Annotation of imach/src/imach.c, revision 1.227
1.227 ! brouard 1: /* $Id: imach.c,v 1.226 2016/07/12 18:42:34 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.227 ! brouard 4: Revision 1.226 2016/07/12 18:42:34 brouard
! 5: Summary: temp
! 6:
1.226 brouard 7: Revision 1.225 2016/07/12 08:40:03 brouard
8: Summary: saving but not running
9:
1.225 brouard 10: Revision 1.224 2016/07/01 13:16:01 brouard
11: Summary: Fixes
12:
1.224 brouard 13: Revision 1.223 2016/02/19 09:23:35 brouard
14: Summary: temporary
15:
1.223 brouard 16: Revision 1.222 2016/02/17 08:14:50 brouard
17: Summary: Probably last 0.98 stable version 0.98r6
18:
1.222 brouard 19: Revision 1.221 2016/02/15 23:35:36 brouard
20: Summary: minor bug
21:
1.220 brouard 22: Revision 1.219 2016/02/15 00:48:12 brouard
23: *** empty log message ***
24:
1.219 brouard 25: Revision 1.218 2016/02/12 11:29:23 brouard
26: Summary: 0.99 Back projections
27:
1.218 brouard 28: Revision 1.217 2015/12/23 17:18:31 brouard
29: Summary: Experimental backcast
30:
1.217 brouard 31: Revision 1.216 2015/12/18 17:32:11 brouard
32: Summary: 0.98r4 Warning and status=-2
33:
34: Version 0.98r4 is now:
35: - displaying an error when status is -1, date of interview unknown and date of death known;
36: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
37: Older changes concerning s=-2, dating from 2005 have been supersed.
38:
1.216 brouard 39: Revision 1.215 2015/12/16 08:52:24 brouard
40: Summary: 0.98r4 working
41:
1.215 brouard 42: Revision 1.214 2015/12/16 06:57:54 brouard
43: Summary: temporary not working
44:
1.214 brouard 45: Revision 1.213 2015/12/11 18:22:17 brouard
46: Summary: 0.98r4
47:
1.213 brouard 48: Revision 1.212 2015/11/21 12:47:24 brouard
49: Summary: minor typo
50:
1.212 brouard 51: Revision 1.211 2015/11/21 12:41:11 brouard
52: Summary: 0.98r3 with some graph of projected cross-sectional
53:
54: Author: Nicolas Brouard
55:
1.211 brouard 56: Revision 1.210 2015/11/18 17:41:20 brouard
57: Summary: Start working on projected prevalences
58:
1.210 brouard 59: Revision 1.209 2015/11/17 22:12:03 brouard
60: Summary: Adding ftolpl parameter
61: Author: N Brouard
62:
63: We had difficulties to get smoothed confidence intervals. It was due
64: to the period prevalence which wasn't computed accurately. The inner
65: parameter ftolpl is now an outer parameter of the .imach parameter
66: file after estepm. If ftolpl is small 1.e-4 and estepm too,
67: computation are long.
68:
1.209 brouard 69: Revision 1.208 2015/11/17 14:31:57 brouard
70: Summary: temporary
71:
1.208 brouard 72: Revision 1.207 2015/10/27 17:36:57 brouard
73: *** empty log message ***
74:
1.207 brouard 75: Revision 1.206 2015/10/24 07:14:11 brouard
76: *** empty log message ***
77:
1.206 brouard 78: Revision 1.205 2015/10/23 15:50:53 brouard
79: Summary: 0.98r3 some clarification for graphs on likelihood contributions
80:
1.205 brouard 81: Revision 1.204 2015/10/01 16:20:26 brouard
82: Summary: Some new graphs of contribution to likelihood
83:
1.204 brouard 84: Revision 1.203 2015/09/30 17:45:14 brouard
85: Summary: looking at better estimation of the hessian
86:
87: Also a better criteria for convergence to the period prevalence And
88: therefore adding the number of years needed to converge. (The
89: prevalence in any alive state shold sum to one
90:
1.203 brouard 91: Revision 1.202 2015/09/22 19:45:16 brouard
92: Summary: Adding some overall graph on contribution to likelihood. Might change
93:
1.202 brouard 94: Revision 1.201 2015/09/15 17:34:58 brouard
95: Summary: 0.98r0
96:
97: - Some new graphs like suvival functions
98: - Some bugs fixed like model=1+age+V2.
99:
1.201 brouard 100: Revision 1.200 2015/09/09 16:53:55 brouard
101: Summary: Big bug thanks to Flavia
102:
103: Even model=1+age+V2. did not work anymore
104:
1.200 brouard 105: Revision 1.199 2015/09/07 14:09:23 brouard
106: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
107:
1.199 brouard 108: Revision 1.198 2015/09/03 07:14:39 brouard
109: Summary: 0.98q5 Flavia
110:
1.198 brouard 111: Revision 1.197 2015/09/01 18:24:39 brouard
112: *** empty log message ***
113:
1.197 brouard 114: Revision 1.196 2015/08/18 23:17:52 brouard
115: Summary: 0.98q5
116:
1.196 brouard 117: Revision 1.195 2015/08/18 16:28:39 brouard
118: Summary: Adding a hack for testing purpose
119:
120: After reading the title, ftol and model lines, if the comment line has
121: a q, starting with #q, the answer at the end of the run is quit. It
122: permits to run test files in batch with ctest. The former workaround was
123: $ echo q | imach foo.imach
124:
1.195 brouard 125: Revision 1.194 2015/08/18 13:32:00 brouard
126: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
127:
1.194 brouard 128: Revision 1.193 2015/08/04 07:17:42 brouard
129: Summary: 0.98q4
130:
1.193 brouard 131: Revision 1.192 2015/07/16 16:49:02 brouard
132: Summary: Fixing some outputs
133:
1.192 brouard 134: Revision 1.191 2015/07/14 10:00:33 brouard
135: Summary: Some fixes
136:
1.191 brouard 137: Revision 1.190 2015/05/05 08:51:13 brouard
138: Summary: Adding digits in output parameters (7 digits instead of 6)
139:
140: Fix 1+age+.
141:
1.190 brouard 142: Revision 1.189 2015/04/30 14:45:16 brouard
143: Summary: 0.98q2
144:
1.189 brouard 145: Revision 1.188 2015/04/30 08:27:53 brouard
146: *** empty log message ***
147:
1.188 brouard 148: Revision 1.187 2015/04/29 09:11:15 brouard
149: *** empty log message ***
150:
1.187 brouard 151: Revision 1.186 2015/04/23 12:01:52 brouard
152: Summary: V1*age is working now, version 0.98q1
153:
154: Some codes had been disabled in order to simplify and Vn*age was
155: working in the optimization phase, ie, giving correct MLE parameters,
156: but, as usual, outputs were not correct and program core dumped.
157:
1.186 brouard 158: Revision 1.185 2015/03/11 13:26:42 brouard
159: Summary: Inclusion of compile and links command line for Intel Compiler
160:
1.185 brouard 161: Revision 1.184 2015/03/11 11:52:39 brouard
162: Summary: Back from Windows 8. Intel Compiler
163:
1.184 brouard 164: Revision 1.183 2015/03/10 20:34:32 brouard
165: Summary: 0.98q0, trying with directest, mnbrak fixed
166:
167: We use directest instead of original Powell test; probably no
168: incidence on the results, but better justifications;
169: We fixed Numerical Recipes mnbrak routine which was wrong and gave
170: wrong results.
171:
1.183 brouard 172: Revision 1.182 2015/02/12 08:19:57 brouard
173: Summary: Trying to keep directest which seems simpler and more general
174: Author: Nicolas Brouard
175:
1.182 brouard 176: Revision 1.181 2015/02/11 23:22:24 brouard
177: Summary: Comments on Powell added
178:
179: Author:
180:
1.181 brouard 181: Revision 1.180 2015/02/11 17:33:45 brouard
182: Summary: Finishing move from main to function (hpijx and prevalence_limit)
183:
1.180 brouard 184: Revision 1.179 2015/01/04 09:57:06 brouard
185: Summary: back to OS/X
186:
1.179 brouard 187: Revision 1.178 2015/01/04 09:35:48 brouard
188: *** empty log message ***
189:
1.178 brouard 190: Revision 1.177 2015/01/03 18:40:56 brouard
191: Summary: Still testing ilc32 on OSX
192:
1.177 brouard 193: Revision 1.176 2015/01/03 16:45:04 brouard
194: *** empty log message ***
195:
1.176 brouard 196: Revision 1.175 2015/01/03 16:33:42 brouard
197: *** empty log message ***
198:
1.175 brouard 199: Revision 1.174 2015/01/03 16:15:49 brouard
200: Summary: Still in cross-compilation
201:
1.174 brouard 202: Revision 1.173 2015/01/03 12:06:26 brouard
203: Summary: trying to detect cross-compilation
204:
1.173 brouard 205: Revision 1.172 2014/12/27 12:07:47 brouard
206: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
207:
1.172 brouard 208: Revision 1.171 2014/12/23 13:26:59 brouard
209: Summary: Back from Visual C
210:
211: Still problem with utsname.h on Windows
212:
1.171 brouard 213: Revision 1.170 2014/12/23 11:17:12 brouard
214: Summary: Cleaning some \%% back to %%
215:
216: The escape was mandatory for a specific compiler (which one?), but too many warnings.
217:
1.170 brouard 218: Revision 1.169 2014/12/22 23:08:31 brouard
219: Summary: 0.98p
220:
221: Outputs some informations on compiler used, OS etc. Testing on different platforms.
222:
1.169 brouard 223: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 224: Summary: update
1.169 brouard 225:
1.168 brouard 226: Revision 1.167 2014/12/22 13:50:56 brouard
227: Summary: Testing uname and compiler version and if compiled 32 or 64
228:
229: Testing on Linux 64
230:
1.167 brouard 231: Revision 1.166 2014/12/22 11:40:47 brouard
232: *** empty log message ***
233:
1.166 brouard 234: Revision 1.165 2014/12/16 11:20:36 brouard
235: Summary: After compiling on Visual C
236:
237: * imach.c (Module): Merging 1.61 to 1.162
238:
1.165 brouard 239: Revision 1.164 2014/12/16 10:52:11 brouard
240: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
241:
242: * imach.c (Module): Merging 1.61 to 1.162
243:
1.164 brouard 244: Revision 1.163 2014/12/16 10:30:11 brouard
245: * imach.c (Module): Merging 1.61 to 1.162
246:
1.163 brouard 247: Revision 1.162 2014/09/25 11:43:39 brouard
248: Summary: temporary backup 0.99!
249:
1.162 brouard 250: Revision 1.1 2014/09/16 11:06:58 brouard
251: Summary: With some code (wrong) for nlopt
252:
253: Author:
254:
255: Revision 1.161 2014/09/15 20:41:41 brouard
256: Summary: Problem with macro SQR on Intel compiler
257:
1.161 brouard 258: Revision 1.160 2014/09/02 09:24:05 brouard
259: *** empty log message ***
260:
1.160 brouard 261: Revision 1.159 2014/09/01 10:34:10 brouard
262: Summary: WIN32
263: Author: Brouard
264:
1.159 brouard 265: Revision 1.158 2014/08/27 17:11:51 brouard
266: *** empty log message ***
267:
1.158 brouard 268: Revision 1.157 2014/08/27 16:26:55 brouard
269: Summary: Preparing windows Visual studio version
270: Author: Brouard
271:
272: In order to compile on Visual studio, time.h is now correct and time_t
273: and tm struct should be used. difftime should be used but sometimes I
274: just make the differences in raw time format (time(&now).
275: Trying to suppress #ifdef LINUX
276: Add xdg-open for __linux in order to open default browser.
277:
1.157 brouard 278: Revision 1.156 2014/08/25 20:10:10 brouard
279: *** empty log message ***
280:
1.156 brouard 281: Revision 1.155 2014/08/25 18:32:34 brouard
282: Summary: New compile, minor changes
283: Author: Brouard
284:
1.155 brouard 285: Revision 1.154 2014/06/20 17:32:08 brouard
286: Summary: Outputs now all graphs of convergence to period prevalence
287:
1.154 brouard 288: Revision 1.153 2014/06/20 16:45:46 brouard
289: Summary: If 3 live state, convergence to period prevalence on same graph
290: Author: Brouard
291:
1.153 brouard 292: Revision 1.152 2014/06/18 17:54:09 brouard
293: Summary: open browser, use gnuplot on same dir than imach if not found in the path
294:
1.152 brouard 295: Revision 1.151 2014/06/18 16:43:30 brouard
296: *** empty log message ***
297:
1.151 brouard 298: Revision 1.150 2014/06/18 16:42:35 brouard
299: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
300: Author: brouard
301:
1.150 brouard 302: Revision 1.149 2014/06/18 15:51:14 brouard
303: Summary: Some fixes in parameter files errors
304: Author: Nicolas Brouard
305:
1.149 brouard 306: Revision 1.148 2014/06/17 17:38:48 brouard
307: Summary: Nothing new
308: Author: Brouard
309:
310: Just a new packaging for OS/X version 0.98nS
311:
1.148 brouard 312: Revision 1.147 2014/06/16 10:33:11 brouard
313: *** empty log message ***
314:
1.147 brouard 315: Revision 1.146 2014/06/16 10:20:28 brouard
316: Summary: Merge
317: Author: Brouard
318:
319: Merge, before building revised version.
320:
1.146 brouard 321: Revision 1.145 2014/06/10 21:23:15 brouard
322: Summary: Debugging with valgrind
323: Author: Nicolas Brouard
324:
325: Lot of changes in order to output the results with some covariates
326: After the Edimburgh REVES conference 2014, it seems mandatory to
327: improve the code.
328: No more memory valgrind error but a lot has to be done in order to
329: continue the work of splitting the code into subroutines.
330: Also, decodemodel has been improved. Tricode is still not
331: optimal. nbcode should be improved. Documentation has been added in
332: the source code.
333:
1.144 brouard 334: Revision 1.143 2014/01/26 09:45:38 brouard
335: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
336:
337: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
338: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
339:
1.143 brouard 340: Revision 1.142 2014/01/26 03:57:36 brouard
341: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
342:
343: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
344:
1.142 brouard 345: Revision 1.141 2014/01/26 02:42:01 brouard
346: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
347:
1.141 brouard 348: Revision 1.140 2011/09/02 10:37:54 brouard
349: Summary: times.h is ok with mingw32 now.
350:
1.140 brouard 351: Revision 1.139 2010/06/14 07:50:17 brouard
352: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
353: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
354:
1.139 brouard 355: Revision 1.138 2010/04/30 18:19:40 brouard
356: *** empty log message ***
357:
1.138 brouard 358: Revision 1.137 2010/04/29 18:11:38 brouard
359: (Module): Checking covariates for more complex models
360: than V1+V2. A lot of change to be done. Unstable.
361:
1.137 brouard 362: Revision 1.136 2010/04/26 20:30:53 brouard
363: (Module): merging some libgsl code. Fixing computation
364: of likelione (using inter/intrapolation if mle = 0) in order to
365: get same likelihood as if mle=1.
366: Some cleaning of code and comments added.
367:
1.136 brouard 368: Revision 1.135 2009/10/29 15:33:14 brouard
369: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
370:
1.135 brouard 371: Revision 1.134 2009/10/29 13:18:53 brouard
372: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
373:
1.134 brouard 374: Revision 1.133 2009/07/06 10:21:25 brouard
375: just nforces
376:
1.133 brouard 377: Revision 1.132 2009/07/06 08:22:05 brouard
378: Many tings
379:
1.132 brouard 380: Revision 1.131 2009/06/20 16:22:47 brouard
381: Some dimensions resccaled
382:
1.131 brouard 383: Revision 1.130 2009/05/26 06:44:34 brouard
384: (Module): Max Covariate is now set to 20 instead of 8. A
385: lot of cleaning with variables initialized to 0. Trying to make
386: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
387:
1.130 brouard 388: Revision 1.129 2007/08/31 13:49:27 lievre
389: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
390:
1.129 lievre 391: Revision 1.128 2006/06/30 13:02:05 brouard
392: (Module): Clarifications on computing e.j
393:
1.128 brouard 394: Revision 1.127 2006/04/28 18:11:50 brouard
395: (Module): Yes the sum of survivors was wrong since
396: imach-114 because nhstepm was no more computed in the age
397: loop. Now we define nhstepma in the age loop.
398: (Module): In order to speed up (in case of numerous covariates) we
399: compute health expectancies (without variances) in a first step
400: and then all the health expectancies with variances or standard
401: deviation (needs data from the Hessian matrices) which slows the
402: computation.
403: In the future we should be able to stop the program is only health
404: expectancies and graph are needed without standard deviations.
405:
1.127 brouard 406: Revision 1.126 2006/04/28 17:23:28 brouard
407: (Module): Yes the sum of survivors was wrong since
408: imach-114 because nhstepm was no more computed in the age
409: loop. Now we define nhstepma in the age loop.
410: Version 0.98h
411:
1.126 brouard 412: Revision 1.125 2006/04/04 15:20:31 lievre
413: Errors in calculation of health expectancies. Age was not initialized.
414: Forecasting file added.
415:
416: Revision 1.124 2006/03/22 17:13:53 lievre
417: Parameters are printed with %lf instead of %f (more numbers after the comma).
418: The log-likelihood is printed in the log file
419:
420: Revision 1.123 2006/03/20 10:52:43 brouard
421: * imach.c (Module): <title> changed, corresponds to .htm file
422: name. <head> headers where missing.
423:
424: * imach.c (Module): Weights can have a decimal point as for
425: English (a comma might work with a correct LC_NUMERIC environment,
426: otherwise the weight is truncated).
427: Modification of warning when the covariates values are not 0 or
428: 1.
429: Version 0.98g
430:
431: Revision 1.122 2006/03/20 09:45:41 brouard
432: (Module): Weights can have a decimal point as for
433: English (a comma might work with a correct LC_NUMERIC environment,
434: otherwise the weight is truncated).
435: Modification of warning when the covariates values are not 0 or
436: 1.
437: Version 0.98g
438:
439: Revision 1.121 2006/03/16 17:45:01 lievre
440: * imach.c (Module): Comments concerning covariates added
441:
442: * imach.c (Module): refinements in the computation of lli if
443: status=-2 in order to have more reliable computation if stepm is
444: not 1 month. Version 0.98f
445:
446: Revision 1.120 2006/03/16 15:10:38 lievre
447: (Module): refinements in the computation of lli if
448: status=-2 in order to have more reliable computation if stepm is
449: not 1 month. Version 0.98f
450:
451: Revision 1.119 2006/03/15 17:42:26 brouard
452: (Module): Bug if status = -2, the loglikelihood was
453: computed as likelihood omitting the logarithm. Version O.98e
454:
455: Revision 1.118 2006/03/14 18:20:07 brouard
456: (Module): varevsij Comments added explaining the second
457: table of variances if popbased=1 .
458: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
459: (Module): Function pstamp added
460: (Module): Version 0.98d
461:
462: Revision 1.117 2006/03/14 17:16:22 brouard
463: (Module): varevsij Comments added explaining the second
464: table of variances if popbased=1 .
465: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
466: (Module): Function pstamp added
467: (Module): Version 0.98d
468:
469: Revision 1.116 2006/03/06 10:29:27 brouard
470: (Module): Variance-covariance wrong links and
471: varian-covariance of ej. is needed (Saito).
472:
473: Revision 1.115 2006/02/27 12:17:45 brouard
474: (Module): One freematrix added in mlikeli! 0.98c
475:
476: Revision 1.114 2006/02/26 12:57:58 brouard
477: (Module): Some improvements in processing parameter
478: filename with strsep.
479:
480: Revision 1.113 2006/02/24 14:20:24 brouard
481: (Module): Memory leaks checks with valgrind and:
482: datafile was not closed, some imatrix were not freed and on matrix
483: allocation too.
484:
485: Revision 1.112 2006/01/30 09:55:26 brouard
486: (Module): Back to gnuplot.exe instead of wgnuplot.exe
487:
488: Revision 1.111 2006/01/25 20:38:18 brouard
489: (Module): Lots of cleaning and bugs added (Gompertz)
490: (Module): Comments can be added in data file. Missing date values
491: can be a simple dot '.'.
492:
493: Revision 1.110 2006/01/25 00:51:50 brouard
494: (Module): Lots of cleaning and bugs added (Gompertz)
495:
496: Revision 1.109 2006/01/24 19:37:15 brouard
497: (Module): Comments (lines starting with a #) are allowed in data.
498:
499: Revision 1.108 2006/01/19 18:05:42 lievre
500: Gnuplot problem appeared...
501: To be fixed
502:
503: Revision 1.107 2006/01/19 16:20:37 brouard
504: Test existence of gnuplot in imach path
505:
506: Revision 1.106 2006/01/19 13:24:36 brouard
507: Some cleaning and links added in html output
508:
509: Revision 1.105 2006/01/05 20:23:19 lievre
510: *** empty log message ***
511:
512: Revision 1.104 2005/09/30 16:11:43 lievre
513: (Module): sump fixed, loop imx fixed, and simplifications.
514: (Module): If the status is missing at the last wave but we know
515: that the person is alive, then we can code his/her status as -2
516: (instead of missing=-1 in earlier versions) and his/her
517: contributions to the likelihood is 1 - Prob of dying from last
518: health status (= 1-p13= p11+p12 in the easiest case of somebody in
519: the healthy state at last known wave). Version is 0.98
520:
521: Revision 1.103 2005/09/30 15:54:49 lievre
522: (Module): sump fixed, loop imx fixed, and simplifications.
523:
524: Revision 1.102 2004/09/15 17:31:30 brouard
525: Add the possibility to read data file including tab characters.
526:
527: Revision 1.101 2004/09/15 10:38:38 brouard
528: Fix on curr_time
529:
530: Revision 1.100 2004/07/12 18:29:06 brouard
531: Add version for Mac OS X. Just define UNIX in Makefile
532:
533: Revision 1.99 2004/06/05 08:57:40 brouard
534: *** empty log message ***
535:
536: Revision 1.98 2004/05/16 15:05:56 brouard
537: New version 0.97 . First attempt to estimate force of mortality
538: directly from the data i.e. without the need of knowing the health
539: state at each age, but using a Gompertz model: log u =a + b*age .
540: This is the basic analysis of mortality and should be done before any
541: other analysis, in order to test if the mortality estimated from the
542: cross-longitudinal survey is different from the mortality estimated
543: from other sources like vital statistic data.
544:
545: The same imach parameter file can be used but the option for mle should be -3.
546:
1.133 brouard 547: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 548: former routines in order to include the new code within the former code.
549:
550: The output is very simple: only an estimate of the intercept and of
551: the slope with 95% confident intervals.
552:
553: Current limitations:
554: A) Even if you enter covariates, i.e. with the
555: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
556: B) There is no computation of Life Expectancy nor Life Table.
557:
558: Revision 1.97 2004/02/20 13:25:42 lievre
559: Version 0.96d. Population forecasting command line is (temporarily)
560: suppressed.
561:
562: Revision 1.96 2003/07/15 15:38:55 brouard
563: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
564: rewritten within the same printf. Workaround: many printfs.
565:
566: Revision 1.95 2003/07/08 07:54:34 brouard
567: * imach.c (Repository):
568: (Repository): Using imachwizard code to output a more meaningful covariance
569: matrix (cov(a12,c31) instead of numbers.
570:
571: Revision 1.94 2003/06/27 13:00:02 brouard
572: Just cleaning
573:
574: Revision 1.93 2003/06/25 16:33:55 brouard
575: (Module): On windows (cygwin) function asctime_r doesn't
576: exist so I changed back to asctime which exists.
577: (Module): Version 0.96b
578:
579: Revision 1.92 2003/06/25 16:30:45 brouard
580: (Module): On windows (cygwin) function asctime_r doesn't
581: exist so I changed back to asctime which exists.
582:
583: Revision 1.91 2003/06/25 15:30:29 brouard
584: * imach.c (Repository): Duplicated warning errors corrected.
585: (Repository): Elapsed time after each iteration is now output. It
586: helps to forecast when convergence will be reached. Elapsed time
587: is stamped in powell. We created a new html file for the graphs
588: concerning matrix of covariance. It has extension -cov.htm.
589:
590: Revision 1.90 2003/06/24 12:34:15 brouard
591: (Module): Some bugs corrected for windows. Also, when
592: mle=-1 a template is output in file "or"mypar.txt with the design
593: of the covariance matrix to be input.
594:
595: Revision 1.89 2003/06/24 12:30:52 brouard
596: (Module): Some bugs corrected for windows. Also, when
597: mle=-1 a template is output in file "or"mypar.txt with the design
598: of the covariance matrix to be input.
599:
600: Revision 1.88 2003/06/23 17:54:56 brouard
601: * 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.
602:
603: Revision 1.87 2003/06/18 12:26:01 brouard
604: Version 0.96
605:
606: Revision 1.86 2003/06/17 20:04:08 brouard
607: (Module): Change position of html and gnuplot routines and added
608: routine fileappend.
609:
610: Revision 1.85 2003/06/17 13:12:43 brouard
611: * imach.c (Repository): Check when date of death was earlier that
612: current date of interview. It may happen when the death was just
613: prior to the death. In this case, dh was negative and likelihood
614: was wrong (infinity). We still send an "Error" but patch by
615: assuming that the date of death was just one stepm after the
616: interview.
617: (Repository): Because some people have very long ID (first column)
618: we changed int to long in num[] and we added a new lvector for
619: memory allocation. But we also truncated to 8 characters (left
620: truncation)
621: (Repository): No more line truncation errors.
622:
623: Revision 1.84 2003/06/13 21:44:43 brouard
624: * imach.c (Repository): Replace "freqsummary" at a correct
625: place. It differs from routine "prevalence" which may be called
626: many times. Probs is memory consuming and must be used with
627: parcimony.
628: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
629:
630: Revision 1.83 2003/06/10 13:39:11 lievre
631: *** empty log message ***
632:
633: Revision 1.82 2003/06/05 15:57:20 brouard
634: Add log in imach.c and fullversion number is now printed.
635:
636: */
637: /*
638: Interpolated Markov Chain
639:
640: Short summary of the programme:
641:
1.227 ! brouard 642: This program computes Healthy Life Expectancies or State-specific
! 643: (if states aren't health statuses) Expectancies from
! 644: cross-longitudinal data. Cross-longitudinal data consist in:
! 645:
! 646: -1- a first survey ("cross") where individuals from different ages
! 647: are interviewed on their health status or degree of disability (in
! 648: the case of a health survey which is our main interest)
! 649:
! 650: -2- at least a second wave of interviews ("longitudinal") which
! 651: measure each change (if any) in individual health status. Health
! 652: expectancies are computed from the time spent in each health state
! 653: according to a model. More health states you consider, more time is
! 654: necessary to reach the Maximum Likelihood of the parameters involved
! 655: in the model. The simplest model is the multinomial logistic model
! 656: where pij is the probability to be observed in state j at the second
! 657: wave conditional to be observed in state i at the first
! 658: wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
! 659: etc , where 'age' is age and 'sex' is a covariate. If you want to
! 660: have a more complex model than "constant and age", you should modify
! 661: the program where the markup *Covariates have to be included here
! 662: again* invites you to do it. More covariates you add, slower the
1.126 brouard 663: convergence.
664:
665: The advantage of this computer programme, compared to a simple
666: multinomial logistic model, is clear when the delay between waves is not
667: identical for each individual. Also, if a individual missed an
668: intermediate interview, the information is lost, but taken into
669: account using an interpolation or extrapolation.
670:
671: hPijx is the probability to be observed in state i at age x+h
672: conditional to the observed state i at age x. The delay 'h' can be
673: split into an exact number (nh*stepm) of unobserved intermediate
674: states. This elementary transition (by month, quarter,
675: semester or year) is modelled as a multinomial logistic. The hPx
676: matrix is simply the matrix product of nh*stepm elementary matrices
677: and the contribution of each individual to the likelihood is simply
678: hPijx.
679:
680: Also this programme outputs the covariance matrix of the parameters but also
1.218 brouard 681: of the life expectancies. It also computes the period (stable) prevalence.
682:
683: Back prevalence and projections:
1.227 ! brouard 684:
! 685: - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
! 686: double agemaxpar, double ftolpl, int *ncvyearp, double
! 687: dateprev1,double dateprev2, int firstpass, int lastpass, int
! 688: mobilavproj)
! 689:
! 690: Computes the back prevalence limit for any combination of
! 691: covariate values k at any age between ageminpar and agemaxpar and
! 692: returns it in **bprlim. In the loops,
! 693:
! 694: - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
! 695: **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
! 696:
! 697: - hBijx Back Probability to be in state i at age x-h being in j at x
1.218 brouard 698: Computes for any combination of covariates k and any age between bage and fage
699: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
700: oldm=oldms;savm=savms;
1.227 ! brouard 701:
! 702: - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.218 brouard 703: Computes the transition matrix starting at age 'age' over
704: 'nhstepm*hstepm*stepm' months (i.e. until
705: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1.227 ! brouard 706: nhstepm*hstepm matrices.
! 707:
! 708: Returns p3mat[i][j][h] after calling
! 709: p3mat[i][j][h]=matprod2(newm,
! 710: bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
! 711: dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
! 712: oldm);
1.226 brouard 713:
714: Important routines
715:
716: - func (or funcone), computes logit (pij) distinguishing
717: o fixed variables (single or product dummies or quantitative);
718: o varying variables by:
719: (1) wave (single, product dummies, quantitative),
720: (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
721: % fixed dummy (treated) or quantitative (not done because time-consuming);
722: % varying dummy (not done) or quantitative (not done);
723: - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
724: and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
725: - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
726: o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
727: race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
1.218 brouard 728:
1.226 brouard 729:
730:
1.133 brouard 731: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
732: Institut national d'études démographiques, Paris.
1.126 brouard 733: This software have been partly granted by Euro-REVES, a concerted action
734: from the European Union.
735: It is copyrighted identically to a GNU software product, ie programme and
736: software can be distributed freely for non commercial use. Latest version
737: can be accessed at http://euroreves.ined.fr/imach .
738:
739: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
740: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
741:
742: **********************************************************************/
743: /*
744: main
745: read parameterfile
746: read datafile
747: concatwav
748: freqsummary
749: if (mle >= 1)
750: mlikeli
751: print results files
752: if mle==1
753: computes hessian
754: read end of parameter file: agemin, agemax, bage, fage, estepm
755: begin-prev-date,...
756: open gnuplot file
757: open html file
1.145 brouard 758: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
759: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
760: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
761: freexexit2 possible for memory heap.
