1.126 brouard 4996: for(ij=1; ij<= nlstate*nlstate; ij++)
1.222 brouard 4997: for(h=0; h<=nhstepm-1; h++){
4998: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
4999: }
1.126 brouard 5000: }/* End theta */
5001:
5002:
5003: for(h=0; h<=nhstepm-1; h++)
5004: for(j=1; j<=nlstate*nlstate;j++)
1.222 brouard 5005: for(theta=1; theta <=npar; theta++)
5006: trgradg[h][j][theta]=gradg[h][theta][j];
1.126 brouard 5007:
1.218 brouard 5008:
1.222 brouard 5009: for(ij=1;ij<=nlstate*nlstate;ij++)
1.126 brouard 5010: for(ji=1;ji<=nlstate*nlstate;ji++)
1.222 brouard 5011: varhe[ij][ji][(int)age] =0.;
1.218 brouard 5012:
1.222 brouard 5013: printf("%d|",(int)age);fflush(stdout);
5014: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5015: for(h=0;h<=nhstepm-1;h++){
1.126 brouard 5016: for(k=0;k<=nhstepm-1;k++){
1.222 brouard 5017: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
5018: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
5019: for(ij=1;ij<=nlstate*nlstate;ij++)
5020: for(ji=1;ji<=nlstate*nlstate;ji++)
5021: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126 brouard 5022: }
5023: }
1.218 brouard 5024:
1.126 brouard 5025: /* Computing expectancies */
5026: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
5027: for(i=1; i<=nlstate;i++)
5028: for(j=1; j<=nlstate;j++)
1.222 brouard 5029: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5030: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.218 brouard 5031:
1.222 brouard 5032: /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
1.218 brouard 5033:
1.222 brouard 5034: }
1.218 brouard 5035:
1.126 brouard 5036: fprintf(ficresstdeij,"%3.0f",age );
5037: for(i=1; i<=nlstate;i++){
5038: eip=0.;
5039: vip=0.;
5040: for(j=1; j<=nlstate;j++){
1.222 brouard 5041: eip += eij[i][j][(int)age];
5042: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
5043: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
5044: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
1.126 brouard 5045: }
5046: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
5047: }
5048: fprintf(ficresstdeij,"\n");
1.218 brouard 5049:
1.126 brouard 5050: fprintf(ficrescveij,"%3.0f",age );
5051: for(i=1; i<=nlstate;i++)
5052: for(j=1; j<=nlstate;j++){
1.222 brouard 5053: cptj= (j-1)*nlstate+i;
5054: for(i2=1; i2<=nlstate;i2++)
5055: for(j2=1; j2<=nlstate;j2++){
5056: cptj2= (j2-1)*nlstate+i2;
5057: if(cptj2 <= cptj)
5058: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
5059: }
1.126 brouard 5060: }
5061: fprintf(ficrescveij,"\n");
1.218 brouard 5062:
1.126 brouard 5063: }
5064: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
5065: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
5066: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
5067: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
5068: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5069: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5070: printf("\n");
5071: fprintf(ficlog,"\n");
1.218 brouard 5072:
1.126 brouard 5073: free_vector(xm,1,npar);
5074: free_vector(xp,1,npar);
5075: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
5076: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
5077: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
5078: }
1.218 brouard 5079:
1.126 brouard 5080: /************ Variance ******************/
1.209 brouard 5081: void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
1.218 brouard 5082: {
5083: /* Variance of health expectancies */
5084: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
5085: /* double **newm;*/
5086: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
5087:
5088: /* int movingaverage(); */
5089: double **dnewm,**doldm;
5090: double **dnewmp,**doldmp;
5091: int i, j, nhstepm, hstepm, h, nstepm ;
5092: int k;
5093: double *xp;
5094: double **gp, **gm; /* for var eij */
5095: double ***gradg, ***trgradg; /*for var eij */
5096: double **gradgp, **trgradgp; /* for var p point j */
5097: double *gpp, *gmp; /* for var p point j */
5098: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
5099: double ***p3mat;
5100: double age,agelim, hf;
5101: /* double ***mobaverage; */
5102: int theta;
5103: char digit[4];
5104: char digitp[25];
5105:
5106: char fileresprobmorprev[FILENAMELENGTH];
5107:
5108: if(popbased==1){
5109: if(mobilav!=0)
5110: strcpy(digitp,"-POPULBASED-MOBILAV_");
5111: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
5112: }
5113: else
5114: strcpy(digitp,"-STABLBASED_");
1.126 brouard 5115:
1.218 brouard 5116: /* if (mobilav!=0) { */
5117: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5118: /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
5119: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
5120: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
5121: /* } */
5122: /* } */
5123:
5124: strcpy(fileresprobmorprev,"PRMORPREV-");
5125: sprintf(digit,"%-d",ij);
5126: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
5127: strcat(fileresprobmorprev,digit); /* Tvar to be done */
5128: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
5129: strcat(fileresprobmorprev,fileresu);
5130: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
5131: printf("Problem with resultfile: %s\n", fileresprobmorprev);
5132: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
5133: }
5134: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5135: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5136: pstamp(ficresprobmorprev);
5137: fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
5138: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
5139: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
5140: fprintf(ficresprobmorprev," p.%-d SE",j);
5141: for(i=1; i<=nlstate;i++)
5142: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
5143: }
5144: fprintf(ficresprobmorprev,"\n");
5145:
5146: fprintf(ficgp,"\n# Routine varevsij");
5147: fprintf(ficgp,"\nunset title \n");
5148: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
5149: fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
5150: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
5151: /* } */
5152: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5153: pstamp(ficresvij);
5154: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
5155: if(popbased==1)
5156: fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
5157: else
5158: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
5159: fprintf(ficresvij,"# Age");
5160: for(i=1; i<=nlstate;i++)
5161: for(j=1; j<=nlstate;j++)
5162: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
5163: fprintf(ficresvij,"\n");
5164:
5165: xp=vector(1,npar);
5166: dnewm=matrix(1,nlstate,1,npar);
5167: doldm=matrix(1,nlstate,1,nlstate);
5168: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
5169: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5170:
5171: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
5172: gpp=vector(nlstate+1,nlstate+ndeath);
5173: gmp=vector(nlstate+1,nlstate+ndeath);
5174: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126 brouard 5175:
1.218 brouard 5176: if(estepm < stepm){
5177: printf ("Problem %d lower than %d\n",estepm, stepm);
5178: }
5179: else hstepm=estepm;
5180: /* For example we decided to compute the life expectancy with the smallest unit */
5181: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5182: nhstepm is the number of hstepm from age to agelim
5183: nstepm is the number of stepm from age to agelim.
5184: Look at function hpijx to understand why because of memory size limitations,
5185: we decided (b) to get a life expectancy respecting the most precise curvature of the
5186: survival function given by stepm (the optimization length). Unfortunately it
5187: means that if the survival funtion is printed every two years of age and if
5188: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5189: results. So we changed our mind and took the option of the best precision.
5190: */
5191: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5192: agelim = AGESUP;
5193: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5194: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5195: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5196: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5197: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
5198: gp=matrix(0,nhstepm,1,nlstate);
5199: gm=matrix(0,nhstepm,1,nlstate);
5200:
5201:
5202: for(theta=1; theta <=npar; theta++){
5203: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
5204: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5205: }
5206:
5207: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5208:
5209: if (popbased==1) {
5210: if(mobilav ==0){
5211: for(i=1; i<=nlstate;i++)
5212: prlim[i][i]=probs[(int)age][i][ij];
5213: }else{ /* mobilav */
5214: for(i=1; i<=nlstate;i++)
5215: prlim[i][i]=mobaverage[(int)age][i][ij];
5216: }
5217: }
5218:
5219: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); /* Returns p3mat[i][j][h] for h=1 to nhstepm */
5220: for(j=1; j<= nlstate; j++){
5221: for(h=0; h<=nhstepm; h++){
5222: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
5223: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
5224: }
5225: }
5226: /* Next for computing probability of death (h=1 means
5227: computed over hstepm matrices product = hstepm*stepm months)
5228: as a weighted average of prlim.
5229: */
5230: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5231: for(i=1,gpp[j]=0.; i<= nlstate; i++)
5232: gpp[j] += prlim[i][i]*p3mat[i][j][1];
5233: }
5234: /* end probability of death */
5235:
5236: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
5237: xp[i] = x[i] - (i==theta ?delti[theta]:0);
5238:
5239: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
5240:
5241: if (popbased==1) {
5242: if(mobilav ==0){
5243: for(i=1; i<=nlstate;i++)
5244: prlim[i][i]=probs[(int)age][i][ij];
5245: }else{ /* mobilav */
5246: for(i=1; i<=nlstate;i++)
5247: prlim[i][i]=mobaverage[(int)age][i][ij];
5248: }
5249: }
5250:
5251: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
5252:
5253: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
5254: for(h=0; h<=nhstepm; h++){
5255: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
5256: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
5257: }
5258: }
5259: /* This for computing probability of death (h=1 means
5260: computed over hstepm matrices product = hstepm*stepm months)
5261: as a weighted average of prlim.
5262: */
5263: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5264: for(i=1,gmp[j]=0.; i<= nlstate; i++)
5265: gmp[j] += prlim[i][i]*p3mat[i][j][1];
5266: }
5267: /* end probability of death */
5268:
5269: for(j=1; j<= nlstate; j++) /* vareij */
5270: for(h=0; h<=nhstepm; h++){
5271: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
5272: }
5273:
5274: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
5275: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
5276: }
5277:
5278: } /* End theta */
5279:
5280: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
5281:
5282: for(h=0; h<=nhstepm; h++) /* veij */
5283: for(j=1; j<=nlstate;j++)
5284: for(theta=1; theta <=npar; theta++)
5285: trgradg[h][j][theta]=gradg[h][theta][j];
5286:
5287: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
5288: for(theta=1; theta <=npar; theta++)
5289: trgradgp[j][theta]=gradgp[theta][j];
5290:
5291:
5292: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
5293: for(i=1;i<=nlstate;i++)
5294: for(j=1;j<=nlstate;j++)
5295: vareij[i][j][(int)age] =0.;
5296:
5297: for(h=0;h<=nhstepm;h++){
5298: for(k=0;k<=nhstepm;k++){
5299: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
5300: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
5301: for(i=1;i<=nlstate;i++)
5302: for(j=1;j<=nlstate;j++)
5303: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
5304: }
5305: }
5306:
5307: /* pptj */
5308: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
5309: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
5310: for(j=nlstate+1;j<=nlstate+ndeath;j++)
5311: for(i=nlstate+1;i<=nlstate+ndeath;i++)
5312: varppt[j][i]=doldmp[j][i];
5313: /* end ppptj */
5314: /* x centered again */
5315:
5316: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
5317:
5318: if (popbased==1) {
5319: if(mobilav ==0){
5320: for(i=1; i<=nlstate;i++)
5321: prlim[i][i]=probs[(int)age][i][ij];
5322: }else{ /* mobilav */
5323: for(i=1; i<=nlstate;i++)
5324: prlim[i][i]=mobaverage[(int)age][i][ij];
5325: }
5326: }
5327:
5328: /* This for computing probability of death (h=1 means
5329: computed over hstepm (estepm) matrices product = hstepm*stepm months)
5330: as a weighted average of prlim.
5331: */
5332: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
5333: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5334: for(i=1,gmp[j]=0.;i<= nlstate; i++)
5335: gmp[j] += prlim[i][i]*p3mat[i][j][1];
5336: }
5337: /* end probability of death */
5338:
5339: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
5340: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
5341: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
5342: for(i=1; i<=nlstate;i++){
5343: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
5344: }
5345: }
5346: fprintf(ficresprobmorprev,"\n");
5347:
5348: fprintf(ficresvij,"%.0f ",age );
5349: for(i=1; i<=nlstate;i++)
5350: for(j=1; j<=nlstate;j++){
5351: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
5352: }
5353: fprintf(ficresvij,"\n");
5354: free_matrix(gp,0,nhstepm,1,nlstate);
5355: free_matrix(gm,0,nhstepm,1,nlstate);
5356: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
5357: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
5358: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5359: } /* End age */
5360: free_vector(gpp,nlstate+1,nlstate+ndeath);
5361: free_vector(gmp,nlstate+1,nlstate+ndeath);
5362: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
5363: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
5364: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
5365: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
5366: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
5367: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
5368: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
5369: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
5370: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
5371: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
5372: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
5373: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
5374: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
5375: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
5376: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.svg\"> <br>\n", estepm,subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
5377: /* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.svg\"> <br>\n", stepm,YEARM,digitp,digit);
1.126 brouard 5378: */
1.218 brouard 5379: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
5380: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 5381:
1.218 brouard 5382: free_vector(xp,1,npar);
5383: free_matrix(doldm,1,nlstate,1,nlstate);
5384: free_matrix(dnewm,1,nlstate,1,npar);
5385: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5386: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
5387: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5388: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5389: fclose(ficresprobmorprev);
5390: fflush(ficgp);
5391: fflush(fichtm);
5392: } /* end varevsij */
1.126 brouard 5393:
5394: /************ Variance of prevlim ******************/
1.209 brouard 5395: void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[])
1.126 brouard 5396: {
1.205 brouard 5397: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 5398: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 5399:
1.126 brouard 5400: double **dnewm,**doldm;
5401: int i, j, nhstepm, hstepm;
5402: double *xp;
5403: double *gp, *gm;
5404: double **gradg, **trgradg;
1.208 brouard 5405: double **mgm, **mgp;
1.126 brouard 5406: double age,agelim;
5407: int theta;
5408:
5409: pstamp(ficresvpl);
5410: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
5411: fprintf(ficresvpl,"# Age");
5412: for(i=1; i<=nlstate;i++)
5413: fprintf(ficresvpl," %1d-%1d",i,i);
5414: fprintf(ficresvpl,"\n");
5415:
5416: xp=vector(1,npar);
5417: dnewm=matrix(1,nlstate,1,npar);
5418: doldm=matrix(1,nlstate,1,nlstate);
5419:
5420: hstepm=1*YEARM; /* Every year of age */
5421: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
5422: agelim = AGESUP;
5423: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5424: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5425: if (stepm >= YEARM) hstepm=1;
5426: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5427: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 5428: mgp=matrix(1,npar,1,nlstate);
5429: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 5430: gp=vector(1,nlstate);
5431: gm=vector(1,nlstate);
5432:
5433: for(theta=1; theta <=npar; theta++){
5434: for(i=1; i<=npar; i++){ /* Computes gradient */
5435: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5436: }
1.209 brouard 5437: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
5438: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5439: else
5440: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 5441: for(i=1;i<=nlstate;i++){
1.126 brouard 5442: gp[i] = prlim[i][i];
1.208 brouard 5443: mgp[theta][i] = prlim[i][i];
5444: }
1.126 brouard 5445: for(i=1; i<=npar; i++) /* Computes gradient */
5446: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 5447: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
5448: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5449: else
5450: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 5451: for(i=1;i<=nlstate;i++){
1.126 brouard 5452: gm[i] = prlim[i][i];
1.208 brouard 5453: mgm[theta][i] = prlim[i][i];
5454: }
1.126 brouard 5455: for(i=1;i<=nlstate;i++)
5456: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 5457: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 5458: } /* End theta */
5459:
5460: trgradg =matrix(1,nlstate,1,npar);
5461:
5462: for(j=1; j<=nlstate;j++)
5463: for(theta=1; theta <=npar; theta++)
5464: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 5465: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5466: /* printf("\nmgm mgp %d ",(int)age); */
5467: /* for(j=1; j<=nlstate;j++){ */
5468: /* printf(" %d ",j); */
5469: /* for(theta=1; theta <=npar; theta++) */
5470: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
5471: /* printf("\n "); */
5472: /* } */
5473: /* } */
5474: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5475: /* printf("\n gradg %d ",(int)age); */
5476: /* for(j=1; j<=nlstate;j++){ */
5477: /* printf("%d ",j); */
5478: /* for(theta=1; theta <=npar; theta++) */
5479: /* printf("%d %lf ",theta,gradg[theta][j]); */
5480: /* printf("\n "); */
5481: /* } */
5482: /* } */
1.126 brouard 5483:
5484: for(i=1;i<=nlstate;i++)
5485: varpl[i][(int)age] =0.;
1.209 brouard 5486: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.205 brouard 5487: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5488: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
5489: }else{
1.126 brouard 5490: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5491: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 5492: }
1.126 brouard 5493: for(i=1;i<=nlstate;i++)
5494: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
5495:
5496: fprintf(ficresvpl,"%.0f ",age );
5497: for(i=1; i<=nlstate;i++)
5498: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
5499: fprintf(ficresvpl,"\n");
5500: free_vector(gp,1,nlstate);
5501: free_vector(gm,1,nlstate);
1.208 brouard 5502: free_matrix(mgm,1,npar,1,nlstate);
5503: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 5504: free_matrix(gradg,1,npar,1,nlstate);
5505: free_matrix(trgradg,1,nlstate,1,npar);
5506: } /* End age */
5507:
5508: free_vector(xp,1,npar);
5509: free_matrix(doldm,1,nlstate,1,npar);
5510: free_matrix(dnewm,1,nlstate,1,nlstate);
5511:
5512: }
5513:
5514: /************ Variance of one-step probabilities ******************/
5515: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
1.222 brouard 5516: {
5517: int i, j=0, k1, l1, tj;
5518: int k2, l2, j1, z1;
5519: int k=0, l;
5520: int first=1, first1, first2;
5521: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
5522: double **dnewm,**doldm;
5523: double *xp;
5524: double *gp, *gm;
5525: double **gradg, **trgradg;
5526: double **mu;
5527: double age, cov[NCOVMAX+1];
5528: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
5529: int theta;
5530: char fileresprob[FILENAMELENGTH];
5531: char fileresprobcov[FILENAMELENGTH];
5532: char fileresprobcor[FILENAMELENGTH];
5533: double ***varpij;
5534:
5535: strcpy(fileresprob,"PROB_");
5536: strcat(fileresprob,fileres);
5537: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
5538: printf("Problem with resultfile: %s\n", fileresprob);
5539: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
5540: }
5541: strcpy(fileresprobcov,"PROBCOV_");
5542: strcat(fileresprobcov,fileresu);
5543: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
5544: printf("Problem with resultfile: %s\n", fileresprobcov);
5545: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
5546: }
5547: strcpy(fileresprobcor,"PROBCOR_");
5548: strcat(fileresprobcor,fileresu);
5549: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
5550: printf("Problem with resultfile: %s\n", fileresprobcor);
5551: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
5552: }
5553: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
5554: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
5555: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
5556: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
5557: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
5558: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
5559: pstamp(ficresprob);
5560: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
5561: fprintf(ficresprob,"# Age");
5562: pstamp(ficresprobcov);
5563: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
5564: fprintf(ficresprobcov,"# Age");
5565: pstamp(ficresprobcor);
5566: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
5567: fprintf(ficresprobcor,"# Age");
1.126 brouard 5568:
5569:
1.222 brouard 5570: for(i=1; i<=nlstate;i++)
5571: for(j=1; j<=(nlstate+ndeath);j++){
5572: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
5573: fprintf(ficresprobcov," p%1d-%1d ",i,j);
5574: fprintf(ficresprobcor," p%1d-%1d ",i,j);
5575: }
5576: /* fprintf(ficresprob,"\n");
5577: fprintf(ficresprobcov,"\n");
5578: fprintf(ficresprobcor,"\n");
5579: */
5580: xp=vector(1,npar);
5581: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
5582: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
5583: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
5584: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
5585: first=1;
5586: fprintf(ficgp,"\n# Routine varprob");
5587: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
5588: fprintf(fichtm,"\n");
5589:
5590: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.</li>\n",optionfilehtmcov);
5591: fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
5592: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 5593: and drawn. It helps understanding how is the covariance between two incidences.\
5594: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.222 brouard 5595: fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
1.126 brouard 5596: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
5597: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
5598: standard deviations wide on each axis. <br>\
5599: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
5600: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
5601: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
5602:
1.222 brouard 5603: cov[1]=1;
5604: /* tj=cptcoveff; */
1.225 brouard 5605: tj = (int) pow(2,cptcoveff);
1.222 brouard 5606: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
5607: j1=0;
1.224 brouard 5608: for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/
1.222 brouard 5609: if (cptcovn>0) {
5610: fprintf(ficresprob, "\n#********** Variable ");
1.225 brouard 5611: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5612: fprintf(ficresprob, "**********\n#\n");
5613: fprintf(ficresprobcov, "\n#********** Variable ");
1.225 brouard 5614: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5615: fprintf(ficresprobcov, "**********\n#\n");
1.220 brouard 5616:
1.222 brouard 5617: fprintf(ficgp, "\n#********** Variable ");
1.225 brouard 5618: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5619: fprintf(ficgp, "**********\n#\n");
1.220 brouard 5620:
5621:
1.222 brouard 5622: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.225 brouard 5623: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5624: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 5625:
1.222 brouard 5626: fprintf(ficresprobcor, "\n#********** Variable ");
1.225 brouard 5627: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5628: fprintf(ficresprobcor, "**********\n#");
5629: if(invalidvarcomb[j1]){
5630: fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
5631: fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
5632: continue;
5633: }
5634: }
5635: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
5636: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
5637: gp=vector(1,(nlstate)*(nlstate+ndeath));
5638: gm=vector(1,(nlstate)*(nlstate+ndeath));
5639: for (age=bage; age<=fage; age ++){
5640: cov[2]=age;
5641: if(nagesqr==1)
5642: cov[3]= age*age;
5643: for (k=1; k<=cptcovn;k++) {
5644: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
5645: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
5646: * 1 1 1 1 1
5647: * 2 2 1 1 1
5648: * 3 1 2 1 1
5649: */
5650: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
5651: }
5652: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5653: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
5654: for (k=1; k<=cptcovprod;k++)
5655: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.220 brouard 5656:
5657:
1.222 brouard 5658: for(theta=1; theta <=npar; theta++){
5659: for(i=1; i<=npar; i++)
5660: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.220 brouard 5661:
1.222 brouard 5662: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1.220 brouard 5663:
1.222 brouard 5664: k=0;
5665: for(i=1; i<= (nlstate); i++){
5666: for(j=1; j<=(nlstate+ndeath);j++){
5667: k=k+1;
5668: gp[k]=pmmij[i][j];
5669: }
5670: }
1.220 brouard 5671:
1.222 brouard 5672: for(i=1; i<=npar; i++)
5673: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.220 brouard 5674:
1.222 brouard 5675: pmij(pmmij,cov,ncovmodel,xp,nlstate);
5676: k=0;
5677: for(i=1; i<=(nlstate); i++){
5678: for(j=1; j<=(nlstate+ndeath);j++){
5679: k=k+1;
5680: gm[k]=pmmij[i][j];
5681: }
5682: }
1.220 brouard 5683:
1.222 brouard 5684: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
5685: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
5686: }
1.126 brouard 5687:
1.222 brouard 5688: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
5689: for(theta=1; theta <=npar; theta++)
5690: trgradg[j][theta]=gradg[theta][j];
1.220 brouard 5691:
1.222 brouard 5692: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
5693: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.220 brouard 5694:
1.222 brouard 5695: pmij(pmmij,cov,ncovmodel,x,nlstate);
1.220 brouard 5696:
1.222 brouard 5697: k=0;
5698: for(i=1; i<=(nlstate); i++){
5699: for(j=1; j<=(nlstate+ndeath);j++){
5700: k=k+1;
5701: mu[k][(int) age]=pmmij[i][j];
5702: }
5703: }
5704: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
5705: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
5706: varpij[i][j][(int)age] = doldm[i][j];
1.220 brouard 5707:
1.222 brouard 5708: /*printf("\n%d ",(int)age);
5709: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
5710: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
5711: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
5712: }*/
1.220 brouard 5713:
1.222 brouard 5714: fprintf(ficresprob,"\n%d ",(int)age);
5715: fprintf(ficresprobcov,"\n%d ",(int)age);
5716: fprintf(ficresprobcor,"\n%d ",(int)age);
1.220 brouard 5717:
1.222 brouard 5718: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
5719: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
5720: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
5721: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
5722: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
5723: }
5724: i=0;
5725: for (k=1; k<=(nlstate);k++){
5726: for (l=1; l<=(nlstate+ndeath);l++){
5727: i++;
5728: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
5729: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
5730: for (j=1; j<=i;j++){
5731: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
5732: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
5733: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
5734: }
5735: }
5736: }/* end of loop for state */
5737: } /* end of loop for age */
5738: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
5739: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
5740: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
5741: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
5742:
5743: /* Confidence intervalle of pij */
5744: /*
5745: fprintf(ficgp,"\nunset parametric;unset label");
5746: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
5747: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
5748: fprintf(fichtm,"\n<br>Probability with confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
5749: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
5750: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
5751: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
5752: */
5753:
5754: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
5755: first1=1;first2=2;
5756: for (k2=1; k2<=(nlstate);k2++){
5757: for (l2=1; l2<=(nlstate+ndeath);l2++){
5758: if(l2==k2) continue;
5759: j=(k2-1)*(nlstate+ndeath)+l2;
5760: for (k1=1; k1<=(nlstate);k1++){
5761: for (l1=1; l1<=(nlstate+ndeath);l1++){
5762: if(l1==k1) continue;
5763: i=(k1-1)*(nlstate+ndeath)+l1;
5764: if(i<=j) continue;
5765: for (age=bage; age<=fage; age ++){
5766: if ((int)age %5==0){
5767: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
5768: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
5769: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
5770: mu1=mu[i][(int) age]/stepm*YEARM ;
5771: mu2=mu[j][(int) age]/stepm*YEARM;
5772: c12=cv12/sqrt(v1*v2);
5773: /* Computing eigen value of matrix of covariance */
5774: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
5775: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
5776: if ((lc2 <0) || (lc1 <0) ){
5777: if(first2==1){
5778: first1=0;
5779: printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
5780: }
5781: fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
5782: /* lc1=fabs(lc1); */ /* If we want to have them positive */
5783: /* lc2=fabs(lc2); */
5784: }
1.220 brouard 5785:
1.222 brouard 5786: /* Eigen vectors */
5787: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
5788: /*v21=sqrt(1.-v11*v11); *//* error */
5789: v21=(lc1-v1)/cv12*v11;
5790: v12=-v21;
5791: v22=v11;
5792: tnalp=v21/v11;
5793: if(first1==1){
5794: first1=0;
5795: printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
5796: }
5797: fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
5798: /*printf(fignu*/
5799: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
5800: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
5801: if(first==1){
5802: first=0;
5803: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
5804: fprintf(ficgp,"\nset parametric;unset label");
5805: fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
5806: fprintf(ficgp,"\nset ter svg size 640, 480");
5807: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.220 brouard 5808: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
1.201 brouard 5809: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.222 brouard 5810: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
5811: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5812: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5813: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
5814: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5815: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
5816: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
5817: fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not", \
5818: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
5819: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
5820: }else{
5821: first=0;
5822: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
5823: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
5824: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
5825: fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not", \
5826: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
5827: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
5828: }/* if first */
5829: } /* age mod 5 */
5830: } /* end loop age */
5831: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5832: first=1;
5833: } /*l12 */
5834: } /* k12 */
5835: } /*l1 */
5836: }/* k1 */
5837: } /* loop on combination of covariates j1 */
5838: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
5839: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
5840: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
5841: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
5842: free_vector(xp,1,npar);
5843: fclose(ficresprob);
5844: fclose(ficresprobcov);
5845: fclose(ficresprobcor);
5846: fflush(ficgp);
5847: fflush(fichtmcov);
5848: }
1.126 brouard 5849:
5850:
5851: /******************* Printing html file ***********/
1.201 brouard 5852: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 5853: int lastpass, int stepm, int weightopt, char model[],\
5854: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.217 brouard 5855: int popforecast, int prevfcast, int backcast, int estepm , \
1.213 brouard 5856: double jprev1, double mprev1,double anprev1, double dateprev1, \
5857: double jprev2, double mprev2,double anprev2, double dateprev2){
1.126 brouard 5858: int jj1, k1, i1, cpt;
5859:
5860: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
5861: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
5862: </ul>");
1.214 brouard 5863: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
5864: fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
5865: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
5866: fprintf(fichtm,"<li> - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",
1.213 brouard 5867: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
5868: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 5869: fprintf(fichtm,"\
5870: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 5871: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 5872: fprintf(fichtm,"\
1.217 brouard 5873: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
5874: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
5875: fprintf(fichtm,"\
1.126 brouard 5876: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5877: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 5878: fprintf(fichtm,"\
1.217 brouard 5879: - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
5880: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
5881: fprintf(fichtm,"\
1.211 brouard 5882: - (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
1.126 brouard 5883: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5884: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 5885: if(prevfcast==1){
5886: fprintf(fichtm,"\
5887: - Prevalence projections by age and states: \
1.201 brouard 5888: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 5889: }
1.126 brouard 5890:
1.222 brouard 5891: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
1.126 brouard 5892:
1.225 brouard 5893: m=pow(2,cptcoveff);
1.222 brouard 5894: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 5895:
1.222 brouard 5896: jj1=0;
5897: for(k1=1; k1<=m;k1++){
1.220 brouard 5898:
1.222 brouard 5899: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
5900: jj1++;
5901: if (cptcovn > 0) {
5902: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 5903: for (cpt=1; cpt<=cptcoveff;cpt++){
1.222 brouard 5904: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
5905: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
5906: }
1.230 ! brouard 5907: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
1.222 brouard 5908: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
5909: if(invalidvarcomb[k1]){
5910: fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
5911: printf("\nCombination (%d) ignored because no cases \n",k1);
5912: continue;
5913: }
5914: }
5915: /* aij, bij */
5916: fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \
1.211 brouard 5917: <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 5918: /* Pij */
5919: fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \
1.201 brouard 5920: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 5921: /* Quasi-incidences */
5922: fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.220 brouard 5923: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211 brouard 5924: incidence (rates) are the limit when h tends to zero of the ratio of the probability <sub>h</sub>P<sub>ij</sub> \
5925: divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
1.201 brouard 5926: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 5927: /* Survival functions (period) in state j */
5928: for(cpt=1; cpt<=nlstate;cpt++){
5929: fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
1.201 brouard 5930: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
1.222 brouard 5931: }
5932: /* State specific survival functions (period) */
5933: for(cpt=1; cpt<=nlstate;cpt++){
5934: fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
1.220 brouard 5935: Or probability to survive in various states (1 to %d) being in state %d at different ages. \
1.201 brouard 5936: <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);
1.222 brouard 5937: }
5938: /* Period (stable) prevalence in each health state */
5939: for(cpt=1; cpt<=nlstate;cpt++){
5940: fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a><br> \
1.201 brouard 5941: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
1.222 brouard 5942: }
5943: if(backcast==1){
5944: /* Period (stable) back prevalence in each health state */
5945: for(cpt=1; cpt<=nlstate;cpt++){
5946: fprintf(fichtm,"<br>\n- Convergence to period (stable) back prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a><br> \
1.217 brouard 5947: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);
1.222 brouard 5948: }
1.217 brouard 5949: }
1.222 brouard 5950: if(prevfcast==1){
5951: /* Projection of prevalence up to period (stable) prevalence in each health state */
5952: for(cpt=1; cpt<=nlstate;cpt++){
5953: fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
1.213 brouard 5954: <img src=\"%s_%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);
1.222 brouard 5955: }
5956: }
1.220 brouard 5957:
1.222 brouard 5958: for(cpt=1; cpt<=nlstate;cpt++) {
5959: fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d%d.svg\">%s_%d%d.svg</a> <br> \
1.201 brouard 5960: <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
1.222 brouard 5961: }
5962: /* } /\* end i1 *\/ */
5963: }/* End k1 */
5964: fprintf(fichtm,"</ul>");
1.126 brouard 5965:
1.222 brouard 5966: fprintf(fichtm,"\
1.126 brouard 5967: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 5968: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 5969: - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \
1.197 brouard 5970: But because parameters are usually highly correlated (a higher incidence of disability \
5971: and a higher incidence of recovery can give very close observed transition) it might \
5972: be very useful to look not only at linear confidence intervals estimated from the \
5973: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
5974: (parameters) of the logistic regression, it might be more meaningful to visualize the \
5975: covariance matrix of the one-step probabilities. \
5976: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 5977:
1.222 brouard 5978: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
5979: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
5980: fprintf(fichtm,"\
1.126 brouard 5981: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 5982: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 5983:
1.222 brouard 5984: fprintf(fichtm,"\
1.126 brouard 5985: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 5986: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
5987: fprintf(fichtm,"\
1.126 brouard 5988: - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
5989: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5990: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.222 brouard 5991: fprintf(fichtm,"\
1.126 brouard 5992: - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
5993: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5994: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.222 brouard 5995: fprintf(fichtm,"\
1.128 brouard 5996: - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
1.222 brouard 5997: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
5998: fprintf(fichtm,"\
1.128 brouard 5999: - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 6000: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
6001: fprintf(fichtm,"\
1.126 brouard 6002: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.222 brouard 6003: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 6004:
6005: /* if(popforecast==1) fprintf(fichtm,"\n */
6006: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
6007: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
6008: /* <br>",fileres,fileres,fileres,fileres); */
6009: /* else */
6010: /* fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
1.222 brouard 6011: fflush(fichtm);
6012: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.126 brouard 6013:
1.225 brouard 6014: m=pow(2,cptcoveff);
1.222 brouard 6015: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 6016:
1.222 brouard 6017: jj1=0;
6018: for(k1=1; k1<=m;k1++){
6019: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
6020: jj1++;
1.126 brouard 6021: if (cptcovn > 0) {
6022: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 6023: for (cpt=1; cpt<=cptcoveff;cpt++) /**< cptcoveff number of variables */
1.222 brouard 6024: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 6025: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 6026:
1.222 brouard 6027: if(invalidvarcomb[k1]){
6028: fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
6029: continue;
6030: }
1.126 brouard 6031: }
6032: for(cpt=1; cpt<=nlstate;cpt++) {
1.218 brouard 6033: fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
6034: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d.svg\"> %s_%d-%d.svg</a>\n <br>\
1.205 brouard 6035: <img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);
1.126 brouard 6036: }
6037: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 6038: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
6039: true period expectancies (those weighted with period prevalences are also\
6040: drawn in addition to the population based expectancies computed using\
1.218 brouard 6041: observed and cahotic prevalences: <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\
1.205 brouard 6042: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.222 brouard 6043: /* } /\* end i1 *\/ */
6044: }/* End k1 */
6045: fprintf(fichtm,"</ul>");
6046: fflush(fichtm);
1.126 brouard 6047: }
6048:
6049: /******************* Gnuplot file **************/
1.223 brouard 6050: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
1.126 brouard 6051:
6052: char dirfileres[132],optfileres[132];
1.223 brouard 6053: char gplotcondition[132];
1.164 brouard 6054: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.211 brouard 6055: int lv=0, vlv=0, kl=0;
1.130 brouard 6056: int ng=0;
1.201 brouard 6057: int vpopbased;
1.223 brouard 6058: int ioffset; /* variable offset for columns */
1.219 brouard 6059:
1.126 brouard 6060: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
6061: /* printf("Problem with file %s",optionfilegnuplot); */
6062: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
6063: /* } */
6064:
6065: /*#ifdef windows */
6066: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.223 brouard 6067: /*#endif */
1.225 brouard 6068: m=pow(2,cptcoveff);
1.126 brouard 6069:
1.202 brouard 6070: /* Contribution to likelihood */
6071: /* Plot the probability implied in the likelihood */
1.223 brouard 6072: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
6073: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
6074: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
6075: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 6076: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 6077: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
6078: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
1.223 brouard 6079: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
6080: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
6081: fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
6082: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
6083: fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
6084: for (i=1; i<= nlstate ; i ++) {
6085: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
6086: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
6087: fprintf(ficgp," u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
6088: for (j=2; j<= nlstate+ndeath ; j ++) {
6089: fprintf(ficgp,",\\\n \"\" u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
6090: }
6091: fprintf(ficgp,";\nset out; unset ylabel;\n");
6092: }
6093: /* unset log; plot "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */
6094: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
6095: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
6096: fprintf(ficgp,"\nset out;unset log\n");
6097: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
1.202 brouard 6098:
1.126 brouard 6099: strcpy(dirfileres,optionfilefiname);
6100: strcpy(optfileres,"vpl");
1.223 brouard 6101: /* 1eme*/
1.211 brouard 6102: for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
1.230 ! brouard 6103: for (k1=1; k1<= m && selected(k1) ; k1 ++) { /* For each valid combination of covariate */
1.211 brouard 6104: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
6105: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
1.225 brouard 6106: for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
6107: lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
1.223 brouard 6108: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6109: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6110: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6111: vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
6112: /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
6113: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6114: }
6115: fprintf(ficgp,"\n#\n");
1.223 brouard 6116: if(invalidvarcomb[k1]){
6117: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6118: continue;
6119: }
1.211 brouard 6120:
1.223 brouard 6121: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
6122: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
6123: fprintf(ficgp,"set xlabel \"Age\" \n\
1.219 brouard 6124: set ylabel \"Probability\" \n \
6125: set ter svg size 640, 480\n \
1.201 brouard 6126: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.219 brouard 6127:
1.223 brouard 6128: for (i=1; i<= nlstate ; i ++) {
6129: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
6130: else fprintf(ficgp," %%*lf (%%*lf)");
6131: }
6132: fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
6133: for (i=1; i<= nlstate ; i ++) {
6134: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
6135: else fprintf(ficgp," %%*lf (%%*lf)");
6136: }
6137: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
6138: for (i=1; i<= nlstate ; i ++) {
6139: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
6140: else fprintf(ficgp," %%*lf (%%*lf)");
6141: }
6142: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
6143: if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
6144: /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
6145: fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
1.225 brouard 6146: if(cptcoveff ==0){
1.223 brouard 6147: fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ", 2+(cpt-1), cpt );
6148: }else{
6149: kl=0;
1.225 brouard 6150: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
6151: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
1.223 brouard 6152: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6153: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6154: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6155: vlv= nbcode[Tvaraff[k]][lv];
6156: kl++;
6157: /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
6158: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
6159: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
6160: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
1.225 brouard 6161: if(k==cptcoveff){
1.227 brouard 6162: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
6163: 4+(cpt-1), cpt ); /* 4 or 6 ?*/
1.223 brouard 6164: }else{
6165: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
6166: kl++;
6167: }
6168: } /* end covariate */
6169: } /* end if no covariate */
6170: } /* end if backcast */
6171: fprintf(ficgp,"\nset out \n");
1.201 brouard 6172: } /* k1 */
6173: } /* cpt */
1.126 brouard 6174: /*2 eme*/
6175: for (k1=1; k1<= m ; k1 ++) {
1.220 brouard 6176:
1.223 brouard 6177: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
1.225 brouard 6178: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6179: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 6180: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6181: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6182: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6183: vlv= nbcode[Tvaraff[k]][lv];
6184: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6185: }
6186: fprintf(ficgp,"\n#\n");
6187: if(invalidvarcomb[k1]){
6188: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6189: continue;
6190: }
1.219 brouard 6191:
1.223 brouard 6192: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
6193: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6194: if(vpopbased==0)
6195: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
6196: else
6197: fprintf(ficgp,"\nreplot ");
6198: for (i=1; i<= nlstate+1 ; i ++) {
6199: k=2*i;
6200: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
6201: for (j=1; j<= nlstate+1 ; j ++) {
6202: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6203: else fprintf(ficgp," %%*lf (%%*lf)");
6204: }
6205: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
6206: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
6207: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
6208: for (j=1; j<= nlstate+1 ; j ++) {
6209: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6210: else fprintf(ficgp," %%*lf (%%*lf)");
6211: }
6212: fprintf(ficgp,"\" t\"\" w l lt 0,");
6213: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
6214: for (j=1; j<= nlstate+1 ; j ++) {
6215: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6216: else fprintf(ficgp," %%*lf (%%*lf)");
6217: }
6218: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
6219: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
6220: } /* state */
6221: } /* vpopbased */
6222: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
1.201 brouard 6223: } /* k1 */
1.219 brouard 6224:
6225:
1.126 brouard 6226: /*3eme*/
6227: for (k1=1; k1<= m ; k1 ++) {
1.220 brouard 6228:
1.126 brouard 6229: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.211 brouard 6230: fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt);
1.225 brouard 6231: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6232: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 6233: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6234: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6235: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6236: vlv= nbcode[Tvaraff[k]][lv];
6237: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6238: }
6239: fprintf(ficgp,"\n#\n");
1.223 brouard 6240: if(invalidvarcomb[k1]){
6241: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6242: continue;
6243: }
1.219 brouard 6244:
1.126 brouard 6245: /* k=2+nlstate*(2*cpt-2); */
6246: k=2+(nlstate+1)*(cpt-1);
1.201 brouard 6247: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
1.199 brouard 6248: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 6249: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.126 brouard 6250: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
1.223 brouard 6251: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
6252: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
6253: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
6254: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
6255: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
1.219 brouard 6256:
1.126 brouard 6257: */
6258: for (i=1; i< nlstate ; i ++) {
1.223 brouard 6259: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);
6260: /* fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
1.219 brouard 6261:
1.126 brouard 6262: }
1.201 brouard 6263: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
1.126 brouard 6264: }
6265: }
6266:
1.223 brouard 6267: /* 4eme */
1.201 brouard 6268: /* Survival functions (period) from state i in state j by initial state i */
6269: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
1.220 brouard 6270:
1.201 brouard 6271: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.211 brouard 6272: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
1.225 brouard 6273: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6274: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 6275: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6276: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6277: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6278: vlv= nbcode[Tvaraff[k]][lv];
6279: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6280: }
6281: fprintf(ficgp,"\n#\n");
1.223 brouard 6282: if(invalidvarcomb[k1]){
6283: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6284: continue;
6285: }
1.220 brouard 6286:
1.201 brouard 6287: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
6288: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
1.220 brouard 6289: set ter svg size 640, 480\n \
6290: unset log y\n \
1.201 brouard 6291: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6292: k=3;
1.201 brouard 6293: for (i=1; i<= nlstate ; i ++){
1.223 brouard 6294: if(i==1){
6295: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6296: }else{
6297: fprintf(ficgp,", '' ");
6298: }
6299: l=(nlstate+ndeath)*(i-1)+1;
6300: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
6301: for (j=2; j<= nlstate+ndeath ; j ++)
6302: fprintf(ficgp,"+$%d",k+l+j-1);
6303: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
1.201 brouard 6304: } /* nlstate */
6305: fprintf(ficgp,"\nset out\n");
6306: } /* end cpt state*/
6307: } /* end covariate */
1.220 brouard 6308:
6309: /* 5eme */
1.201 brouard 6310: /* Survival functions (period) from state i in state j by final state j */
1.202 brouard 6311: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.201 brouard 6312: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
1.223 brouard 6313:
1.201 brouard 6314: fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
1.225 brouard 6315: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 brouard 6316: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6317: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6318: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6319: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6320: vlv= nbcode[Tvaraff[k]][lv];
6321: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6322: }
6323: fprintf(ficgp,"\n#\n");
1.223 brouard 6324: if(invalidvarcomb[k1]){
1.227 brouard 6325: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6326: continue;
1.223 brouard 6327: }
1.227 brouard 6328:
1.201 brouard 6329: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
6330: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
1.227 brouard 6331: set ter svg size 640, 480\n \
6332: unset log y\n \
1.201 brouard 6333: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6334: k=3;
1.201 brouard 6335: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
1.227 brouard 6336: if(j==1)
6337: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6338: else
6339: fprintf(ficgp,", '' ");
6340: l=(nlstate+ndeath)*(cpt-1) +j;
6341: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
6342: /* for (i=2; i<= nlstate+ndeath ; i ++) */
6343: /* fprintf(ficgp,"+$%d",k+l+i-1); */
6344: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
1.201 brouard 6345: } /* nlstate */
6346: fprintf(ficgp,", '' ");
6347: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
6348: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
1.227 brouard 6349: l=(nlstate+ndeath)*(cpt-1) +j;
6350: if(j < nlstate)
6351: fprintf(ficgp,"$%d +",k+l);
6352: else
6353: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
1.201 brouard 6354: }
6355: fprintf(ficgp,"\nset out\n");
6356: } /* end cpt state*/
6357: } /* end covariate */
1.227 brouard 6358:
1.220 brouard 6359: /* 6eme */
1.202 brouard 6360: /* CV preval stable (period) for each covariate */
1.211 brouard 6361: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.153 brouard 6362: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.227 brouard 6363:
1.211 brouard 6364: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
1.225 brouard 6365: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 brouard 6366: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6367: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6368: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6369: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6370: vlv= nbcode[Tvaraff[k]][lv];
6371: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6372: }
6373: fprintf(ficgp,"\n#\n");
1.223 brouard 6374: if(invalidvarcomb[k1]){
1.227 brouard 6375: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6376: continue;
1.223 brouard 6377: }
1.227 brouard 6378:
1.201 brouard 6379: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 6380: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.227 brouard 6381: set ter svg size 640, 480\n \
6382: unset log y\n \
1.153 brouard 6383: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6384: k=3; /* Offset */
1.153 brouard 6385: for (i=1; i<= nlstate ; i ++){
1.227 brouard 6386: if(i==1)
6387: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6388: else
6389: fprintf(ficgp,", '' ");
6390: l=(nlstate+ndeath)*(i-1)+1;
6391: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
6392: for (j=2; j<= nlstate ; j ++)
6393: fprintf(ficgp,"+$%d",k+l+j-1);
6394: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153 brouard 6395: } /* nlstate */
1.201 brouard 6396: fprintf(ficgp,"\nset out\n");
1.153 brouard 6397: } /* end cpt state*/
6398: } /* end covariate */
1.227 brouard 6399:
6400:
1.220 brouard 6401: /* 7eme */
1.218 brouard 6402: if(backcast == 1){
1.217 brouard 6403: /* CV back preval stable (period) for each covariate */
1.218 brouard 6404: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
6405: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.227 brouard 6406: fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
6407: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6408: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6409: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6410: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
1.223 brouard 6411: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.227 brouard 6412: vlv= nbcode[Tvaraff[k]][lv];
6413: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6414: }
6415: fprintf(ficgp,"\n#\n");
6416: if(invalidvarcomb[k1]){
6417: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6418: continue;
6419: }
6420:
6421: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
6422: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
6423: set ter svg size 640, 480\n \
6424: unset log y\n \
1.218 brouard 6425: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 6426: k=3; /* Offset */
6427: for (i=1; i<= nlstate ; i ++){
6428: if(i==1)
6429: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
6430: else
6431: fprintf(ficgp,", '' ");
6432: /* l=(nlstate+ndeath)*(i-1)+1; */
6433: l=(nlstate+ndeath)*(cpt-1)+1;
6434: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
6435: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
6436: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
6437: /* for (j=2; j<= nlstate ; j ++) */
6438: /* fprintf(ficgp,"+$%d",k+l+j-1); */
6439: /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
6440: fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
6441: } /* nlstate */
6442: fprintf(ficgp,"\nset out\n");
1.218 brouard 6443: } /* end cpt state*/
6444: } /* end covariate */
6445: } /* End if backcast */
6446:
1.223 brouard 6447: /* 8eme */
1.218 brouard 6448: if(prevfcast==1){
6449: /* Projection from cross-sectional to stable (period) for each covariate */
6450:
6451: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.211 brouard 6452: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.227 brouard 6453: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
6454: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
6455: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
6456: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6457: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6458: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6459: vlv= nbcode[Tvaraff[k]][lv];
6460: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6461: }
6462: fprintf(ficgp,"\n#\n");
6463: if(invalidvarcomb[k1]){
6464: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6465: continue;
6466: }
6467:
6468: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
6469: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
6470: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
6471: set ter svg size 640, 480\n \
6472: unset log y\n \
1.219 brouard 6473: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 6474: for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
6475: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6476: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6477: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6478: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6479: if(i==1){
6480: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
6481: }else{
6482: fprintf(ficgp,",\\\n '' ");
6483: }
6484: if(cptcoveff ==0){ /* No covariate */
6485: ioffset=2; /* Age is in 2 */
6486: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
6487: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
6488: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
6489: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
6490: fprintf(ficgp," u %d:(", ioffset);
6491: if(i==nlstate+1)
6492: fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ", \
6493: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
6494: else
6495: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
6496: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
6497: }else{ /* more than 2 covariates */
6498: if(cptcoveff ==1){
6499: ioffset=4; /* Age is in 4 */
6500: }else{
6501: ioffset=6; /* Age is in 6 */
6502: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6503: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6504: }
6505: fprintf(ficgp," u %d:(",ioffset);
6506: kl=0;
6507: strcpy(gplotcondition,"(");
6508: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
6509: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
6510: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6511: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6512: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6513: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
6514: kl++;
6515: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
6516: kl++;
6517: if(k <cptcoveff && cptcoveff>1)
6518: sprintf(gplotcondition+strlen(gplotcondition)," && ");
6519: }
6520: strcpy(gplotcondition+strlen(gplotcondition),")");
6521: /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
6522: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
6523: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
6524: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
6525: if(i==nlstate+1){
6526: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
6527: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
6528: }else{
6529: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
6530: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
6531: }
6532: } /* end if covariate */
6533: } /* nlstate */
6534: fprintf(ficgp,"\nset out\n");
1.223 brouard 6535: } /* end cpt state*/
6536: } /* end covariate */
6537: } /* End if prevfcast */
1.227 brouard 6538:
6539:
1.223 brouard 6540: /* proba elementaires */
6541: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 6542: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 6543: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 6544: for(k=1; k <=(nlstate+ndeath); k++){
6545: if (k != i) {
1.227 brouard 6546: fprintf(ficgp,"# current state %d\n",k);
6547: for(j=1; j <=ncovmodel; j++){
6548: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
6549: jk++;
6550: }
6551: fprintf(ficgp,"\n");
1.126 brouard 6552: }
6553: }
1.223 brouard 6554: }
1.187 brouard 6555: fprintf(ficgp,"##############\n#\n");
1.227 brouard 6556:
1.145 brouard 6557: /*goto avoid;*/
1.200 brouard 6558: fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
1.187 brouard 6559: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
6560: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
6561: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
6562: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
6563: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6564: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
6565: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6566: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
6567: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
6568: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6569: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
6570: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
6571: fprintf(ficgp,"#\n");
1.223 brouard 6572: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
6573: fprintf(ficgp,"# ng=%d\n",ng);
1.225 brouard 6574: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.223 brouard 6575: for(jk=1; jk <=m; jk++) {
6576: fprintf(ficgp,"# jk=%d\n",jk);
6577: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
6578: fprintf(ficgp,"\nset ter svg size 640, 480 ");
6579: if (ng==1){
6580: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
6581: fprintf(ficgp,"\nunset log y");
6582: }else if (ng==2){
6583: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
6584: fprintf(ficgp,"\nset log y");
6585: }else if (ng==3){
6586: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
6587: fprintf(ficgp,"\nset log y");
6588: }else
6589: fprintf(ficgp,"\nunset title ");
6590: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
6591: i=1;
6592: for(k2=1; k2<=nlstate; k2++) {
6593: k3=i;
6594: for(k=1; k<=(nlstate+ndeath); k++) {
6595: if (k != k2){
6596: switch( ng) {
6597: case 1:
6598: if(nagesqr==0)
6599: fprintf(ficgp," p%d+p%d*x",i,i+1);
6600: else /* nagesqr =1 */
6601: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
6602: break;
6603: case 2: /* ng=2 */
6604: if(nagesqr==0)
6605: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
6606: else /* nagesqr =1 */
6607: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
6608: break;
6609: case 3:
6610: if(nagesqr==0)
6611: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
6612: else /* nagesqr =1 */
6613: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
6614: break;
6615: }
6616: ij=1;/* To be checked else nbcode[0][0] wrong */
6617: for(j=3; j <=ncovmodel-nagesqr; j++) {
6618: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
6619: if(ij <=cptcovage) { /* Bug valgrind */
6620: if((j-2)==Tage[ij]) { /* Bug valgrind */
6621: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
6622: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
6623: ij++;
6624: }
6625: }
6626: else
1.227 brouard 6627: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); /* Valgrind bug nbcode */
1.223 brouard 6628: }
6629: }else{
6630: i=i-ncovmodel;
6631: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
6632: fprintf(ficgp," (1.");
6633: }
1.227 brouard 6634:
1.223 brouard 6635: if(ng != 1){
6636: fprintf(ficgp,")/(1");
1.227 brouard 6637:
1.223 brouard 6638: for(k1=1; k1 <=nlstate; k1++){
6639: if(nagesqr==0)
6640: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
6641: else /* nagesqr =1 */
6642: fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
1.217 brouard 6643:
1.223 brouard 6644: ij=1;
6645: for(j=3; j <=ncovmodel-nagesqr; j++){
6646: if(ij <=cptcovage) { /* Bug valgrind */
6647: if((j-2)==Tage[ij]) { /* Bug valgrind */
6648: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
6649: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
6650: ij++;
6651: }
6652: }
6653: else
1.225 brouard 6654: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);/* Valgrind bug nbcode */
1.223 brouard 6655: }
6656: fprintf(ficgp,")");
6657: }
6658: fprintf(ficgp,")");
6659: if(ng ==2)
6660: fprintf(ficgp," t \"p%d%d\" ", k2,k);
6661: else /* ng= 3 */
6662: fprintf(ficgp," t \"i%d%d\" ", k2,k);
6663: }else{ /* end ng <> 1 */
6664: if( k !=k2) /* logit p11 is hard to draw */
6665: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
6666: }
6667: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
6668: fprintf(ficgp,",");
6669: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
6670: fprintf(ficgp,",");
6671: i=i+ncovmodel;
6672: } /* end k */
6673: } /* end k2 */
6674: fprintf(ficgp,"\n set out\n");
6675: } /* end jk */
6676: } /* end ng */
6677: /* avoid: */
6678: fflush(ficgp);
1.126 brouard 6679: } /* end gnuplot */
6680:
6681:
6682: /*************** Moving average **************/
1.219 brouard 6683: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.222 brouard 6684: int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
1.218 brouard 6685:
1.222 brouard 6686: int i, cpt, cptcod;
6687: int modcovmax =1;
6688: int mobilavrange, mob;
6689: int iage=0;
6690:
6691: double sum=0.;
6692: double age;
6693: double *sumnewp, *sumnewm;
6694: double *agemingood, *agemaxgood; /* Currently identical for all covariates */
6695:
6696:
1.225 brouard 6697: /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose */
1.222 brouard 6698: /* a covariate has 2 modalities, should be equal to ncovcombmax *\/ */
6699:
6700: sumnewp = vector(1,ncovcombmax);
6701: sumnewm = vector(1,ncovcombmax);
6702: agemingood = vector(1,ncovcombmax);
6703: agemaxgood = vector(1,ncovcombmax);
6704:
6705: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
6706: sumnewm[cptcod]=0.;
6707: sumnewp[cptcod]=0.;
6708: agemingood[cptcod]=0;
6709: agemaxgood[cptcod]=0;
6710: }
6711: if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
6712:
6713: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
6714: if(mobilav==1) mobilavrange=5; /* default */
6715: else mobilavrange=mobilav;
6716: for (age=bage; age<=fage; age++)
6717: for (i=1; i<=nlstate;i++)
6718: for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
6719: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
6720: /* We keep the original values on the extreme ages bage, fage and for
6721: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
6722: we use a 5 terms etc. until the borders are no more concerned.