762:
763: h Pij x | pij_nom ficrestpij
764: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
765: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
766: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
767:
768: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
769: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
770: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
771: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
772: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
773:
1.126 brouard 774: forecasting if prevfcast==1 prevforecast call prevalence()
775: health expectancies
776: Variance-covariance of DFLE
777: prevalence()
778: movingaverage()
779: varevsij()
780: if popbased==1 varevsij(,popbased)
781: total life expectancies
782: Variance of period (stable) prevalence
783: end
784: */
785:
1.187 brouard 786: /* #define DEBUG */
787: /* #define DEBUGBRENT */
1.203 brouard 788: /* #define DEBUGLINMIN */
789: /* #define DEBUGHESS */
790: #define DEBUGHESSIJ
1.224 brouard 791: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan) *\/ */
1.165 brouard 792: #define POWELL /* Instead of NLOPT */
1.224 brouard 793: #define POWELLNOF3INFF1TEST /* Skip test */
1.186 brouard 794: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
795: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 796:
797: #include <math.h>
798: #include <stdio.h>
799: #include <stdlib.h>
800: #include <string.h>
1.226 brouard 801: #include <ctype.h>
1.159 brouard 802:
803: #ifdef _WIN32
804: #include <io.h>
1.172 brouard 805: #include <windows.h>
806: #include <tchar.h>
1.159 brouard 807: #else
1.126 brouard 808: #include <unistd.h>
1.159 brouard 809: #endif
1.126 brouard 810:
811: #include <limits.h>
812: #include <sys/types.h>
1.171 brouard 813:
814: #if defined(__GNUC__)
815: #include <sys/utsname.h> /* Doesn't work on Windows */
816: #endif
817:
1.126 brouard 818: #include <sys/stat.h>
819: #include <errno.h>
1.159 brouard 820: /* extern int errno; */
1.126 brouard 821:
1.157 brouard 822: /* #ifdef LINUX */
823: /* #include <time.h> */
824: /* #include "timeval.h" */
825: /* #else */
826: /* #include <sys/time.h> */
827: /* #endif */
828:
1.126 brouard 829: #include <time.h>
830:
1.136 brouard 831: #ifdef GSL
832: #include <gsl/gsl_errno.h>
833: #include <gsl/gsl_multimin.h>
834: #endif
835:
1.167 brouard 836:
1.162 brouard 837: #ifdef NLOPT
838: #include <nlopt.h>
839: typedef struct {
840: double (* function)(double [] );
841: } myfunc_data ;
842: #endif
843:
1.126 brouard 844: /* #include <libintl.h> */
845: /* #define _(String) gettext (String) */
846:
1.141 brouard 847: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 848:
849: #define GNUPLOTPROGRAM "gnuplot"
850: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
851: #define FILENAMELENGTH 132
852:
853: #define GLOCK_ERROR_NOPATH -1 /* empty path */
854: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
855:
1.144 brouard 856: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
857: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 858:
859: #define NINTERVMAX 8
1.144 brouard 860: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
861: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
862: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 863: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 864: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
865: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.126 brouard 866: #define MAXN 20000
1.144 brouard 867: #define YEARM 12. /**< Number of months per year */
1.218 brouard 868: /* #define AGESUP 130 */
869: #define AGESUP 150
870: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126 brouard 871: #define AGEBASE 40
1.194 brouard 872: #define AGEOVERFLOW 1.e20
1.164 brouard 873: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 874: #ifdef _WIN32
875: #define DIRSEPARATOR '\\'
876: #define CHARSEPARATOR "\\"
877: #define ODIRSEPARATOR '/'
878: #else
1.126 brouard 879: #define DIRSEPARATOR '/'
880: #define CHARSEPARATOR "/"
881: #define ODIRSEPARATOR '\\'
882: #endif
883:
1.227 ! brouard 884: /* $Id: imach.c,v 1.226 2016/07/12 18:42:34 brouard Exp $ */
1.126 brouard 885: /* $State: Exp $ */
1.196 brouard 886: #include "version.h"
887: char version[]=__IMACH_VERSION__;
1.224 brouard 888: 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";
1.227 ! brouard 889: char fullversion[]="$Revision: 1.226 $ $Date: 2016/07/12 18:42:34 $";
1.126 brouard 890: char strstart[80];
891: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 892: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 893: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 894: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
895: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
896: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
1.225 brouard 897: int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
898: int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
1.145 brouard 899: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
900: int cptcovprodnoage=0; /**< Number of covariate products without age */
901: int cptcoveff=0; /* Total number of covariates to vary for printing results */
1.224 brouard 902: int ncoveff=0; /* Total number of effective covariates in the model */
1.225 brouard 903: int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
1.224 brouard 904: int ntveff=0; /**< ntveff number of effective time varying variables */
905: int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
1.145 brouard 906: int cptcov=0; /* Working variable */
1.218 brouard 907: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.126 brouard 908: int npar=NPARMAX;
909: int nlstate=2; /* Number of live states */
910: int ndeath=1; /* Number of dead states */
1.130 brouard 911: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.223 brouard 912: int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
1.126 brouard 913: int popbased=0;
914:
915: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 916: int maxwav=0; /* Maxim number of waves */
917: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
918: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
919: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 920: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 921: int mle=1, weightopt=0;
1.126 brouard 922: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
923: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
924: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
925: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 926: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 927: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 928: double **matprod2(); /* test */
1.126 brouard 929: double **oldm, **newm, **savm; /* Working pointers to matrices */
930: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218 brouard 931: double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
932:
1.136 brouard 933: /*FILE *fic ; */ /* Used in readdata only */
1.217 brouard 934: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 935: FILE *ficlog, *ficrespow;
1.130 brouard 936: int globpr=0; /* Global variable for printing or not */
1.126 brouard 937: double fretone; /* Only one call to likelihood */
1.130 brouard 938: long ipmx=0; /* Number of contributions */
1.126 brouard 939: double sw; /* Sum of weights */
940: char filerespow[FILENAMELENGTH];
941: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
942: FILE *ficresilk;
943: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
944: FILE *ficresprobmorprev;
945: FILE *fichtm, *fichtmcov; /* Html File */
946: FILE *ficreseij;
947: char filerese[FILENAMELENGTH];
948: FILE *ficresstdeij;
949: char fileresstde[FILENAMELENGTH];
950: FILE *ficrescveij;
951: char filerescve[FILENAMELENGTH];
952: FILE *ficresvij;
953: char fileresv[FILENAMELENGTH];
954: FILE *ficresvpl;
955: char fileresvpl[FILENAMELENGTH];
956: char title[MAXLINE];
1.217 brouard 957: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 958: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
959: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
960: char command[FILENAMELENGTH];
961: int outcmd=0;
962:
1.217 brouard 963: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 964: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 965: char filelog[FILENAMELENGTH]; /* Log file */
966: char filerest[FILENAMELENGTH];
967: char fileregp[FILENAMELENGTH];
968: char popfile[FILENAMELENGTH];
969:
970: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
971:
1.157 brouard 972: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
973: /* struct timezone tzp; */
974: /* extern int gettimeofday(); */
975: struct tm tml, *gmtime(), *localtime();
976:
977: extern time_t time();
978:
979: struct tm start_time, end_time, curr_time, last_time, forecast_time;
980: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
981: struct tm tm;
982:
1.126 brouard 983: char strcurr[80], strfor[80];
984:
985: char *endptr;
986: long lval;
987: double dval;
988:
989: #define NR_END 1
990: #define FREE_ARG char*
991: #define FTOL 1.0e-10
992:
993: #define NRANSI
994: #define ITMAX 200
995:
996: #define TOL 2.0e-4
997:
998: #define CGOLD 0.3819660
999: #define ZEPS 1.0e-10
1000: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
1001:
1002: #define GOLD 1.618034
1003: #define GLIMIT 100.0
1004: #define TINY 1.0e-20
1005:
1006: static double maxarg1,maxarg2;
1007: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
1008: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
1009:
1010: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
1011: #define rint(a) floor(a+0.5)
1.166 brouard 1012: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 1013: #define mytinydouble 1.0e-16
1.166 brouard 1014: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
1015: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
1016: /* static double dsqrarg; */
1017: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 1018: static double sqrarg;
1019: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
1020: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1021: int agegomp= AGEGOMP;
1022:
1023: int imx;
1024: int stepm=1;
1025: /* Stepm, step in month: minimum step interpolation*/
1026:
1027: int estepm;
1028: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
1029:
1030: int m,nb;
1031: long *num;
1.197 brouard 1032: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 1033: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
1034: covariate for which somebody answered excluding
1035: undefined. Usually 2: 0 and 1. */
1036: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
1037: covariate for which somebody answered including
1038: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 1039: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218 brouard 1040: double **pmmij, ***probs; /* Global pointer */
1.219 brouard 1041: double ***mobaverage, ***mobaverages; /* New global variable */
1.126 brouard 1042: double *ageexmed,*agecens;
1043: double dateintmean=0;
1044:
1045: double *weight;
1046: int **s; /* Status */
1.141 brouard 1047: double *agedc;
1.145 brouard 1048: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 1049: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 1050: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.225 brouard 1051: double **coqvar; /* Fixed quantitative covariate iqv */
1052: double ***cotvar; /* Time varying covariate itv */
1053: double ***cotqvar; /* Time varying quantitative covariate itqv */
1.141 brouard 1054: double idx;
1055: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.226 brouard 1056: int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
1.227 ! brouard 1057: int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
! 1058: 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 1059: int *Tage;
1.227 ! brouard 1060: int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
! 1061: int *Tmodelind; /** Tmodelind[Tvaraff[3]]=9,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 1062: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 1063: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.227 ! brouard 1064: int **Tvard;
! 1065: int *Tprod;/**< Gives the k position of the k1 product */
! 1066: int *Tposprod; /**< Gives the k1 product from the k position */
! 1067: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
! 1068: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
! 1069: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
! 1070: */
! 1071: int cptcovprod, *Tvaraff, *invalidvarcomb;
1.126 brouard 1072: double *lsurv, *lpop, *tpop;
1073:
1.143 brouard 1074: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
1075: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 1076:
1077: /**************** split *************************/
1078: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1079: {
1080: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1081: the name of the file (name), its extension only (ext) and its first part of the name (finame)
1082: */
1083: char *ss; /* pointer */
1.186 brouard 1084: int l1=0, l2=0; /* length counters */
1.126 brouard 1085:
1086: l1 = strlen(path ); /* length of path */
1087: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1088: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1089: if ( ss == NULL ) { /* no directory, so determine current directory */
1090: strcpy( name, path ); /* we got the fullname name because no directory */
1091: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
1092: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1093: /* get current working directory */
1094: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 1095: #ifdef WIN32
1096: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
1097: #else
1098: if (getcwd(dirc, FILENAME_MAX) == NULL) {
1099: #endif
1.126 brouard 1100: return( GLOCK_ERROR_GETCWD );
1101: }
1102: /* got dirc from getcwd*/
1103: printf(" DIRC = %s \n",dirc);
1.205 brouard 1104: } else { /* strip directory from path */
1.126 brouard 1105: ss++; /* after this, the filename */
1106: l2 = strlen( ss ); /* length of filename */
1107: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1108: strcpy( name, ss ); /* save file name */
1109: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1110: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1111: printf(" DIRC2 = %s \n",dirc);
1112: }
1113: /* We add a separator at the end of dirc if not exists */
1114: l1 = strlen( dirc ); /* length of directory */
1115: if( dirc[l1-1] != DIRSEPARATOR ){
1116: dirc[l1] = DIRSEPARATOR;
1117: dirc[l1+1] = 0;
1118: printf(" DIRC3 = %s \n",dirc);
1119: }
1120: ss = strrchr( name, '.' ); /* find last / */
1121: if (ss >0){
1122: ss++;
1123: strcpy(ext,ss); /* save extension */
1124: l1= strlen( name);
1125: l2= strlen(ss)+1;
1126: strncpy( finame, name, l1-l2);
1127: finame[l1-l2]= 0;
1128: }
1129:
1130: return( 0 ); /* we're done */
1131: }
1132:
1133:
1134: /******************************************/
1135:
1136: void replace_back_to_slash(char *s, char*t)
1137: {
1138: int i;
1139: int lg=0;
1140: i=0;
1141: lg=strlen(t);
1142: for(i=0; i<= lg; i++) {
1143: (s[i] = t[i]);
1144: if (t[i]== '\\') s[i]='/';
1145: }
1146: }
1147:
1.132 brouard 1148: char *trimbb(char *out, char *in)
1.137 brouard 1149: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1150: char *s;
1151: s=out;
1152: while (*in != '\0'){
1.137 brouard 1153: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1154: in++;
1155: }
1156: *out++ = *in++;
1157: }
1158: *out='\0';
1159: return s;
1160: }
1161:
1.187 brouard 1162: /* char *substrchaine(char *out, char *in, char *chain) */
1163: /* { */
1164: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1165: /* char *s, *t; */
1166: /* t=in;s=out; */
1167: /* while ((*in != *chain) && (*in != '\0')){ */
1168: /* *out++ = *in++; */
1169: /* } */
1170:
1171: /* /\* *in matches *chain *\/ */
1172: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1173: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1174: /* } */
1175: /* in--; chain--; */
1176: /* while ( (*in != '\0')){ */
1177: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1178: /* *out++ = *in++; */
1179: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1180: /* } */
1181: /* *out='\0'; */
1182: /* out=s; */
1183: /* return out; */
1184: /* } */
1185: char *substrchaine(char *out, char *in, char *chain)
1186: {
1187: /* Substract chain 'chain' from 'in', return and output 'out' */
1188: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1189:
1190: char *strloc;
1191:
1192: strcpy (out, in);
1193: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1194: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1195: if(strloc != NULL){
1196: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1197: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1198: /* strcpy (strloc, strloc +strlen(chain));*/
1199: }
1200: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1201: return out;
1202: }
1203:
1204:
1.145 brouard 1205: char *cutl(char *blocc, char *alocc, char *in, char occ)
1206: {
1.187 brouard 1207: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1208: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1209: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1210: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1211: */
1.160 brouard 1212: char *s, *t;
1.145 brouard 1213: t=in;s=in;
1214: while ((*in != occ) && (*in != '\0')){
1215: *alocc++ = *in++;
1216: }
1217: if( *in == occ){
1218: *(alocc)='\0';
1219: s=++in;
1220: }
1221:
1222: if (s == t) {/* occ not found */
1223: *(alocc-(in-s))='\0';
1224: in=s;
1225: }
1226: while ( *in != '\0'){
1227: *blocc++ = *in++;
1228: }
1229:
1230: *blocc='\0';
1231: return t;
1232: }
1.137 brouard 1233: char *cutv(char *blocc, char *alocc, char *in, char occ)
1234: {
1.187 brouard 1235: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1236: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1237: gives blocc="abcdef2ghi" and alocc="j".
1238: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1239: */
1240: char *s, *t;
1241: t=in;s=in;
1242: while (*in != '\0'){
1243: while( *in == occ){
1244: *blocc++ = *in++;
1245: s=in;
1246: }
1247: *blocc++ = *in++;
1248: }
1249: if (s == t) /* occ not found */
1250: *(blocc-(in-s))='\0';
1251: else
1252: *(blocc-(in-s)-1)='\0';
1253: in=s;
1254: while ( *in != '\0'){
1255: *alocc++ = *in++;
1256: }
1257:
1258: *alocc='\0';
1259: return s;
1260: }
1261:
1.126 brouard 1262: int nbocc(char *s, char occ)
1263: {
1264: int i,j=0;
1265: int lg=20;
1266: i=0;
1267: lg=strlen(s);
1268: for(i=0; i<= lg; i++) {
1269: if (s[i] == occ ) j++;
1270: }
1271: return j;
1272: }
1273:
1.137 brouard 1274: /* void cutv(char *u,char *v, char*t, char occ) */
1275: /* { */
1276: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1277: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1278: /* gives u="abcdef2ghi" and v="j" *\/ */
1279: /* int i,lg,j,p=0; */
1280: /* i=0; */
1281: /* lg=strlen(t); */
1282: /* for(j=0; j<=lg-1; j++) { */
1283: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1284: /* } */
1.126 brouard 1285:
1.137 brouard 1286: /* for(j=0; j<p; j++) { */
1287: /* (u[j] = t[j]); */
1288: /* } */
1289: /* u[p]='\0'; */
1.126 brouard 1290:
1.137 brouard 1291: /* for(j=0; j<= lg; j++) { */
1292: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1293: /* } */
1294: /* } */
1.126 brouard 1295:
1.160 brouard 1296: #ifdef _WIN32
1297: char * strsep(char **pp, const char *delim)
1298: {
1299: char *p, *q;
1300:
1301: if ((p = *pp) == NULL)
1302: return 0;
1303: if ((q = strpbrk (p, delim)) != NULL)
1304: {
1305: *pp = q + 1;
1306: *q = '\0';
1307: }
1308: else
1309: *pp = 0;
1310: return p;
1311: }
1312: #endif
1313:
1.126 brouard 1314: /********************** nrerror ********************/
1315:
1316: void nrerror(char error_text[])
1317: {
1318: fprintf(stderr,"ERREUR ...\n");
1319: fprintf(stderr,"%s\n",error_text);
1320: exit(EXIT_FAILURE);
1321: }
1322: /*********************** vector *******************/
1323: double *vector(int nl, int nh)
1324: {
1325: double *v;
1326: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1327: if (!v) nrerror("allocation failure in vector");
1328: return v-nl+NR_END;
1329: }
1330:
1331: /************************ free vector ******************/
1332: void free_vector(double*v, int nl, int nh)
1333: {
1334: free((FREE_ARG)(v+nl-NR_END));
1335: }
1336:
1337: /************************ivector *******************************/
1338: int *ivector(long nl,long nh)
1339: {
1340: int *v;
1341: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1342: if (!v) nrerror("allocation failure in ivector");
1343: return v-nl+NR_END;
1344: }
1345:
1346: /******************free ivector **************************/
1347: void free_ivector(int *v, long nl, long nh)
1348: {
1349: free((FREE_ARG)(v+nl-NR_END));
1350: }
1351:
1352: /************************lvector *******************************/
1353: long *lvector(long nl,long nh)
1354: {
1355: long *v;
1356: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1357: if (!v) nrerror("allocation failure in ivector");
1358: return v-nl+NR_END;
1359: }
1360:
1361: /******************free lvector **************************/
1362: void free_lvector(long *v, long nl, long nh)
1363: {
1364: free((FREE_ARG)(v+nl-NR_END));
1365: }
1366:
1367: /******************* imatrix *******************************/
1368: int **imatrix(long nrl, long nrh, long ncl, long nch)
1369: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1370: {
1371: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1372: int **m;
1373:
1374: /* allocate pointers to rows */
1375: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1376: if (!m) nrerror("allocation failure 1 in matrix()");
1377: m += NR_END;
1378: m -= nrl;
1379:
1380:
1381: /* allocate rows and set pointers to them */
1382: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1383: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1384: m[nrl] += NR_END;
1385: m[nrl] -= ncl;
1386:
1387: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1388:
1389: /* return pointer to array of pointers to rows */
1390: return m;
1391: }
1392:
1393: /****************** free_imatrix *************************/
1394: void free_imatrix(m,nrl,nrh,ncl,nch)
1395: int **m;
1396: long nch,ncl,nrh,nrl;
1397: /* free an int matrix allocated by imatrix() */
1398: {
1399: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1400: free((FREE_ARG) (m+nrl-NR_END));
1401: }
1402:
1403: /******************* matrix *******************************/
1404: double **matrix(long nrl, long nrh, long ncl, long nch)
1405: {
1406: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1407: double **m;
1408:
1409: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1410: if (!m) nrerror("allocation failure 1 in matrix()");
1411: m += NR_END;
1412: m -= nrl;
1413:
1414: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1415: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1416: m[nrl] += NR_END;
1417: m[nrl] -= ncl;
1418:
1419: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1420: return m;
1.145 brouard 1421: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1422: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1423: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1424: */
1425: }
1426:
1427: /*************************free matrix ************************/
1428: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1429: {
1430: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1431: free((FREE_ARG)(m+nrl-NR_END));
1432: }
1433:
1434: /******************* ma3x *******************************/
1435: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1436: {
1437: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1438: double ***m;
1439:
1440: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1441: if (!m) nrerror("allocation failure 1 in matrix()");
1442: m += NR_END;
1443: m -= nrl;
1444:
1445: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1446: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1447: m[nrl] += NR_END;
1448: m[nrl] -= ncl;
1449:
1450: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1451:
1452: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1453: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1454: m[nrl][ncl] += NR_END;
1455: m[nrl][ncl] -= nll;
1456: for (j=ncl+1; j<=nch; j++)
1457: m[nrl][j]=m[nrl][j-1]+nlay;
1458:
1459: for (i=nrl+1; i<=nrh; i++) {
1460: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1461: for (j=ncl+1; j<=nch; j++)
1462: m[i][j]=m[i][j-1]+nlay;
1463: }
1464: return m;
1465: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1466: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1467: */
1468: }
1469:
1470: /*************************free ma3x ************************/
1471: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1472: {
1473: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1474: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1475: free((FREE_ARG)(m+nrl-NR_END));
1476: }
1477:
1478: /*************** function subdirf ***********/
1479: char *subdirf(char fileres[])
1480: {
1481: /* Caution optionfilefiname is hidden */
1482: strcpy(tmpout,optionfilefiname);
1483: strcat(tmpout,"/"); /* Add to the right */
1484: strcat(tmpout,fileres);
1485: return tmpout;
1486: }
1487:
1488: /*************** function subdirf2 ***********/
1489: char *subdirf2(char fileres[], char *preop)
1490: {
1491:
1492: /* Caution optionfilefiname is hidden */
1493: strcpy(tmpout,optionfilefiname);
1494: strcat(tmpout,"/");
1495: strcat(tmpout,preop);
1496: strcat(tmpout,fileres);
1497: return tmpout;
1498: }
1499:
1500: /*************** function subdirf3 ***********/
1501: char *subdirf3(char fileres[], char *preop, char *preop2)
1502: {
1503:
1504: /* Caution optionfilefiname is hidden */
1505: strcpy(tmpout,optionfilefiname);
1506: strcat(tmpout,"/");
1507: strcat(tmpout,preop);
1508: strcat(tmpout,preop2);
1509: strcat(tmpout,fileres);
1510: return tmpout;
1511: }
1.213 brouard 1512:
1513: /*************** function subdirfext ***********/
1514: char *subdirfext(char fileres[], char *preop, char *postop)
1515: {
1516:
1517: strcpy(tmpout,preop);
1518: strcat(tmpout,fileres);
1519: strcat(tmpout,postop);
1520: return tmpout;
1521: }
1.126 brouard 1522:
1.213 brouard 1523: /*************** function subdirfext3 ***********/
1524: char *subdirfext3(char fileres[], char *preop, char *postop)
1525: {
1526:
1527: /* Caution optionfilefiname is hidden */
1528: strcpy(tmpout,optionfilefiname);
1529: strcat(tmpout,"/");
1530: strcat(tmpout,preop);
1531: strcat(tmpout,fileres);
1532: strcat(tmpout,postop);
1533: return tmpout;
1534: }
1535:
1.162 brouard 1536: char *asc_diff_time(long time_sec, char ascdiff[])
1537: {
1538: long sec_left, days, hours, minutes;
1539: days = (time_sec) / (60*60*24);
1540: sec_left = (time_sec) % (60*60*24);
1541: hours = (sec_left) / (60*60) ;
1542: sec_left = (sec_left) %(60*60);
1543: minutes = (sec_left) /60;
1544: sec_left = (sec_left) % (60);
1545: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1546: return ascdiff;
1547: }
1548:
1.126 brouard 1549: /***************** f1dim *************************/
1550: extern int ncom;
1551: extern double *pcom,*xicom;
1552: extern double (*nrfunc)(double []);
1553:
1554: double f1dim(double x)
1555: {
1556: int j;
1557: double f;
1558: double *xt;
1559:
1560: xt=vector(1,ncom);
1561: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1562: f=(*nrfunc)(xt);
1563: free_vector(xt,1,ncom);
1564: return f;
1565: }
1566:
1567: /*****************brent *************************/
1568: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1569: {
1570: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1571: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1572: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1573: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1574: * returned function value.
1575: */
1.126 brouard 1576: int iter;
1577: double a,b,d,etemp;
1.159 brouard 1578: double fu=0,fv,fw,fx;
1.164 brouard 1579: double ftemp=0.;
1.126 brouard 1580: double p,q,r,tol1,tol2,u,v,w,x,xm;
1581: double e=0.0;
1582:
1583: a=(ax < cx ? ax : cx);
1584: b=(ax > cx ? ax : cx);
1585: x=w=v=bx;
1586: fw=fv=fx=(*f)(x);
1587: for (iter=1;iter<=ITMAX;iter++) {
1588: xm=0.5*(a+b);
1589: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1590: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1591: printf(".");fflush(stdout);
1592: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1593: #ifdef DEBUGBRENT
1.126 brouard 1594: 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);
1595: 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);
1596: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1597: #endif
1598: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1599: *xmin=x;
1600: return fx;
1601: }
1602: ftemp=fu;
1603: if (fabs(e) > tol1) {
1604: r=(x-w)*(fx-fv);
1605: q=(x-v)*(fx-fw);
1606: p=(x-v)*q-(x-w)*r;
1607: q=2.0*(q-r);
1608: if (q > 0.0) p = -p;
1609: q=fabs(q);
1610: etemp=e;
1611: e=d;
1612: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1.224 brouard 1613: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1.126 brouard 1614: else {
1.224 brouard 1615: d=p/q;
1616: u=x+d;
1617: if (u-a < tol2 || b-u < tol2)
1618: d=SIGN(tol1,xm-x);
1.126 brouard 1619: }
1620: } else {
1621: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1622: }
1623: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1624: fu=(*f)(u);
1625: if (fu <= fx) {
1626: if (u >= x) a=x; else b=x;
1627: SHFT(v,w,x,u)
1.183 brouard 1628: SHFT(fv,fw,fx,fu)
1629: } else {
1630: if (u < x) a=u; else b=u;
1631: if (fu <= fw || w == x) {
1.224 brouard 1632: v=w;
1633: w=u;
1634: fv=fw;
1635: fw=fu;
1.183 brouard 1636: } else if (fu <= fv || v == x || v == w) {
1.224 brouard 1637: v=u;
1638: fv=fu;
1.183 brouard 1639: }
1640: }
1.126 brouard 1641: }
1642: nrerror("Too many iterations in brent");
1643: *xmin=x;
1644: return fx;
1645: }
1646:
1647: /****************** mnbrak ***********************/
1648:
1649: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1650: double (*func)(double))
1.183 brouard 1651: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1652: the downhill direction (defined by the function as evaluated at the initial points) and returns
1653: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1654: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1655: */
1.126 brouard 1656: double ulim,u,r,q, dum;
1657: double fu;
1.187 brouard 1658:
1659: double scale=10.;
1660: int iterscale=0;
1661:
1662: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1663: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1664:
1665:
1666: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1667: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1668: /* *bx = *ax - (*ax - *bx)/scale; */
1669: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1670: /* } */
1671:
1.126 brouard 1672: if (*fb > *fa) {
1673: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1674: SHFT(dum,*fb,*fa,dum)
1675: }
1.126 brouard 1676: *cx=(*bx)+GOLD*(*bx-*ax);
1677: *fc=(*func)(*cx);
1.183 brouard 1678: #ifdef DEBUG
1.224 brouard 1679: printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
1680: 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 1681: #endif
1.224 brouard 1682: 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 1683: r=(*bx-*ax)*(*fb-*fc);
1.224 brouard 1684: q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
1.126 brouard 1685: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1686: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1687: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1688: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1689: fu=(*func)(u);
1.163 brouard 1690: #ifdef DEBUG
1691: /* f(x)=A(x-u)**2+f(u) */
1692: double A, fparabu;
1693: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1694: fparabu= *fa - A*(*ax-u)*(*ax-u);
1.224 brouard 1695: 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);
1696: 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 1697: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1698: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1699: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1700: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1701: #endif
1.184 brouard 1702: #ifdef MNBRAKORIGINAL
1.183 brouard 1703: #else
1.191 brouard 1704: /* if (fu > *fc) { */
1705: /* #ifdef DEBUG */
1706: /* printf("mnbrak4 fu > fc \n"); */
1707: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1708: /* #endif */
1709: /* /\* 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 *\\/ *\/ */
1710: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1711: /* dum=u; /\* Shifting c and u *\/ */
1712: /* u = *cx; */
1713: /* *cx = dum; */
1714: /* dum = fu; */
1715: /* fu = *fc; */
1716: /* *fc =dum; */
1717: /* } else { /\* end *\/ */
1718: /* #ifdef DEBUG */
1719: /* printf("mnbrak3 fu < fc \n"); */
1720: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1721: /* #endif */
1722: /* dum=u; /\* Shifting c and u *\/ */
1723: /* u = *cx; */
1724: /* *cx = dum; */
1725: /* dum = fu; */
1726: /* fu = *fc; */
1727: /* *fc =dum; */
1728: /* } */
1.224 brouard 1729: #ifdef DEBUGMNBRAK
1730: double A, fparabu;
1731: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1732: fparabu= *fa - A*(*ax-u)*(*ax-u);
1733: 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);
1734: 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 1735: #endif
1.191 brouard 1736: dum=u; /* Shifting c and u */
1737: u = *cx;
1738: *cx = dum;
1739: dum = fu;
1740: fu = *fc;
1741: *fc =dum;
1.183 brouard 1742: #endif
1.162 brouard 1743: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1744: #ifdef DEBUG
1.224 brouard 1745: printf("\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1746: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1.183 brouard 1747: #endif
1.126 brouard 1748: fu=(*func)(u);
1749: if (fu < *fc) {
1.183 brouard 1750: #ifdef DEBUG
1.224 brouard 1751: printf("\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
1752: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
1753: #endif
1754: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1755: SHFT(*fb,*fc,fu,(*func)(u))
1756: #ifdef DEBUG
1757: printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
1.183 brouard 1758: #endif
1759: }
1.162 brouard 1760: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1761: #ifdef DEBUG
1.224 brouard 1762: printf("\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1763: fprintf(ficlog,"\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1.183 brouard 1764: #endif
1.126 brouard 1765: u=ulim;
1766: fu=(*func)(u);
1.183 brouard 1767: } else { /* u could be left to b (if r > q parabola has a maximum) */
1768: #ifdef DEBUG
1.224 brouard 1769: printf("\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
1770: 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 1771: #endif
1.126 brouard 1772: u=(*cx)+GOLD*(*cx-*bx);
1773: fu=(*func)(u);
1.224 brouard 1774: #ifdef DEBUG
1775: printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
1776: fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
1777: #endif
1.183 brouard 1778: } /* end tests */
1.126 brouard 1779: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1780: SHFT(*fa,*fb,*fc,fu)
1781: #ifdef DEBUG
1.224 brouard 1782: printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
1783: 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 1784: #endif
1785: } /* 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 1786: }
1787:
1788: /*************** linmin ************************/
1.162 brouard 1789: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1790: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1791: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1792: the value of func at the returned location p . This is actually all accomplished by calling the
1793: routines mnbrak and brent .*/
1.126 brouard 1794: int ncom;
1795: double *pcom,*xicom;
1796: double (*nrfunc)(double []);
1797:
1.224 brouard 1798: #ifdef LINMINORIGINAL
1.126 brouard 1799: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1.224 brouard 1800: #else
1801: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat)
1802: #endif
1.126 brouard 1803: {
1804: double brent(double ax, double bx, double cx,
1805: double (*f)(double), double tol, double *xmin);
1806: double f1dim(double x);
1807: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1808: double *fc, double (*func)(double));
1809: int j;
1810: double xx,xmin,bx,ax;
1811: double fx,fb,fa;
1.187 brouard 1812:
1.203 brouard 1813: #ifdef LINMINORIGINAL
1814: #else
1815: double scale=10., axs, xxs; /* Scale added for infinity */
1816: #endif
1817:
1.126 brouard 1818: ncom=n;
1819: pcom=vector(1,n);
1820: xicom=vector(1,n);
1821: nrfunc=func;
1822: for (j=1;j<=n;j++) {
1823: pcom[j]=p[j];
1.202 brouard 1824: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1825: }
1.187 brouard 1826:
1.203 brouard 1827: #ifdef LINMINORIGINAL
1828: xx=1.;
1829: #else
1830: axs=0.0;
1831: xxs=1.;
1832: do{
1833: xx= xxs;
1834: #endif
1.187 brouard 1835: ax=0.;
1836: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1837: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1838: /* 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)) */
1839: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1840: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1841: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1842: /* 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 1843: #ifdef LINMINORIGINAL
1844: #else
1845: if (fx != fx){
1.224 brouard 1846: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1847: printf("|");
1848: fprintf(ficlog,"|");
1.203 brouard 1849: #ifdef DEBUGLINMIN
1.224 brouard 1850: 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 1851: #endif
1852: }
1.224 brouard 1853: }while(fx != fx && xxs > 1.e-5);
1.203 brouard 1854: #endif
1855:
1.191 brouard 1856: #ifdef DEBUGLINMIN
1857: 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 1858: 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 1859: #endif
1.224 brouard 1860: #ifdef LINMINORIGINAL
1861: #else
1862: if(fb == fx){ /* Flat function in the direction */
1863: xmin=xx;
1864: *flat=1;
1865: }else{
1866: *flat=0;
1867: #endif
1868: /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
1.187 brouard 1869: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1870: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1871: /* fmin = f(p[j] + xmin * xi[j]) */
1872: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1873: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1874: #ifdef DEBUG
1.224 brouard 1875: 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);
1876: 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);
1877: #endif
1878: #ifdef LINMINORIGINAL
1879: #else
1880: }
1.126 brouard 1881: #endif
1.191 brouard 1882: #ifdef DEBUGLINMIN
1883: printf("linmin end ");
1.202 brouard 1884: fprintf(ficlog,"linmin end ");
1.191 brouard 1885: #endif
1.126 brouard 1886: for (j=1;j<=n;j++) {
1.203 brouard 1887: #ifdef LINMINORIGINAL
1888: xi[j] *= xmin;
1889: #else
1890: #ifdef DEBUGLINMIN
1891: if(xxs <1.0)
1892: printf(" before xi[%d]=%12.8f", j,xi[j]);
1893: #endif
1894: 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) */
1895: #ifdef DEBUGLINMIN
1896: if(xxs <1.0)
1897: 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 );
1898: #endif
1899: #endif
1.187 brouard 1900: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1901: }
1.191 brouard 1902: #ifdef DEBUGLINMIN
1.203 brouard 1903: printf("\n");
1.191 brouard 1904: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 1905: 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 1906: for (j=1;j<=n;j++) {
1.202 brouard 1907: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1908: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1909: if(j % ncovmodel == 0){
1.191 brouard 1910: printf("\n");
1.202 brouard 1911: fprintf(ficlog,"\n");
1912: }
1.191 brouard 1913: }
1.203 brouard 1914: #else
1.191 brouard 1915: #endif
1.126 brouard 1916: free_vector(xicom,1,n);
1917: free_vector(pcom,1,n);
1918: }
1919:
1920:
1921: /*************** powell ************************/
1.162 brouard 1922: /*
1923: Minimization of a function func of n variables. Input consists of an initial starting point
1924: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1925: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1926: such that failure to decrease by more than this amount on one iteration signals doneness. On
1927: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1928: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1929: */
1.224 brouard 1930: #ifdef LINMINORIGINAL
1931: #else
1932: int *flatdir; /* Function is vanishing in that direction */
1.225 brouard 1933: int flat=0, flatd=0; /* Function is vanishing in that direction */
1.224 brouard 1934: #endif
1.126 brouard 1935: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1936: double (*func)(double []))
1937: {
1.224 brouard 1938: #ifdef LINMINORIGINAL
1939: void linmin(double p[], double xi[], int n, double *fret,
1.126 brouard 1940: double (*func)(double []));
1.224 brouard 1941: #else
1942: void linmin(double p[], double xi[], int n, double *fret,
1943: double (*func)(double []),int *flat);
1944: #endif
1.126 brouard 1945: int i,ibig,j;
1946: double del,t,*pt,*ptt,*xit;
1.181 brouard 1947: double directest;
1.126 brouard 1948: double fp,fptt;
1949: double *xits;
1950: int niterf, itmp;
1.224 brouard 1951: #ifdef LINMINORIGINAL
1952: #else
1953:
1954: flatdir=ivector(1,n);
1955: for (j=1;j<=n;j++) flatdir[j]=0;
1956: #endif
1.126 brouard 1957:
1958: pt=vector(1,n);
1959: ptt=vector(1,n);
1960: xit=vector(1,n);
1961: xits=vector(1,n);
1962: *fret=(*func)(p);
1963: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 1964: rcurr_time = time(NULL);
1.126 brouard 1965: for (*iter=1;;++(*iter)) {
1.187 brouard 1966: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1967: ibig=0;
1968: del=0.0;
1.157 brouard 1969: rlast_time=rcurr_time;
1970: /* (void) gettimeofday(&curr_time,&tzp); */
1971: rcurr_time = time(NULL);
1972: curr_time = *localtime(&rcurr_time);
1973: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1974: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1975: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1976: for (i=1;i<=n;i++) {
1.126 brouard 1977: printf(" %d %.12f",i, p[i]);
1978: fprintf(ficlog," %d %.12lf",i, p[i]);
1979: fprintf(ficrespow," %.12lf", p[i]);
1980: }
1981: printf("\n");
1982: fprintf(ficlog,"\n");
1983: fprintf(ficrespow,"\n");fflush(ficrespow);
1984: if(*iter <=3){
1.157 brouard 1985: tml = *localtime(&rcurr_time);
1986: strcpy(strcurr,asctime(&tml));
1987: rforecast_time=rcurr_time;
1.126 brouard 1988: itmp = strlen(strcurr);
1989: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.224 brouard 1990: strcurr[itmp-1]='\0';
1.162 brouard 1991: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1992: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1993: for(niterf=10;niterf<=30;niterf+=10){
1.224 brouard 1994: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1995: forecast_time = *localtime(&rforecast_time);
1996: strcpy(strfor,asctime(&forecast_time));
1997: itmp = strlen(strfor);
1998: if(strfor[itmp-1]=='\n')
1999: strfor[itmp-1]='\0';
2000: 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);
2001: 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 2002: }
2003: }
1.187 brouard 2004: for (i=1;i<=n;i++) { /* For each direction i */
2005: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 2006: fptt=(*fret);
2007: #ifdef DEBUG
1.203 brouard 2008: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
2009: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 2010: #endif
1.203 brouard 2011: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 2012: fprintf(ficlog,"%d",i);fflush(ficlog);
1.224 brouard 2013: #ifdef LINMINORIGINAL
1.188 brouard 2014: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1.224 brouard 2015: #else
2016: linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
2017: flatdir[i]=flat; /* Function is vanishing in that direction i */
2018: #endif
2019: /* Outputs are fret(new point p) p is updated and xit rescaled */
1.188 brouard 2020: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1.224 brouard 2021: /* because that direction will be replaced unless the gain del is small */
2022: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
2023: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
2024: /* with the new direction. */
2025: del=fabs(fptt-(*fret));
2026: ibig=i;
1.126 brouard 2027: }
2028: #ifdef DEBUG
2029: printf("%d %.12e",i,(*fret));
2030: fprintf(ficlog,"%d %.12e",i,(*fret));
2031: for (j=1;j<=n;j++) {
1.224 brouard 2032: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
2033: printf(" x(%d)=%.12e",j,xit[j]);
2034: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1.126 brouard 2035: }
2036: for(j=1;j<=n;j++) {
1.225 brouard 2037: printf(" p(%d)=%.12e",j,p[j]);
2038: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 2039: }
2040: printf("\n");
2041: fprintf(ficlog,"\n");
2042: #endif
1.187 brouard 2043: } /* end loop on each direction i */
2044: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 2045: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 2046: /* New value of last point Pn is not computed, P(n-1) */
1.224 brouard 2047: for(j=1;j<=n;j++) {
1.225 brouard 2048: if(flatdir[j] >0){
2049: printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2050: fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2051: }
2052: /* printf("\n"); */
2053: /* fprintf(ficlog,"\n"); */
2054: }
1.182 brouard 2055: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 2056: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
2057: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
2058: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
2059: /* decreased of more than 3.84 */
2060: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
2061: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
2062: /* By adding 10 parameters more the gain should be 18.31 */
1.224 brouard 2063:
1.188 brouard 2064: /* Starting the program with initial values given by a former maximization will simply change */
2065: /* the scales of the directions and the directions, because the are reset to canonical directions */
2066: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
2067: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 2068: #ifdef DEBUG
2069: int k[2],l;
2070: k[0]=1;
2071: k[1]=-1;
2072: printf("Max: %.12e",(*func)(p));
2073: fprintf(ficlog,"Max: %.12e",(*func)(p));
2074: for (j=1;j<=n;j++) {
2075: printf(" %.12e",p[j]);
2076: fprintf(ficlog," %.12e",p[j]);
2077: }
2078: printf("\n");
2079: fprintf(ficlog,"\n");
2080: for(l=0;l<=1;l++) {
2081: for (j=1;j<=n;j++) {
2082: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
2083: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2084: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2085: }
2086: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2087: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2088: }
2089: #endif
2090:
1.224 brouard 2091: #ifdef LINMINORIGINAL
2092: #else
2093: free_ivector(flatdir,1,n);
2094: #endif
1.126 brouard 2095: free_vector(xit,1,n);
2096: free_vector(xits,1,n);
2097: free_vector(ptt,1,n);
2098: free_vector(pt,1,n);
2099: return;
1.192 brouard 2100: } /* enough precision */
1.126 brouard 2101: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 2102: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 2103: ptt[j]=2.0*p[j]-pt[j];
2104: xit[j]=p[j]-pt[j];
2105: pt[j]=p[j];
2106: }
1.181 brouard 2107: fptt=(*func)(ptt); /* f_3 */
1.224 brouard 2108: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
2109: if (*iter <=4) {
1.225 brouard 2110: #else
2111: #endif
1.224 brouard 2112: #ifdef POWELLNOF3INFF1TEST /* skips test F3 <F1 */
1.192 brouard 2113: #else
1.161 brouard 2114: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 2115: #endif
1.162 brouard 2116: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 2117: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 2118: /* Let f"(x2) be the 2nd derivative equal everywhere. */
2119: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
2120: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.224 brouard 2121: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
2122: /* also lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
2123: /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
1.161 brouard 2124: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.224 brouard 2125: /* Even if f3 <f1, directest can be negative and t >0 */
2126: /* mu² and del² are equal when f3=f1 */
2127: /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
2128: /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
2129: /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0 */
2130: /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0 */
1.183 brouard 2131: #ifdef NRCORIGINAL
2132: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
2133: #else
2134: 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 2135: t= t- del*SQR(fp-fptt);
1.183 brouard 2136: #endif
1.202 brouard 2137: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 2138: #ifdef DEBUG
1.181 brouard 2139: 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);
2140: 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 2141: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2142: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2143: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2144: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2145: 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);
2146: 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);
2147: #endif
1.183 brouard 2148: #ifdef POWELLORIGINAL
2149: if (t < 0.0) { /* Then we use it for new direction */
2150: #else
1.182 brouard 2151: if (directest*t < 0.0) { /* Contradiction between both tests */
1.224 brouard 2152: 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 2153: 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 2154: 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 2155: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
2156: }
1.181 brouard 2157: if (directest < 0.0) { /* Then we use it for new direction */
2158: #endif
1.191 brouard 2159: #ifdef DEBUGLINMIN
1.224 brouard 2160: printf("Before linmin in direction P%d-P0\n",n);
2161: for (j=1;j<=n;j++) {
2162: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2163: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2164: if(j % ncovmodel == 0){
2165: printf("\n");
2166: fprintf(ficlog,"\n");
2167: }
2168: }
2169: #endif
2170: #ifdef LINMINORIGINAL
2171: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
2172: #else
2173: linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
2174: flatdir[i]=flat; /* Function is vanishing in that direction i */
1.191 brouard 2175: #endif
1.224 brouard 2176:
1.191 brouard 2177: #ifdef DEBUGLINMIN
1.224 brouard 2178: for (j=1;j<=n;j++) {
2179: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2180: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2181: if(j % ncovmodel == 0){
2182: printf("\n");
2183: fprintf(ficlog,"\n");
2184: }
2185: }
2186: #endif
2187: for (j=1;j<=n;j++) {
2188: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
2189: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
2190: }
2191: #ifdef LINMINORIGINAL
2192: #else
1.225 brouard 2193: for (j=1, flatd=0;j<=n;j++) {
2194: if(flatdir[j]>0)
2195: flatd++;
2196: }
2197: if(flatd >0){
2198: printf("%d flat directions\n",flatd);
2199: fprintf(ficlog,"%d flat directions\n",flatd);
2200: for (j=1;j<=n;j++) {
2201: if(flatdir[j]>0){
2202: printf("%d ",j);
2203: fprintf(ficlog,"%d ",j);
2204: }
2205: }
2206: printf("\n");
2207: fprintf(ficlog,"\n");
2208: }
1.191 brouard 2209: #endif
1.224 brouard 2210: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2211: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2212:
1.126 brouard 2213: #ifdef DEBUG
1.224 brouard 2214: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2215: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2216: for(j=1;j<=n;j++){
2217: printf(" %lf",xit[j]);
2218: fprintf(ficlog," %lf",xit[j]);
2219: }
2220: printf("\n");
2221: fprintf(ficlog,"\n");
1.126 brouard 2222: #endif
1.192 brouard 2223: } /* end of t or directest negative */
1.224 brouard 2224: #ifdef POWELLNOF3INFF1TEST
1.192 brouard 2225: #else
1.162 brouard 2226: } /* end if (fptt < fp) */
1.192 brouard 2227: #endif
1.225 brouard 2228: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
1.224 brouard 2229: } /*NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done */
1.225 brouard 2230: #else
1.224 brouard 2231: #endif
1.192 brouard 2232: } /* loop iteration */
1.126 brouard 2233: }
2234:
2235: /**** Prevalence limit (stable or period prevalence) ****************/
2236:
1.203 brouard 2237: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
1.126 brouard 2238: {
1.218 brouard 2239: /* Computes the prevalence limit in each live state at age x and for covariate ij by left multiplying the unit
1.203 brouard 2240: matrix by transitions matrix until convergence is reached with precision ftolpl */
1.206 brouard 2241: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2242: /* Wx is row vector: population in state 1, population in state 2, population dead */
2243: /* or prevalence in state 1, prevalence in state 2, 0 */
2244: /* newm is the matrix after multiplications, its rows are identical at a factor */
2245: /* Initial matrix pimij */
2246: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2247: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2248: /* 0, 0 , 1} */
2249: /*
2250: * and after some iteration: */
2251: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2252: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2253: /* 0, 0 , 1} */
2254: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2255: /* {0.51571254859325999, 0.4842874514067399, */
2256: /* 0.51326036147820708, 0.48673963852179264} */
2257: /* If we start from prlim again, prlim tends to a constant matrix */
2258:
1.126 brouard 2259: int i, ii,j,k;
1.209 brouard 2260: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2261: /* double **matprod2(); */ /* test */
1.218 brouard 2262: double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126 brouard 2263: double **newm;
1.209 brouard 2264: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2265: int ncvloop=0;
1.169 brouard 2266:
1.209 brouard 2267: min=vector(1,nlstate);
2268: max=vector(1,nlstate);
2269: meandiff=vector(1,nlstate);
2270:
1.218 brouard 2271: /* Starting with matrix unity */
1.126 brouard 2272: for (ii=1;ii<=nlstate+ndeath;ii++)
2273: for (j=1;j<=nlstate+ndeath;j++){
2274: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2275: }
1.169 brouard 2276:
2277: cov[1]=1.;
2278:
2279: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2280: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2281: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2282: ncvloop++;
1.126 brouard 2283: newm=savm;
2284: /* Covariates have to be included here again */
1.138 brouard 2285: cov[2]=agefin;
1.187 brouard 2286: if(nagesqr==1)
2287: cov[3]= agefin*agefin;;
1.138 brouard 2288: for (k=1; k<=cptcovn;k++) {
1.200 brouard 2289: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.218 brouard 2290: /* Here comes the value of the covariate 'ij' */
1.200 brouard 2291: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
1.198 brouard 2292: /* 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 2293: }
1.186 brouard 2294: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2295: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2296: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
1.186 brouard 2297: for (k=1; k<=cptcovprod;k++) /* Useless */
1.200 brouard 2298: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2299: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.138 brouard 2300:
2301: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2302: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2303: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2304: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2305: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2306: /* age and covariate values of ij are in 'cov' */
1.142 brouard 2307: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2308:
1.126 brouard 2309: savm=oldm;
2310: oldm=newm;
1.209 brouard 2311:
2312: for(j=1; j<=nlstate; j++){
2313: max[j]=0.;
2314: min[j]=1.;
2315: }
2316: for(i=1;i<=nlstate;i++){
2317: sumnew=0;
2318: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2319: for(j=1; j<=nlstate; j++){
2320: prlim[i][j]= newm[i][j]/(1-sumnew);
2321: max[j]=FMAX(max[j],prlim[i][j]);
2322: min[j]=FMIN(min[j],prlim[i][j]);
2323: }
2324: }
2325:
1.126 brouard 2326: maxmax=0.;
1.209 brouard 2327: for(j=1; j<=nlstate; j++){
2328: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2329: maxmax=FMAX(maxmax,meandiff[j]);
2330: /* 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 2331: } /* j loop */
1.203 brouard 2332: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2333: /* 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 2334: if(maxmax < ftolpl){
1.209 brouard 2335: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2336: free_vector(min,1,nlstate);
2337: free_vector(max,1,nlstate);
2338: free_vector(meandiff,1,nlstate);
1.126 brouard 2339: return prlim;
2340: }
1.169 brouard 2341: } /* age loop */
1.208 brouard 2342: /* After some age loop it doesn't converge */
1.209 brouard 2343: 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 2344: 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 2345: /* 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); */
2346: free_vector(min,1,nlstate);
2347: free_vector(max,1,nlstate);
2348: free_vector(meandiff,1,nlstate);
1.208 brouard 2349:
1.169 brouard 2350: return prlim; /* should not reach here */
1.126 brouard 2351: }
2352:
1.217 brouard 2353:
2354: /**** Back Prevalence limit (stable or period prevalence) ****************/
2355:
1.218 brouard 2356: /* 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) */
2357: /* 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) */
2358: double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij)
1.217 brouard 2359: {
1.218 brouard 2360: /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit
1.217 brouard 2361: matrix by transitions matrix until convergence is reached with precision ftolpl */
2362: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2363: /* Wx is row vector: population in state 1, population in state 2, population dead */
2364: /* or prevalence in state 1, prevalence in state 2, 0 */
2365: /* newm is the matrix after multiplications, its rows are identical at a factor */
2366: /* Initial matrix pimij */
2367: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2368: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2369: /* 0, 0 , 1} */
2370: /*
2371: * and after some iteration: */
2372: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2373: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2374: /* 0, 0 , 1} */
2375: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2376: /* {0.51571254859325999, 0.4842874514067399, */
2377: /* 0.51326036147820708, 0.48673963852179264} */
2378: /* If we start from prlim again, prlim tends to a constant matrix */
2379:
2380: int i, ii,j,k;
2381: double *min, *max, *meandiff, maxmax,sumnew=0.;
2382: /* double **matprod2(); */ /* test */
2383: double **out, cov[NCOVMAX+1], **bmij();
2384: double **newm;
1.218 brouard 2385: double **dnewm, **doldm, **dsavm; /* for use */
2386: double **oldm, **savm; /* for use */
2387:
1.217 brouard 2388: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
2389: int ncvloop=0;
2390:
2391: min=vector(1,nlstate);
2392: max=vector(1,nlstate);
2393: meandiff=vector(1,nlstate);
2394:
1.218 brouard 2395: dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
2396: oldm=oldms; savm=savms;
2397:
2398: /* Starting with matrix unity */
2399: for (ii=1;ii<=nlstate+ndeath;ii++)
2400: for (j=1;j<=nlstate+ndeath;j++){
1.217 brouard 2401: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2402: }
2403:
2404: cov[1]=1.;
2405:
2406: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2407: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218 brouard 2408: /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
2409: for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217 brouard 2410: ncvloop++;
1.218 brouard 2411: newm=savm; /* oldm should be kept from previous iteration or unity at start */
2412: /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217 brouard 2413: /* Covariates have to be included here again */
2414: cov[2]=agefin;
2415: if(nagesqr==1)
2416: cov[3]= agefin*agefin;;
2417: for (k=1; k<=cptcovn;k++) {
2418: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
2419: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2420: /* 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])]); */
2421: }
2422: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2423: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2424: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
2425: for (k=1; k<=cptcovprod;k++) /* Useless */
2426: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2427: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2428:
2429: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2430: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2431: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
2432: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2433: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2434: /* ij should be linked to the correct index of cov */
2435: /* age and covariate values ij are in 'cov', but we need to pass
2436: * ij for the observed prevalence at age and status and covariate
2437: * number: prevacurrent[(int)agefin][ii][ij]
2438: */
2439: /* 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 *\/ */
2440: /* 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 *\/ */
2441: 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 2442: savm=oldm;
2443: oldm=newm;
2444: for(j=1; j<=nlstate; j++){
2445: max[j]=0.;
2446: min[j]=1.;
2447: }
2448: for(j=1; j<=nlstate; j++){
2449: for(i=1;i<=nlstate;i++){
1.218 brouard 2450: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
2451: bprlim[i][j]= newm[i][j];
2452: max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
2453: min[i]=FMIN(min[i],bprlim[i][j]);
1.217 brouard 2454: }
2455: }
1.218 brouard 2456:
1.217 brouard 2457: maxmax=0.;
2458: for(i=1; i<=nlstate; i++){
2459: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
2460: maxmax=FMAX(maxmax,meandiff[i]);
2461: /* 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); */
2462: } /* j loop */
2463: *ncvyear= -( (int)age- (int)agefin);
1.218 brouard 2464: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/
1.217 brouard 2465: if(maxmax < ftolpl){
1.220 brouard 2466: /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2467: free_vector(min,1,nlstate);
2468: free_vector(max,1,nlstate);
2469: free_vector(meandiff,1,nlstate);
2470: return bprlim;
2471: }
2472: } /* age loop */
2473: /* After some age loop it doesn't converge */
2474: 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\
2475: 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);
2476: /* 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); */
2477: free_vector(min,1,nlstate);
2478: free_vector(max,1,nlstate);
2479: free_vector(meandiff,1,nlstate);
2480:
2481: return bprlim; /* should not reach here */
2482: }
2483:
1.126 brouard 2484: /*************** transition probabilities ***************/
2485:
2486: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2487: {
1.138 brouard 2488: /* According to parameters values stored in x and the covariate's values stored in cov,
2489: computes the probability to be observed in state j being in state i by appying the
2490: model to the ncovmodel covariates (including constant and age).
2491: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2492: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2493: ncth covariate in the global vector x is given by the formula:
2494: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2495: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2496: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2497: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2498: Outputs ps[i][j] the probability to be observed in j being in j according to
2499: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2500: */
2501: double s1, lnpijopii;
1.126 brouard 2502: /*double t34;*/
1.164 brouard 2503: int i,j, nc, ii, jj;
1.126 brouard 2504:
1.223 brouard 2505: for(i=1; i<= nlstate; i++){
2506: for(j=1; j<i;j++){
2507: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2508: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2509: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2510: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2511: }
2512: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2513: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2514: }
2515: for(j=i+1; j<=nlstate+ndeath;j++){
2516: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2517: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2518: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2519: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2520: }
2521: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2522: }
2523: }
1.218 brouard 2524:
1.223 brouard 2525: for(i=1; i<= nlstate; i++){
2526: s1=0;
2527: for(j=1; j<i; j++){
2528: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2529: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2530: }
2531: for(j=i+1; j<=nlstate+ndeath; j++){
2532: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2533: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2534: }
2535: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2536: ps[i][i]=1./(s1+1.);
2537: /* Computing other pijs */
2538: for(j=1; j<i; j++)
2539: ps[i][j]= exp(ps[i][j])*ps[i][i];
2540: for(j=i+1; j<=nlstate+ndeath; j++)
2541: ps[i][j]= exp(ps[i][j])*ps[i][i];
2542: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2543: } /* end i */
1.218 brouard 2544:
1.223 brouard 2545: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2546: for(jj=1; jj<= nlstate+ndeath; jj++){
2547: ps[ii][jj]=0;
2548: ps[ii][ii]=1;
2549: }
2550: }
1.218 brouard 2551:
2552:
1.223 brouard 2553: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2554: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2555: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2556: /* } */
2557: /* printf("\n "); */
2558: /* } */
2559: /* printf("\n ");printf("%lf ",cov[2]);*/
2560: /*
2561: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1.218 brouard 2562: goto end;*/
1.223 brouard 2563: return ps;
1.126 brouard 2564: }
2565:
1.218 brouard 2566: /*************** backward transition probabilities ***************/
2567:
2568: /* 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 ) */
2569: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
2570: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij )
2571: {
1.222 brouard 2572: /* Computes the backward probability at age agefin and covariate ij
2573: * and returns in **ps as well as **bmij.
2574: */
1.218 brouard 2575: int i, ii, j,k;
1.222 brouard 2576:
2577: double **out, **pmij();
2578: double sumnew=0.;
1.218 brouard 2579: double agefin;
1.222 brouard 2580:
2581: double **dnewm, **dsavm, **doldm;
2582: double **bbmij;
2583:
1.218 brouard 2584: doldm=ddoldms; /* global pointers */
1.222 brouard 2585: dnewm=ddnewms;
2586: dsavm=ddsavms;
2587:
2588: agefin=cov[2];
2589: /* bmij *//* age is cov[2], ij is included in cov, but we need for
2590: the observed prevalence (with this covariate ij) */
2591: dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
2592: /* We do have the matrix Px in savm and we need pij */
2593: for (j=1;j<=nlstate+ndeath;j++){
2594: sumnew=0.; /* w1 p11 + w2 p21 only on live states */
2595: for (ii=1;ii<=nlstate;ii++){
2596: sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
2597: } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
2598: for (ii=1;ii<=nlstate+ndeath;ii++){
2599: if(sumnew >= 1.e-10){
2600: /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
2601: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
2602: /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
2603: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
2604: /* }else */
2605: doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
2606: }else{
2607: 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);
2608: }
2609: } /*End ii */
2610: } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
2611: /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
2612: bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
2613: /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
2614: /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
2615: /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
2616: /* left Product of this matrix by diag matrix of prevalences (savm) */
2617: for (j=1;j<=nlstate+ndeath;j++){
2618: for (ii=1;ii<=nlstate+ndeath;ii++){
2619: dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
2620: }
2621: } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
2622: ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
2623: /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
2624: /* end bmij */
2625: return ps;
1.218 brouard 2626: }
1.217 brouard 2627: /*************** transition probabilities ***************/
2628:
1.218 brouard 2629: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217 brouard 2630: {
2631: /* According to parameters values stored in x and the covariate's values stored in cov,
2632: computes the probability to be observed in state j being in state i by appying the
2633: model to the ncovmodel covariates (including constant and age).
2634: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2635: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2636: ncth covariate in the global vector x is given by the formula:
2637: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2638: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2639: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2640: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2641: Outputs ps[i][j] the probability to be observed in j being in j according to
2642: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2643: */
2644: double s1, lnpijopii;
2645: /*double t34;*/
2646: int i,j, nc, ii, jj;
2647:
1.218 brouard 2648: for(i=1; i<= nlstate; i++){
2649: for(j=1; j<i;j++){
2650: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2651: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2652: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2653: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2654: }
2655: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2656: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2657: }
2658: for(j=i+1; j<=nlstate+ndeath;j++){
2659: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2660: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2661: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2662: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2663: }
2664: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2665: }
2666: }
2667:
2668: for(i=1; i<= nlstate; i++){
2669: s1=0;
2670: for(j=1; j<i; j++){
2671: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2672: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2673: }
2674: for(j=i+1; j<=nlstate+ndeath; j++){
2675: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2676: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2677: }
2678: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2679: ps[i][i]=1./(s1+1.);
2680: /* Computing other pijs */
2681: for(j=1; j<i; j++)
2682: ps[i][j]= exp(ps[i][j])*ps[i][i];
2683: for(j=i+1; j<=nlstate+ndeath; j++)
2684: ps[i][j]= exp(ps[i][j])*ps[i][i];
2685: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2686: } /* end i */
2687:
2688: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2689: for(jj=1; jj<= nlstate+ndeath; jj++){
2690: ps[ii][jj]=0;
2691: ps[ii][ii]=1;
2692: }
2693: }
2694: /* Added for backcast */ /* Transposed matrix too */
2695: for(jj=1; jj<= nlstate+ndeath; jj++){
2696: s1=0.;
2697: for(ii=1; ii<= nlstate+ndeath; ii++){
2698: s1+=ps[ii][jj];
2699: }
2700: for(ii=1; ii<= nlstate; ii++){
2701: ps[ii][jj]=ps[ii][jj]/s1;
2702: }
2703: }
2704: /* Transposition */
2705: for(jj=1; jj<= nlstate+ndeath; jj++){
2706: for(ii=jj; ii<= nlstate+ndeath; ii++){
2707: s1=ps[ii][jj];
2708: ps[ii][jj]=ps[jj][ii];
2709: ps[jj][ii]=s1;
2710: }
2711: }
2712: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2713: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2714: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2715: /* } */
2716: /* printf("\n "); */
2717: /* } */
2718: /* printf("\n ");printf("%lf ",cov[2]);*/
2719: /*
2720: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2721: goto end;*/
2722: return ps;
1.217 brouard 2723: }
2724:
2725:
1.126 brouard 2726: /**************** Product of 2 matrices ******************/
2727:
1.145 brouard 2728: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2729: {
2730: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2731: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2732: /* in, b, out are matrice of pointers which should have been initialized
2733: before: only the contents of out is modified. The function returns
2734: a pointer to pointers identical to out */
1.145 brouard 2735: int i, j, k;
1.126 brouard 2736: for(i=nrl; i<= nrh; i++)
1.145 brouard 2737: for(k=ncolol; k<=ncoloh; k++){
2738: out[i][k]=0.;
2739: for(j=ncl; j<=nch; j++)
2740: out[i][k] +=in[i][j]*b[j][k];
2741: }
1.126 brouard 2742: return out;
2743: }
2744:
2745:
2746: /************* Higher Matrix Product ***************/
2747:
2748: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2749: {
1.218 brouard 2750: /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
1.126 brouard 2751: 'nhstepm*hstepm*stepm' months (i.e. until
2752: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2753: nhstepm*hstepm matrices.
2754: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2755: (typically every 2 years instead of every month which is too big
2756: for the memory).
2757: Model is determined by parameters x and covariates have to be
2758: included manually here.
2759:
2760: */
2761:
2762: int i, j, d, h, k;
1.131 brouard 2763: double **out, cov[NCOVMAX+1];
1.126 brouard 2764: double **newm;
1.187 brouard 2765: double agexact;
1.214 brouard 2766: double agebegin, ageend;
1.126 brouard 2767:
2768: /* Hstepm could be zero and should return the unit matrix */
2769: for (i=1;i<=nlstate+ndeath;i++)
2770: for (j=1;j<=nlstate+ndeath;j++){
2771: oldm[i][j]=(i==j ? 1.0 : 0.0);
2772: po[i][j][0]=(i==j ? 1.0 : 0.0);
2773: }
2774: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2775: for(h=1; h <=nhstepm; h++){
2776: for(d=1; d <=hstepm; d++){
2777: newm=savm;
2778: /* Covariates have to be included here again */
2779: cov[1]=1.;
1.214 brouard 2780: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 2781: cov[2]=agexact;
2782: if(nagesqr==1)
1.227 ! brouard 2783: cov[3]= agexact*agexact;
1.131 brouard 2784: for (k=1; k<=cptcovn;k++)
1.227 ! brouard 2785: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
! 2786: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.186 brouard 2787: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1.227 ! brouard 2788: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
! 2789: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
! 2790: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.145 brouard 2791: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.227 ! brouard 2792: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
! 2793: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
! 2794:
! 2795:
1.126 brouard 2796: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2797: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 2798: /* right multiplication of oldm by the current matrix */
1.126 brouard 2799: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2800: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 brouard 2801: /* if((int)age == 70){ */
2802: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
2803: /* for(i=1; i<=nlstate+ndeath; i++) { */
2804: /* printf("%d pmmij ",i); */
2805: /* for(j=1;j<=nlstate+ndeath;j++) { */
2806: /* printf("%f ",pmmij[i][j]); */
2807: /* } */
2808: /* printf(" oldm "); */
2809: /* for(j=1;j<=nlstate+ndeath;j++) { */
2810: /* printf("%f ",oldm[i][j]); */
2811: /* } */
2812: /* printf("\n"); */
2813: /* } */
2814: /* } */
1.126 brouard 2815: savm=oldm;
2816: oldm=newm;
2817: }
2818: for(i=1; i<=nlstate+ndeath; i++)
2819: for(j=1;j<=nlstate+ndeath;j++) {
1.218 brouard 2820: po[i][j][h]=newm[i][j];
2821: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2822: }
1.128 brouard 2823: /*printf("h=%d ",h);*/
1.126 brouard 2824: } /* end h */
1.218 brouard 2825: /* printf("\n H=%d \n",h); */
1.126 brouard 2826: return po;
2827: }
2828:
1.217 brouard 2829: /************* Higher Back Matrix Product ***************/
1.218 brouard 2830: /* 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 2831: double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )
1.217 brouard 2832: {
1.218 brouard 2833: /* Computes the transition matrix starting at age 'age' over
1.217 brouard 2834: 'nhstepm*hstepm*stepm' months (i.e. until
1.218 brouard 2835: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2836: nhstepm*hstepm matrices.
2837: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2838: (typically every 2 years instead of every month which is too big
1.217 brouard 2839: for the memory).
1.218 brouard 2840: Model is determined by parameters x and covariates have to be
2841: included manually here.
1.217 brouard 2842:
1.222 brouard 2843: */
1.217 brouard 2844:
2845: int i, j, d, h, k;
2846: double **out, cov[NCOVMAX+1];
2847: double **newm;
2848: double agexact;
2849: double agebegin, ageend;
1.222 brouard 2850: double **oldm, **savm;
1.217 brouard 2851:
1.222 brouard 2852: oldm=oldms;savm=savms;
1.217 brouard 2853: /* Hstepm could be zero and should return the unit matrix */
2854: for (i=1;i<=nlstate+ndeath;i++)
2855: for (j=1;j<=nlstate+ndeath;j++){
2856: oldm[i][j]=(i==j ? 1.0 : 0.0);
2857: po[i][j][0]=(i==j ? 1.0 : 0.0);
2858: }
2859: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2860: for(h=1; h <=nhstepm; h++){
2861: for(d=1; d <=hstepm; d++){
2862: newm=savm;
2863: /* Covariates have to be included here again */
2864: cov[1]=1.;
2865: agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
2866: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
2867: cov[2]=agexact;
2868: if(nagesqr==1)
1.222 brouard 2869: cov[3]= agexact*agexact;
1.218 brouard 2870: for (k=1; k<=cptcovn;k++)
1.222 brouard 2871: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2872: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.217 brouard 2873: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1.222 brouard 2874: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2875: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2876: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.217 brouard 2877: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.222 brouard 2878: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2879: /* 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 2880:
2881:
1.217 brouard 2882: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2883: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 2884: /* Careful transposed matrix */
1.222 brouard 2885: /* age is in cov[2] */
1.218 brouard 2886: /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
1.222 brouard 2887: /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
1.218 brouard 2888: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1.222 brouard 2889: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217 brouard 2890: /* if((int)age == 70){ */
2891: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
2892: /* for(i=1; i<=nlstate+ndeath; i++) { */
2893: /* printf("%d pmmij ",i); */
2894: /* for(j=1;j<=nlstate+ndeath;j++) { */
2895: /* printf("%f ",pmmij[i][j]); */
2896: /* } */
2897: /* printf(" oldm "); */
2898: /* for(j=1;j<=nlstate+ndeath;j++) { */
2899: /* printf("%f ",oldm[i][j]); */
2900: /* } */
2901: /* printf("\n"); */
2902: /* } */
2903: /* } */
2904: savm=oldm;
2905: oldm=newm;
2906: }
2907: for(i=1; i<=nlstate+ndeath; i++)
2908: for(j=1;j<=nlstate+ndeath;j++) {
1.222 brouard 2909: po[i][j][h]=newm[i][j];
2910: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.217 brouard 2911: }
2912: /*printf("h=%d ",h);*/
2913: } /* end h */
1.222 brouard 2914: /* printf("\n H=%d \n",h); */
1.217 brouard 2915: return po;
2916: }
2917:
2918:
1.162 brouard 2919: #ifdef NLOPT
2920: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2921: double fret;
2922: double *xt;
2923: int j;
2924: myfunc_data *d2 = (myfunc_data *) pd;
2925: /* xt = (p1-1); */
2926: xt=vector(1,n);
2927: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2928:
2929: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2930: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2931: printf("Function = %.12lf ",fret);
2932: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2933: printf("\n");
2934: free_vector(xt,1,n);
2935: return fret;
2936: }
2937: #endif
1.126 brouard 2938:
2939: /*************** log-likelihood *************/
2940: double func( double *x)
2941: {
1.226 brouard 2942: int i, ii, j, k, mi, d, kk;
2943: int ioffset=0;
2944: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
2945: double **out;
2946: double sw; /* Sum of weights */
2947: double lli; /* Individual log likelihood */
2948: int s1, s2;
2949: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quatitative time varying covariate */
2950: double bbh, survp;
2951: long ipmx;
2952: double agexact;
2953: /*extern weight */
2954: /* We are differentiating ll according to initial status */
2955: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2956: /*for(i=1;i<imx;i++)
2957: printf(" %d\n",s[4][i]);
2958: */
1.162 brouard 2959:
1.226 brouard 2960: ++countcallfunc;
1.162 brouard 2961:
1.226 brouard 2962: cov[1]=1.;
1.126 brouard 2963:
1.226 brouard 2964: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 2965: ioffset=0;
1.226 brouard 2966: if(mle==1){
2967: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2968: /* Computes the values of the ncovmodel covariates of the model
2969: depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
2970: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2971: to be observed in j being in i according to the model.
2972: */
2973: ioffset=2+nagesqr+cptcovage;
2974: /* for (k=1; k<=cptcovn;k++){ /\* Simple and product covariates without age* products *\/ */
2975: for (k=1; k<=ncoveff;k++){ /* Simple and product covariates without age* products */
2976: cov[++ioffset]=covar[Tvar[k]][i];
2977: }
2978: for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitatives and Fixed covariates */
2979: cov[++ioffset]=coqvar[iqv][i];
2980: }
2981:
2982: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
2983: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
2984: has been calculated etc */
2985: /* For an individual i, wav[i] gives the number of effective waves */
2986: /* We compute the contribution to Likelihood of each effective transition
2987: mw[mi][i] is real wave of the mi th effectve wave */
2988: /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
2989: s2=s[mw[mi+1][i]][i];
2990: And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
2991: But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
2992: meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
2993: */
2994: for(mi=1; mi<= wav[i]-1; mi++){
2995: for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
2996: cov[ioffset+itv]=cotvar[mw[mi][i]][itv][i];
2997: }
2998: for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
2999: if(cotqvar[mw[mi][i]][iqtv][i] == -1){
3000: printf("i=%d, mi=%d, iqtv=%d, cotqvar[mw[mi][i]][iqtv][i]=%f",i,mi,iqtv,cotqvar[mw[mi][i]][iqtv][i]);
3001: }
3002: cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i];
3003: }
3004: /* ioffset=2+nagesqr+cptcovn+nqv+ntv+nqtv; */
3005: for (ii=1;ii<=nlstate+ndeath;ii++)
3006: for (j=1;j<=nlstate+ndeath;j++){
3007: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3008: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3009: }
3010: for(d=0; d<dh[mi][i]; d++){
3011: newm=savm;
3012: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3013: cov[2]=agexact;
3014: if(nagesqr==1)
3015: cov[3]= agexact*agexact; /* Should be changed here */
3016: for (kk=1; kk<=cptcovage;kk++) {
3017: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
3018: }
3019: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3020: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3021: savm=oldm;
3022: oldm=newm;
3023: } /* end mult */
1.224 brouard 3024:
1.226 brouard 3025: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
3026: /* But now since version 0.9 we anticipate for bias at large stepm.
3027: * If stepm is larger than one month (smallest stepm) and if the exact delay
3028: * (in months) between two waves is not a multiple of stepm, we rounded to
3029: * the nearest (and in case of equal distance, to the lowest) interval but now
3030: * we keep into memory the bias bh[mi][i] and also the previous matrix product
3031: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
3032: * probability in order to take into account the bias as a fraction of the way
3033: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
3034: * -stepm/2 to stepm/2 .
3035: * For stepm=1 the results are the same as for previous versions of Imach.
3036: * For stepm > 1 the results are less biased than in previous versions.
3037: */
3038: s1=s[mw[mi][i]][i];
3039: s2=s[mw[mi+1][i]][i];
3040: bbh=(double)bh[mi][i]/(double)stepm;
3041: /* bias bh is positive if real duration
3042: * is higher than the multiple of stepm and negative otherwise.