6723: */
6724: for (mob=3;mob <=mobilavrange;mob=mob+2){
6725: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
6726: for (i=1; i<=nlstate;i++){
6727: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
6728: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
6729: for (cpt=1;cpt<=(mob-1)/2;cpt++){
6730: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
6731: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
6732: }
6733: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
6734: }
6735: }
6736: }/* end age */
6737: }/* end mob */
6738: }else
6739: return -1;
6740: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
6741: /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
6742: if(invalidvarcomb[cptcod]){
6743: printf("\nCombination (%d) ignored because no cases \n",cptcod);
6744: continue;
6745: }
1.219 brouard 6746:
1.222 brouard 6747: agemingood[cptcod]=fage-(mob-1)/2;
6748: for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
6749: sumnewm[cptcod]=0.;
6750: for (i=1; i<=nlstate;i++){
6751: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6752: }
6753: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
6754: agemingood[cptcod]=age;
6755: }else{ /* bad */
6756: for (i=1; i<=nlstate;i++){
6757: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6758: } /* i */
6759: } /* end bad */
6760: }/* age */
6761: sum=0.;
6762: for (i=1; i<=nlstate;i++){
6763: sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6764: }
6765: if(fabs(sum - 1.) > 1.e-3) { /* bad */
6766: printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);
6767: /* for (i=1; i<=nlstate;i++){ */
6768: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
6769: /* } /\* i *\/ */
6770: } /* end bad */
6771: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
6772: /* From youngest, finding the oldest wrong */
6773: agemaxgood[cptcod]=bage+(mob-1)/2;
6774: for (age=bage+(mob-1)/2; age<=fage; age++){
6775: sumnewm[cptcod]=0.;
6776: for (i=1; i<=nlstate;i++){
6777: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6778: }
6779: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
6780: agemaxgood[cptcod]=age;
6781: }else{ /* bad */
6782: for (i=1; i<=nlstate;i++){
6783: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6784: } /* i */
6785: } /* end bad */
6786: }/* age */
6787: sum=0.;
6788: for (i=1; i<=nlstate;i++){
6789: sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6790: }
6791: if(fabs(sum - 1.) > 1.e-3) { /* bad */
6792: printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod);
6793: /* for (i=1; i<=nlstate;i++){ */
6794: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
6795: /* } /\* i *\/ */
6796: } /* end bad */
6797:
6798: for (age=bage; age<=fage; age++){
6799: printf("%d %d ", cptcod, (int)age);
6800: sumnewp[cptcod]=0.;
6801: sumnewm[cptcod]=0.;
6802: for (i=1; i<=nlstate;i++){
6803: sumnewp[cptcod]+=probs[(int)age][i][cptcod];
6804: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6805: /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
6806: }
6807: /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
6808: }
6809: /* printf("\n"); */
6810: /* } */
6811: /* brutal averaging */
6812: for (i=1; i<=nlstate;i++){
6813: for (age=1; age<=bage; age++){
6814: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6815: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
6816: }
6817: for (age=fage; age<=AGESUP; age++){
6818: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6819: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
6820: }
6821: } /* end i status */
6822: for (i=nlstate+1; i<=nlstate+ndeath;i++){
6823: for (age=1; age<=AGESUP; age++){
6824: /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
6825: mobaverage[(int)age][i][cptcod]=0.;
6826: }
6827: }
6828: }/* end cptcod */
6829: free_vector(sumnewm,1, ncovcombmax);
6830: free_vector(sumnewp,1, ncovcombmax);
6831: free_vector(agemaxgood,1, ncovcombmax);
6832: free_vector(agemingood,1, ncovcombmax);
6833: return 0;
6834: }/* End movingaverage */
1.218 brouard 6835:
1.126 brouard 6836:
6837: /************** Forecasting ******************/
1.225 brouard 6838: void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
1.126 brouard 6839: /* proj1, year, month, day of starting projection
6840: agemin, agemax range of age
6841: dateprev1 dateprev2 range of dates during which prevalence is computed
6842: anproj2 year of en of projection (same day and month as proj1).
6843: */
1.164 brouard 6844: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 6845: double agec; /* generic age */
6846: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
6847: double *popeffectif,*popcount;
6848: double ***p3mat;
1.218 brouard 6849: /* double ***mobaverage; */
1.126 brouard 6850: char fileresf[FILENAMELENGTH];
6851:
6852: agelim=AGESUP;
1.211 brouard 6853: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
6854: in each health status at the date of interview (if between dateprev1 and dateprev2).
6855: We still use firstpass and lastpass as another selection.
6856: */
1.214 brouard 6857: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
6858: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 6859:
1.201 brouard 6860: strcpy(fileresf,"F_");
6861: strcat(fileresf,fileresu);
1.126 brouard 6862: if((ficresf=fopen(fileresf,"w"))==NULL) {
6863: printf("Problem with forecast resultfile: %s\n", fileresf);
6864: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
6865: }
1.215 brouard 6866: printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
6867: fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 6868:
1.225 brouard 6869: if (cptcoveff==0) ncodemax[cptcoveff]=1;
1.126 brouard 6870:
6871:
6872: stepsize=(int) (stepm+YEARM-1)/YEARM;
6873: if (stepm<=12) stepsize=1;
6874: if(estepm < stepm){
6875: printf ("Problem %d lower than %d\n",estepm, stepm);
6876: }
6877: else hstepm=estepm;
6878:
6879: hstepm=hstepm/stepm;
6880: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
6881: fractional in yp1 */
6882: anprojmean=yp;
6883: yp2=modf((yp1*12),&yp);
6884: mprojmean=yp;
6885: yp1=modf((yp2*30.5),&yp);
6886: jprojmean=yp;
6887: if(jprojmean==0) jprojmean=1;
6888: if(mprojmean==0) jprojmean=1;
6889:
1.227 brouard 6890: i1=pow(2,cptcoveff);
1.126 brouard 6891: if (cptcovn < 1){i1=1;}
6892:
6893: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
6894:
6895: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.227 brouard 6896:
1.126 brouard 6897: /* if (h==(int)(YEARM*yearp)){ */
1.227 brouard 6898: for(k=1;k<=i1;k++){
6899: if(invalidvarcomb[k]){
6900: printf("\nCombination (%d) projection ignored because no cases \n",k);
6901: continue;
6902: }
6903: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
6904: for(j=1;j<=cptcoveff;j++) {
6905: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6906: }
6907: fprintf(ficresf," yearproj age");
6908: for(j=1; j<=nlstate+ndeath;j++){
6909: for(i=1; i<=nlstate;i++)
6910: fprintf(ficresf," p%d%d",i,j);
6911: fprintf(ficresf," wp.%d",j);
6912: }
6913: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
6914: fprintf(ficresf,"\n");
6915: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
6916: for (agec=fage; agec>=(ageminpar-1); agec--){
6917: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
6918: nhstepm = nhstepm/hstepm;
6919: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6920: oldm=oldms;savm=savms;
6921: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
6922:
6923: for (h=0; h<=nhstepm; h++){
6924: if (h*hstepm/YEARM*stepm ==yearp) {
6925: fprintf(ficresf,"\n");
6926: for(j=1;j<=cptcoveff;j++)
6927: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6928: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
6929: }
6930: for(j=1; j<=nlstate+ndeath;j++) {
6931: ppij=0.;
6932: for(i=1; i<=nlstate;i++) {
6933: if (mobilav==1)
6934: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];
6935: else {
6936: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
6937: }
6938: if (h*hstepm/YEARM*stepm== yearp) {
6939: fprintf(ficresf," %.3f", p3mat[i][j][h]);
6940: }
6941: } /* end i */
6942: if (h*hstepm/YEARM*stepm==yearp) {
6943: fprintf(ficresf," %.3f", ppij);
6944: }
6945: }/* end j */
6946: } /* end h */
6947: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6948: } /* end agec */
6949: } /* end yearp */
6950: } /* end k */
1.219 brouard 6951:
1.126 brouard 6952: fclose(ficresf);
1.215 brouard 6953: printf("End of Computing forecasting \n");
6954: fprintf(ficlog,"End of Computing forecasting\n");
6955:
1.126 brouard 6956: }
6957:
1.218 brouard 6958: /* /\************** Back Forecasting ******************\/ */
1.225 brouard 6959: /* void prevbackforecast(char fileres[], double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ */
1.218 brouard 6960: /* /\* back1, year, month, day of starting backection */
6961: /* agemin, agemax range of age */
6962: /* dateprev1 dateprev2 range of dates during which prevalence is computed */
6963: /* anback2 year of en of backection (same day and month as back1). */
6964: /* *\/ */
6965: /* int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */
6966: /* double agec; /\* generic age *\/ */
6967: /* double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */
6968: /* double *popeffectif,*popcount; */
6969: /* double ***p3mat; */
6970: /* /\* double ***mobaverage; *\/ */
6971: /* char fileresfb[FILENAMELENGTH]; */
6972:
6973: /* agelim=AGESUP; */
6974: /* /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */
6975: /* in each health status at the date of interview (if between dateprev1 and dateprev2). */
6976: /* We still use firstpass and lastpass as another selection. */
6977: /* *\/ */
6978: /* /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */
6979: /* /\* firstpass, lastpass, stepm, weightopt, model); *\/ */
6980: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
6981:
6982: /* strcpy(fileresfb,"FB_"); */
6983: /* strcat(fileresfb,fileresu); */
6984: /* if((ficresfb=fopen(fileresfb,"w"))==NULL) { */
6985: /* printf("Problem with back forecast resultfile: %s\n", fileresfb); */
6986: /* fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */
6987: /* } */
6988: /* printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
6989: /* fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
6990:
1.225 brouard 6991: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.218 brouard 6992:
6993: /* /\* if (mobilav!=0) { *\/ */
6994: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
6995: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
6996: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
6997: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
6998: /* /\* } *\/ */
6999: /* /\* } *\/ */
7000:
7001: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
7002: /* if (stepm<=12) stepsize=1; */
7003: /* if(estepm < stepm){ */
7004: /* printf ("Problem %d lower than %d\n",estepm, stepm); */
7005: /* } */
7006: /* else hstepm=estepm; */
7007:
7008: /* hstepm=hstepm/stepm; */
7009: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
7010: /* fractional in yp1 *\/ */
7011: /* anprojmean=yp; */
7012: /* yp2=modf((yp1*12),&yp); */
7013: /* mprojmean=yp; */
7014: /* yp1=modf((yp2*30.5),&yp); */
7015: /* jprojmean=yp; */
7016: /* if(jprojmean==0) jprojmean=1; */
7017: /* if(mprojmean==0) jprojmean=1; */
7018:
1.225 brouard 7019: /* i1=cptcoveff; */
1.218 brouard 7020: /* if (cptcovn < 1){i1=1;} */
1.217 brouard 7021:
1.218 brouard 7022: /* fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); */
1.217 brouard 7023:
1.218 brouard 7024: /* fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */
7025:
7026: /* /\* if (h==(int)(YEARM*yearp)){ *\/ */
7027: /* for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
1.225 brouard 7028: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
1.218 brouard 7029: /* k=k+1; */
7030: /* fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
1.225 brouard 7031: /* for(j=1;j<=cptcoveff;j++) { */
1.218 brouard 7032: /* fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
7033: /* } */
7034: /* fprintf(ficresfb," yearbproj age"); */
7035: /* for(j=1; j<=nlstate+ndeath;j++){ */
7036: /* for(i=1; i<=nlstate;i++) */
7037: /* fprintf(ficresfb," p%d%d",i,j); */
7038: /* fprintf(ficresfb," p.%d",j); */
7039: /* } */
7040: /* for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) { */
7041: /* /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { *\/ */
7042: /* fprintf(ficresfb,"\n"); */
7043: /* fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
7044: /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
7045: /* nhstepm=(int) rint((agelim-agec)*YEARM/stepm); */
7046: /* nhstepm = nhstepm/hstepm; */
7047: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7048: /* oldm=oldms;savm=savms; */
7049: /* hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k); */
7050: /* for (h=0; h<=nhstepm; h++){ */
7051: /* if (h*hstepm/YEARM*stepm ==yearp) { */
7052: /* fprintf(ficresfb,"\n"); */
1.225 brouard 7053: /* for(j=1;j<=cptcoveff;j++) */
1.218 brouard 7054: /* fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
7055: /* fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */
7056: /* } */
7057: /* for(j=1; j<=nlstate+ndeath;j++) { */
7058: /* ppij=0.; */
7059: /* for(i=1; i<=nlstate;i++) { */
7060: /* if (mobilav==1) */
7061: /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */
7062: /* else { */
7063: /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */
7064: /* } */
7065: /* if (h*hstepm/YEARM*stepm== yearp) { */
7066: /* fprintf(ficresfb," %.3f", p3mat[i][j][h]); */
7067: /* } */
7068: /* } /\* end i *\/ */
7069: /* if (h*hstepm/YEARM*stepm==yearp) { */
7070: /* fprintf(ficresfb," %.3f", ppij); */
7071: /* } */
7072: /* }/\* end j *\/ */
7073: /* } /\* end h *\/ */
7074: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7075: /* } /\* end agec *\/ */
7076: /* } /\* end yearp *\/ */
7077: /* } /\* end cptcod *\/ */
7078: /* } /\* end cptcov *\/ */
7079:
7080: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
7081:
7082: /* fclose(ficresfb); */
7083: /* printf("End of Computing Back forecasting \n"); */
7084: /* fprintf(ficlog,"End of Computing Back forecasting\n"); */
1.217 brouard 7085:
1.218 brouard 7086: /* } */
1.217 brouard 7087:
1.126 brouard 7088: /************** Forecasting *****not tested NB*************/
1.227 brouard 7089: /* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */
1.126 brouard 7090:
1.227 brouard 7091: /* int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
7092: /* int *popage; */
7093: /* double calagedatem, agelim, kk1, kk2; */
7094: /* double *popeffectif,*popcount; */
7095: /* double ***p3mat,***tabpop,***tabpopprev; */
7096: /* /\* double ***mobaverage; *\/ */
7097: /* char filerespop[FILENAMELENGTH]; */
1.126 brouard 7098:
1.227 brouard 7099: /* tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7100: /* tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7101: /* agelim=AGESUP; */
7102: /* calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
1.126 brouard 7103:
1.227 brouard 7104: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
1.126 brouard 7105:
7106:
1.227 brouard 7107: /* strcpy(filerespop,"POP_"); */
7108: /* strcat(filerespop,fileresu); */
7109: /* if((ficrespop=fopen(filerespop,"w"))==NULL) { */
7110: /* printf("Problem with forecast resultfile: %s\n", filerespop); */
7111: /* fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
7112: /* } */
7113: /* printf("Computing forecasting: result on file '%s' \n", filerespop); */
7114: /* fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
1.126 brouard 7115:
1.227 brouard 7116: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.126 brouard 7117:
1.227 brouard 7118: /* /\* if (mobilav!=0) { *\/ */
7119: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
7120: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
7121: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
7122: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
7123: /* /\* } *\/ */
7124: /* /\* } *\/ */
1.126 brouard 7125:
1.227 brouard 7126: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
7127: /* if (stepm<=12) stepsize=1; */
1.126 brouard 7128:
1.227 brouard 7129: /* agelim=AGESUP; */
1.126 brouard 7130:
1.227 brouard 7131: /* hstepm=1; */
7132: /* hstepm=hstepm/stepm; */
1.218 brouard 7133:
1.227 brouard 7134: /* if (popforecast==1) { */
7135: /* if((ficpop=fopen(popfile,"r"))==NULL) { */
7136: /* printf("Problem with population file : %s\n",popfile);exit(0); */
7137: /* fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
7138: /* } */
7139: /* popage=ivector(0,AGESUP); */
7140: /* popeffectif=vector(0,AGESUP); */
7141: /* popcount=vector(0,AGESUP); */
1.126 brouard 7142:
1.227 brouard 7143: /* i=1; */
7144: /* while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
1.218 brouard 7145:
1.227 brouard 7146: /* imx=i; */
7147: /* for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
7148: /* } */
1.218 brouard 7149:
1.227 brouard 7150: /* for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
7151: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
7152: /* k=k+1; */
7153: /* fprintf(ficrespop,"\n#******"); */
7154: /* for(j=1;j<=cptcoveff;j++) { */
7155: /* fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
7156: /* } */
7157: /* fprintf(ficrespop,"******\n"); */
7158: /* fprintf(ficrespop,"# Age"); */
7159: /* for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
7160: /* if (popforecast==1) fprintf(ficrespop," [Population]"); */
1.126 brouard 7161:
1.227 brouard 7162: /* for (cpt=0; cpt<=0;cpt++) { */
7163: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
1.126 brouard 7164:
1.227 brouard 7165: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
7166: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
7167: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 7168:
1.227 brouard 7169: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7170: /* oldm=oldms;savm=savms; */
7171: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.218 brouard 7172:
1.227 brouard 7173: /* for (h=0; h<=nhstepm; h++){ */
7174: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
7175: /* fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
7176: /* } */
7177: /* for(j=1; j<=nlstate+ndeath;j++) { */
7178: /* kk1=0.;kk2=0; */
7179: /* for(i=1; i<=nlstate;i++) { */
7180: /* if (mobilav==1) */
7181: /* kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
7182: /* else { */
7183: /* kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
7184: /* } */
7185: /* } */
7186: /* if (h==(int)(calagedatem+12*cpt)){ */
7187: /* tabpop[(int)(agedeb)][j][cptcod]=kk1; */
7188: /* /\*fprintf(ficrespop," %.3f", kk1); */
7189: /* if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
7190: /* } */
7191: /* } */
7192: /* for(i=1; i<=nlstate;i++){ */
7193: /* kk1=0.; */
7194: /* for(j=1; j<=nlstate;j++){ */
7195: /* kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; */
7196: /* } */
7197: /* tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
7198: /* } */
1.218 brouard 7199:
1.227 brouard 7200: /* if (h==(int)(calagedatem+12*cpt)) */
7201: /* for(j=1; j<=nlstate;j++) */
7202: /* fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
7203: /* } */
7204: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7205: /* } */
7206: /* } */
1.218 brouard 7207:
1.227 brouard 7208: /* /\******\/ */
1.218 brouard 7209:
1.227 brouard 7210: /* for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { */
7211: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
7212: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
7213: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
7214: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 7215:
1.227 brouard 7216: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7217: /* oldm=oldms;savm=savms; */
7218: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
7219: /* for (h=0; h<=nhstepm; h++){ */
7220: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
7221: /* fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
7222: /* } */
7223: /* for(j=1; j<=nlstate+ndeath;j++) { */
7224: /* kk1=0.;kk2=0; */
7225: /* for(i=1; i<=nlstate;i++) { */
7226: /* kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; */
7227: /* } */
7228: /* if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); */
7229: /* } */
7230: /* } */
7231: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7232: /* } */
7233: /* } */
7234: /* } */
7235: /* } */
1.218 brouard 7236:
1.227 brouard 7237: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
1.218 brouard 7238:
1.227 brouard 7239: /* if (popforecast==1) { */
7240: /* free_ivector(popage,0,AGESUP); */
7241: /* free_vector(popeffectif,0,AGESUP); */
7242: /* free_vector(popcount,0,AGESUP); */
7243: /* } */
7244: /* free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7245: /* free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7246: /* fclose(ficrespop); */
7247: /* } /\* End of popforecast *\/ */
1.218 brouard 7248:
1.126 brouard 7249: int fileappend(FILE *fichier, char *optionfich)
7250: {
7251: if((fichier=fopen(optionfich,"a"))==NULL) {
7252: printf("Problem with file: %s\n", optionfich);
7253: fprintf(ficlog,"Problem with file: %s\n", optionfich);
7254: return (0);
7255: }
7256: fflush(fichier);
7257: return (1);
7258: }
7259:
7260:
7261: /**************** function prwizard **********************/
7262: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
7263: {
7264:
7265: /* Wizard to print covariance matrix template */
7266:
1.164 brouard 7267: char ca[32], cb[32];
7268: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 7269: int numlinepar;
7270:
7271: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7272: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7273: for(i=1; i <=nlstate; i++){
7274: jj=0;
7275: for(j=1; j <=nlstate+ndeath; j++){
7276: if(j==i) continue;
7277: jj++;
7278: /*ca[0]= k+'a'-1;ca[1]='\0';*/
7279: printf("%1d%1d",i,j);
7280: fprintf(ficparo,"%1d%1d",i,j);
7281: for(k=1; k<=ncovmodel;k++){
7282: /* printf(" %lf",param[i][j][k]); */
7283: /* fprintf(ficparo," %lf",param[i][j][k]); */
7284: printf(" 0.");
7285: fprintf(ficparo," 0.");
7286: }
7287: printf("\n");
7288: fprintf(ficparo,"\n");
7289: }
7290: }