3043: */
3044: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
3045: if( s2 > nlstate){
3046: /* i.e. if s2 is a death state and if the date of death is known
3047: then the contribution to the likelihood is the probability to
3048: die between last step unit time and current step unit time,
3049: which is also equal to probability to die before dh
3050: minus probability to die before dh-stepm .
3051: In version up to 0.92 likelihood was computed
3052: as if date of death was unknown. Death was treated as any other
3053: health state: the date of the interview describes the actual state
3054: and not the date of a change in health state. The former idea was
3055: to consider that at each interview the state was recorded
3056: (healthy, disable or death) and IMaCh was corrected; but when we
3057: introduced the exact date of death then we should have modified
3058: the contribution of an exact death to the likelihood. This new
3059: contribution is smaller and very dependent of the step unit
3060: stepm. It is no more the probability to die between last interview
3061: and month of death but the probability to survive from last
3062: interview up to one month before death multiplied by the
3063: probability to die within a month. Thanks to Chris
3064: Jackson for correcting this bug. Former versions increased
3065: mortality artificially. The bad side is that we add another loop
3066: which slows down the processing. The difference can be up to 10%
3067: lower mortality.
3068: */
3069: /* If, at the beginning of the maximization mostly, the
3070: cumulative probability or probability to be dead is
3071: constant (ie = 1) over time d, the difference is equal to
3072: 0. out[s1][3] = savm[s1][3]: probability, being at state
3073: s1 at precedent wave, to be dead a month before current
3074: wave is equal to probability, being at state s1 at
3075: precedent wave, to be dead at mont of the current
3076: wave. Then the observed probability (that this person died)
3077: is null according to current estimated parameter. In fact,
3078: it should be very low but not zero otherwise the log go to
3079: infinity.
3080: */
1.183 brouard 3081: /* #ifdef INFINITYORIGINAL */
3082: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3083: /* #else */
3084: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
3085: /* lli=log(mytinydouble); */
3086: /* else */
3087: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3088: /* #endif */
1.226 brouard 3089: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3090:
1.226 brouard 3091: } else if ( s2==-1 ) { /* alive */
3092: for (j=1,survp=0. ; j<=nlstate; j++)
3093: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3094: /*survp += out[s1][j]; */
3095: lli= log(survp);
3096: }
3097: else if (s2==-4) {
3098: for (j=3,survp=0. ; j<=nlstate; j++)
3099: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3100: lli= log(survp);
3101: }
3102: else if (s2==-5) {
3103: for (j=1,survp=0. ; j<=2; j++)
3104: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3105: lli= log(survp);
3106: }
3107: else{
3108: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3109: /* 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 */
3110: }
3111: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
3112: /*if(lli ==000.0)*/
3113: /*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); */
3114: ipmx +=1;
3115: sw += weight[i];
3116: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3117: /* if (lli < log(mytinydouble)){ */
3118: /* 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); */
3119: /* 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]); */
3120: /* } */
3121: } /* end of wave */
3122: } /* end of individual */
3123: } else if(mle==2){
3124: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3125: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3126: for(mi=1; mi<= wav[i]-1; mi++){
3127: for (ii=1;ii<=nlstate+ndeath;ii++)
3128: for (j=1;j<=nlstate+ndeath;j++){
3129: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3130: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3131: }
3132: for(d=0; d<=dh[mi][i]; d++){
3133: newm=savm;
3134: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3135: cov[2]=agexact;
3136: if(nagesqr==1)
3137: cov[3]= agexact*agexact;
3138: for (kk=1; kk<=cptcovage;kk++) {
3139: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3140: }
3141: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3142: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3143: savm=oldm;
3144: oldm=newm;
3145: } /* end mult */
3146:
3147: s1=s[mw[mi][i]][i];
3148: s2=s[mw[mi+1][i]][i];
3149: bbh=(double)bh[mi][i]/(double)stepm;
3150: 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 */
3151: ipmx +=1;
3152: sw += weight[i];
3153: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3154: } /* end of wave */
3155: } /* end of individual */
3156: } else if(mle==3){ /* exponential inter-extrapolation */
3157: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3158: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3159: for(mi=1; mi<= wav[i]-1; mi++){
3160: for (ii=1;ii<=nlstate+ndeath;ii++)
3161: for (j=1;j<=nlstate+ndeath;j++){
3162: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3163: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3164: }
3165: for(d=0; d<dh[mi][i]; d++){
3166: newm=savm;
3167: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3168: cov[2]=agexact;
3169: if(nagesqr==1)
3170: cov[3]= agexact*agexact;
3171: for (kk=1; kk<=cptcovage;kk++) {
3172: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3173: }
3174: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3175: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3176: savm=oldm;
3177: oldm=newm;
3178: } /* end mult */
3179:
3180: s1=s[mw[mi][i]][i];
3181: s2=s[mw[mi+1][i]][i];
3182: bbh=(double)bh[mi][i]/(double)stepm;
3183: 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 */
3184: ipmx +=1;
3185: sw += weight[i];
3186: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3187: } /* end of wave */
3188: } /* end of individual */
3189: }else if (mle==4){ /* ml=4 no inter-extrapolation */
3190: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3191: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3192: for(mi=1; mi<= wav[i]-1; mi++){
3193: for (ii=1;ii<=nlstate+ndeath;ii++)
3194: for (j=1;j<=nlstate+ndeath;j++){
3195: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3196: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3197: }
3198: for(d=0; d<dh[mi][i]; d++){
3199: newm=savm;
3200: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3201: cov[2]=agexact;
3202: if(nagesqr==1)
3203: cov[3]= agexact*agexact;
3204: for (kk=1; kk<=cptcovage;kk++) {
3205: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3206: }
1.126 brouard 3207:
1.226 brouard 3208: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3209: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3210: savm=oldm;
3211: oldm=newm;
3212: } /* end mult */
3213:
3214: s1=s[mw[mi][i]][i];
3215: s2=s[mw[mi+1][i]][i];
3216: if( s2 > nlstate){
3217: lli=log(out[s1][s2] - savm[s1][s2]);
3218: } else if ( s2==-1 ) { /* alive */
3219: for (j=1,survp=0. ; j<=nlstate; j++)
3220: survp += out[s1][j];
3221: lli= log(survp);
3222: }else{
3223: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3224: }
3225: ipmx +=1;
3226: sw += weight[i];
3227: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.126 brouard 3228: /* 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 3229: } /* end of wave */
3230: } /* end of individual */
3231: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
3232: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3233: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3234: for(mi=1; mi<= wav[i]-1; mi++){
3235: for (ii=1;ii<=nlstate+ndeath;ii++)
3236: for (j=1;j<=nlstate+ndeath;j++){
3237: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3238: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3239: }
3240: for(d=0; d<dh[mi][i]; d++){
3241: newm=savm;
3242: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3243: cov[2]=agexact;
3244: if(nagesqr==1)
3245: cov[3]= agexact*agexact;
3246: for (kk=1; kk<=cptcovage;kk++) {
3247: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3248: }
1.126 brouard 3249:
1.226 brouard 3250: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3251: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3252: savm=oldm;
3253: oldm=newm;
3254: } /* end mult */
3255:
3256: s1=s[mw[mi][i]][i];
3257: s2=s[mw[mi+1][i]][i];
3258: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3259: ipmx +=1;
3260: sw += weight[i];
3261: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3262: /*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]);*/
3263: } /* end of wave */
3264: } /* end of individual */
3265: } /* End of if */
3266: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3267: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3268: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3269: return -l;
1.126 brouard 3270: }
3271:
3272: /*************** log-likelihood *************/
3273: double funcone( double *x)
3274: {
3275: /* Same as likeli but slower because of a lot of printf and if */
3276: int i, ii, j, k, mi, d, kk;
1.224 brouard 3277: int ioffset=0;
1.131 brouard 3278: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 3279: double **out;
3280: double lli; /* Individual log likelihood */
3281: double llt;
3282: int s1, s2;
1.224 brouard 3283: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate */
1.126 brouard 3284: double bbh, survp;
1.187 brouard 3285: double agexact;
1.214 brouard 3286: double agebegin, ageend;
1.126 brouard 3287: /*extern weight */
3288: /* We are differentiating ll according to initial status */
3289: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3290: /*for(i=1;i<imx;i++)
3291: printf(" %d\n",s[4][i]);
3292: */
3293: cov[1]=1.;
3294:
3295: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3296: ioffset=0;
3297: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.225 brouard 3298: ioffset=2+nagesqr+cptcovage;
1.224 brouard 3299: /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
1.226 brouard 3300: for (k=1; k<=ncoveff+nqfveff;k++){ /* Simple and product fixed covariates without age* products */
1.225 brouard 3301: cov[++ioffset]=covar[Tvar[k]][i];
3302: }
1.226 brouard 3303: for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitative fixed covariates */
3304: cov[++ioffset]=coqvar[Tvar[iqv]][i];
1.225 brouard 3305: }
3306:
1.226 brouard 3307: for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */
1.225 brouard 3308: for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
3309: cov[ioffset+itv]=cotvar[mw[mi][i]][itv][i];
3310: }
3311: for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
3312: cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i];
3313: }
1.126 brouard 3314: for (ii=1;ii<=nlstate+ndeath;ii++)
1.225 brouard 3315: for (j=1;j<=nlstate+ndeath;j++){
3316: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3317: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3318: }
1.214 brouard 3319:
3320: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
3321: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
3322: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
1.225 brouard 3323: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3324: and mw[mi+1][i]. dh depends on stepm.*/
3325: newm=savm;
3326: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3327: cov[2]=agexact;
3328: if(nagesqr==1)
3329: cov[3]= agexact*agexact;
3330: for (kk=1; kk<=cptcovage;kk++) {
3331: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3332: }
3333: /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
3334: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
3335: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3336: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3337: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
3338: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
3339: savm=oldm;
3340: oldm=newm;
1.126 brouard 3341: } /* end mult */
3342:
3343: s1=s[mw[mi][i]][i];
3344: s2=s[mw[mi+1][i]][i];
1.217 brouard 3345: /* if(s2==-1){ */
3346: /* printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */
3347: /* /\* exit(1); *\/ */
3348: /* } */
1.126 brouard 3349: bbh=(double)bh[mi][i]/(double)stepm;
3350: /* bias is positive if real duration
3351: * is higher than the multiple of stepm and negative otherwise.
3352: */
3353: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1.225 brouard 3354: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3355: } else if ( s2==-1 ) { /* alive */
1.225 brouard 3356: for (j=1,survp=0. ; j<=nlstate; j++)
3357: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3358: lli= log(survp);
1.126 brouard 3359: }else if (mle==1){
1.225 brouard 3360: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1.126 brouard 3361: } else if(mle==2){
1.225 brouard 3362: 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 3363: } else if(mle==3){ /* exponential inter-extrapolation */
1.225 brouard 3364: 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 3365: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1.225 brouard 3366: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 3367: } else{ /* mle=0 back to 1 */
1.225 brouard 3368: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3369: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 3370: } /* End of if */
3371: ipmx +=1;
3372: sw += weight[i];
3373: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 3374: /*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 3375: if(globpr){
1.225 brouard 3376: fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
1.126 brouard 3377: %11.6f %11.6f %11.6f ", \
1.225 brouard 3378: num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
3379: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
3380: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
3381: llt +=ll[k]*gipmx/gsw;
3382: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
3383: }
3384: fprintf(ficresilk," %10.6f\n", -llt);
1.126 brouard 3385: }
3386: } /* end of wave */
3387: } /* end of individual */
3388: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3389: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3390: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3391: if(globpr==0){ /* First time we count the contributions and weights */
3392: gipmx=ipmx;
3393: gsw=sw;
3394: }
3395: return -l;
3396: }
3397:
3398:
3399: /*************** function likelione ***********/
3400: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
3401: {
3402: /* This routine should help understanding what is done with
3403: the selection of individuals/waves and
3404: to check the exact contribution to the likelihood.
3405: Plotting could be done.
3406: */
3407: int k;
3408:
3409: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 3410: strcpy(fileresilk,"ILK_");
1.202 brouard 3411: strcat(fileresilk,fileresu);
1.126 brouard 3412: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
3413: printf("Problem with resultfile: %s\n", fileresilk);
3414: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
3415: }
1.214 brouard 3416: 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");
3417: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 3418: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
3419: for(k=1; k<=nlstate; k++)
3420: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
3421: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
3422: }
3423:
3424: *fretone=(*funcone)(p);
3425: if(*globpri !=0){
3426: fclose(ficresilk);
1.205 brouard 3427: if (mle ==0)
3428: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
3429: else if(mle >=1)
3430: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
3431: 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 3432:
1.208 brouard 3433:
3434: for (k=1; k<= nlstate ; k++) {
1.211 brouard 3435: 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 3436: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
3437: }
1.207 brouard 3438: 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 3439: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3440: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 3441: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3442: fflush(fichtm);
1.205 brouard 3443: }
1.126 brouard 3444: return;
3445: }
3446:
3447:
3448: /*********** Maximum Likelihood Estimation ***************/
3449:
3450: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
3451: {
1.165 brouard 3452: int i,j, iter=0;
1.126 brouard 3453: double **xi;
3454: double fret;
3455: double fretone; /* Only one call to likelihood */
3456: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 3457:
3458: #ifdef NLOPT
3459: int creturn;
3460: nlopt_opt opt;
3461: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
3462: double *lb;
3463: double minf; /* the minimum objective value, upon return */
3464: double * p1; /* Shifted parameters from 0 instead of 1 */
3465: myfunc_data dinst, *d = &dinst;
3466: #endif
3467:
3468:
1.126 brouard 3469: xi=matrix(1,npar,1,npar);
3470: for (i=1;i<=npar;i++)
3471: for (j=1;j<=npar;j++)
3472: xi[i][j]=(i==j ? 1.0 : 0.0);
3473: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 3474: strcpy(filerespow,"POW_");
1.126 brouard 3475: strcat(filerespow,fileres);
3476: if((ficrespow=fopen(filerespow,"w"))==NULL) {
3477: printf("Problem with resultfile: %s\n", filerespow);
3478: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
3479: }
3480: fprintf(ficrespow,"# Powell\n# iter -2*LL");
3481: for (i=1;i<=nlstate;i++)
3482: for(j=1;j<=nlstate+ndeath;j++)
3483: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
3484: fprintf(ficrespow,"\n");
1.162 brouard 3485: #ifdef POWELL
1.126 brouard 3486: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 3487: #endif
1.126 brouard 3488:
1.162 brouard 3489: #ifdef NLOPT
3490: #ifdef NEWUOA
3491: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
3492: #else
3493: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
3494: #endif
3495: lb=vector(0,npar-1);
3496: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
3497: nlopt_set_lower_bounds(opt, lb);
3498: nlopt_set_initial_step1(opt, 0.1);
3499:
3500: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
3501: d->function = func;
3502: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
3503: nlopt_set_min_objective(opt, myfunc, d);
3504: nlopt_set_xtol_rel(opt, ftol);
3505: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
3506: printf("nlopt failed! %d\n",creturn);
3507: }
3508: else {
3509: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
3510: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
3511: iter=1; /* not equal */
3512: }
3513: nlopt_destroy(opt);
3514: #endif
1.126 brouard 3515: free_matrix(xi,1,npar,1,npar);
3516: fclose(ficrespow);
1.203 brouard 3517: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
3518: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 3519: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 3520:
3521: }
3522:
3523: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 3524: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 3525: {
3526: double **a,**y,*x,pd;
1.203 brouard 3527: /* double **hess; */
1.164 brouard 3528: int i, j;
1.126 brouard 3529: int *indx;
3530:
3531: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 3532: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 3533: void lubksb(double **a, int npar, int *indx, double b[]) ;
3534: void ludcmp(double **a, int npar, int *indx, double *d) ;
3535: double gompertz(double p[]);
1.203 brouard 3536: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 3537:
3538: printf("\nCalculation of the hessian matrix. Wait...\n");
3539: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
3540: for (i=1;i<=npar;i++){
1.203 brouard 3541: printf("%d-",i);fflush(stdout);
3542: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 3543:
3544: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
3545:
3546: /* printf(" %f ",p[i]);
3547: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
3548: }
3549:
3550: for (i=1;i<=npar;i++) {
3551: for (j=1;j<=npar;j++) {
3552: if (j>i) {
1.203 brouard 3553: printf(".%d-%d",i,j);fflush(stdout);
3554: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
3555: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 3556:
3557: hess[j][i]=hess[i][j];
3558: /*printf(" %lf ",hess[i][j]);*/
3559: }
3560: }
3561: }
3562: printf("\n");
3563: fprintf(ficlog,"\n");
3564:
3565: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
3566: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
3567:
3568: a=matrix(1,npar,1,npar);
3569: y=matrix(1,npar,1,npar);
3570: x=vector(1,npar);
3571: indx=ivector(1,npar);
3572: for (i=1;i<=npar;i++)
3573: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
3574: ludcmp(a,npar,indx,&pd);
3575:
3576: for (j=1;j<=npar;j++) {
3577: for (i=1;i<=npar;i++) x[i]=0;
3578: x[j]=1;
3579: lubksb(a,npar,indx,x);
3580: for (i=1;i<=npar;i++){
3581: matcov[i][j]=x[i];
3582: }
3583: }
3584:
3585: printf("\n#Hessian matrix#\n");
3586: fprintf(ficlog,"\n#Hessian matrix#\n");
3587: for (i=1;i<=npar;i++) {
3588: for (j=1;j<=npar;j++) {
1.203 brouard 3589: printf("%.6e ",hess[i][j]);
3590: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 3591: }
3592: printf("\n");
3593: fprintf(ficlog,"\n");
3594: }
3595:
1.203 brouard 3596: /* printf("\n#Covariance matrix#\n"); */
3597: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
3598: /* for (i=1;i<=npar;i++) { */
3599: /* for (j=1;j<=npar;j++) { */
3600: /* printf("%.6e ",matcov[i][j]); */
3601: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
3602: /* } */
3603: /* printf("\n"); */
3604: /* fprintf(ficlog,"\n"); */
3605: /* } */
3606:
1.126 brouard 3607: /* Recompute Inverse */
1.203 brouard 3608: /* for (i=1;i<=npar;i++) */
3609: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
3610: /* ludcmp(a,npar,indx,&pd); */
3611:
3612: /* printf("\n#Hessian matrix recomputed#\n"); */
3613:
3614: /* for (j=1;j<=npar;j++) { */
3615: /* for (i=1;i<=npar;i++) x[i]=0; */
3616: /* x[j]=1; */
3617: /* lubksb(a,npar,indx,x); */
3618: /* for (i=1;i<=npar;i++){ */
3619: /* y[i][j]=x[i]; */
3620: /* printf("%.3e ",y[i][j]); */
3621: /* fprintf(ficlog,"%.3e ",y[i][j]); */
3622: /* } */
3623: /* printf("\n"); */
3624: /* fprintf(ficlog,"\n"); */
3625: /* } */
3626:
3627: /* Verifying the inverse matrix */
3628: #ifdef DEBUGHESS
3629: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 3630:
1.203 brouard 3631: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
3632: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 3633:
3634: for (j=1;j<=npar;j++) {
3635: for (i=1;i<=npar;i++){
1.203 brouard 3636: printf("%.2f ",y[i][j]);
3637: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 3638: }
3639: printf("\n");
3640: fprintf(ficlog,"\n");
3641: }
1.203 brouard 3642: #endif
1.126 brouard 3643:
3644: free_matrix(a,1,npar,1,npar);
3645: free_matrix(y,1,npar,1,npar);
3646: free_vector(x,1,npar);
3647: free_ivector(indx,1,npar);
1.203 brouard 3648: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 3649:
3650:
3651: }
3652:
3653: /*************** hessian matrix ****************/
3654: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 3655: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 3656: int i;
3657: int l=1, lmax=20;
1.203 brouard 3658: double k1,k2, res, fx;
1.132 brouard 3659: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 3660: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
3661: int k=0,kmax=10;
3662: double l1;
3663:
3664: fx=func(x);
3665: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 3666: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 3667: l1=pow(10,l);
3668: delts=delt;
3669: for(k=1 ; k <kmax; k=k+1){
3670: delt = delta*(l1*k);
3671: p2[theta]=x[theta] +delt;
1.145 brouard 3672: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 3673: p2[theta]=x[theta]-delt;
3674: k2=func(p2)-fx;
3675: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 3676: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 3677:
1.203 brouard 3678: #ifdef DEBUGHESSII
1.126 brouard 3679: 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);
3680: 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);
3681: #endif
3682: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
3683: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
3684: k=kmax;
3685: }
3686: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 3687: k=kmax; l=lmax*10;
1.126 brouard 3688: }
3689: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
3690: delts=delt;
3691: }
1.203 brouard 3692: } /* End loop k */
1.126 brouard 3693: }
3694: delti[theta]=delts;
3695: return res;
3696:
3697: }
3698:
1.203 brouard 3699: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 3700: {
3701: int i;
1.164 brouard 3702: int l=1, lmax=20;
1.126 brouard 3703: double k1,k2,k3,k4,res,fx;
1.132 brouard 3704: double p2[MAXPARM+1];
1.203 brouard 3705: int k, kmax=1;
3706: double v1, v2, cv12, lc1, lc2;
1.208 brouard 3707:
3708: int firstime=0;
1.203 brouard 3709:
1.126 brouard 3710: fx=func(x);
1.203 brouard 3711: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 3712: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 3713: p2[thetai]=x[thetai]+delti[thetai]*k;
3714: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3715: k1=func(p2)-fx;
3716:
1.203 brouard 3717: p2[thetai]=x[thetai]+delti[thetai]*k;
3718: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3719: k2=func(p2)-fx;
3720:
1.203 brouard 3721: p2[thetai]=x[thetai]-delti[thetai]*k;
3722: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3723: k3=func(p2)-fx;
3724:
1.203 brouard 3725: p2[thetai]=x[thetai]-delti[thetai]*k;
3726: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3727: k4=func(p2)-fx;
1.203 brouard 3728: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
3729: if(k1*k2*k3*k4 <0.){
1.208 brouard 3730: firstime=1;
1.203 brouard 3731: kmax=kmax+10;
1.208 brouard 3732: }
3733: if(kmax >=10 || firstime ==1){
1.218 brouard 3734: 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);
3735: 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 3736: 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);
3737: 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);
3738: }
3739: #ifdef DEBUGHESSIJ
3740: v1=hess[thetai][thetai];
3741: v2=hess[thetaj][thetaj];
3742: cv12=res;
3743: /* Computing eigen value of Hessian matrix */
3744: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3745: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3746: if ((lc2 <0) || (lc1 <0) ){
3747: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3748: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3749: 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);
3750: 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);
3751: }
1.126 brouard 3752: #endif
3753: }
3754: return res;
3755: }
3756:
1.203 brouard 3757: /* Not done yet: Was supposed to fix if not exactly at the maximum */
3758: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
3759: /* { */
3760: /* int i; */
3761: /* int l=1, lmax=20; */
3762: /* double k1,k2,k3,k4,res,fx; */
3763: /* double p2[MAXPARM+1]; */
3764: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
3765: /* int k=0,kmax=10; */
3766: /* double l1; */
3767:
3768: /* fx=func(x); */
3769: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
3770: /* l1=pow(10,l); */
3771: /* delts=delt; */
3772: /* for(k=1 ; k <kmax; k=k+1){ */
3773: /* delt = delti*(l1*k); */
3774: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
3775: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3776: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3777: /* k1=func(p2)-fx; */
3778:
3779: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3780: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3781: /* k2=func(p2)-fx; */
3782:
3783: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3784: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3785: /* k3=func(p2)-fx; */
3786:
3787: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3788: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3789: /* k4=func(p2)-fx; */
3790: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
3791: /* #ifdef DEBUGHESSIJ */
3792: /* 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); */
3793: /* 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); */
3794: /* #endif */
3795: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
3796: /* k=kmax; */
3797: /* } */
3798: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
3799: /* k=kmax; l=lmax*10; */
3800: /* } */
3801: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
3802: /* delts=delt; */
3803: /* } */
3804: /* } /\* End loop k *\/ */
3805: /* } */
3806: /* delti[theta]=delts; */
3807: /* return res; */
3808: /* } */
3809:
3810:
1.126 brouard 3811: /************** Inverse of matrix **************/
3812: void ludcmp(double **a, int n, int *indx, double *d)
3813: {
3814: int i,imax,j,k;
3815: double big,dum,sum,temp;
3816: double *vv;
3817:
3818: vv=vector(1,n);
3819: *d=1.0;
3820: for (i=1;i<=n;i++) {
3821: big=0.0;
3822: for (j=1;j<=n;j++)
3823: if ((temp=fabs(a[i][j])) > big) big=temp;
3824: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
3825: vv[i]=1.0/big;
3826: }
3827: for (j=1;j<=n;j++) {
3828: for (i=1;i<j;i++) {
3829: sum=a[i][j];
3830: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
3831: a[i][j]=sum;
3832: }
3833: big=0.0;
3834: for (i=j;i<=n;i++) {
3835: sum=a[i][j];
3836: for (k=1;k<j;k++)
3837: sum -= a[i][k]*a[k][j];
3838: a[i][j]=sum;
3839: if ( (dum=vv[i]*fabs(sum)) >= big) {
3840: big=dum;
3841: imax=i;
3842: }
3843: }
3844: if (j != imax) {
3845: for (k=1;k<=n;k++) {
3846: dum=a[imax][k];
3847: a[imax][k]=a[j][k];
3848: a[j][k]=dum;
3849: }
3850: *d = -(*d);
3851: vv[imax]=vv[j];
3852: }
3853: indx[j]=imax;
3854: if (a[j][j] == 0.0) a[j][j]=TINY;
3855: if (j != n) {
3856: dum=1.0/(a[j][j]);
3857: for (i=j+1;i<=n;i++) a[i][j] *= dum;
3858: }
3859: }
3860: free_vector(vv,1,n); /* Doesn't work */
3861: ;
3862: }
3863:
3864: void lubksb(double **a, int n, int *indx, double b[])
3865: {
3866: int i,ii=0,ip,j;
3867: double sum;
3868:
3869: for (i=1;i<=n;i++) {
3870: ip=indx[i];
3871: sum=b[ip];
3872: b[ip]=b[i];
3873: if (ii)
3874: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
3875: else if (sum) ii=i;
3876: b[i]=sum;
3877: }
3878: for (i=n;i>=1;i--) {
3879: sum=b[i];
3880: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
3881: b[i]=sum/a[i][i];
3882: }
3883: }
3884:
3885: void pstamp(FILE *fichier)
3886: {
1.196 brouard 3887: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 3888: }
3889:
3890: /************ Frequencies ********************/
1.226 brouard 3891: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
3892: int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
3893: int firstpass, int lastpass, int stepm, int weightopt, char model[])
3894: { /* Some frequencies */
3895:
1.227 ! brouard 3896: int i, m, jk, j1, bool, z1,j, k, iv;
1.226 brouard 3897: int iind=0, iage=0;
3898: int mi; /* Effective wave */
3899: int first;
3900: double ***freq; /* Frequencies */
3901: double *meanq;
3902: double **meanqt;
3903: double *pp, **prop, *posprop, *pospropt;
3904: double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
3905: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
3906: double agebegin, ageend;
3907:
3908: pp=vector(1,nlstate);
3909: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
3910: posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
3911: pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
3912: /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
3913: meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
3914: meanqt=matrix(1,lastpass,1,nqtveff);
3915: strcpy(fileresp,"P_");
3916: strcat(fileresp,fileresu);
3917: /*strcat(fileresphtm,fileresu);*/
3918: if((ficresp=fopen(fileresp,"w"))==NULL) {
3919: printf("Problem with prevalence resultfile: %s\n", fileresp);
3920: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
3921: exit(0);
3922: }
1.214 brouard 3923:
1.226 brouard 3924: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
3925: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
3926: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3927: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3928: fflush(ficlog);
3929: exit(70);
3930: }
3931: else{
3932: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.214 brouard 3933: <hr size=\"2\" color=\"#EC5E5E\"> \n\
3934: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 3935: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
3936: }
3937: 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 3938:
1.226 brouard 3939: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
3940: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
3941: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
3942: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
3943: fflush(ficlog);
3944: exit(70);
3945: }
3946: else{
3947: 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 3948: <hr size=\"2\" color=\"#EC5E5E\"> \n\
3949: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 3950: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
3951: }
3952: 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 3953:
1.226 brouard 3954: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
3955: j1=0;
1.126 brouard 3956:
1.227 ! brouard 3957: /* j=ncoveff; /\* Only fixed dummy covariates *\/ */
! 3958: j=cptcoveff; /* Only dummy covariates of the model */
1.226 brouard 3959: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.220 brouard 3960:
1.226 brouard 3961: first=1;
1.220 brouard 3962:
1.226 brouard 3963: /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
3964: reference=low_education V1=0,V2=0
3965: med_educ V1=1 V2=0,
3966: high_educ V1=0 V2=1
3967: Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
3968: */
1.126 brouard 3969:
1.227 ! brouard 3970: 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 3971: posproptt=0.;
3972: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
3973: scanf("%d", i);*/
3974: for (i=-5; i<=nlstate+ndeath; i++)
3975: for (jk=-5; jk<=nlstate+ndeath; jk++)
3976: for(m=iagemin; m <= iagemax+3; m++)
3977: freq[i][jk][m]=0;
3978:
3979: for (i=1; i<=nlstate; i++) {
3980: for(m=iagemin; m <= iagemax+3; m++)
3981: prop[i][m]=0;
3982: posprop[i]=0;
3983: pospropt[i]=0;
3984: }
1.227 ! brouard 3985: /* for (z1=1; z1<= nqfveff; z1++) { */
! 3986: /* meanq[z1]+=0.; */
! 3987: /* for(m=1;m<=lastpass;m++){ */
! 3988: /* meanqt[m][z1]=0.; */
! 3989: /* } */
! 3990: /* } */
1.220 brouard 3991:
1.226 brouard 3992: dateintsum=0;
3993: k2cpt=0;
1.227 ! brouard 3994: /* For that combination of covariate j1, we count and print the frequencies in one pass */
1.226 brouard 3995: for (iind=1; iind<=imx; iind++) { /* For each individual iind */
3996: bool=1;
1.227 ! brouard 3997: if(anyvaryingduminmodel==0){ /* If All fixed covariates */
! 3998: if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
! 3999: /* for (z1=1; z1<= nqfveff; z1++) { */
! 4000: /* meanq[z1]+=coqvar[Tvar[z1]][iind]; /\* Computes mean of quantitative with selected filter *\/ */
! 4001: /* } */
! 4002: for (z1=1; z1<=cptcoveff; z1++) {
! 4003: /* if(Tvaraff[z1] ==-20){ */
! 4004: /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
! 4005: /* }else if(Tvaraff[z1] ==-10){ */
! 4006: /* /\* sumnew+=coqvar[z1][iind]; *\/ */
! 4007: /* }else */
! 4008: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
! 4009: /* Tests if this individual iind responded to j1 (V4=1 V3=0) */
! 4010: bool=0;
! 4011: /* 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",
! 4012: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
! 4013: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
! 4014: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
! 4015: } /* Onlyf fixed */
! 4016: } /* end z1 */
! 4017: } /* cptcovn > 0 */
! 4018: } /* end any */
! 4019: if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */
1.226 brouard 4020: /* for(m=firstpass; m<=lastpass; m++){ */
1.227 ! brouard 4021: for(mi=1; mi<wav[iind];mi++){ /* For that wave */
1.226 brouard 4022: m=mw[mi][iind];
1.227 ! brouard 4023: if(anyvaryingduminmodel==1){ /* Some are varying covariates */
! 4024: for (z1=1; z1<=cptcoveff; z1++) {
! 4025: if( Fixed[Tmodelind[z1]]==1){
! 4026: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
! 4027: if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
! 4028: bool=0;
! 4029: }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
! 4030: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
! 4031: bool=0;
! 4032: }
! 4033: }
! 4034: }
! 4035: }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */
! 4036: /* bool =0 we keep that guy which corresponds to the combination of dummy values */
! 4037: if(bool==1){
! 4038: /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
! 4039: and mw[mi+1][iind]. dh depends on stepm. */
! 4040: agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
! 4041: ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
! 4042: if(m >=firstpass && m <=lastpass){
! 4043: k2=anint[m][iind]+(mint[m][iind]/12.);
! 4044: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
! 4045: if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
! 4046: if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
! 4047: if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
! 4048: prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
! 4049: if (m<lastpass) {
! 4050: /* if(s[m][iind]==4 && s[m+1][iind]==4) */
! 4051: /* 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]); */
! 4052: if(s[m][iind]==-1)
! 4053: 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.));
! 4054: freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
! 4055: /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
! 4056: 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 */
! 4057: }
! 4058: } /* end if between passes */
! 4059: if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
! 4060: dateintsum=dateintsum+k2;
! 4061: k2cpt++;
! 4062: /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
1.226 brouard 4063: }
1.227 ! brouard 4064: } /* end bool 2 */
1.226 brouard 4065: } /* end m */
4066: } /* end bool */
4067: } /* end iind = 1 to imx */
4068: /* prop[s][age] is feeded for any initial and valid live state as well as
4069: freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
4070:
4071:
4072: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
4073: pstamp(ficresp);
1.227 ! brouard 4074: /* if (ncoveff>0) { */
! 4075: if (cptcoveff>0) {
1.226 brouard 4076: fprintf(ficresp, "\n#********** Variable ");
4077: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
4078: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
1.227 ! brouard 4079: for (z1=1; z1<=cptcoveff; z1++){
1.226 brouard 4080: fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4081: fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4082: fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4083: }
4084: fprintf(ficresp, "**********\n#");
4085: fprintf(ficresphtm, "**********</h3>\n");
4086: fprintf(ficresphtmfr, "**********</h3>\n");
4087: fprintf(ficlog, "\n#********** Variable ");
1.227 ! brouard 4088: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.226 brouard 4089: fprintf(ficlog, "**********\n");
4090: }
4091: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
4092: for(i=1; i<=nlstate;i++) {
4093: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
4094: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
4095: }
4096: fprintf(ficresp, "\n");
4097: fprintf(ficresphtm, "\n");
4098:
4099: /* Header of frequency table by age */
4100: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
4101: fprintf(ficresphtmfr,"<th>Age</th> ");
4102: for(jk=-1; jk <=nlstate+ndeath; jk++){
4103: for(m=-1; m <=nlstate+ndeath; m++){
4104: if(jk!=0 && m!=0)
4105: fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
4106: }
4107: }
4108: fprintf(ficresphtmfr, "\n");
4109:
4110: /* For each age */
4111: for(iage=iagemin; iage <= iagemax+3; iage++){
4112: fprintf(ficresphtm,"<tr>");
4113: if(iage==iagemax+1){
4114: fprintf(ficlog,"1");
4115: fprintf(ficresphtmfr,"<tr><th>0</th> ");
4116: }else if(iage==iagemax+2){
4117: fprintf(ficlog,"0");
4118: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
4119: }else if(iage==iagemax+3){
4120: fprintf(ficlog,"Total");
4121: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
4122: }else{
4123: if(first==1){
4124: first=0;
4125: printf("See log file for details...\n");
4126: }
4127: fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
4128: fprintf(ficlog,"Age %d", iage);
4129: }
4130: for(jk=1; jk <=nlstate ; jk++){
4131: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
4132: pp[jk] += freq[jk][m][iage];
4133: }
4134: for(jk=1; jk <=nlstate ; jk++){
4135: for(m=-1, pos=0; m <=0 ; m++)
4136: pos += freq[jk][m][iage];
4137: if(pp[jk]>=1.e-10){
4138: if(first==1){
4139: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
4140: }
4141: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
4142: }else{
4143: if(first==1)
4144: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
4145: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
4146: }
4147: }
4148:
4149: for(jk=1; jk <=nlstate ; jk++){
4150: /* posprop[jk]=0; */
4151: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
4152: pp[jk] += freq[jk][m][iage];
4153: } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
4154:
4155: for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
4156: pos += pp[jk]; /* pos is the total number of transitions until this age */
4157: posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
4158: from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4159: pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
4160: from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4161: }
4162: for(jk=1; jk <=nlstate ; jk++){
4163: if(pos>=1.e-5){
4164: if(first==1)
4165: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
4166: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
4167: }else{
4168: if(first==1)
4169: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
4170: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
4171: }
4172: if( iage <= iagemax){
4173: if(pos>=1.e-5){
4174: fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
4175: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
4176: /*probs[iage][jk][j1]= pp[jk]/pos;*/
4177: /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
4178: }
4179: else{
4180: fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
4181: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
4182: }
4183: }
4184: pospropt[jk] +=posprop[jk];
4185: } /* end loop jk */
4186: /* pospropt=0.; */
4187: for(jk=-1; jk <=nlstate+ndeath; jk++){
4188: for(m=-1; m <=nlstate+ndeath; m++){
4189: if(freq[jk][m][iage] !=0 ) { /* minimizing output */
4190: if(first==1){
4191: printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
4192: }
4193: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
4194: }
4195: if(jk!=0 && m!=0)
4196: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
4197: }
4198: } /* end loop jk */
4199: posproptt=0.;
4200: for(jk=1; jk <=nlstate; jk++){
4201: posproptt += pospropt[jk];
4202: }
4203: fprintf(ficresphtmfr,"</tr>\n ");
4204: if(iage <= iagemax){
4205: fprintf(ficresp,"\n");
4206: fprintf(ficresphtm,"</tr>\n");
4207: }
4208: if(first==1)
4209: printf("Others in log...\n");
4210: fprintf(ficlog,"\n");
4211: } /* end loop age iage */
4212: fprintf(ficresphtm,"<tr><th>Tot</th>");
4213: for(jk=1; jk <=nlstate ; jk++){
4214: if(posproptt < 1.e-5){
4215: fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);
4216: }else{
4217: fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);
4218: }
4219: }
4220: fprintf(ficresphtm,"</tr>\n");
4221: fprintf(ficresphtm,"</table>\n");
4222: fprintf(ficresphtmfr,"</table>\n");
4223: if(posproptt < 1.e-5){
4224: fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4225: fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4226: fprintf(ficres,"\n This combination (%d) is not valid and no result will be produced\n\n",j1);
4227: invalidvarcomb[j1]=1;
4228: }else{
4229: fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
4230: invalidvarcomb[j1]=0;
4231: }
4232: fprintf(ficresphtmfr,"</table>\n");
4233: } /* end selected combination of covariate j1 */
4234: dateintmean=dateintsum/k2cpt;
1.220 brouard 4235:
1.226 brouard 4236: fclose(ficresp);
4237: fclose(ficresphtm);
4238: fclose(ficresphtmfr);
4239: free_vector(meanq,1,nqfveff);
4240: free_matrix(meanqt,1,lastpass,1,nqtveff);
4241: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
4242: free_vector(pospropt,1,nlstate);
4243: free_vector(posprop,1,nlstate);
4244: free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
4245: free_vector(pp,1,nlstate);
4246: /* End of freqsummary */
4247: }
1.126 brouard 4248:
4249: /************ Prevalence ********************/
1.227 ! brouard 4250: 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)
! 4251: {
! 4252: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
! 4253: in each health status at the date of interview (if between dateprev1 and dateprev2).
! 4254: We still use firstpass and lastpass as another selection.
! 4255: */
1.126 brouard 4256:
1.227 ! brouard 4257: int i, m, jk, j1, bool, z1,j, iv;
! 4258: int mi; /* Effective wave */
! 4259: int iage;
! 4260: double agebegin, ageend;
! 4261:
! 4262: double **prop;
! 4263: double posprop;
! 4264: double y2; /* in fractional years */
! 4265: int iagemin, iagemax;
! 4266: int first; /** to stop verbosity which is redirected to log file */
! 4267:
! 4268: iagemin= (int) agemin;
! 4269: iagemax= (int) agemax;
! 4270: /*pp=vector(1,nlstate);*/
! 4271: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
! 4272: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
! 4273: j1=0;
1.222 brouard 4274:
1.227 ! brouard 4275: /*j=cptcoveff;*/
! 4276: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.222 brouard 4277:
1.227 ! brouard 4278: first=1;
! 4279: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
! 4280: for (i=1; i<=nlstate; i++)
! 4281: for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
! 4282: prop[i][iage]=0.0;
! 4283: printf("Prevalence combination of varying and fixed dummies %d\n",j1);
! 4284: /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
! 4285: fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
! 4286:
! 4287: for (i=1; i<=imx; i++) { /* Each individual */
! 4288: bool=1;
! 4289: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
! 4290: for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
! 4291: m=mw[mi][i];
! 4292: /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
! 4293: /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
! 4294: for (z1=1; z1<=cptcoveff; z1++){
! 4295: if( Fixed[Tmodelind[z1]]==1){
! 4296: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
! 4297: if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
! 4298: bool=0;
! 4299: }else if( Fixed[Tmodelind[z1]]== 0) /* fixed */
! 4300: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
! 4301: bool=0;
! 4302: }
! 4303: }
! 4304: if(bool==1){ /* Otherwise we skip that wave/person */
! 4305: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
! 4306: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
! 4307: if(m >=firstpass && m <=lastpass){
! 4308: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
! 4309: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
! 4310: if(agev[m][i]==0) agev[m][i]=iagemax+1;
! 4311: if(agev[m][i]==1) agev[m][i]=iagemax+2;
! 4312: if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
! 4313: 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);
! 4314: exit(1);
! 4315: }
! 4316: if (s[m][i]>0 && s[m][i]<=nlstate) {
! 4317: /*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]]);*/
! 4318: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
! 4319: prop[s[m][i]][iagemax+3] += weight[i];
! 4320: } /* end valid statuses */
! 4321: } /* end selection of dates */
! 4322: } /* end selection of waves */
! 4323: } /* end bool */
! 4324: } /* end wave */
! 4325: } /* end individual */
! 4326: for(i=iagemin; i <= iagemax+3; i++){
! 4327: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
! 4328: posprop += prop[jk][i];
! 4329: }
! 4330:
! 4331: for(jk=1; jk <=nlstate ; jk++){
! 4332: if( i <= iagemax){
! 4333: if(posprop>=1.e-5){
! 4334: probs[i][jk][j1]= prop[jk][i]/posprop;
! 4335: } else{
! 4336: if(first==1){
! 4337: first=0;
! 4338: 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]);
! 4339: }
! 4340: }
! 4341: }
! 4342: }/* end jk */
! 4343: }/* end i */
1.222 brouard 4344: /*} *//* end i1 */
1.227 ! brouard 4345: } /* end j1 */
1.222 brouard 4346:
1.227 ! brouard 4347: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
! 4348: /*free_vector(pp,1,nlstate);*/
! 4349: free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
! 4350: } /* End of prevalence */
1.126 brouard 4351:
4352: /************* Waves Concatenation ***************/
4353:
4354: 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)
4355: {
4356: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
4357: Death is a valid wave (if date is known).
4358: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
4359: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
4360: and mw[mi+1][i]. dh depends on stepm.
1.227 ! brouard 4361: */
1.126 brouard 4362:
1.224 brouard 4363: int i=0, mi=0, m=0, mli=0;
1.126 brouard 4364: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
4365: double sum=0., jmean=0.;*/
1.224 brouard 4366: int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
1.126 brouard 4367: int j, k=0,jk, ju, jl;
4368: double sum=0.;
4369: first=0;
1.214 brouard 4370: firstwo=0;
1.217 brouard 4371: firsthree=0;
1.218 brouard 4372: firstfour=0;
1.164 brouard 4373: jmin=100000;
1.126 brouard 4374: jmax=-1;
4375: jmean=0.;
1.224 brouard 4376:
4377: /* Treating live states */
1.214 brouard 4378: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.224 brouard 4379: mi=0; /* First valid wave */
1.227 ! brouard 4380: mli=0; /* Last valid wave */
1.126 brouard 4381: m=firstpass;
1.214 brouard 4382: while(s[m][i] <= nlstate){ /* a live state */
1.227 ! brouard 4383: 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 */
! 4384: mli=m-1;/* mw[++mi][i]=m-1; */
! 4385: }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 */
! 4386: mw[++mi][i]=m;
! 4387: mli=m;
1.224 brouard 4388: } /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
4389: if(m < lastpass){ /* m < lastpass, standard case */
1.227 ! brouard 4390: m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
1.216 brouard 4391: }
1.227 ! brouard 4392: else{ /* m >= lastpass, eventual special issue with warning */
1.224 brouard 4393: #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
1.227 ! brouard 4394: break;
1.224 brouard 4395: #else
1.227 ! brouard 4396: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
! 4397: if(firsthree == 0){
! 4398: 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);
! 4399: firsthree=1;
! 4400: }
! 4401: 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);
! 4402: mw[++mi][i]=m;
! 4403: mli=m;
! 4404: }
! 4405: if(s[m][i]==-2){ /* Vital status is really unknown */
! 4406: nbwarn++;
! 4407: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */
! 4408: 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);
! 4409: 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);
! 4410: }
! 4411: break;
! 4412: }
! 4413: break;
1.224 brouard 4414: #endif
1.227 ! brouard 4415: }/* End m >= lastpass */
1.126 brouard 4416: }/* end while */
1.224 brouard 4417:
1.227 ! brouard 4418: /* 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 4419: /* After last pass */
1.224 brouard 4420: /* Treating death states */
1.214 brouard 4421: if (s[m][i] > nlstate){ /* In a death state */
1.227 ! brouard 4422: /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
! 4423: /* } */
1.126 brouard 4424: mi++; /* Death is another wave */
4425: /* if(mi==0) never been interviewed correctly before death */
1.227 ! brouard 4426: /* Only death is a correct wave */
1.126 brouard 4427: mw[mi][i]=m;
1.224 brouard 4428: }
4429: #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
1.227 ! brouard 4430: 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 4431: /* m++; */
4432: /* mi++; */
4433: /* s[m][i]=nlstate+1; /\* We are setting the status to the last of non live state *\/ */
4434: /* mw[mi][i]=m; */
1.218 brouard 4435: if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
1.227 ! brouard 4436: 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 */
! 4437: nbwarn++;
! 4438: if(firstfiv==0){
! 4439: 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 );
! 4440: firstfiv=1;
! 4441: }else{
! 4442: 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 );
! 4443: }
! 4444: }else{ /* Death occured afer last wave potential bias */
! 4445: nberr++;
! 4446: if(firstwo==0){
! 4447: 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 );
! 4448: firstwo=1;
! 4449: }
! 4450: 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 );
! 4451: }
1.218 brouard 4452: }else{ /* end date of interview is known */
1.227 ! brouard 4453: /* death is known but not confirmed by death status at any wave */
! 4454: if(firstfour==0){
! 4455: 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 );
! 4456: firstfour=1;
! 4457: }
! 4458: 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 4459: }
1.224 brouard 4460: } /* end if date of death is known */
4461: #endif
4462: wav[i]=mi; /* mi should be the last effective wave (or mli) */
4463: /* wav[i]=mw[mi][i]; */
1.126 brouard 4464: if(mi==0){
4465: nbwarn++;
4466: if(first==0){
1.227 ! brouard 4467: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
! 4468: first=1;
1.126 brouard 4469: }
4470: if(first==1){
1.227 ! brouard 4471: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.126 brouard 4472: }
4473: } /* end mi==0 */
4474: } /* End individuals */
1.214 brouard 4475: /* wav and mw are no more changed */
1.223 brouard 4476:
1.214 brouard 4477:
1.126 brouard 4478: for(i=1; i<=imx; i++){
4479: for(mi=1; mi<wav[i];mi++){
4480: if (stepm <=0)
1.227 ! brouard 4481: dh[mi][i]=1;
1.126 brouard 4482: else{
1.227 ! brouard 4483: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
! 4484: if (agedc[i] < 2*AGESUP) {
! 4485: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
! 4486: if(j==0) j=1; /* Survives at least one month after exam */
! 4487: else if(j<0){
! 4488: nberr++;
! 4489: 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]);
! 4490: j=1; /* Temporary Dangerous patch */
! 4491: 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);
! 4492: 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]);
! 4493: 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);
! 4494: }
! 4495: k=k+1;
! 4496: if (j >= jmax){
! 4497: jmax=j;
! 4498: ijmax=i;
! 4499: }
! 4500: if (j <= jmin){
! 4501: jmin=j;
! 4502: ijmin=i;
! 4503: }
! 4504: sum=sum+j;
! 4505: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
! 4506: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
! 4507: }
! 4508: }
! 4509: else{
! 4510: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.126 brouard 4511: /* 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 4512:
1.227 ! brouard 4513: k=k+1;
! 4514: if (j >= jmax) {
! 4515: jmax=j;
! 4516: ijmax=i;
! 4517: }
! 4518: else if (j <= jmin){
! 4519: jmin=j;
! 4520: ijmin=i;
! 4521: }
! 4522: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
! 4523: /*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]);*/
! 4524: if(j<0){
! 4525: nberr++;
! 4526: 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]);
! 4527: 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]);
! 4528: }
! 4529: sum=sum+j;
! 4530: }
! 4531: jk= j/stepm;
! 4532: jl= j -jk*stepm;
! 4533: ju= j -(jk+1)*stepm;
! 4534: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
! 4535: if(jl==0){
! 4536: dh[mi][i]=jk;
! 4537: bh[mi][i]=0;
! 4538: }else{ /* We want a negative bias in order to only have interpolation ie
! 4539: * to avoid the price of an extra matrix product in likelihood */
! 4540: dh[mi][i]=jk+1;
! 4541: bh[mi][i]=ju;
! 4542: }
! 4543: }else{
! 4544: if(jl <= -ju){
! 4545: dh[mi][i]=jk;
! 4546: bh[mi][i]=jl; /* bias is positive if real duration
! 4547: * is higher than the multiple of stepm and negative otherwise.
! 4548: */
! 4549: }
! 4550: else{
! 4551: dh[mi][i]=jk+1;
! 4552: bh[mi][i]=ju;
! 4553: }
! 4554: if(dh[mi][i]==0){
! 4555: dh[mi][i]=1; /* At least one step */
! 4556: bh[mi][i]=ju; /* At least one step */
! 4557: /* 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);*/
! 4558: }
! 4559: } /* end if mle */
1.126 brouard 4560: }
4561: } /* end wave */
4562: }
4563: jmean=sum/k;
4564: 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 4565: 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 4566: }
1.126 brouard 4567:
4568: /*********** Tricode ****************************/
1.220 brouard 4569: void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 4570: {
1.144 brouard 4571: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
4572: /* 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 4573: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.224 brouard 4574: * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
4575: * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
1.144 brouard 4576: */
1.130 brouard 4577:
1.145 brouard 4578: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 4579: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 4580: int cptcode=0; /* Modality max of covariates j */
4581: int modmincovj=0; /* Modality min of covariates j */
4582:
4583:
1.220 brouard 4584: /* cptcoveff=0; */
1.224 brouard 4585: /* *cptcov=0; */
1.126 brouard 4586:
1.144 brouard 4587: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 4588:
1.224 brouard 4589: /* Loop on covariates without age and products and no quantitative variable */
4590: /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
1.227 ! brouard 4591: for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
! 4592: for (j=-1; (j < maxncov); j++) Ndum[j]=0;
! 4593: if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
! 4594: switch(Fixed[k]) {
! 4595: case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
! 4596: 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*/
! 4597: ij=(int)(covar[Tvar[k]][i]);
! 4598: /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
! 4599: * If product of Vn*Vm, still boolean *:
! 4600: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
! 4601: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
! 4602: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
! 4603: modality of the nth covariate of individual i. */
! 4604: if (ij > modmaxcovj)
! 4605: modmaxcovj=ij;
! 4606: else if (ij < modmincovj)
! 4607: modmincovj=ij;
! 4608: if ((ij < -1) && (ij > NCOVMAX)){
! 4609: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
! 4610: exit(1);
! 4611: }else
! 4612: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
! 4613: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
! 4614: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
! 4615: /* getting the maximum value of the modality of the covariate
! 4616: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
! 4617: female ies 1, then modmaxcovj=1.
! 4618: */
! 4619: } /* end for loop on individuals i */
! 4620: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
! 4621: fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
! 4622: cptcode=modmaxcovj;
! 4623: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
! 4624: /*for (i=0; i<=cptcode; i++) {*/
! 4625: for (j=modmincovj; j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
! 4626: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
! 4627: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
! 4628: if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
! 4629: if( j != -1){
! 4630: ncodemax[k]++; /* ncodemax[k]= Number of modalities of the k th
! 4631: covariate for which somebody answered excluding
! 4632: undefined. Usually 2: 0 and 1. */
! 4633: }
! 4634: ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
! 4635: covariate for which somebody answered including
! 4636: undefined. Usually 3: -1, 0 and 1. */
! 4637: }
! 4638: /* In fact ncodemax[k]=2 (dichotom. variables only) but it could be more for
! 4639: * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
! 4640: } /* Ndum[-1] number of undefined modalities */
! 4641:
! 4642: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
! 4643: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
! 4644: If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
! 4645: modmincovj=3; modmaxcovj = 7;
! 4646: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
! 4647: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
! 4648: defining two dummy variables: variables V1_1 and V1_2.
! 4649: nbcode[Tvar[j]][ij]=k;
! 4650: nbcode[Tvar[j]][1]=0;
! 4651: nbcode[Tvar[j]][2]=1;
! 4652: nbcode[Tvar[j]][3]=2;
! 4653: To be continued (not working yet).
! 4654: */
! 4655: ij=0; /* ij is similar to i but can jump over null modalities */
! 4656: 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*/
! 4657: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
! 4658: break;
! 4659: }
! 4660: ij++;
! 4661: 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*/
! 4662: cptcode = ij; /* New max modality for covar j */
! 4663: } /* end of loop on modality i=-1 to 1 or more */
! 4664: break;
! 4665: case 1: /* Testing on varying covariate, could be simple and
! 4666: * should look at waves or product of fixed *
! 4667: * varying. No time to test -1, assuming 0 and 1 only */
! 4668: ij=0;
! 4669: for(i=0; i<=1;i++){
! 4670: nbcode[Tvar[k]][++ij]=i;
! 4671: }
1.225 brouard 4672: break;
1.227 ! brouard 4673: default:
1.225 brouard 4674: break;
1.227 ! brouard 4675: } /* end switch */
! 4676: } /* end dummy test */
1.225 brouard 4677:
1.192 brouard 4678: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
4679: /* /\*recode from 0 *\/ */
4680: /* k is a modality. If we have model=V1+V1*sex */
4681: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
4682: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
4683: /* } */
4684: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
4685: /* if (ij > ncodemax[j]) { */
4686: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4687: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4688: /* break; */
4689: /* } */
4690: /* } /\* end of loop on modality k *\/ */
1.137 brouard 4691: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
4692:
1.225 brouard 4693: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.227 ! brouard 4694: /* Look at fixed dummy (single or product) covariates to check empty modalities */
1.187 brouard 4695: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.225 brouard 4696: /* 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 4697: 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 */
! 4698: 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 */
! 4699: /* 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 4700: } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
4701:
4702: ij=0;
1.227 ! brouard 4703: /* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
! 4704: 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 4705: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.227 ! brouard 4706: /* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? *\/ */
! 4707: if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */
! 4708: /* If product not in single variable we don't print results */
1.225 brouard 4709: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
1.227 ! brouard 4710: ++ij;
! 4711: Tvaraff[ij]=Tvar[k]; /*For printing */
! 4712: Tmodelind[ij]=k;
! 4713: if(Fixed[k]!=0)
! 4714: anyvaryingduminmodel=1;
! 4715: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
! 4716: /* Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
! 4717: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
! 4718: /* Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
! 4719: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
! 4720: /* Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
! 4721: }
1.225 brouard 4722: } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
4723: /* ij--; */
4724: /* cptcoveff=ij; /\*Number of total covariates*\/ */
4725: *cptcov=ij; /*Number of total real effective covariates: effective
4726: * because they can be excluded from the model and real
1.227 ! brouard 4727: * if in the model but excluded because missing values, but how to get k from ij?*/
! 4728: for(j=ij+1; j<= cptcovt; j++){
! 4729: Tvaraff[j]=0;
! 4730: Tmodelind[j]=0;
! 4731: }
! 4732: /* To be sorted */
! 4733: ;
1.126 brouard 4734: }
4735:
1.145 brouard 4736:
1.126 brouard 4737: /*********** Health Expectancies ****************/
4738:
1.127 brouard 4739: 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 4740:
4741: {
4742: /* Health expectancies, no variances */
1.164 brouard 4743: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 4744: int nhstepma, nstepma; /* Decreasing with age */
4745: double age, agelim, hf;
4746: double ***p3mat;
4747: double eip;
4748:
4749: pstamp(ficreseij);
4750: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
4751: fprintf(ficreseij,"# Age");
4752: for(i=1; i<=nlstate;i++){
4753: for(j=1; j<=nlstate;j++){
4754: fprintf(ficreseij," e%1d%1d ",i,j);
4755: }
4756: fprintf(ficreseij," e%1d. ",i);
4757: }
4758: fprintf(ficreseij,"\n");
4759:
4760:
4761: if(estepm < stepm){
4762: printf ("Problem %d lower than %d\n",estepm, stepm);
4763: }
4764: else hstepm=estepm;
4765: /* We compute the life expectancy from trapezoids spaced every estepm months
4766: * This is mainly to measure the difference between two models: for example
4767: * if stepm=24 months pijx are given only every 2 years and by summing them
4768: * we are calculating an estimate of the Life Expectancy assuming a linear
4769: * progression in between and thus overestimating or underestimating according
4770: * to the curvature of the survival function. If, for the same date, we
4771: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4772: * to compare the new estimate of Life expectancy with the same linear
4773: * hypothesis. A more precise result, taking into account a more precise
4774: * curvature will be obtained if estepm is as small as stepm. */
4775:
4776: /* For example we decided to compute the life expectancy with the smallest unit */
4777: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4778: nhstepm is the number of hstepm from age to agelim
4779: nstepm is the number of stepm from age to agelin.
4780: Look at hpijx to understand the reason of that which relies in memory size
4781: and note for a fixed period like estepm months */
4782: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4783: survival function given by stepm (the optimization length). Unfortunately it
4784: means that if the survival funtion is printed only each two years of age and if
4785: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4786: results. So we changed our mind and took the option of the best precision.
4787: */
4788: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4789:
4790: agelim=AGESUP;
4791: /* If stepm=6 months */
4792: /* Computed by stepm unit matrices, product of hstepm matrices, stored
4793: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
4794:
4795: /* nhstepm age range expressed in number of stepm */
4796: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4797: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4798: /* if (stepm >= YEARM) hstepm=1;*/
4799: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4800: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4801:
4802: for (age=bage; age<=fage; age ++){
4803: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4804: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4805: /* if (stepm >= YEARM) hstepm=1;*/
4806: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
4807:
4808: /* If stepm=6 months */
4809: /* Computed by stepm unit matrices, product of hstepma matrices, stored
4810: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
4811:
4812: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
4813:
4814: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4815:
4816: printf("%d|",(int)age);fflush(stdout);
4817: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
4818:
4819: /* Computing expectancies */
4820: for(i=1; i<=nlstate;i++)
4821: for(j=1; j<=nlstate;j++)
4822: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
4823: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
4824:
4825: /* 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]);*/
4826:
4827: }
4828:
4829: fprintf(ficreseij,"%3.0f",age );
4830: for(i=1; i<=nlstate;i++){
4831: eip=0;
4832: for(j=1; j<=nlstate;j++){
4833: eip +=eij[i][j][(int)age];
4834: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
4835: }
4836: fprintf(ficreseij,"%9.4f", eip );
4837: }
4838: fprintf(ficreseij,"\n");
4839:
4840: }
4841: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4842: printf("\n");
4843: fprintf(ficlog,"\n");
4844:
4845: }
4846:
1.127 brouard 4847: 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 4848:
4849: {
4850: /* Covariances of health expectancies eij and of total life expectancies according
1.222 brouard 4851: to initial status i, ei. .
1.126 brouard 4852: */
4853: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
4854: int nhstepma, nstepma; /* Decreasing with age */
4855: double age, agelim, hf;
4856: double ***p3matp, ***p3matm, ***varhe;
4857: double **dnewm,**doldm;
4858: double *xp, *xm;
4859: double **gp, **gm;
4860: double ***gradg, ***trgradg;
4861: int theta;
4862:
4863: double eip, vip;
4864:
4865: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
4866: xp=vector(1,npar);
4867: xm=vector(1,npar);
4868: dnewm=matrix(1,nlstate*nlstate,1,npar);
4869: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
4870:
4871: pstamp(ficresstdeij);
4872: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
4873: fprintf(ficresstdeij,"# Age");
4874: for(i=1; i<=nlstate;i++){
4875: for(j=1; j<=nlstate;j++)
4876: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
4877: fprintf(ficresstdeij," e%1d. ",i);
4878: }
4879: fprintf(ficresstdeij,"\n");
4880:
4881: pstamp(ficrescveij);
4882: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
4883: fprintf(ficrescveij,"# Age");
4884: for(i=1; i<=nlstate;i++)
4885: for(j=1; j<=nlstate;j++){
4886: cptj= (j-1)*nlstate+i;
4887: for(i2=1; i2<=nlstate;i2++)
4888: for(j2=1; j2<=nlstate;j2++){
4889: cptj2= (j2-1)*nlstate+i2;
4890: if(cptj2 <= cptj)
4891: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
4892: }
4893: }
4894: fprintf(ficrescveij,"\n");
4895:
4896: if(estepm < stepm){
4897: printf ("Problem %d lower than %d\n",estepm, stepm);
4898: }
4899: else hstepm=estepm;
4900: /* We compute the life expectancy from trapezoids spaced every estepm months
4901: * This is mainly to measure the difference between two models: for example
4902: * if stepm=24 months pijx are given only every 2 years and by summing them
4903: * we are calculating an estimate of the Life Expectancy assuming a linear
4904: * progression in between and thus overestimating or underestimating according
4905: * to the curvature of the survival function. If, for the same date, we
4906: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4907: * to compare the new estimate of Life expectancy with the same linear
4908: * hypothesis. A more precise result, taking into account a more precise
4909: * curvature will be obtained if estepm is as small as stepm. */
4910:
4911: /* For example we decided to compute the life expectancy with the smallest unit */
4912: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4913: nhstepm is the number of hstepm from age to agelim
4914: nstepm is the number of stepm from age to agelin.
4915: Look at hpijx to understand the reason of that which relies in memory size
4916: and note for a fixed period like estepm months */
4917: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4918: survival function given by stepm (the optimization length). Unfortunately it
4919: means that if the survival funtion is printed only each two years of age and if
4920: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4921: results. So we changed our mind and took the option of the best precision.
4922: */
4923: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4924:
4925: /* If stepm=6 months */
4926: /* nhstepm age range expressed in number of stepm */
4927: agelim=AGESUP;
4928: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
4929: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4930: /* if (stepm >= YEARM) hstepm=1;*/
4931: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4932:
4933: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4934: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4935: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
4936: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
4937: gp=matrix(0,nhstepm,1,nlstate*nlstate);
4938: gm=matrix(0,nhstepm,1,nlstate*nlstate);
4939:
4940: for (age=bage; age<=fage; age ++){
4941: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4942: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4943: /* if (stepm >= YEARM) hstepm=1;*/
4944: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218 brouard 4945:
1.126 brouard 4946: /* If stepm=6 months */
4947: /* Computed by stepm unit matrices, product of hstepma matrices, stored
4948: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
4949:
4950: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.218 brouard 4951:
1.126 brouard 4952: /* Computing Variances of health expectancies */
4953: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
4954: decrease memory allocation */
4955: for(theta=1; theta <=npar; theta++){
4956: for(i=1; i<=npar; i++){
1.222 brouard 4957: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4958: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126 brouard 4959: }
4960: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
4961: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
1.218 brouard 4962:
1.126 brouard 4963: for(j=1; j<= nlstate; j++){
1.222 brouard 4964: for(i=1; i<=nlstate; i++){
4965: for(h=0; h<=nhstepm-1; h++){
4966: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
4967: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
4968: }
4969: }
1.126 brouard 4970: }
1.218 brouard 4971:
1.126 brouard 4972: for(ij=1; ij<= nlstate*nlstate; ij++)
1.222 brouard 4973: for(h=0; h<=nhstepm-1; h++){
4974: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
4975: }
1.126 brouard 4976: }/* End theta */
4977:
4978:
4979: for(h=0; h<=nhstepm-1; h++)
4980: for(j=1; j<=nlstate*nlstate;j++)
1.222 brouard 4981: for(theta=1; theta <=npar; theta++)
4982: trgradg[h][j][theta]=gradg[h][theta][j];
1.126 brouard 4983:
1.218 brouard 4984:
1.222 brouard 4985: for(ij=1;ij<=nlstate*nlstate;ij++)
1.126 brouard 4986: for(ji=1;ji<=nlstate*nlstate;ji++)
1.222 brouard 4987: varhe[ij][ji][(int)age] =0.;
1.218 brouard 4988:
1.222 brouard 4989: printf("%d|",(int)age);fflush(stdout);
4990: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
4991: for(h=0;h<=nhstepm-1;h++){
1.126 brouard 4992: for(k=0;k<=nhstepm-1;k++){
1.222 brouard 4993: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
4994: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
4995: for(ij=1;ij<=nlstate*nlstate;ij++)
4996: for(ji=1;ji<=nlstate*nlstate;ji++)
4997: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126 brouard 4998: }
4999: }
1.218 brouard 5000:
1.126 brouard 5001: /* Computing expectancies */
5002: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
5003: for(i=1; i<=nlstate;i++)
5004: for(j=1; j<=nlstate;j++)
1.222 brouard 5005: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5006: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.218 brouard 5007:
1.222 brouard 5008: /* 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 5009:
1.222 brouard 5010: }
1.218 brouard 5011:
1.126 brouard 5012: fprintf(ficresstdeij,"%3.0f",age );
5013: for(i=1; i<=nlstate;i++){
5014: eip=0.;
5015: vip=0.;
5016: for(j=1; j<=nlstate;j++){
1.222 brouard 5017: eip += eij[i][j][(int)age];
5018: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
5019: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
5020: 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 5021: }
5022: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
5023: }
5024: fprintf(ficresstdeij,"\n");
1.218 brouard 5025:
1.126 brouard 5026: fprintf(ficrescveij,"%3.0f",age );
5027: for(i=1; i<=nlstate;i++)
5028: for(j=1; j<=nlstate;j++){
1.222 brouard 5029: cptj= (j-1)*nlstate+i;
5030: for(i2=1; i2<=nlstate;i2++)
5031: for(j2=1; j2<=nlstate;j2++){
5032: cptj2= (j2-1)*nlstate+i2;
5033: if(cptj2 <= cptj)
5034: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
5035: }
1.126 brouard 5036: }
5037: fprintf(ficrescveij,"\n");
1.218 brouard 5038:
1.126 brouard 5039: }
5040: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
5041: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
5042: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
5043: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
5044: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5045: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5046: printf("\n");
5047: fprintf(ficlog,"\n");
1.218 brouard 5048:
1.126 brouard 5049: free_vector(xm,1,npar);
5050: free_vector(xp,1,npar);
5051: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
5052: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
5053: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
5054: }
1.218 brouard 5055:
1.126 brouard 5056: /************ Variance ******************/
1.209 brouard 5057: 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 5058: {
5059: /* Variance of health expectancies */
5060: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
5061: /* double **newm;*/
5062: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
5063:
5064: /* int movingaverage(); */
5065: double **dnewm,**doldm;
5066: double **dnewmp,**doldmp;
5067: int i, j, nhstepm, hstepm, h, nstepm ;
5068: int k;
5069: double *xp;
5070: double **gp, **gm; /* for var eij */
5071: double ***gradg, ***trgradg; /*for var eij */
5072: double **gradgp, **trgradgp; /* for var p point j */
5073: double *gpp, *gmp; /* for var p point j */
5074: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
5075: double ***p3mat;
5076: double age,agelim, hf;
5077: /* double ***mobaverage; */
5078: int theta;
5079: char digit[4];
5080: char digitp[25];
5081:
5082: char fileresprobmorprev[FILENAMELENGTH];
5083:
5084: if(popbased==1){
5085: if(mobilav!=0)
5086: strcpy(digitp,"-POPULBASED-MOBILAV_");
5087: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
5088: }
5089: else
5090: strcpy(digitp,"-STABLBASED_");
1.126 brouard 5091:
1.218 brouard 5092: /* if (mobilav!=0) { */
5093: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5094: /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
5095: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
5096: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
5097: /* } */
5098: /* } */
5099:
5100: strcpy(fileresprobmorprev,"PRMORPREV-");
5101: sprintf(digit,"%-d",ij);
5102: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
5103: strcat(fileresprobmorprev,digit); /* Tvar to be done */
5104: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
5105: strcat(fileresprobmorprev,fileresu);
5106: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
5107: printf("Problem with resultfile: %s\n", fileresprobmorprev);
5108: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
5109: }
5110: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5111: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5112: pstamp(ficresprobmorprev);
5113: 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);
5114: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
5115: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
5116: fprintf(ficresprobmorprev," p.%-d SE",j);
5117: for(i=1; i<=nlstate;i++)
5118: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
5119: }
5120: fprintf(ficresprobmorprev,"\n");
5121:
5122: fprintf(ficgp,"\n# Routine varevsij");
5123: fprintf(ficgp,"\nunset title \n");
5124: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
5125: 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");
5126: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
5127: /* } */
5128: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5129: pstamp(ficresvij);
5130: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
5131: if(popbased==1)
5132: 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);
5133: else
5134: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
5135: fprintf(ficresvij,"# Age");
5136: for(i=1; i<=nlstate;i++)
5137: for(j=1; j<=nlstate;j++)
5138: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
5139: fprintf(ficresvij,"\n");
5140:
5141: xp=vector(1,npar);
5142: dnewm=matrix(1,nlstate,1,npar);
5143: doldm=matrix(1,nlstate,1,nlstate);
5144: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
5145: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5146:
5147: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
5148: gpp=vector(nlstate+1,nlstate+ndeath);
5149: gmp=vector(nlstate+1,nlstate+ndeath);
5150: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126 brouard 5151:
1.218 brouard 5152: if(estepm < stepm){
5153: printf ("Problem %d lower than %d\n",estepm, stepm);
5154: }
5155: else hstepm=estepm;
5156: /* For example we decided to compute the life expectancy with the smallest unit */
5157: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5158: nhstepm is the number of hstepm from age to agelim
5159: nstepm is the number of stepm from age to agelim.