7291: printf("# Scales (for hessian or gradient estimation)\n");
7292: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
7293: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
7294: for(i=1; i <=nlstate; i++){
7295: jj=0;
7296: for(j=1; j <=nlstate+ndeath; j++){
7297: if(j==i) continue;
7298: jj++;
7299: fprintf(ficparo,"%1d%1d",i,j);
7300: printf("%1d%1d",i,j);
7301: fflush(stdout);
7302: for(k=1; k<=ncovmodel;k++){
7303: /* printf(" %le",delti3[i][j][k]); */
7304: /* fprintf(ficparo," %le",delti3[i][j][k]); */
7305: printf(" 0.");
7306: fprintf(ficparo," 0.");
7307: }
7308: numlinepar++;
7309: printf("\n");
7310: fprintf(ficparo,"\n");
7311: }
7312: }
7313: printf("# Covariance matrix\n");
7314: /* # 121 Var(a12)\n\ */
7315: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7316: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7317: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7318: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7319: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7320: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7321: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7322: fflush(stdout);
7323: fprintf(ficparo,"# Covariance matrix\n");
7324: /* # 121 Var(a12)\n\ */
7325: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7326: /* # ...\n\ */
7327: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7328:
7329: for(itimes=1;itimes<=2;itimes++){
7330: jj=0;
7331: for(i=1; i <=nlstate; i++){
7332: for(j=1; j <=nlstate+ndeath; j++){
7333: if(j==i) continue;
7334: for(k=1; k<=ncovmodel;k++){
7335: jj++;
7336: ca[0]= k+'a'-1;ca[1]='\0';
7337: if(itimes==1){
7338: printf("#%1d%1d%d",i,j,k);
7339: fprintf(ficparo,"#%1d%1d%d",i,j,k);
7340: }else{
7341: printf("%1d%1d%d",i,j,k);
7342: fprintf(ficparo,"%1d%1d%d",i,j,k);
7343: /* printf(" %.5le",matcov[i][j]); */
7344: }
7345: ll=0;
7346: for(li=1;li <=nlstate; li++){
7347: for(lj=1;lj <=nlstate+ndeath; lj++){
7348: if(lj==li) continue;
7349: for(lk=1;lk<=ncovmodel;lk++){
7350: ll++;
7351: if(ll<=jj){
7352: cb[0]= lk +'a'-1;cb[1]='\0';
7353: if(ll<jj){
7354: if(itimes==1){
7355: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7356: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7357: }else{
7358: printf(" 0.");
7359: fprintf(ficparo," 0.");
7360: }
7361: }else{
7362: if(itimes==1){
7363: printf(" Var(%s%1d%1d)",ca,i,j);
7364: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
7365: }else{
7366: printf(" 0.");
7367: fprintf(ficparo," 0.");
7368: }
7369: }
7370: }
7371: } /* end lk */
7372: } /* end lj */
7373: } /* end li */
7374: printf("\n");
7375: fprintf(ficparo,"\n");
7376: numlinepar++;
7377: } /* end k*/
7378: } /*end j */
7379: } /* end i */
7380: } /* end itimes */
7381:
7382: } /* end of prwizard */
7383: /******************* Gompertz Likelihood ******************************/
7384: double gompertz(double x[])
7385: {
7386: double A,B,L=0.0,sump=0.,num=0.;
7387: int i,n=0; /* n is the size of the sample */
7388:
1.220 brouard 7389: for (i=1;i<=imx ; i++) {
1.126 brouard 7390: sump=sump+weight[i];
7391: /* sump=sump+1;*/
7392: num=num+1;
7393: }
7394:
7395:
7396: /* for (i=0; i<=imx; i++)
7397: if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
7398:
7399: for (i=1;i<=imx ; i++)
7400: {
7401: if (cens[i] == 1 && wav[i]>1)
7402: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
7403:
7404: if (cens[i] == 0 && wav[i]>1)
7405: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
7406: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
7407:
7408: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
7409: if (wav[i] > 1 ) { /* ??? */
7410: L=L+A*weight[i];
7411: /* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
7412: }
7413: }
7414:
7415: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
7416:
7417: return -2*L*num/sump;
7418: }
7419:
1.136 brouard 7420: #ifdef GSL
7421: /******************* Gompertz_f Likelihood ******************************/
7422: double gompertz_f(const gsl_vector *v, void *params)
7423: {
7424: double A,B,LL=0.0,sump=0.,num=0.;
7425: double *x= (double *) v->data;
7426: int i,n=0; /* n is the size of the sample */
7427:
7428: for (i=0;i<=imx-1 ; i++) {
7429: sump=sump+weight[i];
7430: /* sump=sump+1;*/
7431: num=num+1;
7432: }
7433:
7434:
7435: /* for (i=0; i<=imx; i++)
7436: if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
7437: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
7438: for (i=1;i<=imx ; i++)
7439: {
7440: if (cens[i] == 1 && wav[i]>1)
7441: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
7442:
7443: if (cens[i] == 0 && wav[i]>1)
7444: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
7445: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
7446:
7447: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
7448: if (wav[i] > 1 ) { /* ??? */
7449: LL=LL+A*weight[i];
7450: /* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
7451: }
7452: }
7453:
7454: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
7455: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
7456:
7457: return -2*LL*num/sump;
7458: }
7459: #endif
7460:
1.126 brouard 7461: /******************* Printing html file ***********/
1.201 brouard 7462: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 7463: int lastpass, int stepm, int weightopt, char model[],\
7464: int imx, double p[],double **matcov,double agemortsup){
7465: int i,k;
7466:
7467: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
7468: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
7469: for (i=1;i<=2;i++)
7470: fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.199 brouard 7471: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 7472: fprintf(fichtm,"</ul>");
7473:
7474: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
7475:
7476: fprintf(fichtm,"\nAge l<inf>x</inf> q<inf>x</inf> d(x,x+1) L<inf>x</inf> T<inf>x</inf> e<infx</inf><br>");
7477:
7478: for (k=agegomp;k<(agemortsup-2);k++)
7479: fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
7480:
7481:
7482: fflush(fichtm);
7483: }
7484:
7485: /******************* Gnuplot file **************/
1.201 brouard 7486: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 7487:
7488: char dirfileres[132],optfileres[132];
1.164 brouard 7489:
1.126 brouard 7490: int ng;
7491:
7492:
7493: /*#ifdef windows */
7494: fprintf(ficgp,"cd \"%s\" \n",pathc);
7495: /*#endif */
7496:
7497:
7498: strcpy(dirfileres,optionfilefiname);
7499: strcpy(optfileres,"vpl");
1.199 brouard 7500: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 7501: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 7502: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 7503: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 7504: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
7505:
7506: }
7507:
1.136 brouard 7508: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
7509: {
1.126 brouard 7510:
1.136 brouard 7511: /*-------- data file ----------*/
7512: FILE *fic;
7513: char dummy[]=" ";
1.223 brouard 7514: int i=0, j=0, n=0, iv=0;
7515: int lstra;
1.136 brouard 7516: int linei, month, year,iout;
7517: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 7518: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 7519: char *stratrunc;
1.223 brouard 7520:
1.126 brouard 7521:
7522:
1.136 brouard 7523: if((fic=fopen(datafile,"r"))==NULL) {
1.218 brouard 7524: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
7525: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136 brouard 7526: }
1.126 brouard 7527:
1.136 brouard 7528: i=1;
7529: linei=0;
7530: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
7531: linei=linei+1;
7532: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
7533: if(line[j] == '\t')
7534: line[j] = ' ';
7535: }
7536: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
7537: ;
7538: };
7539: line[j+1]=0; /* Trims blanks at end of line */
7540: if(line[0]=='#'){
7541: fprintf(ficlog,"Comment line\n%s\n",line);
7542: printf("Comment line\n%s\n",line);
7543: continue;
7544: }
7545: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 7546: strcpy(line, linetmp);
1.223 brouard 7547:
7548: /* Loops on waves */
7549: for (j=maxwav;j>=1;j--){
7550: for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */
1.225 brouard 7551: cutv(stra, strb, line, ' ');
7552: if(strb[0]=='.') { /* Missing value */
7553: lval=-1;
7554: cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
7555: if(isalpha(strb[1])) { /* .m or .d Really Missing value */
7556: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j);
7557: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);
7558: return 1;
7559: }
7560: }else{
7561: errno=0;
7562: /* what_kind_of_number(strb); */
7563: dval=strtod(strb,&endptr);
7564: /* if( strb[0]=='\0' || (*endptr != '\0')){ */
7565: /* if(strb != endptr && *endptr == '\0') */
7566: /* dval=dlval; */
7567: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
7568: if( strb[0]=='\0' || (*endptr != '\0')){
7569: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav);
7570: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog);
7571: return 1;
7572: }
7573: cotqvar[j][iv][i]=dval;
7574: }
7575: strcpy(line,stra);
1.223 brouard 7576: }/* end loop ntqv */
1.225 brouard 7577:
1.223 brouard 7578: for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */
1.225 brouard 7579: cutv(stra, strb, line, ' ');
7580: if(strb[0]=='.') { /* Missing value */
7581: lval=-1;
7582: }else{
7583: errno=0;
7584: lval=strtol(strb,&endptr,10);
7585: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
7586: if( strb[0]=='\0' || (*endptr != '\0')){
7587: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav);
7588: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);fflush(ficlog);
7589: return 1;
7590: }
7591: }
7592: if(lval <-1 || lval >1){
7593: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 7594: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7595: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 7596: For example, for multinomial values like 1, 2 and 3,\n \
7597: build V1=0 V2=0 for the reference value (1),\n \
7598: V1=1 V2=0 for (2) \n \
1.223 brouard 7599: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 7600: output of IMaCh is often meaningless.\n \
1.223 brouard 7601: Exiting.\n",lval,linei, i,line,j);
1.225 brouard 7602: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 7603: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7604: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 7605: For example, for multinomial values like 1, 2 and 3,\n \
7606: build V1=0 V2=0 for the reference value (1),\n \
7607: V1=1 V2=0 for (2) \n \
1.223 brouard 7608: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
7609: output of IMaCh is often meaningless.\n \
7610: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.225 brouard 7611: return 1;
7612: }
7613: cotvar[j][iv][i]=(double)(lval);
7614: strcpy(line,stra);
1.223 brouard 7615: }/* end loop ntv */
1.225 brouard 7616:
1.223 brouard 7617: /* Statuses at wave */
1.137 brouard 7618: cutv(stra, strb, line, ' ');
1.223 brouard 7619: if(strb[0]=='.') { /* Missing value */
1.225 brouard 7620: lval=-1;
1.136 brouard 7621: }else{
1.225 brouard 7622: errno=0;
7623: lval=strtol(strb,&endptr,10);
7624: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
7625: if( strb[0]=='\0' || (*endptr != '\0')){
7626: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);
7627: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
7628: return 1;
7629: }
1.136 brouard 7630: }
1.225 brouard 7631:
1.136 brouard 7632: s[j][i]=lval;
1.225 brouard 7633:
1.223 brouard 7634: /* Date of Interview */
1.136 brouard 7635: strcpy(line,stra);
7636: cutv(stra, strb,line,' ');
1.169 brouard 7637: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7638: }
1.169 brouard 7639: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.225 brouard 7640: month=99;
7641: year=9999;
1.136 brouard 7642: }else{
1.225 brouard 7643: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
7644: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
7645: return 1;
1.136 brouard 7646: }
7647: anint[j][i]= (double) year;
7648: mint[j][i]= (double)month;
7649: strcpy(line,stra);
1.223 brouard 7650: } /* End loop on waves */
1.225 brouard 7651:
1.223 brouard 7652: /* Date of death */
1.136 brouard 7653: cutv(stra, strb,line,' ');
1.169 brouard 7654: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7655: }
1.169 brouard 7656: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 7657: month=99;
7658: year=9999;
7659: }else{
1.141 brouard 7660: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
1.225 brouard 7661: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
7662: return 1;
1.136 brouard 7663: }
7664: andc[i]=(double) year;
7665: moisdc[i]=(double) month;
7666: strcpy(line,stra);
7667:
1.223 brouard 7668: /* Date of birth */
1.136 brouard 7669: cutv(stra, strb,line,' ');
1.169 brouard 7670: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7671: }
1.169 brouard 7672: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 7673: month=99;
7674: year=9999;
7675: }else{
1.141 brouard 7676: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
7677: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.225 brouard 7678: return 1;
1.136 brouard 7679: }
7680: if (year==9999) {
1.141 brouard 7681: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);
7682: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.225 brouard 7683: return 1;
7684:
1.136 brouard 7685: }
7686: annais[i]=(double)(year);
7687: moisnais[i]=(double)(month);
7688: strcpy(line,stra);
1.225 brouard 7689:
1.223 brouard 7690: /* Sample weight */
1.136 brouard 7691: cutv(stra, strb,line,' ');
7692: errno=0;
7693: dval=strtod(strb,&endptr);
7694: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 7695: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
7696: fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
1.136 brouard 7697: fflush(ficlog);
7698: return 1;
7699: }
7700: weight[i]=dval;
7701: strcpy(line,stra);
1.225 brouard 7702:
1.223 brouard 7703: for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */
7704: cutv(stra, strb, line, ' ');
7705: if(strb[0]=='.') { /* Missing value */
1.225 brouard 7706: lval=-1;
1.223 brouard 7707: }else{
1.225 brouard 7708: errno=0;
7709: /* what_kind_of_number(strb); */
7710: dval=strtod(strb,&endptr);
7711: /* if(strb != endptr && *endptr == '\0') */
7712: /* dval=dlval; */
7713: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
7714: if( strb[0]=='\0' || (*endptr != '\0')){
7715: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);
7716: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);fflush(ficlog);
7717: return 1;
7718: }
7719: coqvar[iv][i]=dval;
1.226 brouard 7720: covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */
1.223 brouard 7721: }
7722: strcpy(line,stra);
7723: }/* end loop nqv */
1.136 brouard 7724:
1.223 brouard 7725: /* Covariate values */
1.136 brouard 7726: for (j=ncovcol;j>=1;j--){
7727: cutv(stra, strb,line,' ');
1.223 brouard 7728: if(strb[0]=='.') { /* Missing covariate value */
1.225 brouard 7729: lval=-1;
1.136 brouard 7730: }else{
1.225 brouard 7731: errno=0;
7732: lval=strtol(strb,&endptr,10);
7733: if( strb[0]=='\0' || (*endptr != '\0')){
7734: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);
7735: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);fflush(ficlog);
7736: return 1;
7737: }
1.136 brouard 7738: }
7739: if(lval <-1 || lval >1){
1.225 brouard 7740: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 7741: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7742: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 7743: For example, for multinomial values like 1, 2 and 3,\n \
7744: build V1=0 V2=0 for the reference value (1),\n \
7745: V1=1 V2=0 for (2) \n \
1.136 brouard 7746: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 7747: output of IMaCh is often meaningless.\n \
1.136 brouard 7748: Exiting.\n",lval,linei, i,line,j);
1.225 brouard 7749: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 7750: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7751: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 7752: For example, for multinomial values like 1, 2 and 3,\n \
7753: build V1=0 V2=0 for the reference value (1),\n \
7754: V1=1 V2=0 for (2) \n \
1.136 brouard 7755: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 7756: output of IMaCh is often meaningless.\n \
1.136 brouard 7757: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.225 brouard 7758: return 1;
1.136 brouard 7759: }
7760: covar[j][i]=(double)(lval);
7761: strcpy(line,stra);
7762: }
7763: lstra=strlen(stra);
1.225 brouard 7764:
1.136 brouard 7765: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
7766: stratrunc = &(stra[lstra-9]);
7767: num[i]=atol(stratrunc);
7768: }
7769: else
7770: num[i]=atol(stra);
7771: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
7772: printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
7773:
7774: i=i+1;
7775: } /* End loop reading data */
1.225 brouard 7776:
1.136 brouard 7777: *imax=i-1; /* Number of individuals */
7778: fclose(fic);
1.225 brouard 7779:
1.136 brouard 7780: return (0);
1.164 brouard 7781: /* endread: */
1.225 brouard 7782: printf("Exiting readdata: ");
7783: fclose(fic);
7784: return (1);
1.223 brouard 7785: }
1.126 brouard 7786:
1.230 ! brouard 7787: void removespace(char **stri){/*, char stro[]) {*/
! 7788: char *p1 = *stri, *p2 = *stri;
1.145 brouard 7789: do
7790: while (*p2 == ' ')
7791: p2++;
1.169 brouard 7792: while (*p1++ == *p2++);
1.230 ! brouard 7793: *stri=p1;
1.145 brouard 7794: }
7795:
1.230 ! brouard 7796: int decoderesult ( char resultline[])
! 7797: /**< This routine decode one result line and returns the combination # of dummy covariates only **/
! 7798: {
! 7799: int j=0, k=0;
! 7800: char resultsav[MAXLINE];
! 7801: char stra[80], strb[80], strc[80], strd[80],stre[80];
! 7802:
! 7803: removespace(&resultline);
! 7804: printf("decoderesult=%s\n",resultline);
! 7805:
! 7806: if (strstr(resultline,"v") !=0){
! 7807: printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
! 7808: fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
! 7809: return 1;
! 7810: }
! 7811: trimbb(resultsav, resultline);
! 7812: if (strlen(resultsav) >1){
! 7813: j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
! 7814: }
! 7815:
! 7816: for(k=1; k<=j;k++){ /* Loop on total covariates of the model */
! 7817: cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '
! 7818: resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
! 7819: cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */
! 7820: Tvalsel[k]=atof(strc); /* 1 */
! 7821:
! 7822: cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
! 7823: Tvarsel[k]=atoi(strc);
! 7824: /* Typevarsel[k]=1; /\* 1 for age product *\/ */
! 7825: /* cptcovsel++; */
! 7826: if (nbocc(stra,'=') >0)
! 7827: strcpy(resultsav,stra); /* and analyzes it */
! 7828: }
! 7829: return (0);
! 7830: }
! 7831: int selected( int kvar){ /* Selected combination of covariates */
! 7832: if(Tvarsel[kvar])
! 7833: return (0);
! 7834: else
! 7835: return(1);
! 7836: }
! 7837: int decodemodel( char model[], int lastobs)
! 7838: /**< This routine decodes the model and returns:
1.224 brouard 7839: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
7840: * - nagesqr = 1 if age*age in the model, otherwise 0.
7841: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
7842: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
7843: * - cptcovage number of covariates with age*products =2
7844: * - cptcovs number of simple covariates
7845: * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
7846: * which is a new column after the 9 (ncovcol) variables.
7847: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
7848: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
7849: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
7850: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
7851: */
1.136 brouard 7852: {
1.145 brouard 7853: int i, j, k, ks;
1.227 brouard 7854: int j1, k1, k2, k3, k4;
1.136 brouard 7855: char modelsav[80];
1.145 brouard 7856: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 7857: char *strpt;
1.136 brouard 7858:
1.145 brouard 7859: /*removespace(model);*/
1.136 brouard 7860: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 7861: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 7862: if (strstr(model,"AGE") !=0){
1.192 brouard 7863: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
7864: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 7865: return 1;
7866: }
1.141 brouard 7867: if (strstr(model,"v") !=0){
7868: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
7869: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
7870: return 1;
7871: }
1.187 brouard 7872: strcpy(modelsav,model);
7873: if ((strpt=strstr(model,"age*age")) !=0){
7874: printf(" strpt=%s, model=%s\n",strpt, model);
7875: if(strpt != model){
1.225 brouard 7876: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 7877: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 7878: corresponding column of parameters.\n",model);
1.225 brouard 7879: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 7880: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 7881: corresponding column of parameters.\n",model); fflush(ficlog);
1.225 brouard 7882: return 1;
7883: }
1.187 brouard 7884: nagesqr=1;
7885: if (strstr(model,"+age*age") !=0)
1.225 brouard 7886: substrchaine(modelsav, model, "+age*age");
1.187 brouard 7887: else if (strstr(model,"age*age+") !=0)
1.225 brouard 7888: substrchaine(modelsav, model, "age*age+");
1.187 brouard 7889: else
1.225 brouard 7890: substrchaine(modelsav, model, "age*age");
1.187 brouard 7891: }else
7892: nagesqr=0;
7893: if (strlen(modelsav) >1){
7894: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
7895: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
1.224 brouard 7896: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2 */
1.187 brouard 7897: cptcovt= j+1; /* Number of total covariates in the model, not including
1.225 brouard 7898: * cst, age and age*age
7899: * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
7900: /* including age products which are counted in cptcovage.
7901: * but the covariates which are products must be treated
7902: * separately: ncovn=4- 2=2 (V1+V3). */
1.187 brouard 7903: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
7904: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.225 brouard 7905:
7906:
1.187 brouard 7907: /* Design
7908: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
7909: * < ncovcol=8 >
7910: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
7911: * k= 1 2 3 4 5 6 7 8
7912: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
7913: * covar[k,i], value of kth covariate if not including age for individual i:
1.224 brouard 7914: * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
7915: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
1.187 brouard 7916: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
7917: * Tage[++cptcovage]=k
7918: * if products, new covar are created after ncovcol with k1
7919: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
7920: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
7921: * Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
7922: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
7923: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
7924: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
7925: * < ncovcol=8 >
7926: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
7927: * k= 1 2 3 4 5 6 7 8 9 10 11 12
7928: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
7929: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
7930: * p Tprod[1]@2={ 6, 5}
7931: *p Tvard[1][1]@4= {7, 8, 5, 6}
7932: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
7933: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
7934: *How to reorganize?
7935: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
7936: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
7937: * {2, 1, 4, 8, 5, 6, 3, 7}
7938: * Struct []
7939: */
1.225 brouard 7940:
1.187 brouard 7941: /* This loop fills the array Tvar from the string 'model'.*/
7942: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
7943: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
7944: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
7945: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
7946: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
7947: /* k=1 Tvar[1]=2 (from V2) */
7948: /* k=5 Tvar[5] */
7949: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 7950: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 7951: /* } */
1.198 brouard 7952: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 7953: /*
7954: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
1.227 brouard 7955: for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
7956: Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
7957: }
1.187 brouard 7958: cptcovage=0;
7959: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
1.225 brouard 7960: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
7961: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
7962: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
7963: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
7964: /*scanf("%d",i);*/
7965: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
7966: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
7967: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
7968: /* covar is not filled and then is empty */
7969: cptcovprod--;
7970: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
7971: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
1.226 brouard 7972: Typevar[k]=1; /* 1 for age product */
1.225 brouard 7973: cptcovage++; /* Sums the number of covariates which include age as a product */
7974: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
7975: /*printf("stre=%s ", stre);*/
7976: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
7977: cptcovprod--;
7978: cutl(stre,strb,strc,'V');
7979: Tvar[k]=atoi(stre);
7980: Typevar[k]=1; /* 1 for age product */
7981: cptcovage++;
7982: Tage[cptcovage]=k;
7983: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
7984: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
7985: cptcovn++;
7986: cptcovprodnoage++;k1++;
7987: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
7988: Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
7989: because this model-covariate is a construction we invent a new column
7990: which is after existing variables ncovcol+nqv+ntv+nqtv + k1
7991: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
7992: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
7993: Typevar[k]=2; /* 2 for double fixed dummy covariates */
7994: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
7995: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
1.227 brouard 7996: Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
1.225 brouard 7997: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
7998: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
7999: k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
8000: /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
8001: /* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
8002: /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
8003: /* 1 2 3 4 5 | Tvar[5+1)=1, Tvar[7]=2 */
8004: for (i=1; i<=lastobs;i++){
8005: /* Computes the new covariate which is a product of
8006: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
8007: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
8008: }
8009: } /* End age is not in the model */
8010: } /* End if model includes a product */
8011: else { /* no more sum */
8012: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
8013: /* scanf("%d",i);*/
8014: cutl(strd,strc,strb,'V');
1.227 brouard 8015: ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
1.225 brouard 8016: cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
8017: Tvar[k]=atoi(strd);
8018: Typevar[k]=0; /* 0 for simple covariates */
8019: }
8020: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.223 brouard 8021: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
1.225 brouard 8022: scanf("%d",i);*/
1.187 brouard 8023: } /* end of loop + on total covariates */
8024: } /* end if strlen(modelsave == 0) age*age might exist */
8025: } /* end if strlen(model == 0) */
1.136 brouard 8026:
8027: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
8028: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
1.225 brouard 8029:
1.136 brouard 8030: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.225 brouard 8031: printf("cptcovprod=%d ", cptcovprod);
8032: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
8033: scanf("%d ",i);*/
8034:
8035:
1.230 ! brouard 8036: /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
! 8037: of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
1.226 brouard 8038: /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1 = 5 possible variables data: 2 fixed 3, varying
8039: model= V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
8040: k = 1 2 3 4 5 6 7 8 9
8041: Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5
8042: Typevar[k]= 0 0 0 2 1 0 2 1 1
1.227 brouard 8043: Fixed[k] 1 1 1 1 3 0 0 or 2 2 3
8044: Dummy[k] 1 0 0 0 3 1 1 2 3
8045: Tmodelind[combination of covar]=k;
1.225 brouard 8046: */
8047: /* Dispatching between quantitative and time varying covariates */
1.226 brouard 8048: /* If Tvar[k] >ncovcol it is a product */
1.225 brouard 8049: /* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p Vp=Vn*Vm for product */
1.226 brouard 8050: /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
1.227 brouard 8051: printf("Model=%s\n\
8052: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
8053: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
8054: Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
8055: fprintf(ficlog,"Model=%s\n\
8056: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
8057: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
8058: Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
8059:
1.225 brouard 8060: for(k=1, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
1.226 brouard 8061: if (Tvar[k] <=ncovcol && (Typevar[k]==0 || Typevar[k]==2)){ /* Simple or product fixed dummy covariatee */
1.227 brouard 8062: Fixed[k]= 0;
8063: Dummy[k]= 0;
1.225 brouard 8064: ncoveff++;
1.230 ! brouard 8065: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
! 8066: TvarFDind[ncoveff]=Tvar[k]; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.225 brouard 8067: }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){ /* Remind that product Vn*Vm are added in k*/
1.227 brouard 8068: Fixed[k]= 0;
8069: Dummy[k]= 1;
1.230 ! brouard 8070: nqfveff++;
! 8071: TvarFQ[nqfveff]=Tvar[k]; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
! 8072: TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1.225 brouard 8073: }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){
1.227 brouard 8074: Fixed[k]= 1;
8075: Dummy[k]= 0;
1.225 brouard 8076: ntveff++; /* Only simple time varying dummy variable */
1.230 ! brouard 8077: TvarVD[ntvveff]=Tvar[k]; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
! 8078: TvarVDind[ntveff++]=k; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1.228 brouard 8079: printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv);
8080: printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
1.227 brouard 8081: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){
8082: Fixed[k]= 1;
8083: Dummy[k]= 1;
1.228 brouard 8084: TmodelInvQind[++nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
8085: /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
8086: printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%d,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv);
8087: printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
1.227 brouard 8088: }else if (Typevar[k] == 1) { /* product with age */
8089: if (Tvar[k] <=ncovcol ){ /* Simple or product fixed dummy covariatee */
8090: Fixed[k]= 2;
8091: Dummy[k]= 2;
8092: /* ncoveff++; */
8093: }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
8094: Fixed[k]= 2;
8095: Dummy[k]= 3;
8096: /* nqfveff++; /\* Only simple fixed quantitative variable *\/ */
8097: }else if( Tvar[k] <=ncovcol+nqv+ntv ){
8098: Fixed[k]= 3;
8099: Dummy[k]= 2;
8100: /* ntveff++; /\* Only simple time varying dummy variable *\/ */
8101: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
8102: Fixed[k]= 3;
8103: Dummy[k]= 3;
8104: /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
8105: }
8106: }else if (Typevar[k] == 2) { /* product without age */
8107: k1=Tposprod[k];
8108: if(Tvard[k1][1] <=ncovcol){
8109: if(Tvard[k1][2] <=ncovcol){
8110: Fixed[k]= 1;
8111: Dummy[k]= 0;
8112: }else if(Tvard[k1][2] <=ncovcol+nqv){
8113: Fixed[k]= 0; /* or 2 ?*/
8114: Dummy[k]= 1;
8115: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
8116: Fixed[k]= 1;
8117: Dummy[k]= 0;
8118: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
8119: Fixed[k]= 1;
8120: Dummy[k]= 1;
8121: }
8122: }else if(Tvard[k1][1] <=ncovcol+nqv){
8123: if(Tvard[k1][2] <=ncovcol){
8124: Fixed[k]= 0; /* or 2 ?*/
8125: Dummy[k]= 1;
8126: }else if(Tvard[k1][2] <=ncovcol+nqv){
8127: Fixed[k]= 0; /* or 2 ?*/
8128: Dummy[k]= 1;
8129: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
8130: Fixed[k]= 1;
8131: Dummy[k]= 1;
8132: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
8133: Fixed[k]= 1;
8134: Dummy[k]= 1;
8135: }
8136: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
8137: if(Tvard[k1][2] <=ncovcol){
8138: Fixed[k]= 1;
8139: Dummy[k]= 1;
8140: }else if(Tvard[k1][2] <=ncovcol+nqv){
8141: Fixed[k]= 1;
8142: Dummy[k]= 1;
8143: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
8144: Fixed[k]= 1;
8145: Dummy[k]= 0;
8146: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
8147: Fixed[k]= 1;
8148: Dummy[k]= 1;
8149: }
8150: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
8151: if(Tvard[k1][2] <=ncovcol){
8152: Fixed[k]= 1;
8153: Dummy[k]= 1;
8154: }else if(Tvard[k1][2] <=ncovcol+nqv){
8155: Fixed[k]= 1;
8156: Dummy[k]= 1;
8157: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
8158: Fixed[k]= 1;
8159: Dummy[k]= 1;
8160: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
8161: Fixed[k]= 1;
8162: Dummy[k]= 1;
8163: }
8164: }else{
8165: printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
8166: fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
1.226 brouard 8167: } /* end k1 */
1.225 brouard 8168: }else{
1.226 brouard 8169: printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
8170: fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
1.225 brouard 8171: }
1.227 brouard 8172: printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
8173: fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
8174: }
8175: /* Searching for doublons in the model */
8176: for(k1=1; k1<= cptcovt;k1++){
8177: for(k2=1; k2 <k1;k2++){
8178: if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){
8179: if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
8180: if(Tvar[k1]==Tvar[k2]){
8181: printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
8182: fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
8183: return(1);
8184: }
8185: }else if (Typevar[k1] ==2){
8186: k3=Tposprod[k1];
8187: k4=Tposprod[k2];
8188: if( ((Tvard[k3][1]== Tvard[k4][1])&&(Tvard[k3][2]== Tvard[k4][2])) || ((Tvard[k3][1]== Tvard[k4][2])&&(Tvard[k3][2]== Tvard[k4][1])) ){
8189: printf("Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
8190: fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
8191: return(1);
8192: }
8193: }
8194: }
8195: }
1.225 brouard 8196: }
8197: printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
8198: fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
1.137 brouard 8199: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 8200: /*endread:*/
1.225 brouard 8201: printf("Exiting decodemodel: ");
8202: return (1);
1.136 brouard 8203: }
8204:
1.169 brouard 8205: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 8206: {
8207: int i, m;
1.218 brouard 8208: int firstone=0;
8209:
1.136 brouard 8210: for (i=1; i<=imx; i++) {
8211: for(m=2; (m<= maxwav); m++) {
8212: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
8213: anint[m][i]=9999;
1.216 brouard 8214: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
8215: s[m][i]=-1;
1.136 brouard 8216: }
8217: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 8218: *nberr = *nberr + 1;
1.218 brouard 8219: if(firstone == 0){
8220: firstone=1;
8221: printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\nOther similar cases in log file\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
8222: }
8223: fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
1.136 brouard 8224: s[m][i]=-1;
8225: }
8226: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 8227: (*nberr)++;
1.136 brouard 8228: printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
8229: fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
8230: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
8231: }
8232: }
8233: }
8234:
8235: for (i=1; i<=imx; i++) {
8236: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
8237: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 8238: if(s[m][i] >0 || s[m][i]==-1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ /* What if s[m][i]=-1 */
1.136 brouard 8239: if (s[m][i] >= nlstate+1) {
1.169 brouard 8240: if(agedc[i]>0){
8241: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 8242: agev[m][i]=agedc[i];
1.214 brouard 8243: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 8244: }else {
1.136 brouard 8245: if ((int)andc[i]!=9999){
8246: nbwarn++;
8247: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
8248: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
8249: agev[m][i]=-1;
8250: }
8251: }
1.169 brouard 8252: } /* agedc > 0 */
1.214 brouard 8253: } /* end if */
1.136 brouard 8254: else if(s[m][i] !=9){ /* Standard case, age in fractional
8255: years but with the precision of a month */
8256: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
8257: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
8258: agev[m][i]=1;
8259: else if(agev[m][i] < *agemin){
8260: *agemin=agev[m][i];
8261: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
8262: }
8263: else if(agev[m][i] >*agemax){
8264: *agemax=agev[m][i];
1.156 brouard 8265: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 8266: }
8267: /*agev[m][i]=anint[m][i]-annais[i];*/
8268: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 8269: } /* en if 9*/
1.136 brouard 8270: else { /* =9 */
1.214 brouard 8271: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 8272: agev[m][i]=1;
8273: s[m][i]=-1;
8274: }
8275: }
1.214 brouard 8276: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 8277: agev[m][i]=1;
1.214 brouard 8278: else{
8279: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
8280: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
8281: agev[m][i]=0;
8282: }
8283: } /* End for lastpass */
8284: }
1.136 brouard 8285:
8286: for (i=1; i<=imx; i++) {
8287: for(m=firstpass; (m<=lastpass); m++){
8288: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 8289: (*nberr)++;
1.136 brouard 8290: printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
8291: fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
8292: return 1;
8293: }
8294: }
8295: }
8296:
8297: /*for (i=1; i<=imx; i++){
8298: for (m=firstpass; (m<lastpass); m++){
8299: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
8300: }
8301:
8302: }*/
8303:
8304:
1.139 brouard 8305: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
8306: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 8307:
8308: return (0);
1.164 brouard 8309: /* endread:*/
1.136 brouard 8310: printf("Exiting calandcheckages: ");
8311: return (1);
8312: }
8313:
1.172 brouard 8314: #if defined(_MSC_VER)
8315: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
8316: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
8317: //#include "stdafx.h"
8318: //#include <stdio.h>
8319: //#include <tchar.h>
8320: //#include <windows.h>
8321: //#include <iostream>
8322: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
8323:
8324: LPFN_ISWOW64PROCESS fnIsWow64Process;
8325:
8326: BOOL IsWow64()
8327: {
8328: BOOL bIsWow64 = FALSE;
8329:
8330: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
8331: // (HANDLE, PBOOL);
8332:
8333: //LPFN_ISWOW64PROCESS fnIsWow64Process;
8334:
8335: HMODULE module = GetModuleHandle(_T("kernel32"));
8336: const char funcName[] = "IsWow64Process";
8337: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
8338: GetProcAddress(module, funcName);
8339:
8340: if (NULL != fnIsWow64Process)
8341: {
8342: if (!fnIsWow64Process(GetCurrentProcess(),
8343: &bIsWow64))
8344: //throw std::exception("Unknown error");
8345: printf("Unknown error\n");
8346: }
8347: return bIsWow64 != FALSE;
8348: }
8349: #endif
1.177 brouard 8350:
1.191 brouard 8351: void syscompilerinfo(int logged)
1.167 brouard 8352: {
8353: /* #include "syscompilerinfo.h"*/
1.185 brouard 8354: /* command line Intel compiler 32bit windows, XP compatible:*/
8355: /* /GS /W3 /Gy
8356: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
8357: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
8358: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 8359: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
8360: */
8361: /* 64 bits */
1.185 brouard 8362: /*
8363: /GS /W3 /Gy
8364: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
8365: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
8366: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
8367: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
8368: /* Optimization are useless and O3 is slower than O2 */
8369: /*
8370: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
8371: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
8372: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
8373: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
8374: */
1.186 brouard 8375: /* Link is */ /* /OUT:"visual studio
1.185 brouard 8376: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
8377: /PDB:"visual studio
8378: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
8379: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
8380: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
8381: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
8382: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
8383: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
8384: uiAccess='false'"
8385: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
8386: /NOLOGO /TLBID:1
8387: */
1.177 brouard 8388: #if defined __INTEL_COMPILER
1.178 brouard 8389: #if defined(__GNUC__)
8390: struct utsname sysInfo; /* For Intel on Linux and OS/X */
8391: #endif
1.177 brouard 8392: #elif defined(__GNUC__)
1.179 brouard 8393: #ifndef __APPLE__
1.174 brouard 8394: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 8395: #endif
1.177 brouard 8396: struct utsname sysInfo;
1.178 brouard 8397: int cross = CROSS;
8398: if (cross){
8399: printf("Cross-");
1.191 brouard 8400: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 8401: }
1.174 brouard 8402: #endif
8403:
1.171 brouard 8404: #include <stdint.h>
1.178 brouard 8405:
1.191 brouard 8406: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 8407: #if defined(__clang__)
1.191 brouard 8408: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 8409: #endif
8410: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 8411: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 8412: #endif
8413: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 8414: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 8415: #endif
8416: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 8417: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 8418: #endif
8419: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 8420: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 8421: #endif
8422: #if defined(_MSC_VER)
1.191 brouard 8423: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 8424: #endif
8425: #if defined(__PGI)
1.191 brouard 8426: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 8427: #endif
8428: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 8429: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 8430: #endif
1.191 brouard 8431: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 8432:
1.167 brouard 8433: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
8434: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
8435: // Windows (x64 and x86)
1.191 brouard 8436: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 8437: #elif __unix__ // all unices, not all compilers
8438: // Unix
1.191 brouard 8439: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 8440: #elif __linux__
8441: // linux
1.191 brouard 8442: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 8443: #elif __APPLE__
1.174 brouard 8444: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 8445: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 8446: #endif
8447:
8448: /* __MINGW32__ */
8449: /* __CYGWIN__ */
8450: /* __MINGW64__ */
8451: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
8452: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
8453: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
8454: /* _WIN64 // Defined for applications for Win64. */
8455: /* _M_X64 // Defined for compilations that target x64 processors. */
8456: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 8457:
1.167 brouard 8458: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 8459: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 8460: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 8461: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 8462: #else
1.191 brouard 8463: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 8464: #endif
8465:
1.169 brouard 8466: #if defined(__GNUC__)
8467: # if defined(__GNUC_PATCHLEVEL__)
8468: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
8469: + __GNUC_MINOR__ * 100 \
8470: + __GNUC_PATCHLEVEL__)
8471: # else
8472: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
8473: + __GNUC_MINOR__ * 100)
8474: # endif
1.174 brouard 8475: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 8476: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 8477:
8478: if (uname(&sysInfo) != -1) {
8479: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 8480: if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.176 brouard 8481: }
8482: else
8483: perror("uname() error");
1.179 brouard 8484: //#ifndef __INTEL_COMPILER
8485: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 8486: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 8487: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 8488: #endif
1.169 brouard 8489: #endif
1.172 brouard 8490:
8491: // void main()
8492: // {
1.169 brouard 8493: #if defined(_MSC_VER)
1.174 brouard 8494: if (IsWow64()){
1.191 brouard 8495: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
8496: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 8497: }
8498: else{
1.191 brouard 8499: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
8500: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 8501: }
1.172 brouard 8502: // printf("\nPress Enter to continue...");
8503: // getchar();
8504: // }
8505:
1.169 brouard 8506: #endif
8507:
1.167 brouard 8508:
1.219 brouard 8509: }
1.136 brouard 8510:
1.219 brouard 8511: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.180 brouard 8512: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
8513: int i, j, k, i1 ;
1.202 brouard 8514: /* double ftolpl = 1.e-10; */
1.180 brouard 8515: double age, agebase, agelim;
1.203 brouard 8516: double tot;
1.180 brouard 8517:
1.202 brouard 8518: strcpy(filerespl,"PL_");
8519: strcat(filerespl,fileresu);
8520: if((ficrespl=fopen(filerespl,"w"))==NULL) {
8521: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
8522: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
8523: }
1.227 brouard 8524: printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
8525: fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
1.202 brouard 8526: pstamp(ficrespl);
1.203 brouard 8527: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 8528: fprintf(ficrespl,"#Age ");
8529: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
8530: fprintf(ficrespl,"\n");
1.180 brouard 8531:
1.219 brouard 8532: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180 brouard 8533:
1.219 brouard 8534: agebase=ageminpar;
8535: agelim=agemaxpar;
1.180 brouard 8536:
1.227 brouard 8537: /* i1=pow(2,ncoveff); */
8538: i1=pow(2,cptcoveff); /* Number of dummy covariates */
1.219 brouard 8539: if (cptcovn < 1){i1=1;}
1.180 brouard 8540:
1.220 brouard 8541: for(k=1; k<=i1;k++){
8542: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
1.180 brouard 8543: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
1.219 brouard 8544: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.220 brouard 8545: /* k=k+1; */
1.219 brouard 8546: /* to clean */
8547: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
8548: fprintf(ficrespl,"#******");
8549: printf("#******");
8550: fprintf(ficlog,"#******");
1.227 brouard 8551: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
8552: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
1.219 brouard 8553: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8554: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8555: }
8556: fprintf(ficrespl,"******\n");
8557: printf("******\n");
8558: fprintf(ficlog,"******\n");
1.227 brouard 8559: if(invalidvarcomb[k]){
8560: printf("\nCombination (%d) ignored because no case \n",k);
8561: fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
8562: fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
1.220 brouard 8563: continue;
1.227 brouard 8564: }
1.219 brouard 8565:
8566: fprintf(ficrespl,"#Age ");
1.227 brouard 8567: for(j=1;j<=cptcoveff;j++) {
1.219 brouard 8568: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8569: }
8570: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
8571: fprintf(ficrespl,"Total Years_to_converge\n");
1.227 brouard 8572:
1.219 brouard 8573: for (age=agebase; age<=agelim; age++){
8574: /* for (age=agebase; age<=agebase; age++){ */
8575: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
8576: fprintf(ficrespl,"%.0f ",age );
1.227 brouard 8577: for(j=1;j<=cptcoveff;j++)
8578: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.219 brouard 8579: tot=0.;
8580: for(i=1; i<=nlstate;i++){
1.227 brouard 8581: tot += prlim[i][i];
8582: fprintf(ficrespl," %.5f", prlim[i][i]);
1.219 brouard 8583: }
8584: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
8585: } /* Age */
8586: /* was end of cptcod */
8587: } /* cptcov */
8588: return 0;
1.180 brouard 8589: }
8590:
1.218 brouard 8591: int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){
8592: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
8593:
8594: /* Computes the back prevalence limit for any combination of covariate values
8595: * at any age between ageminpar and agemaxpar
8596: */
1.217 brouard 8597: int i, j, k, i1 ;
8598: /* double ftolpl = 1.e-10; */
8599: double age, agebase, agelim;
8600: double tot;
1.218 brouard 8601: /* double ***mobaverage; */
8602: /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
1.217 brouard 8603:
8604: strcpy(fileresplb,"PLB_");
8605: strcat(fileresplb,fileresu);
8606: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
8607: printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
8608: fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
8609: }
8610: printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
8611: fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
8612: pstamp(ficresplb);
8613: fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
8614: fprintf(ficresplb,"#Age ");
8615: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
8616: fprintf(ficresplb,"\n");
8617:
1.218 brouard 8618:
8619: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
8620:
8621: agebase=ageminpar;
8622: agelim=agemaxpar;
8623:
8624:
1.227 brouard 8625: i1=pow(2,cptcoveff);
1.218 brouard 8626: if (cptcovn < 1){i1=1;}
1.227 brouard 8627:
8628: for(k=1; k<=i1;k++){
1.218 brouard 8629: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
8630: fprintf(ficresplb,"#******");
8631: printf("#******");
8632: fprintf(ficlog,"#******");
1.227 brouard 8633: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
1.218 brouard 8634: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8635: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8636: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8637: }
8638: fprintf(ficresplb,"******\n");
8639: printf("******\n");
8640: fprintf(ficlog,"******\n");
1.227 brouard 8641: if(invalidvarcomb[k]){
8642: printf("\nCombination (%d) ignored because no cases \n",k);
8643: fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
8644: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
8645: continue;
8646: }
1.218 brouard 8647:
8648: fprintf(ficresplb,"#Age ");
1.227 brouard 8649: for(j=1;j<=cptcoveff;j++) {
1.218 brouard 8650: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8651: }
8652: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
8653: fprintf(ficresplb,"Total Years_to_converge\n");
8654:
8655:
8656: for (age=agebase; age<=agelim; age++){
8657: /* for (age=agebase; age<=agebase; age++){ */
8658: if(mobilavproj > 0){
8659: /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
8660: /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.227 brouard 8661: bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);
1.218 brouard 8662: }else if (mobilavproj == 0){
1.227 brouard 8663: printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
8664: fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
8665: exit(1);
1.218 brouard 8666: }else{
1.227 brouard 8667: /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
8668: bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);
1.218 brouard 8669: }
8670: fprintf(ficresplb,"%.0f ",age );
1.227 brouard 8671: for(j=1;j<=cptcoveff;j++)
8672: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.218 brouard 8673: tot=0.;
8674: for(i=1; i<=nlstate;i++){
1.227 brouard 8675: tot += bprlim[i][i];
8676: fprintf(ficresplb," %.5f", bprlim[i][i]);
1.218 brouard 8677: }
8678: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
8679: } /* Age */