5160: Look at function hpijx to understand why because of memory size limitations,
5161: we decided (b) to get a life expectancy respecting the most precise curvature of the
5162: survival function given by stepm (the optimization length). Unfortunately it
5163: means that if the survival funtion is printed every two years of age and if
5164: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5165: results. So we changed our mind and took the option of the best precision.
5166: */
5167: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5168: agelim = AGESUP;
5169: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5170: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5171: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5172: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5173: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
5174: gp=matrix(0,nhstepm,1,nlstate);
5175: gm=matrix(0,nhstepm,1,nlstate);
5176:
5177:
5178: for(theta=1; theta <=npar; theta++){
5179: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
5180: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5181: }
5182:
5183: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5184:
5185: if (popbased==1) {
5186: if(mobilav ==0){
5187: for(i=1; i<=nlstate;i++)
5188: prlim[i][i]=probs[(int)age][i][ij];
5189: }else{ /* mobilav */
5190: for(i=1; i<=nlstate;i++)
5191: prlim[i][i]=mobaverage[(int)age][i][ij];
5192: }
5193: }
5194:
5195: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); /* Returns p3mat[i][j][h] for h=1 to nhstepm */
5196: for(j=1; j<= nlstate; j++){
5197: for(h=0; h<=nhstepm; h++){
5198: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
5199: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
5200: }
5201: }
5202: /* Next for computing probability of death (h=1 means
5203: computed over hstepm matrices product = hstepm*stepm months)
5204: as a weighted average of prlim.
5205: */
5206: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5207: for(i=1,gpp[j]=0.; i<= nlstate; i++)
5208: gpp[j] += prlim[i][i]*p3mat[i][j][1];
5209: }
5210: /* end probability of death */
5211:
5212: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
5213: xp[i] = x[i] - (i==theta ?delti[theta]:0);
5214:
5215: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
5216:
5217: if (popbased==1) {
5218: if(mobilav ==0){
5219: for(i=1; i<=nlstate;i++)
5220: prlim[i][i]=probs[(int)age][i][ij];
5221: }else{ /* mobilav */
5222: for(i=1; i<=nlstate;i++)
5223: prlim[i][i]=mobaverage[(int)age][i][ij];
5224: }
5225: }
5226:
5227: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
5228:
5229: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
5230: for(h=0; h<=nhstepm; h++){
5231: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
5232: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
5233: }
5234: }
5235: /* This for computing probability of death (h=1 means
5236: computed over hstepm matrices product = hstepm*stepm months)
5237: as a weighted average of prlim.
5238: */
5239: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5240: for(i=1,gmp[j]=0.; i<= nlstate; i++)
5241: gmp[j] += prlim[i][i]*p3mat[i][j][1];
5242: }
5243: /* end probability of death */
5244:
5245: for(j=1; j<= nlstate; j++) /* vareij */
5246: for(h=0; h<=nhstepm; h++){
5247: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
5248: }
5249:
5250: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
5251: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
5252: }
5253:
5254: } /* End theta */
5255:
5256: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
5257:
5258: for(h=0; h<=nhstepm; h++) /* veij */
5259: for(j=1; j<=nlstate;j++)
5260: for(theta=1; theta <=npar; theta++)
5261: trgradg[h][j][theta]=gradg[h][theta][j];
5262:
5263: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
5264: for(theta=1; theta <=npar; theta++)
5265: trgradgp[j][theta]=gradgp[theta][j];
5266:
5267:
5268: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
5269: for(i=1;i<=nlstate;i++)
5270: for(j=1;j<=nlstate;j++)
5271: vareij[i][j][(int)age] =0.;
5272:
5273: for(h=0;h<=nhstepm;h++){
5274: for(k=0;k<=nhstepm;k++){
5275: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
5276: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
5277: for(i=1;i<=nlstate;i++)
5278: for(j=1;j<=nlstate;j++)
5279: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
5280: }
5281: }
5282:
5283: /* pptj */
5284: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
5285: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
5286: for(j=nlstate+1;j<=nlstate+ndeath;j++)
5287: for(i=nlstate+1;i<=nlstate+ndeath;i++)
5288: varppt[j][i]=doldmp[j][i];
5289: /* end ppptj */
5290: /* x centered again */
5291:
5292: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
5293:
5294: if (popbased==1) {
5295: if(mobilav ==0){
5296: for(i=1; i<=nlstate;i++)
5297: prlim[i][i]=probs[(int)age][i][ij];
5298: }else{ /* mobilav */
5299: for(i=1; i<=nlstate;i++)
5300: prlim[i][i]=mobaverage[(int)age][i][ij];
5301: }
5302: }
5303:
5304: /* This for computing probability of death (h=1 means
5305: computed over hstepm (estepm) matrices product = hstepm*stepm months)
5306: as a weighted average of prlim.
5307: */
5308: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
5309: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5310: for(i=1,gmp[j]=0.;i<= nlstate; i++)
5311: gmp[j] += prlim[i][i]*p3mat[i][j][1];
5312: }
5313: /* end probability of death */
5314:
5315: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
5316: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
5317: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
5318: for(i=1; i<=nlstate;i++){
5319: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
5320: }
5321: }
5322: fprintf(ficresprobmorprev,"\n");
5323:
5324: fprintf(ficresvij,"%.0f ",age );
5325: for(i=1; i<=nlstate;i++)
5326: for(j=1; j<=nlstate;j++){
5327: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
5328: }
5329: fprintf(ficresvij,"\n");
5330: free_matrix(gp,0,nhstepm,1,nlstate);
5331: free_matrix(gm,0,nhstepm,1,nlstate);
5332: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
5333: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
5334: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5335: } /* End age */
5336: free_vector(gpp,nlstate+1,nlstate+ndeath);
5337: free_vector(gmp,nlstate+1,nlstate+ndeath);
5338: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
5339: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
5340: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
5341: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
5342: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
5343: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
5344: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
5345: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
5346: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
5347: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
5348: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
5349: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
5350: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
5351: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
5352: 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);
5353: /* 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 5354: */
1.218 brouard 5355: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
5356: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 5357:
1.218 brouard 5358: free_vector(xp,1,npar);
5359: free_matrix(doldm,1,nlstate,1,nlstate);
5360: free_matrix(dnewm,1,nlstate,1,npar);
5361: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5362: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
5363: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5364: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5365: fclose(ficresprobmorprev);
5366: fflush(ficgp);
5367: fflush(fichtm);
5368: } /* end varevsij */
1.126 brouard 5369:
5370: /************ Variance of prevlim ******************/
1.209 brouard 5371: 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 5372: {
1.205 brouard 5373: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 5374: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 5375:
1.126 brouard 5376: double **dnewm,**doldm;
5377: int i, j, nhstepm, hstepm;
5378: double *xp;
5379: double *gp, *gm;
5380: double **gradg, **trgradg;
1.208 brouard 5381: double **mgm, **mgp;
1.126 brouard 5382: double age,agelim;
5383: int theta;
5384:
5385: pstamp(ficresvpl);
5386: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
5387: fprintf(ficresvpl,"# Age");
5388: for(i=1; i<=nlstate;i++)
5389: fprintf(ficresvpl," %1d-%1d",i,i);
5390: fprintf(ficresvpl,"\n");
5391:
5392: xp=vector(1,npar);
5393: dnewm=matrix(1,nlstate,1,npar);
5394: doldm=matrix(1,nlstate,1,nlstate);
5395:
5396: hstepm=1*YEARM; /* Every year of age */
5397: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
5398: agelim = AGESUP;
5399: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5400: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5401: if (stepm >= YEARM) hstepm=1;
5402: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5403: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 5404: mgp=matrix(1,npar,1,nlstate);
5405: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 5406: gp=vector(1,nlstate);
5407: gm=vector(1,nlstate);
5408:
5409: for(theta=1; theta <=npar; theta++){
5410: for(i=1; i<=npar; i++){ /* Computes gradient */
5411: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5412: }
1.209 brouard 5413: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
5414: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5415: else
5416: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 5417: for(i=1;i<=nlstate;i++){
1.126 brouard 5418: gp[i] = prlim[i][i];
1.208 brouard 5419: mgp[theta][i] = prlim[i][i];
5420: }
1.126 brouard 5421: for(i=1; i<=npar; i++) /* Computes gradient */
5422: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 5423: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
5424: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5425: else
5426: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 5427: for(i=1;i<=nlstate;i++){
1.126 brouard 5428: gm[i] = prlim[i][i];
1.208 brouard 5429: mgm[theta][i] = prlim[i][i];
5430: }
1.126 brouard 5431: for(i=1;i<=nlstate;i++)
5432: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 5433: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 5434: } /* End theta */
5435:
5436: trgradg =matrix(1,nlstate,1,npar);
5437:
5438: for(j=1; j<=nlstate;j++)
5439: for(theta=1; theta <=npar; theta++)
5440: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 5441: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5442: /* printf("\nmgm mgp %d ",(int)age); */
5443: /* for(j=1; j<=nlstate;j++){ */
5444: /* printf(" %d ",j); */
5445: /* for(theta=1; theta <=npar; theta++) */
5446: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
5447: /* printf("\n "); */
5448: /* } */
5449: /* } */
5450: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5451: /* printf("\n gradg %d ",(int)age); */
5452: /* for(j=1; j<=nlstate;j++){ */
5453: /* printf("%d ",j); */
5454: /* for(theta=1; theta <=npar; theta++) */
5455: /* printf("%d %lf ",theta,gradg[theta][j]); */
5456: /* printf("\n "); */
5457: /* } */
5458: /* } */
1.126 brouard 5459:
5460: for(i=1;i<=nlstate;i++)
5461: varpl[i][(int)age] =0.;
1.209 brouard 5462: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.205 brouard 5463: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5464: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
5465: }else{
1.126 brouard 5466: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5467: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 5468: }
1.126 brouard 5469: for(i=1;i<=nlstate;i++)
5470: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
5471:
5472: fprintf(ficresvpl,"%.0f ",age );
5473: for(i=1; i<=nlstate;i++)
5474: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
5475: fprintf(ficresvpl,"\n");
5476: free_vector(gp,1,nlstate);
5477: free_vector(gm,1,nlstate);
1.208 brouard 5478: free_matrix(mgm,1,npar,1,nlstate);
5479: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 5480: free_matrix(gradg,1,npar,1,nlstate);
5481: free_matrix(trgradg,1,nlstate,1,npar);
5482: } /* End age */
5483:
5484: free_vector(xp,1,npar);
5485: free_matrix(doldm,1,nlstate,1,npar);
5486: free_matrix(dnewm,1,nlstate,1,nlstate);
5487:
5488: }
5489:
5490: /************ Variance of one-step probabilities ******************/
5491: 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 5492: {
5493: int i, j=0, k1, l1, tj;
5494: int k2, l2, j1, z1;
5495: int k=0, l;
5496: int first=1, first1, first2;
5497: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
5498: double **dnewm,**doldm;
5499: double *xp;
5500: double *gp, *gm;
5501: double **gradg, **trgradg;
5502: double **mu;
5503: double age, cov[NCOVMAX+1];
5504: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
5505: int theta;
5506: char fileresprob[FILENAMELENGTH];
5507: char fileresprobcov[FILENAMELENGTH];
5508: char fileresprobcor[FILENAMELENGTH];
5509: double ***varpij;
5510:
5511: strcpy(fileresprob,"PROB_");
5512: strcat(fileresprob,fileres);
5513: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
5514: printf("Problem with resultfile: %s\n", fileresprob);
5515: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
5516: }
5517: strcpy(fileresprobcov,"PROBCOV_");
5518: strcat(fileresprobcov,fileresu);
5519: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
5520: printf("Problem with resultfile: %s\n", fileresprobcov);
5521: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
5522: }
5523: strcpy(fileresprobcor,"PROBCOR_");
5524: strcat(fileresprobcor,fileresu);
5525: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
5526: printf("Problem with resultfile: %s\n", fileresprobcor);
5527: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
5528: }
5529: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
5530: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
5531: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
5532: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
5533: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
5534: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
5535: pstamp(ficresprob);
5536: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
5537: fprintf(ficresprob,"# Age");
5538: pstamp(ficresprobcov);
5539: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
5540: fprintf(ficresprobcov,"# Age");
5541: pstamp(ficresprobcor);
5542: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
5543: fprintf(ficresprobcor,"# Age");
1.126 brouard 5544:
5545:
1.222 brouard 5546: for(i=1; i<=nlstate;i++)
5547: for(j=1; j<=(nlstate+ndeath);j++){
5548: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
5549: fprintf(ficresprobcov," p%1d-%1d ",i,j);
5550: fprintf(ficresprobcor," p%1d-%1d ",i,j);
5551: }
5552: /* fprintf(ficresprob,"\n");
5553: fprintf(ficresprobcov,"\n");
5554: fprintf(ficresprobcor,"\n");
5555: */
5556: xp=vector(1,npar);
5557: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
5558: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
5559: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
5560: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
5561: first=1;
5562: fprintf(ficgp,"\n# Routine varprob");
5563: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
5564: fprintf(fichtm,"\n");
5565:
5566: 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);
5567: 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);
5568: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 5569: and drawn. It helps understanding how is the covariance between two incidences.\
5570: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.222 brouard 5571: 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 5572: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
5573: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
5574: standard deviations wide on each axis. <br>\
5575: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
5576: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
5577: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
5578:
1.222 brouard 5579: cov[1]=1;
5580: /* tj=cptcoveff; */
1.225 brouard 5581: tj = (int) pow(2,cptcoveff);
1.222 brouard 5582: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
5583: j1=0;
1.224 brouard 5584: for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/
1.222 brouard 5585: if (cptcovn>0) {
5586: fprintf(ficresprob, "\n#********** Variable ");
1.225 brouard 5587: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5588: fprintf(ficresprob, "**********\n#\n");
5589: fprintf(ficresprobcov, "\n#********** Variable ");
1.225 brouard 5590: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5591: fprintf(ficresprobcov, "**********\n#\n");
1.220 brouard 5592:
1.222 brouard 5593: fprintf(ficgp, "\n#********** Variable ");
1.225 brouard 5594: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5595: fprintf(ficgp, "**********\n#\n");
1.220 brouard 5596:
5597:
1.222 brouard 5598: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.225 brouard 5599: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5600: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 5601:
1.222 brouard 5602: fprintf(ficresprobcor, "\n#********** Variable ");
1.225 brouard 5603: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5604: fprintf(ficresprobcor, "**********\n#");
5605: if(invalidvarcomb[j1]){
5606: fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
5607: fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
5608: continue;
5609: }
5610: }
5611: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
5612: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
5613: gp=vector(1,(nlstate)*(nlstate+ndeath));
5614: gm=vector(1,(nlstate)*(nlstate+ndeath));
5615: for (age=bage; age<=fage; age ++){
5616: cov[2]=age;
5617: if(nagesqr==1)
5618: cov[3]= age*age;
5619: for (k=1; k<=cptcovn;k++) {
5620: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
5621: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
5622: * 1 1 1 1 1
5623: * 2 2 1 1 1
5624: * 3 1 2 1 1
5625: */
5626: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
5627: }
5628: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5629: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
5630: for (k=1; k<=cptcovprod;k++)
5631: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.220 brouard 5632:
5633:
1.222 brouard 5634: for(theta=1; theta <=npar; theta++){
5635: for(i=1; i<=npar; i++)
5636: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.220 brouard 5637:
1.222 brouard 5638: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1.220 brouard 5639:
1.222 brouard 5640: k=0;
5641: for(i=1; i<= (nlstate); i++){
5642: for(j=1; j<=(nlstate+ndeath);j++){
5643: k=k+1;
5644: gp[k]=pmmij[i][j];
5645: }
5646: }
1.220 brouard 5647:
1.222 brouard 5648: for(i=1; i<=npar; i++)
5649: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.220 brouard 5650:
1.222 brouard 5651: pmij(pmmij,cov,ncovmodel,xp,nlstate);
5652: k=0;
5653: for(i=1; i<=(nlstate); i++){
5654: for(j=1; j<=(nlstate+ndeath);j++){
5655: k=k+1;
5656: gm[k]=pmmij[i][j];
5657: }
5658: }
1.220 brouard 5659:
1.222 brouard 5660: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
5661: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
5662: }
1.126 brouard 5663:
1.222 brouard 5664: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
5665: for(theta=1; theta <=npar; theta++)
5666: trgradg[j][theta]=gradg[theta][j];
1.220 brouard 5667:
1.222 brouard 5668: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
5669: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.220 brouard 5670:
1.222 brouard 5671: pmij(pmmij,cov,ncovmodel,x,nlstate);
1.220 brouard 5672:
1.222 brouard 5673: k=0;
5674: for(i=1; i<=(nlstate); i++){
5675: for(j=1; j<=(nlstate+ndeath);j++){
5676: k=k+1;
5677: mu[k][(int) age]=pmmij[i][j];
5678: }
5679: }
5680: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
5681: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
5682: varpij[i][j][(int)age] = doldm[i][j];
1.220 brouard 5683:
1.222 brouard 5684: /*printf("\n%d ",(int)age);
5685: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
5686: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
5687: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
5688: }*/
1.220 brouard 5689:
1.222 brouard 5690: fprintf(ficresprob,"\n%d ",(int)age);
5691: fprintf(ficresprobcov,"\n%d ",(int)age);
5692: fprintf(ficresprobcor,"\n%d ",(int)age);
1.220 brouard 5693:
1.222 brouard 5694: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
5695: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
5696: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
5697: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
5698: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
5699: }
5700: i=0;
5701: for (k=1; k<=(nlstate);k++){
5702: for (l=1; l<=(nlstate+ndeath);l++){
5703: i++;
5704: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
5705: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
5706: for (j=1; j<=i;j++){
5707: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
5708: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
5709: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
5710: }
5711: }
5712: }/* end of loop for state */
5713: } /* end of loop for age */
5714: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
5715: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
5716: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
5717: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
5718:
5719: /* Confidence intervalle of pij */
5720: /*
5721: fprintf(ficgp,"\nunset parametric;unset label");
5722: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
5723: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
5724: 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);
5725: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
5726: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
5727: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
5728: */
5729:
5730: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
5731: first1=1;first2=2;
5732: for (k2=1; k2<=(nlstate);k2++){
5733: for (l2=1; l2<=(nlstate+ndeath);l2++){
5734: if(l2==k2) continue;
5735: j=(k2-1)*(nlstate+ndeath)+l2;
5736: for (k1=1; k1<=(nlstate);k1++){
5737: for (l1=1; l1<=(nlstate+ndeath);l1++){
5738: if(l1==k1) continue;
5739: i=(k1-1)*(nlstate+ndeath)+l1;
5740: if(i<=j) continue;
5741: for (age=bage; age<=fage; age ++){
5742: if ((int)age %5==0){
5743: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
5744: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
5745: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
5746: mu1=mu[i][(int) age]/stepm*YEARM ;
5747: mu2=mu[j][(int) age]/stepm*YEARM;
5748: c12=cv12/sqrt(v1*v2);
5749: /* Computing eigen value of matrix of covariance */
5750: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
5751: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
5752: if ((lc2 <0) || (lc1 <0) ){
5753: if(first2==1){
5754: first1=0;
5755: 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);
5756: }
5757: 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);
5758: /* lc1=fabs(lc1); */ /* If we want to have them positive */
5759: /* lc2=fabs(lc2); */
5760: }
1.220 brouard 5761:
1.222 brouard 5762: /* Eigen vectors */
5763: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
5764: /*v21=sqrt(1.-v11*v11); *//* error */
5765: v21=(lc1-v1)/cv12*v11;
5766: v12=-v21;
5767: v22=v11;
5768: tnalp=v21/v11;
5769: if(first1==1){
5770: first1=0;
5771: 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);
5772: }
5773: 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);
5774: /*printf(fignu*/
5775: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
5776: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
5777: if(first==1){
5778: first=0;
5779: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
5780: fprintf(ficgp,"\nset parametric;unset label");
5781: 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);
5782: fprintf(ficgp,"\nset ter svg size 640, 480");
5783: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.220 brouard 5784: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
1.201 brouard 5785: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.222 brouard 5786: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
5787: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5788: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5789: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
5790: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5791: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
5792: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
5793: 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", \
5794: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
5795: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
5796: }else{
5797: first=0;
5798: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
5799: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
5800: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
5801: 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", \
5802: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
5803: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
5804: }/* if first */
5805: } /* age mod 5 */
5806: } /* end loop age */
5807: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5808: first=1;
5809: } /*l12 */
5810: } /* k12 */
5811: } /*l1 */
5812: }/* k1 */
5813: } /* loop on combination of covariates j1 */
5814: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
5815: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
5816: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
5817: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
5818: free_vector(xp,1,npar);
5819: fclose(ficresprob);
5820: fclose(ficresprobcov);
5821: fclose(ficresprobcor);
5822: fflush(ficgp);
5823: fflush(fichtmcov);
5824: }
1.126 brouard 5825:
5826:
5827: /******************* Printing html file ***********/
1.201 brouard 5828: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 5829: int lastpass, int stepm, int weightopt, char model[],\
5830: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.217 brouard 5831: int popforecast, int prevfcast, int backcast, int estepm , \
1.213 brouard 5832: double jprev1, double mprev1,double anprev1, double dateprev1, \
5833: double jprev2, double mprev2,double anprev2, double dateprev2){
1.126 brouard 5834: int jj1, k1, i1, cpt;
5835:
5836: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
5837: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
5838: </ul>");
1.214 brouard 5839: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
5840: 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",
5841: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
5842: 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 5843: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
5844: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 5845: fprintf(fichtm,"\
5846: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 5847: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 5848: fprintf(fichtm,"\
1.217 brouard 5849: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
5850: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
5851: fprintf(fichtm,"\
1.126 brouard 5852: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5853: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 5854: fprintf(fichtm,"\
1.217 brouard 5855: - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
5856: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
5857: fprintf(fichtm,"\
1.211 brouard 5858: - (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 5859: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5860: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 5861: if(prevfcast==1){
5862: fprintf(fichtm,"\
5863: - Prevalence projections by age and states: \
1.201 brouard 5864: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 5865: }
1.126 brouard 5866:
1.222 brouard 5867: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
1.126 brouard 5868:
1.225 brouard 5869: m=pow(2,cptcoveff);
1.222 brouard 5870: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 5871:
1.222 brouard 5872: jj1=0;
5873: for(k1=1; k1<=m;k1++){
1.220 brouard 5874:
1.222 brouard 5875: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
5876: jj1++;
5877: if (cptcovn > 0) {
5878: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 5879: for (cpt=1; cpt<=cptcoveff;cpt++){
1.222 brouard 5880: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
5881: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
5882: }
5883: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
5884: if(invalidvarcomb[k1]){
5885: fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
5886: printf("\nCombination (%d) ignored because no cases \n",k1);
5887: continue;
5888: }
5889: }
5890: /* aij, bij */
5891: 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 5892: <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 5893: /* Pij */
5894: 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 5895: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 5896: /* Quasi-incidences */
5897: 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 5898: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211 brouard 5899: incidence (rates) are the limit when h tends to zero of the ratio of the probability <sub>h</sub>P<sub>ij</sub> \
5900: 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 5901: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 5902: /* Survival functions (period) in state j */
5903: for(cpt=1; cpt<=nlstate;cpt++){
5904: 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 5905: <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 5906: }
5907: /* State specific survival functions (period) */
5908: for(cpt=1; cpt<=nlstate;cpt++){
5909: fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
1.220 brouard 5910: Or probability to survive in various states (1 to %d) being in state %d at different ages. \
1.201 brouard 5911: <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 5912: }
5913: /* Period (stable) prevalence in each health state */
5914: for(cpt=1; cpt<=nlstate;cpt++){
5915: 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 5916: <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 5917: }
5918: if(backcast==1){
5919: /* Period (stable) back prevalence in each health state */
5920: for(cpt=1; cpt<=nlstate;cpt++){
5921: 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 5922: <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 5923: }
1.217 brouard 5924: }
1.222 brouard 5925: if(prevfcast==1){
5926: /* Projection of prevalence up to period (stable) prevalence in each health state */
5927: for(cpt=1; cpt<=nlstate;cpt++){
5928: 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 5929: <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 5930: }
5931: }
1.220 brouard 5932:
1.222 brouard 5933: for(cpt=1; cpt<=nlstate;cpt++) {
5934: 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 5935: <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 5936: }
5937: /* } /\* end i1 *\/ */
5938: }/* End k1 */
5939: fprintf(fichtm,"</ul>");
1.126 brouard 5940:
1.222 brouard 5941: fprintf(fichtm,"\
1.126 brouard 5942: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 5943: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 5944: - 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 5945: But because parameters are usually highly correlated (a higher incidence of disability \
5946: and a higher incidence of recovery can give very close observed transition) it might \
5947: be very useful to look not only at linear confidence intervals estimated from the \
5948: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
5949: (parameters) of the logistic regression, it might be more meaningful to visualize the \
5950: covariance matrix of the one-step probabilities. \
5951: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 5952:
1.222 brouard 5953: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
5954: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
5955: fprintf(fichtm,"\
1.126 brouard 5956: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 5957: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 5958:
1.222 brouard 5959: fprintf(fichtm,"\
1.126 brouard 5960: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 5961: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
5962: fprintf(fichtm,"\
1.126 brouard 5963: - 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): \
5964: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5965: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.222 brouard 5966: fprintf(fichtm,"\
1.126 brouard 5967: - (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): \
5968: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5969: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.222 brouard 5970: fprintf(fichtm,"\
1.128 brouard 5971: - 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 5972: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
5973: fprintf(fichtm,"\
1.128 brouard 5974: - 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 5975: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
5976: fprintf(fichtm,"\
1.126 brouard 5977: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.222 brouard 5978: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 5979:
5980: /* if(popforecast==1) fprintf(fichtm,"\n */
5981: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
5982: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
5983: /* <br>",fileres,fileres,fileres,fileres); */
5984: /* else */
5985: /* 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 5986: fflush(fichtm);
5987: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.126 brouard 5988:
1.225 brouard 5989: m=pow(2,cptcoveff);
1.222 brouard 5990: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 5991:
1.222 brouard 5992: jj1=0;
5993: for(k1=1; k1<=m;k1++){
5994: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
5995: jj1++;
1.126 brouard 5996: if (cptcovn > 0) {
5997: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 5998: for (cpt=1; cpt<=cptcoveff;cpt++) /**< cptcoveff number of variables */
1.222 brouard 5999: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 6000: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 6001:
1.222 brouard 6002: if(invalidvarcomb[k1]){
6003: fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
6004: continue;
6005: }
1.126 brouard 6006: }
6007: for(cpt=1; cpt<=nlstate;cpt++) {
1.218 brouard 6008: fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
6009: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d.svg\"> %s_%d-%d.svg</a>\n <br>\
1.205 brouard 6010: <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 6011: }
6012: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 6013: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
6014: true period expectancies (those weighted with period prevalences are also\
6015: drawn in addition to the population based expectancies computed using\
1.218 brouard 6016: observed and cahotic prevalences: <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\
1.205 brouard 6017: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.222 brouard 6018: /* } /\* end i1 *\/ */
6019: }/* End k1 */
6020: fprintf(fichtm,"</ul>");
6021: fflush(fichtm);
1.126 brouard 6022: }
6023:
6024: /******************* Gnuplot file **************/
1.223 brouard 6025: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
1.126 brouard 6026:
6027: char dirfileres[132],optfileres[132];
1.223 brouard 6028: char gplotcondition[132];
1.164 brouard 6029: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.211 brouard 6030: int lv=0, vlv=0, kl=0;
1.130 brouard 6031: int ng=0;
1.201 brouard 6032: int vpopbased;
1.223 brouard 6033: int ioffset; /* variable offset for columns */
1.219 brouard 6034:
1.126 brouard 6035: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
6036: /* printf("Problem with file %s",optionfilegnuplot); */
6037: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
6038: /* } */
6039:
6040: /*#ifdef windows */
6041: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.223 brouard 6042: /*#endif */
1.225 brouard 6043: m=pow(2,cptcoveff);
1.126 brouard 6044:
1.202 brouard 6045: /* Contribution to likelihood */
6046: /* Plot the probability implied in the likelihood */
1.223 brouard 6047: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
6048: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
6049: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
6050: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 6051: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 6052: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
6053: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
1.223 brouard 6054: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
6055: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
6056: 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));
6057: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
6058: 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));
6059: for (i=1; i<= nlstate ; i ++) {
6060: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
6061: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
6062: 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);
6063: for (j=2; j<= nlstate+ndeath ; j ++) {
6064: 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);
6065: }
6066: fprintf(ficgp,";\nset out; unset ylabel;\n");
6067: }
6068: /* 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 */
6069: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
6070: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
6071: fprintf(ficgp,"\nset out;unset log\n");
6072: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
1.202 brouard 6073:
1.126 brouard 6074: strcpy(dirfileres,optionfilefiname);
6075: strcpy(optfileres,"vpl");
1.223 brouard 6076: /* 1eme*/
1.211 brouard 6077: for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
1.220 brouard 6078: for (k1=1; k1<= m ; k1 ++) { /* For each valid combination of covariate */
1.211 brouard 6079: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
6080: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
1.225 brouard 6081: for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
6082: lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
1.223 brouard 6083: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6084: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6085: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6086: vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
6087: /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
6088: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6089: }
6090: fprintf(ficgp,"\n#\n");
1.223 brouard 6091: if(invalidvarcomb[k1]){
6092: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6093: continue;
6094: }
1.211 brouard 6095:
1.223 brouard 6096: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
6097: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
6098: fprintf(ficgp,"set xlabel \"Age\" \n\
1.219 brouard 6099: set ylabel \"Probability\" \n \
6100: set ter svg size 640, 480\n \
1.201 brouard 6101: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.219 brouard 6102:
1.223 brouard 6103: for (i=1; i<= nlstate ; i ++) {
6104: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
6105: else fprintf(ficgp," %%*lf (%%*lf)");
6106: }
6107: 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);
6108: for (i=1; i<= nlstate ; i ++) {
6109: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
6110: else fprintf(ficgp," %%*lf (%%*lf)");
6111: }
6112: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
6113: for (i=1; i<= nlstate ; i ++) {
6114: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
6115: else fprintf(ficgp," %%*lf (%%*lf)");
6116: }
6117: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
6118: if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
6119: /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
6120: fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
1.225 brouard 6121: if(cptcoveff ==0){
1.223 brouard 6122: fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ", 2+(cpt-1), cpt );
6123: }else{
6124: kl=0;
1.225 brouard 6125: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
6126: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
1.223 brouard 6127: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6128: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6129: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6130: vlv= nbcode[Tvaraff[k]][lv];
6131: kl++;
6132: /* 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 *\/ */
6133: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
6134: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
6135: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
1.225 brouard 6136: if(k==cptcoveff){
1.227 ! brouard 6137: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
! 6138: 4+(cpt-1), cpt ); /* 4 or 6 ?*/
1.223 brouard 6139: }else{
6140: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
6141: kl++;
6142: }
6143: } /* end covariate */
6144: } /* end if no covariate */
6145: } /* end if backcast */
6146: fprintf(ficgp,"\nset out \n");
1.201 brouard 6147: } /* k1 */