8680: /* was end of cptcod */
8681: } /* cptcov */
8682:
8683: /* hBijx(p, bage, fage); */
8684: /* fclose(ficrespijb); */
8685:
8686: return 0;
1.217 brouard 8687: }
1.218 brouard 8688:
1.180 brouard 8689: int hPijx(double *p, int bage, int fage){
8690: /*------------- h Pij x at various ages ------------*/
8691:
8692: int stepsize;
8693: int agelim;
8694: int hstepm;
8695: int nhstepm;
8696: int h, i, i1, j, k;
8697:
8698: double agedeb;
8699: double ***p3mat;
8700:
1.201 brouard 8701: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 8702: if((ficrespij=fopen(filerespij,"w"))==NULL) {
8703: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
8704: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
8705: }
8706: printf("Computing pij: result on file '%s' \n", filerespij);
8707: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
8708:
8709: stepsize=(int) (stepm+YEARM-1)/YEARM;
8710: /*if (stepm<=24) stepsize=2;*/
8711:
8712: agelim=AGESUP;
8713: hstepm=stepsize*YEARM; /* Every year of age */
8714: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.218 brouard 8715:
1.180 brouard 8716: /* hstepm=1; aff par mois*/
8717: pstamp(ficrespij);
8718: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.227 brouard 8719: i1= pow(2,cptcoveff);
1.218 brouard 8720: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
8721: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
8722: /* k=k+1; */
1.227 brouard 8723: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.183 brouard 8724: fprintf(ficrespij,"\n#****** ");
1.227 brouard 8725: for(j=1;j<=cptcoveff;j++)
1.198 brouard 8726: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.183 brouard 8727: fprintf(ficrespij,"******\n");
8728:
8729: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
8730: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
8731: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
8732:
8733: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 8734:
1.183 brouard 8735: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8736: oldm=oldms;savm=savms;
8737: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
8738: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
8739: for(i=1; i<=nlstate;i++)
8740: for(j=1; j<=nlstate+ndeath;j++)
8741: fprintf(ficrespij," %1d-%1d",i,j);
8742: fprintf(ficrespij,"\n");
8743: for (h=0; h<=nhstepm; h++){
8744: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
8745: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 8746: for(i=1; i<=nlstate;i++)
8747: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 8748: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 8749: fprintf(ficrespij,"\n");
8750: }
1.183 brouard 8751: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8752: fprintf(ficrespij,"\n");
8753: }
1.180 brouard 8754: /*}*/
8755: }
1.218 brouard 8756: return 0;
1.180 brouard 8757: }
1.218 brouard 8758:
8759: int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217 brouard 8760: /*------------- h Bij x at various ages ------------*/
8761:
8762: int stepsize;
1.218 brouard 8763: /* int agelim; */
8764: int ageminl;
1.217 brouard 8765: int hstepm;
8766: int nhstepm;
8767: int h, i, i1, j, k;
1.218 brouard 8768:
1.217 brouard 8769: double agedeb;
8770: double ***p3mat;
1.218 brouard 8771:
8772: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
8773: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
8774: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
8775: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
8776: }
8777: printf("Computing pij back: result on file '%s' \n", filerespijb);
8778: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
8779:
8780: stepsize=(int) (stepm+YEARM-1)/YEARM;
8781: /*if (stepm<=24) stepsize=2;*/
1.217 brouard 8782:
1.218 brouard 8783: /* agelim=AGESUP; */
8784: ageminl=30;
8785: hstepm=stepsize*YEARM; /* Every year of age */
8786: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
8787:
8788: /* hstepm=1; aff par mois*/
8789: pstamp(ficrespijb);
8790: fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");
1.227 brouard 8791: i1= pow(2,cptcoveff);
1.218 brouard 8792: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
8793: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
8794: /* k=k+1; */
1.227 brouard 8795: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.218 brouard 8796: fprintf(ficrespijb,"\n#****** ");
1.227 brouard 8797: for(j=1;j<=cptcoveff;j++)
1.218 brouard 8798: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8799: fprintf(ficrespijb,"******\n");
1.222 brouard 8800: if(invalidvarcomb[k]){
8801: fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
8802: continue;
8803: }
1.218 brouard 8804:
8805: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
8806: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
8807: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
8808: nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
8809: nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
8810:
8811: /* nhstepm=nhstepm*YEARM; aff par mois*/
8812:
8813: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8814: /* oldm=oldms;savm=savms; */
8815: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
8816: hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
8817: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
8818: fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
8819: for(i=1; i<=nlstate;i++)
8820: for(j=1; j<=nlstate+ndeath;j++)
8821: fprintf(ficrespijb," %1d-%1d",i,j);
8822: fprintf(ficrespijb,"\n");
8823: for (h=0; h<=nhstepm; h++){
8824: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
8825: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
8826: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
1.217 brouard 8827: for(i=1; i<=nlstate;i++)
8828: for(j=1; j<=nlstate+ndeath;j++)
1.218 brouard 8829: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
1.217 brouard 8830: fprintf(ficrespijb,"\n");
8831: }
1.218 brouard 8832: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8833: fprintf(ficrespijb,"\n");
1.217 brouard 8834: }
1.218 brouard 8835: /*}*/
8836: }
8837: return 0;
8838: } /* hBijx */
1.217 brouard 8839:
1.180 brouard 8840:
1.136 brouard 8841: /***********************************************/
8842: /**************** Main Program *****************/
8843: /***********************************************/
8844:
8845: int main(int argc, char *argv[])
8846: {
8847: #ifdef GSL
8848: const gsl_multimin_fminimizer_type *T;
8849: size_t iteri = 0, it;
8850: int rval = GSL_CONTINUE;
8851: int status = GSL_SUCCESS;
8852: double ssval;
8853: #endif
8854: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 8855: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.209 brouard 8856: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 8857: int jj, ll, li, lj, lk;
1.136 brouard 8858: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 8859: int num_filled;
1.136 brouard 8860: int itimes;
8861: int NDIM=2;
8862: int vpopbased=0;
8863:
1.164 brouard 8864: char ca[32], cb[32];
1.136 brouard 8865: /* FILE *fichtm; *//* Html File */
8866: /* FILE *ficgp;*/ /*Gnuplot File */
8867: struct stat info;
1.191 brouard 8868: double agedeb=0.;
1.194 brouard 8869:
8870: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219 brouard 8871: double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136 brouard 8872:
1.165 brouard 8873: double fret;
1.191 brouard 8874: double dum=0.; /* Dummy variable */
1.136 brouard 8875: double ***p3mat;
1.218 brouard 8876: /* double ***mobaverage; */
1.164 brouard 8877:
8878: char line[MAXLINE];
1.197 brouard 8879: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
8880:
8881: char model[MAXLINE], modeltemp[MAXLINE];
1.230 ! brouard 8882: char resultline[MAXLINE];
! 8883:
1.136 brouard 8884: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 8885: char *tok, *val; /* pathtot */
1.136 brouard 8886: int firstobs=1, lastobs=10;
1.195 brouard 8887: int c, h , cpt, c2;
1.191 brouard 8888: int jl=0;
8889: int i1, j1, jk, stepsize=0;
1.194 brouard 8890: int count=0;
8891:
1.164 brouard 8892: int *tab;
1.136 brouard 8893: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.217 brouard 8894: int backcast=0;
1.136 brouard 8895: int mobilav=0,popforecast=0;
1.191 brouard 8896: int hstepm=0, nhstepm=0;
1.136 brouard 8897: int agemortsup;
8898: float sumlpop=0.;
8899: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
8900: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
8901:
1.191 brouard 8902: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 8903: double ftolpl=FTOL;
8904: double **prlim;
1.217 brouard 8905: double **bprlim;
1.136 brouard 8906: double ***param; /* Matrix of parameters */
8907: double *p;
8908: double **matcov; /* Matrix of covariance */
1.203 brouard 8909: double **hess; /* Hessian matrix */
1.136 brouard 8910: double ***delti3; /* Scale */
8911: double *delti; /* Scale */
8912: double ***eij, ***vareij;
8913: double **varpl; /* Variances of prevalence limits by age */
8914: double *epj, vepp;
1.164 brouard 8915:
1.136 brouard 8916: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.217 brouard 8917: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;
8918:
1.136 brouard 8919: double **ximort;
1.145 brouard 8920: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 8921: int *dcwave;
8922:
1.164 brouard 8923: char z[1]="c";
1.136 brouard 8924:
8925: /*char *strt;*/
8926: char strtend[80];
1.126 brouard 8927:
1.164 brouard 8928:
1.126 brouard 8929: /* setlocale (LC_ALL, ""); */
8930: /* bindtextdomain (PACKAGE, LOCALEDIR); */
8931: /* textdomain (PACKAGE); */
8932: /* setlocale (LC_CTYPE, ""); */
8933: /* setlocale (LC_MESSAGES, ""); */
8934:
8935: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 8936: rstart_time = time(NULL);
8937: /* (void) gettimeofday(&start_time,&tzp);*/
8938: start_time = *localtime(&rstart_time);
1.126 brouard 8939: curr_time=start_time;
1.157 brouard 8940: /*tml = *localtime(&start_time.tm_sec);*/
8941: /* strcpy(strstart,asctime(&tml)); */
8942: strcpy(strstart,asctime(&start_time));
1.126 brouard 8943:
8944: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 8945: /* tp.tm_sec = tp.tm_sec +86400; */
8946: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 8947: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
8948: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
8949: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 8950: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 8951: /* strt=asctime(&tmg); */
8952: /* printf("Time(after) =%s",strstart); */
8953: /* (void) time (&time_value);
8954: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
8955: * tm = *localtime(&time_value);
8956: * strstart=asctime(&tm);
8957: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
8958: */
8959:
8960: nberr=0; /* Number of errors and warnings */
8961: nbwarn=0;
1.184 brouard 8962: #ifdef WIN32
8963: _getcwd(pathcd, size);
8964: #else
1.126 brouard 8965: getcwd(pathcd, size);
1.184 brouard 8966: #endif
1.191 brouard 8967: syscompilerinfo(0);
1.196 brouard 8968: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 8969: if(argc <=1){
8970: printf("\nEnter the parameter file name: ");
1.205 brouard 8971: if(!fgets(pathr,FILENAMELENGTH,stdin)){
8972: printf("ERROR Empty parameter file name\n");
8973: goto end;
8974: }
1.126 brouard 8975: i=strlen(pathr);
8976: if(pathr[i-1]=='\n')
8977: pathr[i-1]='\0';
1.156 brouard 8978: i=strlen(pathr);
1.205 brouard 8979: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 8980: pathr[i-1]='\0';
1.205 brouard 8981: }
8982: i=strlen(pathr);
8983: if( i==0 ){
8984: printf("ERROR Empty parameter file name\n");
8985: goto end;
8986: }
8987: for (tok = pathr; tok != NULL; ){
1.126 brouard 8988: printf("Pathr |%s|\n",pathr);
8989: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
8990: printf("val= |%s| pathr=%s\n",val,pathr);
8991: strcpy (pathtot, val);
8992: if(pathr[0] == '\0') break; /* Dirty */
8993: }
8994: }
8995: else{
8996: strcpy(pathtot,argv[1]);
8997: }
8998: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
8999: /*cygwin_split_path(pathtot,path,optionfile);
9000: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
9001: /* cutv(path,optionfile,pathtot,'\\');*/
9002:
9003: /* Split argv[0], imach program to get pathimach */
9004: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
9005: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
9006: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
9007: /* strcpy(pathimach,argv[0]); */
9008: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
9009: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
9010: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 9011: #ifdef WIN32
9012: _chdir(path); /* Can be a relative path */
9013: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
9014: #else
1.126 brouard 9015: chdir(path); /* Can be a relative path */
1.184 brouard 9016: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
9017: #endif
9018: printf("Current directory %s!\n",pathcd);
1.126 brouard 9019: strcpy(command,"mkdir ");
9020: strcat(command,optionfilefiname);
9021: if((outcmd=system(command)) != 0){
1.169 brouard 9022: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 9023: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
9024: /* fclose(ficlog); */
9025: /* exit(1); */
9026: }
9027: /* if((imk=mkdir(optionfilefiname))<0){ */
9028: /* perror("mkdir"); */
9029: /* } */
9030:
9031: /*-------- arguments in the command line --------*/
9032:
1.186 brouard 9033: /* Main Log file */
1.126 brouard 9034: strcat(filelog, optionfilefiname);
9035: strcat(filelog,".log"); /* */
9036: if((ficlog=fopen(filelog,"w"))==NULL) {
9037: printf("Problem with logfile %s\n",filelog);
9038: goto end;
9039: }
9040: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 9041: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 9042: fprintf(ficlog,"\nEnter the parameter file name: \n");
9043: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
9044: path=%s \n\
9045: optionfile=%s\n\
9046: optionfilext=%s\n\
1.156 brouard 9047: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 9048:
1.197 brouard 9049: syscompilerinfo(1);
1.167 brouard 9050:
1.126 brouard 9051: printf("Local time (at start):%s",strstart);
9052: fprintf(ficlog,"Local time (at start): %s",strstart);
9053: fflush(ficlog);
9054: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 9055: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 9056:
9057: /* */
9058: strcpy(fileres,"r");
9059: strcat(fileres, optionfilefiname);
1.201 brouard 9060: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 9061: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 9062: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 9063:
1.186 brouard 9064: /* Main ---------arguments file --------*/
1.126 brouard 9065:
9066: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 9067: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
9068: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 9069: fflush(ficlog);
1.149 brouard 9070: /* goto end; */
9071: exit(70);
1.126 brouard 9072: }
9073:
9074:
9075:
9076: strcpy(filereso,"o");
1.201 brouard 9077: strcat(filereso,fileresu);
1.126 brouard 9078: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
9079: printf("Problem with Output resultfile: %s\n", filereso);
9080: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
9081: fflush(ficlog);
9082: goto end;
9083: }
9084:
9085: /* Reads comments: lines beginning with '#' */
9086: numlinepar=0;
1.197 brouard 9087:
9088: /* First parameter line */
9089: while(fgets(line, MAXLINE, ficpar)) {
9090: /* If line starts with a # it is a comment */
9091: if (line[0] == '#') {
9092: numlinepar++;
9093: fputs(line,stdout);
9094: fputs(line,ficparo);
9095: fputs(line,ficlog);
9096: continue;
9097: }else
9098: break;
9099: }
9100: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
9101: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
9102: if (num_filled != 5) {
9103: printf("Should be 5 parameters\n");
9104: }
1.126 brouard 9105: numlinepar++;
1.197 brouard 9106: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
9107: }
9108: /* Second parameter line */
9109: while(fgets(line, MAXLINE, ficpar)) {
9110: /* If line starts with a # it is a comment */
9111: if (line[0] == '#') {
9112: numlinepar++;
9113: fputs(line,stdout);
9114: fputs(line,ficparo);
9115: fputs(line,ficlog);
9116: continue;
9117: }else
9118: break;
9119: }
1.223 brouard 9120: if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
9121: &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
9122: if (num_filled != 11) {
9123: printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
1.209 brouard 9124: printf("but line=%s\n",line);
1.197 brouard 9125: }
1.223 brouard 9126: printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
1.126 brouard 9127: }
1.203 brouard 9128: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 9129: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 9130: /* Third parameter line */
9131: while(fgets(line, MAXLINE, ficpar)) {
9132: /* If line starts with a # it is a comment */
9133: if (line[0] == '#') {
9134: numlinepar++;
9135: fputs(line,stdout);
9136: fputs(line,ficparo);
9137: fputs(line,ficlog);
9138: continue;
9139: }else
9140: break;
9141: }
1.201 brouard 9142: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
9143: if (num_filled == 0)
9144: model[0]='\0';
9145: else if (num_filled != 1){
1.197 brouard 9146: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
9147: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
9148: model[0]='\0';
9149: goto end;
9150: }
9151: else{
9152: if (model[0]=='+'){
9153: for(i=1; i<=strlen(model);i++)
9154: modeltemp[i-1]=model[i];
1.201 brouard 9155: strcpy(model,modeltemp);
1.197 brouard 9156: }
9157: }
1.199 brouard 9158: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 9159: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 9160: }
9161: /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
9162: /* numlinepar=numlinepar+3; /\* In general *\/ */
9163: /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
1.223 brouard 9164: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
9165: fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
1.126 brouard 9166: fflush(ficlog);
1.190 brouard 9167: /* if(model[0]=='#'|| model[0]== '\0'){ */
9168: if(model[0]=='#'){
1.187 brouard 9169: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
9170: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
9171: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
9172: if(mle != -1){
9173: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
9174: exit(1);
9175: }
9176: }
1.126 brouard 9177: while((c=getc(ficpar))=='#' && c!= EOF){
9178: ungetc(c,ficpar);
9179: fgets(line, MAXLINE, ficpar);
9180: numlinepar++;
1.195 brouard 9181: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
9182: z[0]=line[1];
9183: }
9184: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 9185: fputs(line, stdout);
9186: //puts(line);
1.126 brouard 9187: fputs(line,ficparo);
9188: fputs(line,ficlog);
9189: }
9190: ungetc(c,ficpar);
9191:
9192:
1.145 brouard 9193: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.225 brouard 9194: coqvar=matrix(1,nqv,1,n); /**< Fixed quantitative covariate */
9195: cotvar=ma3x(1,maxwav,1,ntv,1,n); /**< Time varying covariate */
9196: cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /**< Time varying quantitative covariate */
1.136 brouard 9197: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
9198: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
9199: v1+v2*age+v2*v3 makes cptcovn = 3
9200: */
9201: if (strlen(model)>1)
1.187 brouard 9202: ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7,age*age makes 3*/
1.145 brouard 9203: else
1.187 brouard 9204: ncovmodel=2; /* Constant and age */
1.133 brouard 9205: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
9206: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 9207: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
9208: printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
9209: fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
9210: fflush(stdout);
9211: fclose (ficlog);
9212: goto end;
9213: }
1.126 brouard 9214: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
9215: delti=delti3[1][1];
9216: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
9217: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
9218: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 9219: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
9220: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 9221: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
9222: fclose (ficparo);
9223: fclose (ficlog);
9224: goto end;
9225: exit(0);
1.220 brouard 9226: } else if(mle==-5) { /* Main Wizard */
1.126 brouard 9227: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 9228: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
9229: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 9230: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
9231: matcov=matrix(1,npar,1,npar);
1.203 brouard 9232: hess=matrix(1,npar,1,npar);
1.220 brouard 9233: } else{ /* Begin of mle != -1 or -5 */
1.145 brouard 9234: /* Read guessed parameters */
1.126 brouard 9235: /* Reads comments: lines beginning with '#' */
9236: while((c=getc(ficpar))=='#' && c!= EOF){
9237: ungetc(c,ficpar);
9238: fgets(line, MAXLINE, ficpar);
9239: numlinepar++;
1.141 brouard 9240: fputs(line,stdout);
1.126 brouard 9241: fputs(line,ficparo);
9242: fputs(line,ficlog);
9243: }
9244: ungetc(c,ficpar);
9245:
9246: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
9247: for(i=1; i <=nlstate; i++){
1.220 brouard 9248: j=0;
1.126 brouard 9249: for(jj=1; jj <=nlstate+ndeath; jj++){
1.220 brouard 9250: if(jj==i) continue;
9251: j++;
9252: fscanf(ficpar,"%1d%1d",&i1,&j1);
9253: if ((i1 != i) || (j1 != jj)){
9254: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126 brouard 9255: It might be a problem of design; if ncovcol and the model are correct\n \
9256: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.220 brouard 9257: exit(1);
9258: }
9259: fprintf(ficparo,"%1d%1d",i1,j1);
9260: if(mle==1)
9261: printf("%1d%1d",i,jj);
9262: fprintf(ficlog,"%1d%1d",i,jj);
9263: for(k=1; k<=ncovmodel;k++){
9264: fscanf(ficpar," %lf",¶m[i][j][k]);
9265: if(mle==1){
9266: printf(" %lf",param[i][j][k]);
9267: fprintf(ficlog," %lf",param[i][j][k]);
9268: }
9269: else
9270: fprintf(ficlog," %lf",param[i][j][k]);
9271: fprintf(ficparo," %lf",param[i][j][k]);
9272: }
9273: fscanf(ficpar,"\n");
9274: numlinepar++;
9275: if(mle==1)
9276: printf("\n");
9277: fprintf(ficlog,"\n");
9278: fprintf(ficparo,"\n");
1.126 brouard 9279: }
9280: }
9281: fflush(ficlog);
9282:
1.145 brouard 9283: /* Reads scales values */
1.126 brouard 9284: p=param[1][1];
9285:
9286: /* Reads comments: lines beginning with '#' */
9287: while((c=getc(ficpar))=='#' && c!= EOF){
9288: ungetc(c,ficpar);
9289: fgets(line, MAXLINE, ficpar);
9290: numlinepar++;
1.141 brouard 9291: fputs(line,stdout);
1.126 brouard 9292: fputs(line,ficparo);
9293: fputs(line,ficlog);
9294: }
9295: ungetc(c,ficpar);
9296:
9297: for(i=1; i <=nlstate; i++){
9298: for(j=1; j <=nlstate+ndeath-1; j++){
1.220 brouard 9299: fscanf(ficpar,"%1d%1d",&i1,&j1);
9300: if ( (i1-i) * (j1-j) != 0){
9301: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
9302: exit(1);
9303: }
9304: printf("%1d%1d",i,j);
9305: fprintf(ficparo,"%1d%1d",i1,j1);
9306: fprintf(ficlog,"%1d%1d",i1,j1);
9307: for(k=1; k<=ncovmodel;k++){
9308: fscanf(ficpar,"%le",&delti3[i][j][k]);
9309: printf(" %le",delti3[i][j][k]);
9310: fprintf(ficparo," %le",delti3[i][j][k]);
9311: fprintf(ficlog," %le",delti3[i][j][k]);
9312: }
9313: fscanf(ficpar,"\n");
9314: numlinepar++;
9315: printf("\n");
9316: fprintf(ficparo,"\n");
9317: fprintf(ficlog,"\n");
1.126 brouard 9318: }
9319: }
9320: fflush(ficlog);
1.220 brouard 9321:
1.145 brouard 9322: /* Reads covariance matrix */
1.126 brouard 9323: delti=delti3[1][1];
1.220 brouard 9324:
9325:
1.126 brouard 9326: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
1.220 brouard 9327:
1.126 brouard 9328: /* Reads comments: lines beginning with '#' */
9329: while((c=getc(ficpar))=='#' && c!= EOF){
9330: ungetc(c,ficpar);
9331: fgets(line, MAXLINE, ficpar);
9332: numlinepar++;
1.141 brouard 9333: fputs(line,stdout);
1.126 brouard 9334: fputs(line,ficparo);
9335: fputs(line,ficlog);
9336: }
9337: ungetc(c,ficpar);
1.220 brouard 9338:
1.126 brouard 9339: matcov=matrix(1,npar,1,npar);
1.203 brouard 9340: hess=matrix(1,npar,1,npar);
1.131 brouard 9341: for(i=1; i <=npar; i++)
9342: for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220 brouard 9343:
1.194 brouard 9344: /* Scans npar lines */
1.126 brouard 9345: for(i=1; i <=npar; i++){
1.226 brouard 9346: count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
1.194 brouard 9347: if(count != 3){
1.226 brouard 9348: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 9349: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
9350: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 9351: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 9352: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
9353: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 9354: exit(1);
1.220 brouard 9355: }else{
1.226 brouard 9356: if(mle==1)
9357: printf("%1d%1d%d",i1,j1,jk);
9358: }
9359: fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
9360: fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
1.126 brouard 9361: for(j=1; j <=i; j++){
1.226 brouard 9362: fscanf(ficpar," %le",&matcov[i][j]);
9363: if(mle==1){
9364: printf(" %.5le",matcov[i][j]);
9365: }
9366: fprintf(ficlog," %.5le",matcov[i][j]);
9367: fprintf(ficparo," %.5le",matcov[i][j]);
1.126 brouard 9368: }
9369: fscanf(ficpar,"\n");
9370: numlinepar++;
9371: if(mle==1)
1.220 brouard 9372: printf("\n");
1.126 brouard 9373: fprintf(ficlog,"\n");
9374: fprintf(ficparo,"\n");
9375: }
1.194 brouard 9376: /* End of read covariance matrix npar lines */
1.126 brouard 9377: for(i=1; i <=npar; i++)
9378: for(j=i+1;j<=npar;j++)
1.226 brouard 9379: matcov[i][j]=matcov[j][i];
1.126 brouard 9380:
9381: if(mle==1)
9382: printf("\n");
9383: fprintf(ficlog,"\n");
9384:
9385: fflush(ficlog);
9386:
9387: /*-------- Rewriting parameter file ----------*/
9388: strcpy(rfileres,"r"); /* "Rparameterfile */
9389: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
9390: strcat(rfileres,"."); /* */
9391: strcat(rfileres,optionfilext); /* Other files have txt extension */
9392: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 9393: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
9394: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 9395: }
9396: fprintf(ficres,"#%s\n",version);
9397: } /* End of mle != -3 */
1.218 brouard 9398:
1.186 brouard 9399: /* Main data
9400: */
1.126 brouard 9401: n= lastobs;
9402: num=lvector(1,n);
9403: moisnais=vector(1,n);
9404: annais=vector(1,n);
9405: moisdc=vector(1,n);
9406: andc=vector(1,n);
1.220 brouard 9407: weight=vector(1,n);
1.126 brouard 9408: agedc=vector(1,n);
9409: cod=ivector(1,n);
1.220 brouard 9410: for(i=1;i<=n;i++){
9411: num[i]=0;
9412: moisnais[i]=0;
9413: annais[i]=0;
9414: moisdc[i]=0;
9415: andc[i]=0;
9416: agedc[i]=0;
9417: cod[i]=0;
9418: weight[i]=1.0; /* Equal weights, 1 by default */
9419: }
1.126 brouard 9420: mint=matrix(1,maxwav,1,n);
9421: anint=matrix(1,maxwav,1,n);
1.131 brouard 9422: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 9423: tab=ivector(1,NCOVMAX);
1.144 brouard 9424: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 9425: ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.126 brouard 9426:
1.136 brouard 9427: /* Reads data from file datafile */
9428: if (readdata(datafile, firstobs, lastobs, &imx)==1)
9429: goto end;
9430:
9431: /* Calculation of the number of parameters from char model */
1.137 brouard 9432: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
9433: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
9434: k=3 V4 Tvar[k=3]= 4 (from V4)
9435: k=2 V1 Tvar[k=2]= 1 (from V1)
9436: k=1 Tvar[1]=2 (from V2)
9437: */
9438: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
1.230 ! brouard 9439: Tvarsel=ivector(1,NCOVMAX); /* */
! 9440: Tvalsel=vector(1,NCOVMAX); /* */
1.226 brouard 9441: Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
9442: Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
9443: Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
1.137 brouard 9444: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
9445: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
9446: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
9447: */
9448: /* For model-covariate k tells which data-covariate to use but
9449: because this model-covariate is a construction we invent a new column
9450: ncovcol + k1
9451: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
9452: Tvar[3=V1*V4]=4+1 etc */
1.227 brouard 9453: Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
9454: Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
1.137 brouard 9455: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
9456: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
1.227 brouard 9457: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
1.137 brouard 9458: */
1.145 brouard 9459: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
9460: Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1] and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
1.141 brouard 9461: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
9462: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 9463: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 9464: 4 covariates (3 plus signs)
9465: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
9466: */
1.230 ! brouard 9467: Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
1.227 brouard 9468: * individual dummy, fixed or varying:
9469: * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
9470: * 3, 1, 0, 0, 0, 0, 0, 0},
1.230 ! brouard 9471: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 ,
! 9472: * V1 df, V2 qf, V3 & V4 dv, V5 qv
! 9473: * Tmodelind[1]@9={9,0,3,2,}*/
! 9474: TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
! 9475: TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
1.228 brouard 9476: * individual quantitative, fixed or varying:
9477: * Tmodelqind[1]=1,Tvaraff[1]@9={4,
9478: * 3, 1, 0, 0, 0, 0, 0, 0},
9479: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.186 brouard 9480: /* Main decodemodel */
9481:
1.187 brouard 9482:
1.223 brouard 9483: if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/
1.136 brouard 9484: goto end;
9485:
1.137 brouard 9486: if((double)(lastobs-imx)/(double)imx > 1.10){
9487: nbwarn++;
9488: printf("Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx);
9489: fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx);
9490: }
1.136 brouard 9491: /* if(mle==1){*/
1.137 brouard 9492: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
9493: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 9494: }
9495:
9496: /*-calculation of age at interview from date of interview and age at death -*/
9497: agev=matrix(1,maxwav,1,imx);
9498:
9499: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
9500: goto end;
9501:
1.126 brouard 9502:
1.136 brouard 9503: agegomp=(int)agemin;
9504: free_vector(moisnais,1,n);
9505: free_vector(annais,1,n);
1.126 brouard 9506: /* free_matrix(mint,1,maxwav,1,n);
9507: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 9508: /* free_vector(moisdc,1,n); */
9509: /* free_vector(andc,1,n); */
1.145 brouard 9510: /* */
9511:
1.126 brouard 9512: wav=ivector(1,imx);
1.214 brouard 9513: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
9514: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
9515: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
9516: dh=imatrix(1,lastpass-firstpass+2,1,imx); /* We are adding a wave if status is unknown at last wave but death occurs after last wave.*/
9517: bh=imatrix(1,lastpass-firstpass+2,1,imx);
9518: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 9519:
9520: /* Concatenates waves */
1.214 brouard 9521: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
9522: Death is a valid wave (if date is known).