6148: } /* cpt */
1.126 brouard 6149: /*2 eme*/
6150: for (k1=1; k1<= m ; k1 ++) {
1.220 brouard 6151:
1.223 brouard 6152: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
1.225 brouard 6153: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6154: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 6155: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6156: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6157: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6158: vlv= nbcode[Tvaraff[k]][lv];
6159: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6160: }
6161: fprintf(ficgp,"\n#\n");
6162: if(invalidvarcomb[k1]){
6163: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6164: continue;
6165: }
1.219 brouard 6166:
1.223 brouard 6167: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
6168: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6169: if(vpopbased==0)
6170: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
6171: else
6172: fprintf(ficgp,"\nreplot ");
6173: for (i=1; i<= nlstate+1 ; i ++) {
6174: k=2*i;
6175: 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);
6176: for (j=1; j<= nlstate+1 ; j ++) {
6177: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6178: else fprintf(ficgp," %%*lf (%%*lf)");
6179: }
6180: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
6181: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
6182: 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);
6183: for (j=1; j<= nlstate+1 ; j ++) {
6184: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6185: else fprintf(ficgp," %%*lf (%%*lf)");
6186: }
6187: fprintf(ficgp,"\" t\"\" w l lt 0,");
6188: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
6189: for (j=1; j<= nlstate+1 ; j ++) {
6190: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6191: else fprintf(ficgp," %%*lf (%%*lf)");
6192: }
6193: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
6194: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
6195: } /* state */
6196: } /* vpopbased */
6197: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
1.201 brouard 6198: } /* k1 */
1.219 brouard 6199:
6200:
1.126 brouard 6201: /*3eme*/
6202: for (k1=1; k1<= m ; k1 ++) {
1.220 brouard 6203:
1.126 brouard 6204: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.211 brouard 6205: fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt);
1.225 brouard 6206: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6207: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 6208: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6209: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6210: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6211: vlv= nbcode[Tvaraff[k]][lv];
6212: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6213: }
6214: fprintf(ficgp,"\n#\n");
1.223 brouard 6215: if(invalidvarcomb[k1]){
6216: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6217: continue;
6218: }
1.219 brouard 6219:
1.126 brouard 6220: /* k=2+nlstate*(2*cpt-2); */
6221: k=2+(nlstate+1)*(cpt-1);
1.201 brouard 6222: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
1.199 brouard 6223: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 6224: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.126 brouard 6225: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
1.223 brouard 6226: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
6227: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
6228: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
6229: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
6230: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
1.219 brouard 6231:
1.126 brouard 6232: */
6233: for (i=1; i< nlstate ; i ++) {
1.223 brouard 6234: 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);
6235: /* 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 6236:
1.126 brouard 6237: }
1.201 brouard 6238: 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 6239: }
6240: }
6241:
1.223 brouard 6242: /* 4eme */
1.201 brouard 6243: /* Survival functions (period) from state i in state j by initial state i */
6244: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
1.220 brouard 6245:
1.201 brouard 6246: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.211 brouard 6247: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
1.225 brouard 6248: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6249: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 6250: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6251: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6252: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6253: vlv= nbcode[Tvaraff[k]][lv];
6254: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6255: }
6256: fprintf(ficgp,"\n#\n");
1.223 brouard 6257: if(invalidvarcomb[k1]){
6258: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6259: continue;
6260: }
1.220 brouard 6261:
1.201 brouard 6262: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
6263: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
1.220 brouard 6264: set ter svg size 640, 480\n \
6265: unset log y\n \
1.201 brouard 6266: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6267: k=3;
1.201 brouard 6268: for (i=1; i<= nlstate ; i ++){
1.223 brouard 6269: if(i==1){
6270: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6271: }else{
6272: fprintf(ficgp,", '' ");
6273: }
6274: l=(nlstate+ndeath)*(i-1)+1;
6275: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
6276: for (j=2; j<= nlstate+ndeath ; j ++)
6277: fprintf(ficgp,"+$%d",k+l+j-1);
6278: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
1.201 brouard 6279: } /* nlstate */
6280: fprintf(ficgp,"\nset out\n");
6281: } /* end cpt state*/
6282: } /* end covariate */
1.220 brouard 6283:
6284: /* 5eme */
1.201 brouard 6285: /* Survival functions (period) from state i in state j by final state j */
1.202 brouard 6286: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.201 brouard 6287: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
1.223 brouard 6288:
1.201 brouard 6289: 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 6290: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 ! brouard 6291: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
! 6292: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
! 6293: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
! 6294: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
! 6295: vlv= nbcode[Tvaraff[k]][lv];
! 6296: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6297: }
6298: fprintf(ficgp,"\n#\n");
1.223 brouard 6299: if(invalidvarcomb[k1]){
1.227 ! brouard 6300: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
! 6301: continue;
1.223 brouard 6302: }
1.227 ! brouard 6303:
1.201 brouard 6304: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
6305: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
1.227 ! brouard 6306: set ter svg size 640, 480\n \
! 6307: unset log y\n \
1.201 brouard 6308: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6309: k=3;
1.201 brouard 6310: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
1.227 ! brouard 6311: if(j==1)
! 6312: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
! 6313: else
! 6314: fprintf(ficgp,", '' ");
! 6315: l=(nlstate+ndeath)*(cpt-1) +j;
! 6316: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
! 6317: /* for (i=2; i<= nlstate+ndeath ; i ++) */
! 6318: /* fprintf(ficgp,"+$%d",k+l+i-1); */
! 6319: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
1.201 brouard 6320: } /* nlstate */
6321: fprintf(ficgp,", '' ");
6322: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
6323: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
1.227 ! brouard 6324: l=(nlstate+ndeath)*(cpt-1) +j;
! 6325: if(j < nlstate)
! 6326: fprintf(ficgp,"$%d +",k+l);
! 6327: else
! 6328: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
1.201 brouard 6329: }
6330: fprintf(ficgp,"\nset out\n");
6331: } /* end cpt state*/
6332: } /* end covariate */
1.227 ! brouard 6333:
1.220 brouard 6334: /* 6eme */
1.202 brouard 6335: /* CV preval stable (period) for each covariate */
1.211 brouard 6336: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.153 brouard 6337: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.227 ! brouard 6338:
1.211 brouard 6339: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
1.225 brouard 6340: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 ! brouard 6341: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
! 6342: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
! 6343: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
! 6344: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
! 6345: vlv= nbcode[Tvaraff[k]][lv];
! 6346: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6347: }
6348: fprintf(ficgp,"\n#\n");
1.223 brouard 6349: if(invalidvarcomb[k1]){
1.227 ! brouard 6350: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
! 6351: continue;
1.223 brouard 6352: }
1.227 ! brouard 6353:
1.201 brouard 6354: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 6355: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.227 ! brouard 6356: set ter svg size 640, 480\n \
! 6357: unset log y\n \
1.153 brouard 6358: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6359: k=3; /* Offset */
1.153 brouard 6360: for (i=1; i<= nlstate ; i ++){
1.227 ! brouard 6361: if(i==1)
! 6362: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
! 6363: else
! 6364: fprintf(ficgp,", '' ");
! 6365: l=(nlstate+ndeath)*(i-1)+1;
! 6366: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
! 6367: for (j=2; j<= nlstate ; j ++)
! 6368: fprintf(ficgp,"+$%d",k+l+j-1);
! 6369: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153 brouard 6370: } /* nlstate */
1.201 brouard 6371: fprintf(ficgp,"\nset out\n");
1.153 brouard 6372: } /* end cpt state*/
6373: } /* end covariate */
1.227 ! brouard 6374:
! 6375:
1.220 brouard 6376: /* 7eme */
1.218 brouard 6377: if(backcast == 1){
1.217 brouard 6378: /* CV back preval stable (period) for each covariate */
1.218 brouard 6379: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
6380: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.227 ! brouard 6381: fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
! 6382: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
! 6383: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
! 6384: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
! 6385: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
1.223 brouard 6386: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.227 ! brouard 6387: vlv= nbcode[Tvaraff[k]][lv];
! 6388: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
! 6389: }
! 6390: fprintf(ficgp,"\n#\n");
! 6391: if(invalidvarcomb[k1]){
! 6392: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
! 6393: continue;
! 6394: }
! 6395:
! 6396: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
! 6397: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
! 6398: set ter svg size 640, 480\n \
! 6399: unset log y\n \
1.218 brouard 6400: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 ! brouard 6401: k=3; /* Offset */
! 6402: for (i=1; i<= nlstate ; i ++){
! 6403: if(i==1)
! 6404: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
! 6405: else
! 6406: fprintf(ficgp,", '' ");
! 6407: /* l=(nlstate+ndeath)*(i-1)+1; */
! 6408: l=(nlstate+ndeath)*(cpt-1)+1;
! 6409: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
! 6410: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
! 6411: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
! 6412: /* for (j=2; j<= nlstate ; j ++) */
! 6413: /* fprintf(ficgp,"+$%d",k+l+j-1); */
! 6414: /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
! 6415: fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
! 6416: } /* nlstate */
! 6417: fprintf(ficgp,"\nset out\n");
1.218 brouard 6418: } /* end cpt state*/
6419: } /* end covariate */
6420: } /* End if backcast */
6421:
1.223 brouard 6422: /* 8eme */
1.218 brouard 6423: if(prevfcast==1){
6424: /* Projection from cross-sectional to stable (period) for each covariate */
6425:
6426: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.211 brouard 6427: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.227 ! brouard 6428: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
! 6429: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
! 6430: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
! 6431: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
! 6432: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
! 6433: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
! 6434: vlv= nbcode[Tvaraff[k]][lv];
! 6435: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
! 6436: }
! 6437: fprintf(ficgp,"\n#\n");
! 6438: if(invalidvarcomb[k1]){
! 6439: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
! 6440: continue;
! 6441: }
! 6442:
! 6443: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
! 6444: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
! 6445: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
! 6446: set ter svg size 640, 480\n \
! 6447: unset log y\n \
1.219 brouard 6448: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 ! brouard 6449: for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
! 6450: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
! 6451: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
! 6452: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
! 6453: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
! 6454: if(i==1){
! 6455: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
! 6456: }else{
! 6457: fprintf(ficgp,",\\\n '' ");
! 6458: }
! 6459: if(cptcoveff ==0){ /* No covariate */
! 6460: ioffset=2; /* Age is in 2 */
! 6461: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
! 6462: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
! 6463: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
! 6464: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
! 6465: fprintf(ficgp," u %d:(", ioffset);
! 6466: if(i==nlstate+1)
! 6467: fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ", \
! 6468: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
! 6469: else
! 6470: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
! 6471: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
! 6472: }else{ /* more than 2 covariates */
! 6473: if(cptcoveff ==1){
! 6474: ioffset=4; /* Age is in 4 */
! 6475: }else{
! 6476: ioffset=6; /* Age is in 6 */
! 6477: /*# V1 = 1 V2 = 0 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: }
! 6480: fprintf(ficgp," u %d:(",ioffset);
! 6481: kl=0;
! 6482: strcpy(gplotcondition,"(");
! 6483: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
! 6484: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
! 6485: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
! 6486: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
! 6487: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
! 6488: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
! 6489: kl++;
! 6490: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
! 6491: kl++;
! 6492: if(k <cptcoveff && cptcoveff>1)
! 6493: sprintf(gplotcondition+strlen(gplotcondition)," && ");
! 6494: }
! 6495: strcpy(gplotcondition+strlen(gplotcondition),")");
! 6496: /* 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 *\/ */
! 6497: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
! 6498: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
! 6499: /* '' 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*/
! 6500: if(i==nlstate+1){
! 6501: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
! 6502: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
! 6503: }else{
! 6504: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
! 6505: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
! 6506: }
! 6507: } /* end if covariate */
! 6508: } /* nlstate */
! 6509: fprintf(ficgp,"\nset out\n");
1.223 brouard 6510: } /* end cpt state*/
6511: } /* end covariate */
6512: } /* End if prevfcast */
1.227 ! brouard 6513:
! 6514:
1.223 brouard 6515: /* proba elementaires */
6516: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 6517: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 6518: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 6519: for(k=1; k <=(nlstate+ndeath); k++){
6520: if (k != i) {
1.227 ! brouard 6521: fprintf(ficgp,"# current state %d\n",k);
! 6522: for(j=1; j <=ncovmodel; j++){
! 6523: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
! 6524: jk++;
! 6525: }
! 6526: fprintf(ficgp,"\n");
1.126 brouard 6527: }
6528: }
1.223 brouard 6529: }
1.187 brouard 6530: fprintf(ficgp,"##############\n#\n");
1.227 ! brouard 6531:
1.145 brouard 6532: /*goto avoid;*/
1.200 brouard 6533: fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
1.187 brouard 6534: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
6535: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
6536: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
6537: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
6538: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6539: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
6540: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6541: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
6542: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
6543: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6544: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
6545: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
6546: fprintf(ficgp,"#\n");
1.223 brouard 6547: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
6548: fprintf(ficgp,"# ng=%d\n",ng);
1.225 brouard 6549: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.223 brouard 6550: for(jk=1; jk <=m; jk++) {
6551: fprintf(ficgp,"# jk=%d\n",jk);
6552: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
6553: fprintf(ficgp,"\nset ter svg size 640, 480 ");
6554: if (ng==1){
6555: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
6556: fprintf(ficgp,"\nunset log y");
6557: }else if (ng==2){
6558: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
6559: fprintf(ficgp,"\nset log y");
6560: }else if (ng==3){
6561: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
6562: fprintf(ficgp,"\nset log y");
6563: }else
6564: fprintf(ficgp,"\nunset title ");
6565: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
6566: i=1;
6567: for(k2=1; k2<=nlstate; k2++) {
6568: k3=i;
6569: for(k=1; k<=(nlstate+ndeath); k++) {
6570: if (k != k2){
6571: switch( ng) {
6572: case 1:
6573: if(nagesqr==0)
6574: fprintf(ficgp," p%d+p%d*x",i,i+1);
6575: else /* nagesqr =1 */
6576: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
6577: break;
6578: case 2: /* ng=2 */
6579: if(nagesqr==0)
6580: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
6581: else /* nagesqr =1 */
6582: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
6583: break;
6584: case 3:
6585: if(nagesqr==0)
6586: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
6587: else /* nagesqr =1 */
6588: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
6589: break;
6590: }
6591: ij=1;/* To be checked else nbcode[0][0] wrong */
6592: for(j=3; j <=ncovmodel-nagesqr; j++) {
6593: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
6594: if(ij <=cptcovage) { /* Bug valgrind */
6595: if((j-2)==Tage[ij]) { /* Bug valgrind */
6596: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
6597: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
6598: ij++;
6599: }
6600: }
6601: else
1.227 ! brouard 6602: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); /* Valgrind bug nbcode */
1.223 brouard 6603: }
6604: }else{
6605: i=i-ncovmodel;
6606: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
6607: fprintf(ficgp," (1.");
6608: }
1.227 ! brouard 6609:
1.223 brouard 6610: if(ng != 1){
6611: fprintf(ficgp,")/(1");
1.227 ! brouard 6612:
1.223 brouard 6613: for(k1=1; k1 <=nlstate; k1++){
6614: if(nagesqr==0)
6615: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
6616: else /* nagesqr =1 */
6617: 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 6618:
1.223 brouard 6619: ij=1;
6620: for(j=3; j <=ncovmodel-nagesqr; j++){
6621: if(ij <=cptcovage) { /* Bug valgrind */
6622: if((j-2)==Tage[ij]) { /* Bug valgrind */
6623: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
6624: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
6625: ij++;
6626: }
6627: }
6628: else
1.225 brouard 6629: 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 6630: }
6631: fprintf(ficgp,")");
6632: }
6633: fprintf(ficgp,")");
6634: if(ng ==2)
6635: fprintf(ficgp," t \"p%d%d\" ", k2,k);
6636: else /* ng= 3 */
6637: fprintf(ficgp," t \"i%d%d\" ", k2,k);
6638: }else{ /* end ng <> 1 */
6639: if( k !=k2) /* logit p11 is hard to draw */
6640: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
6641: }
6642: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
6643: fprintf(ficgp,",");
6644: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
6645: fprintf(ficgp,",");
6646: i=i+ncovmodel;
6647: } /* end k */
6648: } /* end k2 */
6649: fprintf(ficgp,"\n set out\n");
6650: } /* end jk */
6651: } /* end ng */
6652: /* avoid: */
6653: fflush(ficgp);
1.126 brouard 6654: } /* end gnuplot */
6655:
6656:
6657: /*************** Moving average **************/
1.219 brouard 6658: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.222 brouard 6659: int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
1.218 brouard 6660:
1.222 brouard 6661: int i, cpt, cptcod;
6662: int modcovmax =1;
6663: int mobilavrange, mob;
6664: int iage=0;
6665:
6666: double sum=0.;
6667: double age;
6668: double *sumnewp, *sumnewm;
6669: double *agemingood, *agemaxgood; /* Currently identical for all covariates */
6670:
6671:
1.225 brouard 6672: /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose */
1.222 brouard 6673: /* a covariate has 2 modalities, should be equal to ncovcombmax *\/ */
6674:
6675: sumnewp = vector(1,ncovcombmax);
6676: sumnewm = vector(1,ncovcombmax);
6677: agemingood = vector(1,ncovcombmax);
6678: agemaxgood = vector(1,ncovcombmax);
6679:
6680: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
6681: sumnewm[cptcod]=0.;
6682: sumnewp[cptcod]=0.;
6683: agemingood[cptcod]=0;
6684: agemaxgood[cptcod]=0;
6685: }
6686: if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
6687:
6688: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
6689: if(mobilav==1) mobilavrange=5; /* default */
6690: else mobilavrange=mobilav;
6691: for (age=bage; age<=fage; age++)
6692: for (i=1; i<=nlstate;i++)
6693: for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
6694: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
6695: /* We keep the original values on the extreme ages bage, fage and for
6696: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
6697: we use a 5 terms etc. until the borders are no more concerned.
6698: */
6699: for (mob=3;mob <=mobilavrange;mob=mob+2){
6700: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
6701: for (i=1; i<=nlstate;i++){
6702: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
6703: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
6704: for (cpt=1;cpt<=(mob-1)/2;cpt++){
6705: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
6706: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
6707: }
6708: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
6709: }
6710: }
6711: }/* end age */
6712: }/* end mob */
6713: }else
6714: return -1;
6715: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
6716: /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
6717: if(invalidvarcomb[cptcod]){
6718: printf("\nCombination (%d) ignored because no cases \n",cptcod);
6719: continue;
6720: }
1.219 brouard 6721:
1.222 brouard 6722: agemingood[cptcod]=fage-(mob-1)/2;
6723: for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
6724: sumnewm[cptcod]=0.;
6725: for (i=1; i<=nlstate;i++){
6726: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6727: }
6728: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
6729: agemingood[cptcod]=age;
6730: }else{ /* bad */
6731: for (i=1; i<=nlstate;i++){
6732: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6733: } /* i */
6734: } /* end bad */
6735: }/* age */
6736: sum=0.;
6737: for (i=1; i<=nlstate;i++){
6738: sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6739: }
6740: if(fabs(sum - 1.) > 1.e-3) { /* bad */
6741: 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);
6742: /* for (i=1; i<=nlstate;i++){ */
6743: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
6744: /* } /\* i *\/ */
6745: } /* end bad */
6746: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
6747: /* From youngest, finding the oldest wrong */
6748: agemaxgood[cptcod]=bage+(mob-1)/2;
6749: for (age=bage+(mob-1)/2; age<=fage; age++){
6750: sumnewm[cptcod]=0.;
6751: for (i=1; i<=nlstate;i++){
6752: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6753: }
6754: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
6755: agemaxgood[cptcod]=age;
6756: }else{ /* bad */
6757: for (i=1; i<=nlstate;i++){
6758: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6759: } /* i */
6760: } /* end bad */
6761: }/* age */
6762: sum=0.;
6763: for (i=1; i<=nlstate;i++){
6764: sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6765: }
6766: if(fabs(sum - 1.) > 1.e-3) { /* bad */
6767: 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);
6768: /* for (i=1; i<=nlstate;i++){ */
6769: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
6770: /* } /\* i *\/ */
6771: } /* end bad */
6772:
6773: for (age=bage; age<=fage; age++){
6774: printf("%d %d ", cptcod, (int)age);
6775: sumnewp[cptcod]=0.;
6776: sumnewm[cptcod]=0.;
6777: for (i=1; i<=nlstate;i++){
6778: sumnewp[cptcod]+=probs[(int)age][i][cptcod];
6779: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6780: /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
6781: }
6782: /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
6783: }
6784: /* printf("\n"); */
6785: /* } */
6786: /* brutal averaging */
6787: for (i=1; i<=nlstate;i++){
6788: for (age=1; age<=bage; age++){
6789: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6790: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
6791: }
6792: for (age=fage; age<=AGESUP; age++){
6793: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6794: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
6795: }
6796: } /* end i status */
6797: for (i=nlstate+1; i<=nlstate+ndeath;i++){
6798: for (age=1; age<=AGESUP; age++){
6799: /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
6800: mobaverage[(int)age][i][cptcod]=0.;
6801: }
6802: }
6803: }/* end cptcod */
6804: free_vector(sumnewm,1, ncovcombmax);
6805: free_vector(sumnewp,1, ncovcombmax);
6806: free_vector(agemaxgood,1, ncovcombmax);
6807: free_vector(agemingood,1, ncovcombmax);
6808: return 0;
6809: }/* End movingaverage */
1.218 brouard 6810:
1.126 brouard 6811:
6812: /************** Forecasting ******************/
1.225 brouard 6813: 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 6814: /* proj1, year, month, day of starting projection
6815: agemin, agemax range of age
6816: dateprev1 dateprev2 range of dates during which prevalence is computed
6817: anproj2 year of en of projection (same day and month as proj1).
6818: */
1.164 brouard 6819: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 6820: double agec; /* generic age */
6821: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
6822: double *popeffectif,*popcount;
6823: double ***p3mat;
1.218 brouard 6824: /* double ***mobaverage; */
1.126 brouard 6825: char fileresf[FILENAMELENGTH];
6826:
6827: agelim=AGESUP;
1.211 brouard 6828: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
6829: in each health status at the date of interview (if between dateprev1 and dateprev2).
6830: We still use firstpass and lastpass as another selection.
6831: */
1.214 brouard 6832: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
6833: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 6834:
1.201 brouard 6835: strcpy(fileresf,"F_");
6836: strcat(fileresf,fileresu);
1.126 brouard 6837: if((ficresf=fopen(fileresf,"w"))==NULL) {
6838: printf("Problem with forecast resultfile: %s\n", fileresf);
6839: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
6840: }
1.215 brouard 6841: printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
6842: fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 6843:
1.225 brouard 6844: if (cptcoveff==0) ncodemax[cptcoveff]=1;
1.126 brouard 6845:
6846:
6847: stepsize=(int) (stepm+YEARM-1)/YEARM;
6848: if (stepm<=12) stepsize=1;
6849: if(estepm < stepm){
6850: printf ("Problem %d lower than %d\n",estepm, stepm);
6851: }
6852: else hstepm=estepm;
6853:
6854: hstepm=hstepm/stepm;
6855: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
6856: fractional in yp1 */
6857: anprojmean=yp;
6858: yp2=modf((yp1*12),&yp);
6859: mprojmean=yp;
6860: yp1=modf((yp2*30.5),&yp);
6861: jprojmean=yp;
6862: if(jprojmean==0) jprojmean=1;
6863: if(mprojmean==0) jprojmean=1;
6864:
1.227 ! brouard 6865: i1=pow(2,cptcoveff);
1.126 brouard 6866: if (cptcovn < 1){i1=1;}
6867:
6868: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
6869:
6870: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.227 ! brouard 6871:
1.126 brouard 6872: /* if (h==(int)(YEARM*yearp)){ */
1.227 ! brouard 6873: for(k=1;k<=i1;k++){
! 6874: if(invalidvarcomb[k]){
! 6875: printf("\nCombination (%d) projection ignored because no cases \n",k);
! 6876: continue;
! 6877: }
! 6878: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
! 6879: for(j=1;j<=cptcoveff;j++) {
! 6880: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 6881: }
! 6882: fprintf(ficresf," yearproj age");
! 6883: for(j=1; j<=nlstate+ndeath;j++){
! 6884: for(i=1; i<=nlstate;i++)
! 6885: fprintf(ficresf," p%d%d",i,j);
! 6886: fprintf(ficresf," wp.%d",j);
! 6887: }
! 6888: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
! 6889: fprintf(ficresf,"\n");
! 6890: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
! 6891: for (agec=fage; agec>=(ageminpar-1); agec--){
! 6892: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
! 6893: nhstepm = nhstepm/hstepm;
! 6894: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 6895: oldm=oldms;savm=savms;
! 6896: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
! 6897:
! 6898: for (h=0; h<=nhstepm; h++){
! 6899: if (h*hstepm/YEARM*stepm ==yearp) {
! 6900: fprintf(ficresf,"\n");
! 6901: for(j=1;j<=cptcoveff;j++)
! 6902: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 6903: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
! 6904: }
! 6905: for(j=1; j<=nlstate+ndeath;j++) {
! 6906: ppij=0.;
! 6907: for(i=1; i<=nlstate;i++) {
! 6908: if (mobilav==1)
! 6909: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];
! 6910: else {
! 6911: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
! 6912: }
! 6913: if (h*hstepm/YEARM*stepm== yearp) {
! 6914: fprintf(ficresf," %.3f", p3mat[i][j][h]);
! 6915: }
! 6916: } /* end i */
! 6917: if (h*hstepm/YEARM*stepm==yearp) {
! 6918: fprintf(ficresf," %.3f", ppij);
! 6919: }
! 6920: }/* end j */
! 6921: } /* end h */
! 6922: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 6923: } /* end agec */
! 6924: } /* end yearp */
! 6925: } /* end k */
1.219 brouard 6926:
1.126 brouard 6927: fclose(ficresf);
1.215 brouard 6928: printf("End of Computing forecasting \n");
6929: fprintf(ficlog,"End of Computing forecasting\n");
6930:
1.126 brouard 6931: }
6932:
1.218 brouard 6933: /* /\************** Back Forecasting ******************\/ */
1.225 brouard 6934: /* 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 6935: /* /\* back1, year, month, day of starting backection */
6936: /* agemin, agemax range of age */
6937: /* dateprev1 dateprev2 range of dates during which prevalence is computed */
6938: /* anback2 year of en of backection (same day and month as back1). */
6939: /* *\/ */
6940: /* int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */
6941: /* double agec; /\* generic age *\/ */
6942: /* double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */
6943: /* double *popeffectif,*popcount; */
6944: /* double ***p3mat; */
6945: /* /\* double ***mobaverage; *\/ */
6946: /* char fileresfb[FILENAMELENGTH]; */
6947:
6948: /* agelim=AGESUP; */
6949: /* /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */
6950: /* in each health status at the date of interview (if between dateprev1 and dateprev2). */
6951: /* We still use firstpass and lastpass as another selection. */
6952: /* *\/ */
6953: /* /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */
6954: /* /\* firstpass, lastpass, stepm, weightopt, model); *\/ */
6955: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
6956:
6957: /* strcpy(fileresfb,"FB_"); */
6958: /* strcat(fileresfb,fileresu); */
6959: /* if((ficresfb=fopen(fileresfb,"w"))==NULL) { */
6960: /* printf("Problem with back forecast resultfile: %s\n", fileresfb); */
6961: /* fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */
6962: /* } */
6963: /* printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
6964: /* fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
6965:
1.225 brouard 6966: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.218 brouard 6967:
6968: /* /\* if (mobilav!=0) { *\/ */
6969: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
6970: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
6971: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
6972: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
6973: /* /\* } *\/ */
6974: /* /\* } *\/ */
6975:
6976: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
6977: /* if (stepm<=12) stepsize=1; */
6978: /* if(estepm < stepm){ */
6979: /* printf ("Problem %d lower than %d\n",estepm, stepm); */
6980: /* } */
6981: /* else hstepm=estepm; */
6982:
6983: /* hstepm=hstepm/stepm; */
6984: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
6985: /* fractional in yp1 *\/ */
6986: /* anprojmean=yp; */
6987: /* yp2=modf((yp1*12),&yp); */
6988: /* mprojmean=yp; */
6989: /* yp1=modf((yp2*30.5),&yp); */
6990: /* jprojmean=yp; */
6991: /* if(jprojmean==0) jprojmean=1; */
6992: /* if(mprojmean==0) jprojmean=1; */
6993:
1.225 brouard 6994: /* i1=cptcoveff; */
1.218 brouard 6995: /* if (cptcovn < 1){i1=1;} */
1.217 brouard 6996:
1.218 brouard 6997: /* fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); */
1.217 brouard 6998:
1.218 brouard 6999: /* fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */
7000:
7001: /* /\* if (h==(int)(YEARM*yearp)){ *\/ */
7002: /* for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
1.225 brouard 7003: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
1.218 brouard 7004: /* k=k+1; */
7005: /* fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
1.225 brouard 7006: /* for(j=1;j<=cptcoveff;j++) { */
1.218 brouard 7007: /* fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
7008: /* } */
7009: /* fprintf(ficresfb," yearbproj age"); */
7010: /* for(j=1; j<=nlstate+ndeath;j++){ */
7011: /* for(i=1; i<=nlstate;i++) */
7012: /* fprintf(ficresfb," p%d%d",i,j); */
7013: /* fprintf(ficresfb," p.%d",j); */
7014: /* } */
7015: /* for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) { */
7016: /* /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { *\/ */
7017: /* fprintf(ficresfb,"\n"); */
7018: /* fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
7019: /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
7020: /* nhstepm=(int) rint((agelim-agec)*YEARM/stepm); */
7021: /* nhstepm = nhstepm/hstepm; */
7022: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7023: /* oldm=oldms;savm=savms; */
7024: /* hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k); */
7025: /* for (h=0; h<=nhstepm; h++){ */
7026: /* if (h*hstepm/YEARM*stepm ==yearp) { */
7027: /* fprintf(ficresfb,"\n"); */
1.225 brouard 7028: /* for(j=1;j<=cptcoveff;j++) */
1.218 brouard 7029: /* fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
7030: /* fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */
7031: /* } */
7032: /* for(j=1; j<=nlstate+ndeath;j++) { */
7033: /* ppij=0.; */
7034: /* for(i=1; i<=nlstate;i++) { */
7035: /* if (mobilav==1) */
7036: /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */
7037: /* else { */
7038: /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */
7039: /* } */
7040: /* if (h*hstepm/YEARM*stepm== yearp) { */
7041: /* fprintf(ficresfb," %.3f", p3mat[i][j][h]); */
7042: /* } */
7043: /* } /\* end i *\/ */
7044: /* if (h*hstepm/YEARM*stepm==yearp) { */
7045: /* fprintf(ficresfb," %.3f", ppij); */
7046: /* } */
7047: /* }/\* end j *\/ */
7048: /* } /\* end h *\/ */
7049: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7050: /* } /\* end agec *\/ */
7051: /* } /\* end yearp *\/ */
7052: /* } /\* end cptcod *\/ */
7053: /* } /\* end cptcov *\/ */
7054:
7055: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
7056:
7057: /* fclose(ficresfb); */
7058: /* printf("End of Computing Back forecasting \n"); */
7059: /* fprintf(ficlog,"End of Computing Back forecasting\n"); */
1.217 brouard 7060:
1.218 brouard 7061: /* } */
1.217 brouard 7062:
1.126 brouard 7063: /************** Forecasting *****not tested NB*************/
1.227 ! brouard 7064: /* 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 7065:
1.227 ! brouard 7066: /* int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
! 7067: /* int *popage; */
! 7068: /* double calagedatem, agelim, kk1, kk2; */
! 7069: /* double *popeffectif,*popcount; */
! 7070: /* double ***p3mat,***tabpop,***tabpopprev; */
! 7071: /* /\* double ***mobaverage; *\/ */
! 7072: /* char filerespop[FILENAMELENGTH]; */
1.126 brouard 7073:
1.227 ! brouard 7074: /* tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
! 7075: /* tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
! 7076: /* agelim=AGESUP; */
! 7077: /* calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
1.126 brouard 7078:
1.227 ! brouard 7079: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
1.126 brouard 7080:
7081:
1.227 ! brouard 7082: /* strcpy(filerespop,"POP_"); */
! 7083: /* strcat(filerespop,fileresu); */
! 7084: /* if((ficrespop=fopen(filerespop,"w"))==NULL) { */
! 7085: /* printf("Problem with forecast resultfile: %s\n", filerespop); */
! 7086: /* fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
! 7087: /* } */
! 7088: /* printf("Computing forecasting: result on file '%s' \n", filerespop); */
! 7089: /* fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
1.126 brouard 7090:
1.227 ! brouard 7091: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.126 brouard 7092:
1.227 ! brouard 7093: /* /\* if (mobilav!=0) { *\/ */
! 7094: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
! 7095: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
! 7096: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
! 7097: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
! 7098: /* /\* } *\/ */
! 7099: /* /\* } *\/ */
1.126 brouard 7100:
1.227 ! brouard 7101: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
! 7102: /* if (stepm<=12) stepsize=1; */
1.126 brouard 7103:
1.227 ! brouard 7104: /* agelim=AGESUP; */
1.126 brouard 7105:
1.227 ! brouard 7106: /* hstepm=1; */
! 7107: /* hstepm=hstepm/stepm; */
1.218 brouard 7108:
1.227 ! brouard 7109: /* if (popforecast==1) { */
! 7110: /* if((ficpop=fopen(popfile,"r"))==NULL) { */
! 7111: /* printf("Problem with population file : %s\n",popfile);exit(0); */
! 7112: /* fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
! 7113: /* } */
! 7114: /* popage=ivector(0,AGESUP); */
! 7115: /* popeffectif=vector(0,AGESUP); */
! 7116: /* popcount=vector(0,AGESUP); */
1.126 brouard 7117:
1.227 ! brouard 7118: /* i=1; */
! 7119: /* while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
1.218 brouard 7120:
1.227 ! brouard 7121: /* imx=i; */
! 7122: /* for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
! 7123: /* } */
1.218 brouard 7124:
1.227 ! brouard 7125: /* for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
! 7126: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
! 7127: /* k=k+1; */
! 7128: /* fprintf(ficrespop,"\n#******"); */
! 7129: /* for(j=1;j<=cptcoveff;j++) { */
! 7130: /* fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
! 7131: /* } */
! 7132: /* fprintf(ficrespop,"******\n"); */
! 7133: /* fprintf(ficrespop,"# Age"); */
! 7134: /* for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
! 7135: /* if (popforecast==1) fprintf(ficrespop," [Population]"); */
1.126 brouard 7136:
1.227 ! brouard 7137: /* for (cpt=0; cpt<=0;cpt++) { */
! 7138: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
1.126 brouard 7139:
1.227 ! brouard 7140: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
! 7141: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
! 7142: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 7143:
1.227 ! brouard 7144: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
! 7145: /* oldm=oldms;savm=savms; */
! 7146: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.218 brouard 7147:
1.227 ! brouard 7148: /* for (h=0; h<=nhstepm; h++){ */
! 7149: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
! 7150: /* fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
! 7151: /* } */
! 7152: /* for(j=1; j<=nlstate+ndeath;j++) { */
! 7153: /* kk1=0.;kk2=0; */
! 7154: /* for(i=1; i<=nlstate;i++) { */
! 7155: /* if (mobilav==1) */
! 7156: /* kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
! 7157: /* else { */
! 7158: /* kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
! 7159: /* } */
! 7160: /* } */
! 7161: /* if (h==(int)(calagedatem+12*cpt)){ */