9523: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
9524: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
9525: and mw[mi+1][i]. dh depends on stepm.
9526: */
9527:
1.126 brouard 9528: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 9529: /* */
9530:
1.215 brouard 9531: free_vector(moisdc,1,n);
9532: free_vector(andc,1,n);
9533:
1.126 brouard 9534: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
9535: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
9536: ncodemax[1]=1;
1.145 brouard 9537: Ndum =ivector(-1,NCOVMAX);
1.225 brouard 9538: cptcoveff=0;
1.220 brouard 9539: if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
9540: tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.227 brouard 9541: }
9542:
9543: ncovcombmax=pow(2,cptcoveff);
9544: invalidvarcomb=ivector(1, ncovcombmax);
9545: for(i=1;i<ncovcombmax;i++)
9546: invalidvarcomb[i]=0;
9547:
1.211 brouard 9548: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 9549: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 9550: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.227 brouard 9551:
1.200 brouard 9552: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 9553: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 9554: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 9555: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
9556: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
9557: * (currently 0 or 1) in the data.
9558: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
9559: * corresponding modality (h,j).
9560: */
9561:
1.145 brouard 9562: h=0;
9563: /*if (cptcovn > 0) */
1.126 brouard 9564: m=pow(2,cptcoveff);
9565:
1.144 brouard 9566: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 9567: * For k=4 covariates, h goes from 1 to m=2**k
9568: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
9569: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 9570: * h\k 1 2 3 4
1.143 brouard 9571: *______________________________
9572: * 1 i=1 1 i=1 1 i=1 1 i=1 1
9573: * 2 2 1 1 1
9574: * 3 i=2 1 2 1 1
9575: * 4 2 2 1 1
9576: * 5 i=3 1 i=2 1 2 1
9577: * 6 2 1 2 1
9578: * 7 i=4 1 2 2 1
9579: * 8 2 2 2 1
1.197 brouard 9580: * 9 i=5 1 i=3 1 i=2 1 2
9581: * 10 2 1 1 2
9582: * 11 i=6 1 2 1 2
9583: * 12 2 2 1 2
9584: * 13 i=7 1 i=4 1 2 2
9585: * 14 2 1 2 2
9586: * 15 i=8 1 2 2 2
9587: * 16 2 2 2 2
1.143 brouard 9588: */
1.212 brouard 9589: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 9590: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
9591: * and the value of each covariate?
9592: * V1=1, V2=1, V3=2, V4=1 ?
9593: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
9594: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
9595: * In order to get the real value in the data, we use nbcode
9596: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
9597: * We are keeping this crazy system in order to be able (in the future?)
9598: * to have more than 2 values (0 or 1) for a covariate.
9599: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
9600: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
9601: * bbbbbbbb
9602: * 76543210
9603: * h-1 00000101 (6-1=5)
1.219 brouard 9604: *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211 brouard 9605: * &
9606: * 1 00000001 (1)
1.219 brouard 9607: * 00000000 = 1 & ((h-1) >> (k-1))
9608: * +1= 00000001 =1
1.211 brouard 9609: *
9610: * h=14, k=3 => h'=h-1=13, k'=k-1=2
9611: * h' 1101 =2^3+2^2+0x2^1+2^0
9612: * >>k' 11
9613: * & 00000001
9614: * = 00000001
9615: * +1 = 00000010=2 = codtabm(14,3)
9616: * Reverse h=6 and m=16?
9617: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
9618: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
9619: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
9620: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
9621: * V3=decodtabm(14,3,2**4)=2
9622: * h'=13 1101 =2^3+2^2+0x2^1+2^0
9623: *(h-1) >> (j-1) 0011 =13 >> 2
9624: * &1 000000001
9625: * = 000000001
9626: * +1= 000000010 =2
9627: * 2211
9628: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
9629: * V3=2
1.220 brouard 9630: * codtabm and decodtabm are identical
1.211 brouard 9631: */
9632:
1.145 brouard 9633:
9634: free_ivector(Ndum,-1,NCOVMAX);
9635:
9636:
1.126 brouard 9637:
1.186 brouard 9638: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 9639: strcpy(optionfilegnuplot,optionfilefiname);
9640: if(mle==-3)
1.201 brouard 9641: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 9642: strcat(optionfilegnuplot,".gp");
9643:
9644: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
9645: printf("Problem with file %s",optionfilegnuplot);
9646: }
9647: else{
1.204 brouard 9648: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 9649: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 9650: //fprintf(ficgp,"set missing 'NaNq'\n");
9651: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 9652: }
9653: /* fclose(ficgp);*/
1.186 brouard 9654:
9655:
9656: /* Initialisation of --------- index.htm --------*/
1.126 brouard 9657:
9658: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
9659: if(mle==-3)
1.201 brouard 9660: strcat(optionfilehtm,"-MORT_");
1.126 brouard 9661: strcat(optionfilehtm,".htm");
9662: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 9663: printf("Problem with %s \n",optionfilehtm);
9664: exit(0);
1.126 brouard 9665: }
9666:
9667: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
9668: strcat(optionfilehtmcov,"-cov.htm");
9669: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
9670: printf("Problem with %s \n",optionfilehtmcov), exit(0);
9671: }
9672: else{
9673: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
9674: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 9675: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 9676: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
9677: }
9678:
1.213 brouard 9679: fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C) 2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br> \
1.204 brouard 9680: <hr size=\"2\" color=\"#EC5E5E\"> \n\
9681: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 9682: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 9683: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 9684: \n\
9685: <hr size=\"2\" color=\"#EC5E5E\">\
9686: <ul><li><h4>Parameter files</h4>\n\
9687: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
9688: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
9689: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
9690: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
9691: - Date and time at start: %s</ul>\n",\
9692: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
9693: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
9694: fileres,fileres,\
9695: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
9696: fflush(fichtm);
9697:
9698: strcpy(pathr,path);
9699: strcat(pathr,optionfilefiname);
1.184 brouard 9700: #ifdef WIN32
9701: _chdir(optionfilefiname); /* Move to directory named optionfile */
9702: #else
1.126 brouard 9703: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 9704: #endif
9705:
1.126 brouard 9706:
1.220 brouard 9707: /* Calculates basic frequencies. Computes observed prevalence at single age
9708: and for any valid combination of covariates
1.126 brouard 9709: and prints on file fileres'p'. */
1.227 brouard 9710: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
9711: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 9712:
9713: fprintf(fichtm,"\n");
9714: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
9715: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
9716: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
9717: imx,agemin,agemax,jmin,jmax,jmean);
9718: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.220 brouard 9719: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9720: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9721: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9722: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218 brouard 9723:
1.126 brouard 9724: /* For Powell, parameters are in a vector p[] starting at p[1]
9725: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
9726: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
9727:
9728: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 9729: /* For mortality only */
1.126 brouard 9730: if (mle==-3){
1.136 brouard 9731: ximort=matrix(1,NDIM,1,NDIM);
1.220 brouard 9732: for(i=1;i<=NDIM;i++)
9733: for(j=1;j<=NDIM;j++)
9734: ximort[i][j]=0.;
1.186 brouard 9735: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 9736: cens=ivector(1,n);
9737: ageexmed=vector(1,n);
9738: agecens=vector(1,n);
9739: dcwave=ivector(1,n);
1.223 brouard 9740:
1.126 brouard 9741: for (i=1; i<=imx; i++){
9742: dcwave[i]=-1;
9743: for (m=firstpass; m<=lastpass; m++)
1.226 brouard 9744: if (s[m][i]>nlstate) {
9745: dcwave[i]=m;
9746: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
9747: break;
9748: }
1.126 brouard 9749: }
1.226 brouard 9750:
1.126 brouard 9751: for (i=1; i<=imx; i++) {
9752: if (wav[i]>0){
1.226 brouard 9753: ageexmed[i]=agev[mw[1][i]][i];
9754: j=wav[i];
9755: agecens[i]=1.;
9756:
9757: if (ageexmed[i]> 1 && wav[i] > 0){
9758: agecens[i]=agev[mw[j][i]][i];
9759: cens[i]= 1;
9760: }else if (ageexmed[i]< 1)
9761: cens[i]= -1;
9762: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
9763: cens[i]=0 ;
1.126 brouard 9764: }
9765: else cens[i]=-1;
9766: }
9767:
9768: for (i=1;i<=NDIM;i++) {
9769: for (j=1;j<=NDIM;j++)
1.226 brouard 9770: ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126 brouard 9771: }
9772:
1.145 brouard 9773: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 9774: /*printf("%lf %lf", p[1], p[2]);*/
9775:
9776:
1.136 brouard 9777: #ifdef GSL
9778: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 9779: #else
1.126 brouard 9780: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 9781: #endif
1.201 brouard 9782: strcpy(filerespow,"POW-MORT_");
9783: strcat(filerespow,fileresu);
1.126 brouard 9784: if((ficrespow=fopen(filerespow,"w"))==NULL) {
9785: printf("Problem with resultfile: %s\n", filerespow);
9786: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
9787: }
1.136 brouard 9788: #ifdef GSL
9789: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 9790: #else
1.126 brouard 9791: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 9792: #endif
1.126 brouard 9793: /* for (i=1;i<=nlstate;i++)
9794: for(j=1;j<=nlstate+ndeath;j++)
9795: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
9796: */
9797: fprintf(ficrespow,"\n");
1.136 brouard 9798: #ifdef GSL
9799: /* gsl starts here */
9800: T = gsl_multimin_fminimizer_nmsimplex;
9801: gsl_multimin_fminimizer *sfm = NULL;
9802: gsl_vector *ss, *x;
9803: gsl_multimin_function minex_func;
9804:
9805: /* Initial vertex size vector */
9806: ss = gsl_vector_alloc (NDIM);
9807:
9808: if (ss == NULL){
9809: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
9810: }
9811: /* Set all step sizes to 1 */
9812: gsl_vector_set_all (ss, 0.001);
9813:
9814: /* Starting point */
1.126 brouard 9815:
1.136 brouard 9816: x = gsl_vector_alloc (NDIM);
9817:
9818: if (x == NULL){
9819: gsl_vector_free(ss);
9820: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
9821: }
9822:
9823: /* Initialize method and iterate */
9824: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 9825: /* gsl_vector_set(x, 0, 0.0268); */
9826: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 9827: gsl_vector_set(x, 0, p[1]);
9828: gsl_vector_set(x, 1, p[2]);
9829:
9830: minex_func.f = &gompertz_f;
9831: minex_func.n = NDIM;
9832: minex_func.params = (void *)&p; /* ??? */
9833:
9834: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
9835: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
9836:
9837: printf("Iterations beginning .....\n\n");
9838: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
9839:
9840: iteri=0;
9841: while (rval == GSL_CONTINUE){
9842: iteri++;
9843: status = gsl_multimin_fminimizer_iterate(sfm);
9844:
9845: if (status) printf("error: %s\n", gsl_strerror (status));
9846: fflush(0);
9847:
9848: if (status)
9849: break;
9850:
9851: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
9852: ssval = gsl_multimin_fminimizer_size (sfm);
9853:
9854: if (rval == GSL_SUCCESS)
9855: printf ("converged to a local maximum at\n");
9856:
9857: printf("%5d ", iteri);
9858: for (it = 0; it < NDIM; it++){
9859: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
9860: }
9861: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
9862: }
9863:
9864: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
9865:
9866: gsl_vector_free(x); /* initial values */
9867: gsl_vector_free(ss); /* inital step size */
9868: for (it=0; it<NDIM; it++){
9869: p[it+1]=gsl_vector_get(sfm->x,it);
9870: fprintf(ficrespow," %.12lf", p[it]);
9871: }
9872: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
9873: #endif
9874: #ifdef POWELL
9875: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
9876: #endif
1.126 brouard 9877: fclose(ficrespow);
9878:
1.203 brouard 9879: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 9880:
9881: for(i=1; i <=NDIM; i++)
9882: for(j=i+1;j<=NDIM;j++)
1.220 brouard 9883: matcov[i][j]=matcov[j][i];
1.126 brouard 9884:
9885: printf("\nCovariance matrix\n ");
1.203 brouard 9886: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 9887: for(i=1; i <=NDIM; i++) {
9888: for(j=1;j<=NDIM;j++){
1.220 brouard 9889: printf("%f ",matcov[i][j]);
9890: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 9891: }
1.203 brouard 9892: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 9893: }
9894:
9895: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 9896: for (i=1;i<=NDIM;i++) {
1.126 brouard 9897: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 9898: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
9899: }
1.126 brouard 9900: lsurv=vector(1,AGESUP);
9901: lpop=vector(1,AGESUP);
9902: tpop=vector(1,AGESUP);
9903: lsurv[agegomp]=100000;
9904:
9905: for (k=agegomp;k<=AGESUP;k++) {
9906: agemortsup=k;
9907: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
9908: }
9909:
9910: for (k=agegomp;k<agemortsup;k++)
9911: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
9912:
9913: for (k=agegomp;k<agemortsup;k++){
9914: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
9915: sumlpop=sumlpop+lpop[k];
9916: }
9917:
9918: tpop[agegomp]=sumlpop;
9919: for (k=agegomp;k<(agemortsup-3);k++){
9920: /* tpop[k+1]=2;*/
9921: tpop[k+1]=tpop[k]-lpop[k];
9922: }
9923:
9924:
9925: printf("\nAge lx qx dx Lx Tx e(x)\n");
9926: for (k=agegomp;k<(agemortsup-2);k++)
9927: printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
9928:
9929:
9930: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220 brouard 9931: ageminpar=50;
9932: agemaxpar=100;
1.194 brouard 9933: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
9934: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
9935: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9936: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
9937: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
9938: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9939: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 9940: }else{
9941: printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
9942: fprintf(ficlog,"Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
1.201 brouard 9943: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220 brouard 9944: }
1.201 brouard 9945: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 9946: stepm, weightopt,\
9947: model,imx,p,matcov,agemortsup);
9948:
9949: free_vector(lsurv,1,AGESUP);
9950: free_vector(lpop,1,AGESUP);
9951: free_vector(tpop,1,AGESUP);
1.220 brouard 9952: free_matrix(ximort,1,NDIM,1,NDIM);
1.136 brouard 9953: free_ivector(cens,1,n);
9954: free_vector(agecens,1,n);
9955: free_ivector(dcwave,1,n);
1.220 brouard 9956: #ifdef GSL
1.136 brouard 9957: #endif
1.186 brouard 9958: } /* Endof if mle==-3 mortality only */
1.205 brouard 9959: /* Standard */
9960: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
9961: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
9962: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 9963: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 9964: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
9965: for (k=1; k<=npar;k++)
9966: printf(" %d %8.5f",k,p[k]);
9967: printf("\n");
1.205 brouard 9968: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
9969: /* mlikeli uses func not funcone */
9970: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
9971: }
9972: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
9973: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
9974: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
9975: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
9976: }
9977: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 9978: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
9979: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
9980: for (k=1; k<=npar;k++)
9981: printf(" %d %8.5f",k,p[k]);
9982: printf("\n");
9983:
9984: /*--------- results files --------------*/
1.224 brouard 9985: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model);
1.126 brouard 9986:
9987:
9988: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9989: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9990: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9991: for(i=1,jk=1; i <=nlstate; i++){
9992: for(k=1; k <=(nlstate+ndeath); k++){
1.225 brouard 9993: if (k != i) {
9994: printf("%d%d ",i,k);
9995: fprintf(ficlog,"%d%d ",i,k);
9996: fprintf(ficres,"%1d%1d ",i,k);
9997: for(j=1; j <=ncovmodel; j++){
9998: printf("%12.7f ",p[jk]);
9999: fprintf(ficlog,"%12.7f ",p[jk]);
10000: fprintf(ficres,"%12.7f ",p[jk]);
10001: jk++;
10002: }
10003: printf("\n");
10004: fprintf(ficlog,"\n");
10005: fprintf(ficres,"\n");
10006: }
1.126 brouard 10007: }
10008: }
1.203 brouard 10009: if(mle != 0){
10010: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 10011: ftolhess=ftol; /* Usually correct */
1.203 brouard 10012: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
10013: printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
10014: fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
10015: for(i=1,jk=1; i <=nlstate; i++){
1.225 brouard 10016: for(k=1; k <=(nlstate+ndeath); k++){
10017: if (k != i) {
10018: printf("%d%d ",i,k);
10019: fprintf(ficlog,"%d%d ",i,k);
10020: for(j=1; j <=ncovmodel; j++){
10021: printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
10022: fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
10023: jk++;
10024: }
10025: printf("\n");
10026: fprintf(ficlog,"\n");
10027: }
10028: }
1.193 brouard 10029: }
1.203 brouard 10030: } /* end of hesscov and Wald tests */
1.225 brouard 10031:
1.203 brouard 10032: /* */
1.126 brouard 10033: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
10034: printf("# Scales (for hessian or gradient estimation)\n");
10035: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
10036: for(i=1,jk=1; i <=nlstate; i++){
10037: for(j=1; j <=nlstate+ndeath; j++){
1.225 brouard 10038: if (j!=i) {
10039: fprintf(ficres,"%1d%1d",i,j);
10040: printf("%1d%1d",i,j);
10041: fprintf(ficlog,"%1d%1d",i,j);
10042: for(k=1; k<=ncovmodel;k++){
10043: printf(" %.5e",delti[jk]);
10044: fprintf(ficlog," %.5e",delti[jk]);
10045: fprintf(ficres," %.5e",delti[jk]);
10046: jk++;
10047: }
10048: printf("\n");
10049: fprintf(ficlog,"\n");
10050: fprintf(ficres,"\n");
10051: }
1.126 brouard 10052: }
10053: }
10054:
10055: fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
1.203 brouard 10056: if(mle >= 1) /* To big for the screen */
1.126 brouard 10057: printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
10058: fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
10059: /* # 121 Var(a12)\n\ */
10060: /* # 122 Cov(b12,a12) Var(b12)\n\ */
10061: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
10062: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
10063: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
10064: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
10065: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
10066: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
10067:
10068:
10069: /* Just to have a covariance matrix which will be more understandable
10070: even is we still don't want to manage dictionary of variables
10071: */
10072: for(itimes=1;itimes<=2;itimes++){
10073: jj=0;
10074: for(i=1; i <=nlstate; i++){
1.225 brouard 10075: for(j=1; j <=nlstate+ndeath; j++){
10076: if(j==i) continue;
10077: for(k=1; k<=ncovmodel;k++){
10078: jj++;
10079: ca[0]= k+'a'-1;ca[1]='\0';
10080: if(itimes==1){
10081: if(mle>=1)
10082: printf("#%1d%1d%d",i,j,k);
10083: fprintf(ficlog,"#%1d%1d%d",i,j,k);
10084: fprintf(ficres,"#%1d%1d%d",i,j,k);
10085: }else{
10086: if(mle>=1)
10087: printf("%1d%1d%d",i,j,k);
10088: fprintf(ficlog,"%1d%1d%d",i,j,k);
10089: fprintf(ficres,"%1d%1d%d",i,j,k);
10090: }
10091: ll=0;
10092: for(li=1;li <=nlstate; li++){
10093: for(lj=1;lj <=nlstate+ndeath; lj++){
10094: if(lj==li) continue;
10095: for(lk=1;lk<=ncovmodel;lk++){
10096: ll++;
10097: if(ll<=jj){
10098: cb[0]= lk +'a'-1;cb[1]='\0';
10099: if(ll<jj){
10100: if(itimes==1){
10101: if(mle>=1)
10102: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
10103: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
10104: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
10105: }else{
10106: if(mle>=1)
10107: printf(" %.5e",matcov[jj][ll]);
10108: fprintf(ficlog," %.5e",matcov[jj][ll]);
10109: fprintf(ficres," %.5e",matcov[jj][ll]);
10110: }
10111: }else{
10112: if(itimes==1){
10113: if(mle>=1)
10114: printf(" Var(%s%1d%1d)",ca,i,j);
10115: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
10116: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
10117: }else{
10118: if(mle>=1)
10119: printf(" %.7e",matcov[jj][ll]);
10120: fprintf(ficlog," %.7e",matcov[jj][ll]);
10121: fprintf(ficres," %.7e",matcov[jj][ll]);
10122: }
10123: }
10124: }
10125: } /* end lk */
10126: } /* end lj */
10127: } /* end li */
10128: if(mle>=1)
10129: printf("\n");
10130: fprintf(ficlog,"\n");
10131: fprintf(ficres,"\n");
10132: numlinepar++;
10133: } /* end k*/
10134: } /*end j */
1.126 brouard 10135: } /* end i */
10136: } /* end itimes */
10137:
10138: fflush(ficlog);
10139: fflush(ficres);
1.225 brouard 10140: while(fgets(line, MAXLINE, ficpar)) {
10141: /* If line starts with a # it is a comment */
10142: if (line[0] == '#') {
10143: numlinepar++;
10144: fputs(line,stdout);
10145: fputs(line,ficparo);
10146: fputs(line,ficlog);
10147: continue;
10148: }else
10149: break;
10150: }
10151:
1.209 brouard 10152: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
10153: /* ungetc(c,ficpar); */
10154: /* fgets(line, MAXLINE, ficpar); */
10155: /* fputs(line,stdout); */
10156: /* fputs(line,ficparo); */
10157: /* } */
10158: /* ungetc(c,ficpar); */
1.126 brouard 10159:
10160: estepm=0;
1.209 brouard 10161: if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){
1.225 brouard 10162:
10163: if (num_filled != 6) {
10164: printf("Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
10165: fprintf(ficlog,"Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
10166: goto end;
10167: }
10168: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
10169: }
10170: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
10171: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
10172:
1.209 brouard 10173: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 10174: if (estepm==0 || estepm < stepm) estepm=stepm;
10175: if (fage <= 2) {
10176: bage = ageminpar;
10177: fage = agemaxpar;
10178: }
10179:
10180: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 10181: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
10182: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220 brouard 10183:
1.186 brouard 10184: /* Other stuffs, more or less useful */
1.126 brouard 10185: while((c=getc(ficpar))=='#' && c!= EOF){
10186: ungetc(c,ficpar);
10187: fgets(line, MAXLINE, ficpar);
1.141 brouard 10188: fputs(line,stdout);
1.126 brouard 10189: fputs(line,ficparo);
10190: }
10191: ungetc(c,ficpar);
10192:
10193: fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
10194: fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
10195: fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
10196: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
10197: fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
10198:
10199: while((c=getc(ficpar))=='#' && c!= EOF){
10200: ungetc(c,ficpar);
10201: fgets(line, MAXLINE, ficpar);
1.141 brouard 10202: fputs(line,stdout);
1.126 brouard 10203: fputs(line,ficparo);
10204: }
10205: ungetc(c,ficpar);
10206:
10207:
10208: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
10209: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
10210:
10211: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 10212: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 10213: fprintf(ficparo,"pop_based=%d\n",popbased);
10214: fprintf(ficres,"pop_based=%d\n",popbased);
10215:
10216: while((c=getc(ficpar))=='#' && c!= EOF){
10217: ungetc(c,ficpar);
10218: fgets(line, MAXLINE, ficpar);
1.141 brouard 10219: fputs(line,stdout);
1.126 brouard 10220: fputs(line,ficparo);
10221: }
10222: ungetc(c,ficpar);
10223:
10224: fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
10225: fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
10226: printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
10227: fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
10228: fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
10229: /* day and month of proj2 are not used but only year anproj2.*/
10230:
1.217 brouard 10231: while((c=getc(ficpar))=='#' && c!= EOF){
10232: ungetc(c,ficpar);
10233: fgets(line, MAXLINE, ficpar);
10234: fputs(line,stdout);
10235: fputs(line,ficparo);
10236: }
10237: ungetc(c,ficpar);
10238:
10239: fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);
1.223 brouard 10240: fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
10241: fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
10242: fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
1.217 brouard 10243: /* day and month of proj2 are not used but only year anproj2.*/
1.126 brouard 10244:
1.230 ! brouard 10245: /* Results */
! 10246: while(fgets(line, MAXLINE, ficpar)) {
! 10247: /* If line starts with a # it is a comment */
! 10248: if (line[0] == '#') {
! 10249: numlinepar++;
! 10250: fputs(line,stdout);
! 10251: fputs(line,ficparo);
! 10252: fputs(line,ficlog);
! 10253: continue;
! 10254: }else
! 10255: break;
! 10256: }
! 10257: while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
! 10258: if (num_filled == 0)
! 10259: resultline[0]='\0';
! 10260: else if (num_filled != 1){
! 10261: printf("ERROR %d: result line should be at minimum 'result=' %s\n",num_filled, line);
! 10262: }
! 10263: printf("Result %d: result line should be at minimum 'line=' %s, result=%s\n",num_filled, line, resultline);
! 10264: decoderesult(resultline);
! 10265: while(fgets(line, MAXLINE, ficpar)) {
! 10266: /* If line starts with a # it is a comment */
! 10267: if (line[0] == '#') {
! 10268: numlinepar++;
! 10269: fputs(line,stdout);
! 10270: fputs(line,ficparo);
! 10271: fputs(line,ficlog);
! 10272: continue;
! 10273: }else
! 10274: break;
! 10275: }
! 10276: if (feof(ficpar))
! 10277: break;
! 10278: else{ /* Processess output results for this combination of covariate values */
! 10279: }
! 10280: }
! 10281:
! 10282:
1.126 brouard 10283:
1.230 ! brouard 10284: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145 brouard 10285: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 10286:
10287: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 10288: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.230 ! brouard 10289: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 10290: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
10291: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.230 ! brouard 10292: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 10293: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
10294: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 10295: }else{
1.218 brouard 10296: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
1.220 brouard 10297: }
10298: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
1.225 brouard 10299: model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
10300: jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
1.220 brouard 10301:
1.225 brouard 10302: /*------------ free_vector -------------*/
10303: /* chdir(path); */
1.220 brouard 10304:
1.215 brouard 10305: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
10306: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
10307: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
10308: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.126 brouard 10309: free_lvector(num,1,n);
10310: free_vector(agedc,1,n);
10311: /*free_matrix(covar,0,NCOVMAX,1,n);*/
10312: /*free_matrix(covar,1,NCOVMAX,1,n);*/
10313: fclose(ficparo);
10314: fclose(ficres);
1.220 brouard 10315:
10316:
1.186 brouard 10317: /* Other results (useful)*/
1.220 brouard 10318:
10319:
1.126 brouard 10320: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 10321: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
10322: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 10323: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 10324: fclose(ficrespl);
10325:
10326: /*------------- h Pij x at various ages ------------*/
1.180 brouard 10327: /*#include "hpijx.h"*/
10328: hPijx(p, bage, fage);
1.145 brouard 10329: fclose(ficrespij);
1.227 brouard 10330:
1.220 brouard 10331: /* ncovcombmax= pow(2,cptcoveff); */
1.219 brouard 10332: /*-------------- Variance of one-step probabilities---*/
1.145 brouard 10333: k=1;
1.126 brouard 10334: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.227 brouard 10335:
1.219 brouard 10336: /* Prevalence for each covariates in probs[age][status][cov] */
1.218 brouard 10337: probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.126 brouard 10338: for(i=1;i<=AGESUP;i++)
1.219 brouard 10339: for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.225 brouard 10340: for(k=1;k<=ncovcombmax;k++)
10341: probs[i][j][k]=0.;
1.219 brouard 10342: prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
10343: if (mobilav!=0 ||mobilavproj !=0 ) {
10344: mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.227 brouard 10345: for(i=1;i<=AGESUP;i++)
10346: for(j=1;j<=nlstate;j++)
10347: for(k=1;k<=ncovcombmax;k++)
10348: mobaverages[i][j][k]=0.;
1.219 brouard 10349: mobaverage=mobaverages;
10350: if (mobilav!=0) {
1.227 brouard 10351: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
10352: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
10353: printf(" Error in movingaverage mobilav=%d\n",mobilav);
10354: }
1.219 brouard 10355: }
10356: /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
10357: /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
10358: else if (mobilavproj !=0) {
1.227 brouard 10359: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
10360: fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
10361: printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
10362: }
1.219 brouard 10363: }
10364: }/* end if moving average */
1.227 brouard 10365:
1.126 brouard 10366: /*---------- Forecasting ------------------*/
10367: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
10368: if(prevfcast==1){
10369: /* if(stepm ==1){*/
1.225 brouard 10370: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 10371: }
1.217 brouard 10372: if(backcast==1){
1.219 brouard 10373: ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
10374: ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
10375: ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
10376:
10377: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
10378:
10379: bprlim=matrix(1,nlstate,1,nlstate);
10380: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
10381: fclose(ficresplb);
10382:
1.222 brouard 10383: hBijx(p, bage, fage, mobaverage);
10384: fclose(ficrespijb);
1.219 brouard 10385: free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
10386:
10387: /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
1.225 brouard 10388: bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
1.219 brouard 10389: free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
10390: free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
10391: free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
10392: }
1.217 brouard 10393:
1.186 brouard 10394:
10395: /* ------ Other prevalence ratios------------ */
1.126 brouard 10396:
1.215 brouard 10397: free_ivector(wav,1,imx);
10398: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
10399: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
10400: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.218 brouard 10401:
10402:
1.127 brouard 10403: /*---------- Health expectancies, no variances ------------*/
1.218 brouard 10404:
1.201 brouard 10405: strcpy(filerese,"E_");
10406: strcat(filerese,fileresu);
1.126 brouard 10407: if((ficreseij=fopen(filerese,"w"))==NULL) {
10408: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
10409: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
10410: }
1.208 brouard 10411: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
10412: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.219 brouard 10413:
1.227 brouard 10414: for (k=1; k <= (int) pow(2,cptcoveff); k++){ /* For any combination of dummy covariates, fixed and varying */
1.219 brouard 10415: fprintf(ficreseij,"\n#****** ");
1.225 brouard 10416: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 10417: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.219 brouard 10418: }
10419: fprintf(ficreseij,"******\n");
10420:
10421: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
10422: oldm=oldms;savm=savms;
10423: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
1.127 brouard 10424:
1.219 brouard 10425: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127 brouard 10426: }
10427: fclose(ficreseij);
1.208 brouard 10428: printf("done evsij\n");fflush(stdout);
10429: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.218 brouard 10430:
1.227 brouard 10431: /*---------- State-specific expectancies and variances ------------*/
1.218 brouard 10432:
10433:
1.201 brouard 10434: strcpy(filerest,"T_");
10435: strcat(filerest,fileresu);
1.127 brouard 10436: if((ficrest=fopen(filerest,"w"))==NULL) {
10437: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
10438: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
10439: }
1.208 brouard 10440: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
10441: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.218 brouard 10442:
1.126 brouard 10443:
1.201 brouard 10444: strcpy(fileresstde,"STDE_");
10445: strcat(fileresstde,fileresu);
1.126 brouard 10446: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
1.227 brouard 10447: printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
10448: fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
1.126 brouard 10449: }
1.227 brouard 10450: printf(" Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
10451: fprintf(ficlog," Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 10452:
1.201 brouard 10453: strcpy(filerescve,"CVE_");
10454: strcat(filerescve,fileresu);
1.126 brouard 10455: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
1.227 brouard 10456: printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
10457: fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
1.126 brouard 10458: }
1.227 brouard 10459: printf(" Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
10460: fprintf(ficlog," Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 10461:
1.201 brouard 10462: strcpy(fileresv,"V_");
10463: strcat(fileresv,fileresu);
1.126 brouard 10464: if((ficresvij=fopen(fileresv,"w"))==NULL) {
10465: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
10466: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
10467: }
1.227 brouard 10468: printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
10469: fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 10470:
1.145 brouard 10471: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
10472: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
10473:
1.225 brouard 10474: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.227 brouard 10475: printf("\n#****** ");
1.208 brouard 10476: fprintf(ficrest,"\n#****** ");
1.227 brouard 10477: fprintf(ficlog,"\n#****** ");
10478: for(j=1;j<=cptcoveff;j++){
10479: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10480: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10481: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10482: }
1.208 brouard 10483: fprintf(ficrest,"******\n");
1.227 brouard 10484: fprintf(ficlog,"******\n");
10485: printf("******\n");
1.208 brouard 10486:
10487: fprintf(ficresstdeij,"\n#****** ");
10488: fprintf(ficrescveij,"\n#****** ");
1.225 brouard 10489: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 10490: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10491: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 10492: }
10493: fprintf(ficresstdeij,"******\n");
10494: fprintf(ficrescveij,"******\n");
10495:
10496: fprintf(ficresvij,"\n#****** ");
1.225 brouard 10497: for(j=1;j<=cptcoveff;j++)
1.227 brouard 10498: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 10499: fprintf(ficresvij,"******\n");
10500:
10501: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
10502: oldm=oldms;savm=savms;
1.227 brouard 10503: printf(" cvevsij combination#=%d, ",k);
10504: fprintf(ficlog, " cvevsij combination#=%d, ",k);
1.208 brouard 10505: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
10506: printf(" end cvevsij \n ");
10507: fprintf(ficlog, " end cvevsij \n ");
10508:
10509: /*
10510: */
10511: /* goto endfree; */
10512:
10513: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
10514: pstamp(ficrest);
10515:
10516:
10517: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.227 brouard 10518: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
10519: cptcod= 0; /* To be deleted */
10520: printf("varevsij vpopbased=%d \n",vpopbased);
10521: fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
10522: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
10523: fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");
10524: if(vpopbased==1)
10525: fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
10526: else
10527: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
10528: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
10529: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
10530: fprintf(ficrest,"\n");
10531: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
10532: epj=vector(1,nlstate+1);
10533: printf("Computing age specific period (stable) prevalences in each health state \n");
10534: fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
10535: for(age=bage; age <=fage ;age++){
10536: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
10537: if (vpopbased==1) {
10538: if(mobilav ==0){
10539: for(i=1; i<=nlstate;i++)
10540: prlim[i][i]=probs[(int)age][i][k];
10541: }else{ /* mobilav */
10542: for(i=1; i<=nlstate;i++)
10543: prlim[i][i]=mobaverage[(int)age][i][k];
10544: }
10545: }
1.219 brouard 10546:
1.227 brouard 10547: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
10548: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
10549: /* printf(" age %4.0f ",age); */
10550: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
10551: for(i=1, epj[j]=0.;i <=nlstate;i++) {
10552: epj[j] += prlim[i][i]*eij[i][j][(int)age];
10553: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
10554: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
10555: }
10556: epj[nlstate+1] +=epj[j];
10557: }
10558: /* printf(" age %4.0f \n",age); */
1.219 brouard 10559:
1.227 brouard 10560: for(i=1, vepp=0.;i <=nlstate;i++)
10561: for(j=1;j <=nlstate;j++)
10562: vepp += vareij[i][j][(int)age];
10563: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
10564: for(j=1;j <=nlstate;j++){
10565: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
10566: }
10567: fprintf(ficrest,"\n");
10568: }
1.208 brouard 10569: } /* End vpopbased */
10570: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
10571: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
10572: free_vector(epj,1,nlstate+1);
10573: printf("done \n");fflush(stdout);
10574: fprintf(ficlog,"done\n");fflush(ficlog);
10575:
1.145 brouard 10576: /*}*/
1.208 brouard 10577: } /* End k */
1.227 brouard 10578:
10579: printf("done State-specific expectancies\n");fflush(stdout);
10580: fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
10581:
1.126 brouard 10582: /*------- Variance of period (stable) prevalence------*/
1.227 brouard 10583:
1.201 brouard 10584: strcpy(fileresvpl,"VPL_");
10585: strcat(fileresvpl,fileresu);
1.126 brouard 10586: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
10587: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
10588: exit(0);
10589: }
1.208 brouard 10590: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
10591: fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.227 brouard 10592:
1.145 brouard 10593: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
10594: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
1.227 brouard 10595:
1.225 brouard 10596: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.227 brouard 10597: fprintf(ficresvpl,"\n#****** ");
10598: printf("\n#****** ");
10599: fprintf(ficlog,"\n#****** ");
10600: for(j=1;j<=cptcoveff;j++) {
10601: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10602: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10603: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10604: }
10605: fprintf(ficresvpl,"******\n");
10606: printf("******\n");
10607: fprintf(ficlog,"******\n");
10608:
10609: varpl=matrix(1,nlstate,(int) bage, (int) fage);
10610: oldm=oldms;savm=savms;
10611: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
10612: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 10613: /*}*/
1.126 brouard 10614: }
1.227 brouard 10615:
1.126 brouard 10616: fclose(ficresvpl);
1.208 brouard 10617: printf("done variance-covariance of period prevalence\n");fflush(stdout);
10618: fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
1.227 brouard 10619:
10620: free_vector(weight,1,n);
10621: free_imatrix(Tvard,1,NCOVMAX,1,2);
10622: free_imatrix(s,1,maxwav+1,1,n);
10623: free_matrix(anint,1,maxwav,1,n);
10624: free_matrix(mint,1,maxwav,1,n);
10625: free_ivector(cod,1,n);
10626: free_ivector(tab,1,NCOVMAX);
10627: fclose(ficresstdeij);
10628: fclose(ficrescveij);
10629: fclose(ficresvij);
10630: fclose(ficrest);
10631: fclose(ficpar);
10632:
10633:
1.126 brouard 10634: /*---------- End : free ----------------*/
1.219 brouard 10635: if (mobilav!=0 ||mobilavproj !=0)
10636: free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
1.218 brouard 10637: free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220 brouard 10638: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
10639: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126 brouard 10640: } /* mle==-3 arrives here for freeing */
1.227 brouard 10641: /* endfree:*/
10642: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
10643: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
10644: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
10645: free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
10646: free_ma3x(cotvar,1,maxwav,1,ntv,1,n);
10647: free_matrix(coqvar,1,maxwav,1,n);
10648: free_matrix(covar,0,NCOVMAX,1,n);
10649: free_matrix(matcov,1,npar,1,npar);
10650: free_matrix(hess,1,npar,1,npar);
10651: /*free_vector(delti,1,npar);*/
10652: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
10653: free_matrix(agev,1,maxwav,1,imx);
10654: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
10655:
10656: free_ivector(ncodemax,1,NCOVMAX);
10657: free_ivector(ncodemaxwundef,1,NCOVMAX);
10658: free_ivector(Dummy,-1,NCOVMAX);
10659: free_ivector(Fixed,-1,NCOVMAX);
10660: free_ivector(Typevar,-1,NCOVMAX);
10661: free_ivector(Tvar,1,NCOVMAX);
1.230 ! brouard 10662: free_ivector(Tvarsel,1,NCOVMAX);
! 10663: free_vector(Tvalsel,1,NCOVMAX);
1.227 brouard 10664: free_ivector(Tposprod,1,NCOVMAX);
10665: free_ivector(Tprod,1,NCOVMAX);
10666: free_ivector(Tvaraff,1,NCOVMAX);
10667: free_ivector(invalidvarcomb,1,ncovcombmax);
10668: free_ivector(Tage,1,NCOVMAX);
10669: free_ivector(Tmodelind,1,NCOVMAX);
1.228 brouard 10670: free_ivector(TmodelInvind,1,NCOVMAX);
10671: free_ivector(TmodelInvQind,1,NCOVMAX);
1.227 brouard 10672:
10673: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
10674: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 10675: fflush(fichtm);
10676: fflush(ficgp);
10677:
1.227 brouard 10678:
1.126 brouard 10679: if((nberr >0) || (nbwarn>0)){
1.216 brouard 10680: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
10681: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d. Please look at the log file for details.\n",nberr,nbwarn);
1.126 brouard 10682: }else{
10683: printf("End of Imach\n");
10684: fprintf(ficlog,"End of Imach\n");
10685: }
10686: printf("See log file on %s\n",filelog);
10687: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 10688: /*(void) gettimeofday(&end_time,&tzp);*/
10689: rend_time = time(NULL);
10690: end_time = *localtime(&rend_time);
10691: /* tml = *localtime(&end_time.tm_sec); */
10692: strcpy(strtend,asctime(&end_time));
1.126 brouard 10693: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
10694: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 10695: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.227 brouard 10696:
1.157 brouard 10697: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
10698: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
10699: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 10700: /* printf("Total time was %d uSec.\n", total_usecs);*/
10701: /* if(fileappend(fichtm,optionfilehtm)){ */
10702: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
10703: fclose(fichtm);
10704: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
10705: fclose(fichtmcov);
10706: fclose(ficgp);
10707: fclose(ficlog);
10708: /*------ End -----------*/
1.227 brouard 10709:
10710:
10711: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 10712: #ifdef WIN32
1.227 brouard 10713: if (_chdir(pathcd) != 0)
10714: printf("Can't move to directory %s!\n",path);
10715: if(_getcwd(pathcd,MAXLINE) > 0)
1.184 brouard 10716: #else
1.227 brouard 10717: if(chdir(pathcd) != 0)
10718: printf("Can't move to directory %s!\n", path);
10719: if (getcwd(pathcd, MAXLINE) > 0)
1.184 brouard 10720: #endif
1.126 brouard 10721: printf("Current directory %s!\n",pathcd);
10722: /*strcat(plotcmd,CHARSEPARATOR);*/
10723: sprintf(plotcmd,"gnuplot");
1.157 brouard 10724: #ifdef _WIN32
1.126 brouard 10725: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
10726: #endif
10727: if(!stat(plotcmd,&info)){
1.158 brouard 10728: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 10729: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 10730: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 10731: }else
10732: strcpy(pplotcmd,plotcmd);
1.157 brouard 10733: #ifdef __unix
1.126 brouard 10734: strcpy(plotcmd,GNUPLOTPROGRAM);
10735: if(!stat(plotcmd,&info)){
1.158 brouard 10736: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 10737: }else
10738: strcpy(pplotcmd,plotcmd);
10739: #endif
10740: }else
10741: strcpy(pplotcmd,plotcmd);
10742:
10743: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 10744: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.227 brouard 10745:
1.126 brouard 10746: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 10747: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 10748: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 10749: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 10750: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 10751: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 10752: }
1.158 brouard 10753: printf(" Successful, please wait...");
1.126 brouard 10754: while (z[0] != 'q') {
10755: /* chdir(path); */
1.154 brouard 10756: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 10757: scanf("%s",z);
10758: /* if (z[0] == 'c') system("./imach"); */
10759: if (z[0] == 'e') {
1.158 brouard 10760: #ifdef __APPLE__
1.152 brouard 10761: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 10762: #elif __linux
10763: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 10764: #else
1.152 brouard 10765: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 10766: #endif
10767: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
10768: system(pplotcmd);
1.126 brouard 10769: }
10770: else if (z[0] == 'g') system(plotcmd);
10771: else if (z[0] == 'q') exit(0);
10772: }
1.227 brouard 10773: end:
1.126 brouard 10774: while (z[0] != 'q') {
1.195 brouard 10775: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 10776: scanf("%s",z);
10777: }
10778: }
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