! 7162: /* tabpop[(int)(agedeb)][j][cptcod]=kk1; */
! 7163: /* /\*fprintf(ficrespop," %.3f", kk1); */
! 7164: /* if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
! 7165: /* } */
! 7166: /* } */
! 7167: /* for(i=1; i<=nlstate;i++){ */
! 7168: /* kk1=0.; */
! 7169: /* for(j=1; j<=nlstate;j++){ */
! 7170: /* kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; */
! 7171: /* } */
! 7172: /* tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
! 7173: /* } */
1.218 brouard 7174:
1.227 ! brouard 7175: /* if (h==(int)(calagedatem+12*cpt)) */
! 7176: /* for(j=1; j<=nlstate;j++) */
! 7177: /* fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
! 7178: /* } */
! 7179: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
! 7180: /* } */
! 7181: /* } */
1.218 brouard 7182:
1.227 ! brouard 7183: /* /\******\/ */
1.218 brouard 7184:
1.227 ! brouard 7185: /* for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { */
! 7186: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
! 7187: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
! 7188: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
! 7189: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 7190:
1.227 ! brouard 7191: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
! 7192: /* oldm=oldms;savm=savms; */
! 7193: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
! 7194: /* for (h=0; h<=nhstepm; h++){ */
! 7195: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
! 7196: /* fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
! 7197: /* } */
! 7198: /* for(j=1; j<=nlstate+ndeath;j++) { */
! 7199: /* kk1=0.;kk2=0; */
! 7200: /* for(i=1; i<=nlstate;i++) { */
! 7201: /* kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; */
! 7202: /* } */
! 7203: /* if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); */
! 7204: /* } */
! 7205: /* } */
! 7206: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
! 7207: /* } */
! 7208: /* } */
! 7209: /* } */
! 7210: /* } */
1.218 brouard 7211:
1.227 ! brouard 7212: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
1.218 brouard 7213:
1.227 ! brouard 7214: /* if (popforecast==1) { */
! 7215: /* free_ivector(popage,0,AGESUP); */
! 7216: /* free_vector(popeffectif,0,AGESUP); */
! 7217: /* free_vector(popcount,0,AGESUP); */
! 7218: /* } */
! 7219: /* free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
! 7220: /* free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
! 7221: /* fclose(ficrespop); */
! 7222: /* } /\* End of popforecast *\/ */
1.218 brouard 7223:
1.126 brouard 7224: int fileappend(FILE *fichier, char *optionfich)
7225: {
7226: if((fichier=fopen(optionfich,"a"))==NULL) {
7227: printf("Problem with file: %s\n", optionfich);
7228: fprintf(ficlog,"Problem with file: %s\n", optionfich);
7229: return (0);
7230: }
7231: fflush(fichier);
7232: return (1);
7233: }
7234:
7235:
7236: /**************** function prwizard **********************/
7237: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
7238: {
7239:
7240: /* Wizard to print covariance matrix template */
7241:
1.164 brouard 7242: char ca[32], cb[32];
7243: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 7244: int numlinepar;
7245:
7246: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7247: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7248: for(i=1; i <=nlstate; i++){
7249: jj=0;
7250: for(j=1; j <=nlstate+ndeath; j++){
7251: if(j==i) continue;
7252: jj++;
7253: /*ca[0]= k+'a'-1;ca[1]='\0';*/
7254: printf("%1d%1d",i,j);
7255: fprintf(ficparo,"%1d%1d",i,j);
7256: for(k=1; k<=ncovmodel;k++){
7257: /* printf(" %lf",param[i][j][k]); */
7258: /* fprintf(ficparo," %lf",param[i][j][k]); */
7259: printf(" 0.");
7260: fprintf(ficparo," 0.");
7261: }
7262: printf("\n");
7263: fprintf(ficparo,"\n");
7264: }
7265: }
7266: printf("# Scales (for hessian or gradient estimation)\n");
7267: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
7268: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
7269: for(i=1; i <=nlstate; i++){
7270: jj=0;
7271: for(j=1; j <=nlstate+ndeath; j++){
7272: if(j==i) continue;
7273: jj++;
7274: fprintf(ficparo,"%1d%1d",i,j);
7275: printf("%1d%1d",i,j);
7276: fflush(stdout);
7277: for(k=1; k<=ncovmodel;k++){
7278: /* printf(" %le",delti3[i][j][k]); */
7279: /* fprintf(ficparo," %le",delti3[i][j][k]); */
7280: printf(" 0.");
7281: fprintf(ficparo," 0.");
7282: }
7283: numlinepar++;
7284: printf("\n");
7285: fprintf(ficparo,"\n");
7286: }
7287: }
7288: printf("# Covariance matrix\n");
7289: /* # 121 Var(a12)\n\ */
7290: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7291: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7292: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7293: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7294: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7295: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7296: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7297: fflush(stdout);
7298: fprintf(ficparo,"# Covariance matrix\n");
7299: /* # 121 Var(a12)\n\ */
7300: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7301: /* # ...\n\ */
7302: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7303:
7304: for(itimes=1;itimes<=2;itimes++){
7305: jj=0;
7306: for(i=1; i <=nlstate; i++){
7307: for(j=1; j <=nlstate+ndeath; j++){
7308: if(j==i) continue;
7309: for(k=1; k<=ncovmodel;k++){
7310: jj++;
7311: ca[0]= k+'a'-1;ca[1]='\0';
7312: if(itimes==1){
7313: printf("#%1d%1d%d",i,j,k);
7314: fprintf(ficparo,"#%1d%1d%d",i,j,k);
7315: }else{
7316: printf("%1d%1d%d",i,j,k);
7317: fprintf(ficparo,"%1d%1d%d",i,j,k);
7318: /* printf(" %.5le",matcov[i][j]); */
7319: }
7320: ll=0;
7321: for(li=1;li <=nlstate; li++){
7322: for(lj=1;lj <=nlstate+ndeath; lj++){
7323: if(lj==li) continue;
7324: for(lk=1;lk<=ncovmodel;lk++){
7325: ll++;
7326: if(ll<=jj){
7327: cb[0]= lk +'a'-1;cb[1]='\0';
7328: if(ll<jj){
7329: if(itimes==1){
7330: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7331: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7332: }else{
7333: printf(" 0.");
7334: fprintf(ficparo," 0.");
7335: }
7336: }else{
7337: if(itimes==1){
7338: printf(" Var(%s%1d%1d)",ca,i,j);
7339: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
7340: }else{
7341: printf(" 0.");
7342: fprintf(ficparo," 0.");
7343: }
7344: }
7345: }
7346: } /* end lk */
7347: } /* end lj */
7348: } /* end li */
7349: printf("\n");
7350: fprintf(ficparo,"\n");
7351: numlinepar++;
7352: } /* end k*/
7353: } /*end j */
7354: } /* end i */
7355: } /* end itimes */
7356:
7357: } /* end of prwizard */
7358: /******************* Gompertz Likelihood ******************************/
7359: double gompertz(double x[])
7360: {
7361: double A,B,L=0.0,sump=0.,num=0.;
7362: int i,n=0; /* n is the size of the sample */
7363:
1.220 brouard 7364: for (i=1;i<=imx ; i++) {
1.126 brouard 7365: sump=sump+weight[i];
7366: /* sump=sump+1;*/
7367: num=num+1;
7368: }
7369:
7370:
7371: /* for (i=0; i<=imx; i++)
7372: 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]);*/
7373:
7374: for (i=1;i<=imx ; i++)
7375: {
7376: if (cens[i] == 1 && wav[i]>1)
7377: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
7378:
7379: if (cens[i] == 0 && wav[i]>1)
7380: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
7381: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
7382:
7383: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
7384: if (wav[i] > 1 ) { /* ??? */
7385: L=L+A*weight[i];
7386: /* 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]);*/
7387: }
7388: }
7389:
7390: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
7391:
7392: return -2*L*num/sump;
7393: }
7394:
1.136 brouard 7395: #ifdef GSL
7396: /******************* Gompertz_f Likelihood ******************************/
7397: double gompertz_f(const gsl_vector *v, void *params)
7398: {
7399: double A,B,LL=0.0,sump=0.,num=0.;
7400: double *x= (double *) v->data;
7401: int i,n=0; /* n is the size of the sample */
7402:
7403: for (i=0;i<=imx-1 ; i++) {
7404: sump=sump+weight[i];
7405: /* sump=sump+1;*/
7406: num=num+1;
7407: }
7408:
7409:
7410: /* for (i=0; i<=imx; i++)
7411: 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]);*/
7412: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
7413: for (i=1;i<=imx ; i++)
7414: {
7415: if (cens[i] == 1 && wav[i]>1)
7416: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
7417:
7418: if (cens[i] == 0 && wav[i]>1)
7419: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
7420: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
7421:
7422: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
7423: if (wav[i] > 1 ) { /* ??? */
7424: LL=LL+A*weight[i];
7425: /* 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]);*/
7426: }
7427: }
7428:
7429: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
7430: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
7431:
7432: return -2*LL*num/sump;
7433: }
7434: #endif
7435:
1.126 brouard 7436: /******************* Printing html file ***********/
1.201 brouard 7437: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 7438: int lastpass, int stepm, int weightopt, char model[],\
7439: int imx, double p[],double **matcov,double agemortsup){
7440: int i,k;
7441:
7442: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
7443: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
7444: for (i=1;i<=2;i++)
7445: 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 7446: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 7447: fprintf(fichtm,"</ul>");
7448:
7449: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
7450:
7451: 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>");
7452:
7453: for (k=agegomp;k<(agemortsup-2);k++)
7454: 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]);
7455:
7456:
7457: fflush(fichtm);
7458: }
7459:
7460: /******************* Gnuplot file **************/
1.201 brouard 7461: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 7462:
7463: char dirfileres[132],optfileres[132];
1.164 brouard 7464:
1.126 brouard 7465: int ng;
7466:
7467:
7468: /*#ifdef windows */
7469: fprintf(ficgp,"cd \"%s\" \n",pathc);
7470: /*#endif */
7471:
7472:
7473: strcpy(dirfileres,optionfilefiname);
7474: strcpy(optfileres,"vpl");
1.199 brouard 7475: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 7476: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 7477: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 7478: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 7479: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
7480:
7481: }
7482:
1.136 brouard 7483: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
7484: {
1.126 brouard 7485:
1.136 brouard 7486: /*-------- data file ----------*/
7487: FILE *fic;
7488: char dummy[]=" ";
1.223 brouard 7489: int i=0, j=0, n=0, iv=0;
7490: int lstra;
1.136 brouard 7491: int linei, month, year,iout;
7492: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 7493: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 7494: char *stratrunc;
1.223 brouard 7495:
1.126 brouard 7496:
7497:
1.136 brouard 7498: if((fic=fopen(datafile,"r"))==NULL) {
1.218 brouard 7499: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
7500: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136 brouard 7501: }
1.126 brouard 7502:
1.136 brouard 7503: i=1;
7504: linei=0;
7505: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
7506: linei=linei+1;
7507: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
7508: if(line[j] == '\t')
7509: line[j] = ' ';
7510: }
7511: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
7512: ;
7513: };
7514: line[j+1]=0; /* Trims blanks at end of line */
7515: if(line[0]=='#'){
7516: fprintf(ficlog,"Comment line\n%s\n",line);
7517: printf("Comment line\n%s\n",line);
7518: continue;
7519: }
7520: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 7521: strcpy(line, linetmp);
1.223 brouard 7522:
7523: /* Loops on waves */
7524: for (j=maxwav;j>=1;j--){
7525: for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */
1.225 brouard 7526: cutv(stra, strb, line, ' ');
7527: if(strb[0]=='.') { /* Missing value */
7528: lval=-1;
7529: cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
7530: if(isalpha(strb[1])) { /* .m or .d Really Missing value */
7531: 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);
7532: 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);
7533: return 1;
7534: }
7535: }else{
7536: errno=0;
7537: /* what_kind_of_number(strb); */
7538: dval=strtod(strb,&endptr);
7539: /* if( strb[0]=='\0' || (*endptr != '\0')){ */
7540: /* if(strb != endptr && *endptr == '\0') */
7541: /* dval=dlval; */
7542: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
7543: if( strb[0]=='\0' || (*endptr != '\0')){
7544: 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);
7545: 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);
7546: return 1;
7547: }
7548: cotqvar[j][iv][i]=dval;
7549: }
7550: strcpy(line,stra);
1.223 brouard 7551: }/* end loop ntqv */
1.225 brouard 7552:
1.223 brouard 7553: for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */
1.225 brouard 7554: cutv(stra, strb, line, ' ');
7555: if(strb[0]=='.') { /* Missing value */
7556: lval=-1;
7557: }else{
7558: errno=0;
7559: lval=strtol(strb,&endptr,10);
7560: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
7561: if( strb[0]=='\0' || (*endptr != '\0')){
7562: 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);
7563: 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);
7564: return 1;
7565: }
7566: }
7567: if(lval <-1 || lval >1){
7568: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 7569: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7570: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 7571: For example, for multinomial values like 1, 2 and 3,\n \
7572: build V1=0 V2=0 for the reference value (1),\n \
7573: V1=1 V2=0 for (2) \n \
1.223 brouard 7574: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 7575: output of IMaCh is often meaningless.\n \
1.223 brouard 7576: Exiting.\n",lval,linei, i,line,j);
1.225 brouard 7577: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 7578: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7579: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 7580: For example, for multinomial values like 1, 2 and 3,\n \
7581: build V1=0 V2=0 for the reference value (1),\n \
7582: V1=1 V2=0 for (2) \n \
1.223 brouard 7583: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
7584: output of IMaCh is often meaningless.\n \
7585: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.225 brouard 7586: return 1;
7587: }
7588: cotvar[j][iv][i]=(double)(lval);
7589: strcpy(line,stra);
1.223 brouard 7590: }/* end loop ntv */
1.225 brouard 7591:
1.223 brouard 7592: /* Statuses at wave */
1.137 brouard 7593: cutv(stra, strb, line, ' ');
1.223 brouard 7594: if(strb[0]=='.') { /* Missing value */
1.225 brouard 7595: lval=-1;
1.136 brouard 7596: }else{
1.225 brouard 7597: errno=0;
7598: lval=strtol(strb,&endptr,10);
7599: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
7600: if( strb[0]=='\0' || (*endptr != '\0')){
7601: 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);
7602: 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);
7603: return 1;
7604: }
1.136 brouard 7605: }
1.225 brouard 7606:
1.136 brouard 7607: s[j][i]=lval;
1.225 brouard 7608:
1.223 brouard 7609: /* Date of Interview */
1.136 brouard 7610: strcpy(line,stra);
7611: cutv(stra, strb,line,' ');
1.169 brouard 7612: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7613: }
1.169 brouard 7614: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.225 brouard 7615: month=99;
7616: year=9999;
1.136 brouard 7617: }else{
1.225 brouard 7618: 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);
7619: 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);
7620: return 1;
1.136 brouard 7621: }
7622: anint[j][i]= (double) year;
7623: mint[j][i]= (double)month;
7624: strcpy(line,stra);
1.223 brouard 7625: } /* End loop on waves */
1.225 brouard 7626:
1.223 brouard 7627: /* Date of death */
1.136 brouard 7628: cutv(stra, strb,line,' ');
1.169 brouard 7629: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7630: }
1.169 brouard 7631: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 7632: month=99;
7633: year=9999;
7634: }else{
1.141 brouard 7635: 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 7636: 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);
7637: return 1;
1.136 brouard 7638: }
7639: andc[i]=(double) year;
7640: moisdc[i]=(double) month;
7641: strcpy(line,stra);
7642:
1.223 brouard 7643: /* Date of birth */
1.136 brouard 7644: cutv(stra, strb,line,' ');
1.169 brouard 7645: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7646: }
1.169 brouard 7647: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 7648: month=99;
7649: year=9999;
7650: }else{
1.141 brouard 7651: 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);
7652: 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 7653: return 1;
1.136 brouard 7654: }
7655: if (year==9999) {
1.141 brouard 7656: 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);
7657: 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 7658: return 1;
7659:
1.136 brouard 7660: }
7661: annais[i]=(double)(year);
7662: moisnais[i]=(double)(month);
7663: strcpy(line,stra);
1.225 brouard 7664:
1.223 brouard 7665: /* Sample weight */
1.136 brouard 7666: cutv(stra, strb,line,' ');
7667: errno=0;
7668: dval=strtod(strb,&endptr);
7669: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 7670: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
7671: 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 7672: fflush(ficlog);
7673: return 1;
7674: }
7675: weight[i]=dval;
7676: strcpy(line,stra);
1.225 brouard 7677:
1.223 brouard 7678: for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */
7679: cutv(stra, strb, line, ' ');
7680: if(strb[0]=='.') { /* Missing value */
1.225 brouard 7681: lval=-1;
1.223 brouard 7682: }else{
1.225 brouard 7683: errno=0;
7684: /* what_kind_of_number(strb); */
7685: dval=strtod(strb,&endptr);
7686: /* if(strb != endptr && *endptr == '\0') */
7687: /* dval=dlval; */
7688: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
7689: if( strb[0]=='\0' || (*endptr != '\0')){
7690: 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);
7691: 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);
7692: return 1;
7693: }
7694: coqvar[iv][i]=dval;
1.226 brouard 7695: covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */
1.223 brouard 7696: }
7697: strcpy(line,stra);
7698: }/* end loop nqv */
1.136 brouard 7699:
1.223 brouard 7700: /* Covariate values */
1.136 brouard 7701: for (j=ncovcol;j>=1;j--){
7702: cutv(stra, strb,line,' ');
1.223 brouard 7703: if(strb[0]=='.') { /* Missing covariate value */
1.225 brouard 7704: lval=-1;
1.136 brouard 7705: }else{
1.225 brouard 7706: errno=0;
7707: lval=strtol(strb,&endptr,10);
7708: if( strb[0]=='\0' || (*endptr != '\0')){
7709: 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);
7710: 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);
7711: return 1;
7712: }
1.136 brouard 7713: }
7714: if(lval <-1 || lval >1){
1.225 brouard 7715: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 7716: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7717: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 7718: For example, for multinomial values like 1, 2 and 3,\n \
7719: build V1=0 V2=0 for the reference value (1),\n \
7720: V1=1 V2=0 for (2) \n \
1.136 brouard 7721: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 7722: output of IMaCh is often meaningless.\n \
1.136 brouard 7723: Exiting.\n",lval,linei, i,line,j);
1.225 brouard 7724: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 7725: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7726: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 7727: For example, for multinomial values like 1, 2 and 3,\n \
7728: build V1=0 V2=0 for the reference value (1),\n \
7729: V1=1 V2=0 for (2) \n \
1.136 brouard 7730: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 7731: output of IMaCh is often meaningless.\n \
1.136 brouard 7732: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.225 brouard 7733: return 1;
1.136 brouard 7734: }
7735: covar[j][i]=(double)(lval);
7736: strcpy(line,stra);
7737: }
7738: lstra=strlen(stra);
1.225 brouard 7739:
1.136 brouard 7740: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
7741: stratrunc = &(stra[lstra-9]);
7742: num[i]=atol(stratrunc);
7743: }
7744: else
7745: num[i]=atol(stra);
7746: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
7747: 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;}*/
7748:
7749: i=i+1;
7750: } /* End loop reading data */
1.225 brouard 7751:
1.136 brouard 7752: *imax=i-1; /* Number of individuals */
7753: fclose(fic);
1.225 brouard 7754:
1.136 brouard 7755: return (0);
1.164 brouard 7756: /* endread: */
1.225 brouard 7757: printf("Exiting readdata: ");
7758: fclose(fic);
7759: return (1);
1.223 brouard 7760: }
1.126 brouard 7761:
1.145 brouard 7762: void removespace(char *str) {
7763: char *p1 = str, *p2 = str;
7764: do
7765: while (*p2 == ' ')
7766: p2++;
1.169 brouard 7767: while (*p1++ == *p2++);
1.145 brouard 7768: }
7769:
1.224 brouard 7770: int decodemodel ( char model[], int lastobs)
7771: /**< This routine decode the model and returns:
7772: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
7773: * - nagesqr = 1 if age*age in the model, otherwise 0.
7774: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
7775: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
7776: * - cptcovage number of covariates with age*products =2
7777: * - cptcovs number of simple covariates
7778: * - 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
7779: * which is a new column after the 9 (ncovcol) variables.
7780: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
7781: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
7782: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
7783: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
7784: */
1.136 brouard 7785: {
1.145 brouard 7786: int i, j, k, ks;
1.227 ! brouard 7787: int j1, k1, k2, k3, k4;
1.136 brouard 7788: char modelsav[80];
1.145 brouard 7789: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 7790: char *strpt;
1.136 brouard 7791:
1.145 brouard 7792: /*removespace(model);*/
1.136 brouard 7793: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 7794: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 7795: if (strstr(model,"AGE") !=0){
1.192 brouard 7796: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
7797: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 7798: return 1;
7799: }
1.141 brouard 7800: if (strstr(model,"v") !=0){
7801: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
7802: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
7803: return 1;
7804: }
1.187 brouard 7805: strcpy(modelsav,model);
7806: if ((strpt=strstr(model,"age*age")) !=0){
7807: printf(" strpt=%s, model=%s\n",strpt, model);
7808: if(strpt != model){
1.225 brouard 7809: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 7810: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 7811: corresponding column of parameters.\n",model);
1.225 brouard 7812: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 7813: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 7814: corresponding column of parameters.\n",model); fflush(ficlog);
1.225 brouard 7815: return 1;
7816: }
1.187 brouard 7817: nagesqr=1;
7818: if (strstr(model,"+age*age") !=0)
1.225 brouard 7819: substrchaine(modelsav, model, "+age*age");
1.187 brouard 7820: else if (strstr(model,"age*age+") !=0)
1.225 brouard 7821: substrchaine(modelsav, model, "age*age+");
1.187 brouard 7822: else
1.225 brouard 7823: substrchaine(modelsav, model, "age*age");
1.187 brouard 7824: }else
7825: nagesqr=0;
7826: if (strlen(modelsav) >1){
7827: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
7828: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
1.224 brouard 7829: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2 */
1.187 brouard 7830: cptcovt= j+1; /* Number of total covariates in the model, not including
1.225 brouard 7831: * cst, age and age*age
7832: * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
7833: /* including age products which are counted in cptcovage.
7834: * but the covariates which are products must be treated
7835: * separately: ncovn=4- 2=2 (V1+V3). */
1.187 brouard 7836: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
7837: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.225 brouard 7838:
7839:
1.187 brouard 7840: /* Design
7841: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
7842: * < ncovcol=8 >
7843: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
7844: * k= 1 2 3 4 5 6 7 8
7845: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
7846: * covar[k,i], value of kth covariate if not including age for individual i:
1.224 brouard 7847: * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
7848: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
1.187 brouard 7849: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
7850: * Tage[++cptcovage]=k
7851: * if products, new covar are created after ncovcol with k1
7852: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
7853: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
7854: * 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
7855: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
7856: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
7857: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
7858: * < ncovcol=8 >
7859: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
7860: * k= 1 2 3 4 5 6 7 8 9 10 11 12
7861: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
7862: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
7863: * p Tprod[1]@2={ 6, 5}
7864: *p Tvard[1][1]@4= {7, 8, 5, 6}
7865: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
7866: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
7867: *How to reorganize?
7868: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
7869: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
7870: * {2, 1, 4, 8, 5, 6, 3, 7}
7871: * Struct []
7872: */
1.225 brouard 7873:
1.187 brouard 7874: /* This loop fills the array Tvar from the string 'model'.*/
7875: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
7876: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
7877: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
7878: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
7879: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
7880: /* k=1 Tvar[1]=2 (from V2) */
7881: /* k=5 Tvar[5] */
7882: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 7883: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 7884: /* } */
1.198 brouard 7885: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 7886: /*
7887: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
1.227 ! brouard 7888: for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
! 7889: Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
! 7890: }
1.187 brouard 7891: cptcovage=0;
7892: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
1.225 brouard 7893: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
7894: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
7895: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
7896: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
7897: /*scanf("%d",i);*/
7898: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
7899: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
7900: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
7901: /* covar is not filled and then is empty */
7902: cptcovprod--;
7903: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
7904: 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 7905: Typevar[k]=1; /* 1 for age product */
1.225 brouard 7906: cptcovage++; /* Sums the number of covariates which include age as a product */
7907: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
7908: /*printf("stre=%s ", stre);*/
7909: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
7910: cptcovprod--;
7911: cutl(stre,strb,strc,'V');
7912: Tvar[k]=atoi(stre);
7913: Typevar[k]=1; /* 1 for age product */
7914: cptcovage++;
7915: Tage[cptcovage]=k;
7916: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
7917: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
7918: cptcovn++;
7919: cptcovprodnoage++;k1++;
7920: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
7921: Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
7922: because this model-covariate is a construction we invent a new column
7923: which is after existing variables ncovcol+nqv+ntv+nqtv + k1
7924: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
7925: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
7926: Typevar[k]=2; /* 2 for double fixed dummy covariates */
7927: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
7928: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
1.227 ! brouard 7929: Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
1.225 brouard 7930: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
7931: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
7932: k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
7933: /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
7934: /* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
7935: /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
7936: /* 1 2 3 4 5 | Tvar[5+1)=1, Tvar[7]=2 */
7937: for (i=1; i<=lastobs;i++){
7938: /* Computes the new covariate which is a product of
7939: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
7940: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
7941: }
7942: } /* End age is not in the model */
7943: } /* End if model includes a product */
7944: else { /* no more sum */
7945: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
7946: /* scanf("%d",i);*/
7947: cutl(strd,strc,strb,'V');
1.227 ! brouard 7948: ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
1.225 brouard 7949: cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
7950: Tvar[k]=atoi(strd);
7951: Typevar[k]=0; /* 0 for simple covariates */
7952: }
7953: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.223 brouard 7954: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
1.225 brouard 7955: scanf("%d",i);*/
1.187 brouard 7956: } /* end of loop + on total covariates */
7957: } /* end if strlen(modelsave == 0) age*age might exist */
7958: } /* end if strlen(model == 0) */
1.136 brouard 7959:
7960: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
7961: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
1.225 brouard 7962:
1.136 brouard 7963: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.225 brouard 7964: printf("cptcovprod=%d ", cptcovprod);
7965: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
7966: scanf("%d ",i);*/
7967:
7968:
7969: /* Decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
7970: of variable (dummy vs quantitative, fixed vs time varying) is behind */
1.226 brouard 7971: /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1 = 5 possible variables data: 2 fixed 3, varying
7972: model= V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
7973: k = 1 2 3 4 5 6 7 8 9
7974: Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5
7975: Typevar[k]= 0 0 0 2 1 0 2 1 1
1.227 ! brouard 7976: Fixed[k] 1 1 1 1 3 0 0 or 2 2 3
! 7977: Dummy[k] 1 0 0 0 3 1 1 2 3
! 7978: Tmodelind[combination of covar]=k;
1.225 brouard 7979: */
7980: /* Dispatching between quantitative and time varying covariates */
1.226 brouard 7981: /* If Tvar[k] >ncovcol it is a product */
1.225 brouard 7982: /* 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 7983: /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
1.227 ! brouard 7984: printf("Model=%s\n\
! 7985: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
! 7986: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
! 7987: 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);
! 7988: fprintf(ficlog,"Model=%s\n\
! 7989: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
! 7990: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
! 7991: 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);
! 7992:
1.225 brouard 7993: for(k=1, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
1.226 brouard 7994: if (Tvar[k] <=ncovcol && (Typevar[k]==0 || Typevar[k]==2)){ /* Simple or product fixed dummy covariatee */
1.227 ! brouard 7995: Fixed[k]= 0;
! 7996: Dummy[k]= 0;
1.225 brouard 7997: ncoveff++;
7998: }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){ /* Remind that product Vn*Vm are added in k*/
1.227 ! brouard 7999: Fixed[k]= 0;
! 8000: Dummy[k]= 1;
1.225 brouard 8001: nqfveff++; /* Only simple fixed quantitative variable */
8002: }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){
1.227 ! brouard 8003: Fixed[k]= 1;
! 8004: Dummy[k]= 0;
1.225 brouard 8005: ntveff++; /* Only simple time varying dummy variable */
1.227 ! brouard 8006: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){
! 8007: Fixed[k]= 1;
! 8008: Dummy[k]= 1;
1.226 brouard 8009: nqtveff++;/* Only simple time varying quantitative variable */
1.227 ! brouard 8010: }else if (Typevar[k] == 1) { /* product with age */
! 8011: if (Tvar[k] <=ncovcol ){ /* Simple or product fixed dummy covariatee */
! 8012: Fixed[k]= 2;
! 8013: Dummy[k]= 2;
! 8014: /* ncoveff++; */
! 8015: }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
! 8016: Fixed[k]= 2;
! 8017: Dummy[k]= 3;
! 8018: /* nqfveff++; /\* Only simple fixed quantitative variable *\/ */
! 8019: }else if( Tvar[k] <=ncovcol+nqv+ntv ){
! 8020: Fixed[k]= 3;
! 8021: Dummy[k]= 2;
! 8022: /* ntveff++; /\* Only simple time varying dummy variable *\/ */
! 8023: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
! 8024: Fixed[k]= 3;
! 8025: Dummy[k]= 3;
! 8026: /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
! 8027: }
! 8028: }else if (Typevar[k] == 2) { /* product without age */
! 8029: k1=Tposprod[k];
! 8030: if(Tvard[k1][1] <=ncovcol){
! 8031: if(Tvard[k1][2] <=ncovcol){
! 8032: Fixed[k]= 1;
! 8033: Dummy[k]= 0;
! 8034: }else if(Tvard[k1][2] <=ncovcol+nqv){
! 8035: Fixed[k]= 0; /* or 2 ?*/
! 8036: Dummy[k]= 1;
! 8037: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
! 8038: Fixed[k]= 1;
! 8039: Dummy[k]= 0;
! 8040: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
! 8041: Fixed[k]= 1;
! 8042: Dummy[k]= 1;
! 8043: }
! 8044: }else if(Tvard[k1][1] <=ncovcol+nqv){
! 8045: if(Tvard[k1][2] <=ncovcol){
! 8046: Fixed[k]= 0; /* or 2 ?*/
! 8047: Dummy[k]= 1;
! 8048: }else if(Tvard[k1][2] <=ncovcol+nqv){
! 8049: Fixed[k]= 0; /* or 2 ?*/
! 8050: Dummy[k]= 1;
! 8051: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
! 8052: Fixed[k]= 1;
! 8053: Dummy[k]= 1;
! 8054: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
! 8055: Fixed[k]= 1;
! 8056: Dummy[k]= 1;
! 8057: }
! 8058: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
! 8059: if(Tvard[k1][2] <=ncovcol){
! 8060: Fixed[k]= 1;
! 8061: Dummy[k]= 1;
! 8062: }else if(Tvard[k1][2] <=ncovcol+nqv){
! 8063: Fixed[k]= 1;
! 8064: Dummy[k]= 1;
! 8065: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
! 8066: Fixed[k]= 1;
! 8067: Dummy[k]= 0;
! 8068: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
! 8069: Fixed[k]= 1;
! 8070: Dummy[k]= 1;
! 8071: }
! 8072: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
! 8073: if(Tvard[k1][2] <=ncovcol){
! 8074: Fixed[k]= 1;
! 8075: Dummy[k]= 1;
! 8076: }else if(Tvard[k1][2] <=ncovcol+nqv){
! 8077: Fixed[k]= 1;
! 8078: Dummy[k]= 1;
! 8079: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
! 8080: Fixed[k]= 1;
! 8081: Dummy[k]= 1;
! 8082: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
! 8083: Fixed[k]= 1;
! 8084: Dummy[k]= 1;
! 8085: }
! 8086: }else{
! 8087: printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
! 8088: 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 8089: } /* end k1 */
1.225 brouard 8090: }else{
1.226 brouard 8091: printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
8092: 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 8093: }
1.227 ! brouard 8094: 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]);
! 8095: 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]);
! 8096: }
! 8097: /* Searching for doublons in the model */
! 8098: for(k1=1; k1<= cptcovt;k1++){
! 8099: for(k2=1; k2 <k1;k2++){
! 8100: if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){
! 8101: if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
! 8102: if(Tvar[k1]==Tvar[k2]){
! 8103: 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]]);
! 8104: 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);
! 8105: return(1);
! 8106: }
! 8107: }else if (Typevar[k1] ==2){
! 8108: k3=Tposprod[k1];
! 8109: k4=Tposprod[k2];
! 8110: 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])) ){
! 8111: 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]]);
! 8112: 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);
! 8113: return(1);
! 8114: }
! 8115: }
! 8116: }
! 8117: }
1.225 brouard 8118: }
8119: printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
8120: fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
1.137 brouard 8121: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 8122: /*endread:*/
1.225 brouard 8123: printf("Exiting decodemodel: ");
8124: return (1);
1.136 brouard 8125: }
8126:
1.169 brouard 8127: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 8128: {
8129: int i, m;
1.218 brouard 8130: int firstone=0;
8131:
1.136 brouard 8132: for (i=1; i<=imx; i++) {
8133: for(m=2; (m<= maxwav); m++) {
8134: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
8135: anint[m][i]=9999;
1.216 brouard 8136: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
8137: s[m][i]=-1;
1.136 brouard 8138: }
8139: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 8140: *nberr = *nberr + 1;
1.218 brouard 8141: if(firstone == 0){
8142: firstone=1;
8143: 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);
8144: }
8145: 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 8146: s[m][i]=-1;
8147: }
8148: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 8149: (*nberr)++;
1.136 brouard 8150: 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]);
8151: 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]);
8152: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
8153: }
8154: }
8155: }
8156:
8157: for (i=1; i<=imx; i++) {
8158: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
8159: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 8160: 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 8161: if (s[m][i] >= nlstate+1) {
1.169 brouard 8162: if(agedc[i]>0){
8163: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 8164: agev[m][i]=agedc[i];
1.214 brouard 8165: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 8166: }else {
1.136 brouard 8167: if ((int)andc[i]!=9999){
8168: nbwarn++;
8169: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
8170: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
8171: agev[m][i]=-1;
8172: }
8173: }
1.169 brouard 8174: } /* agedc > 0 */
1.214 brouard 8175: } /* end if */
1.136 brouard 8176: else if(s[m][i] !=9){ /* Standard case, age in fractional
8177: years but with the precision of a month */
8178: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
8179: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
8180: agev[m][i]=1;
8181: else if(agev[m][i] < *agemin){
8182: *agemin=agev[m][i];
8183: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
8184: }
8185: else if(agev[m][i] >*agemax){
8186: *agemax=agev[m][i];
1.156 brouard 8187: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 8188: }
8189: /*agev[m][i]=anint[m][i]-annais[i];*/
8190: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 8191: } /* en if 9*/
1.136 brouard 8192: else { /* =9 */
1.214 brouard 8193: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 8194: agev[m][i]=1;
8195: s[m][i]=-1;
8196: }
8197: }
1.214 brouard 8198: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 8199: agev[m][i]=1;
1.214 brouard 8200: else{
8201: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
8202: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
8203: agev[m][i]=0;
8204: }
8205: } /* End for lastpass */
8206: }
1.136 brouard 8207:
8208: for (i=1; i<=imx; i++) {
8209: for(m=firstpass; (m<=lastpass); m++){
8210: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 8211: (*nberr)++;
1.136 brouard 8212: 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);
8213: 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);
8214: return 1;
8215: }
8216: }
8217: }
8218:
8219: /*for (i=1; i<=imx; i++){
8220: for (m=firstpass; (m<lastpass); m++){
8221: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
8222: }
8223:
8224: }*/
8225:
8226:
1.139 brouard 8227: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
8228: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 8229:
8230: return (0);
1.164 brouard 8231: /* endread:*/
1.136 brouard 8232: printf("Exiting calandcheckages: ");
8233: return (1);
8234: }
8235:
1.172 brouard 8236: #if defined(_MSC_VER)
8237: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
8238: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
8239: //#include "stdafx.h"
8240: //#include <stdio.h>
8241: //#include <tchar.h>
8242: //#include <windows.h>
8243: //#include <iostream>
8244: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
8245:
8246: LPFN_ISWOW64PROCESS fnIsWow64Process;
8247:
8248: BOOL IsWow64()
8249: {
8250: BOOL bIsWow64 = FALSE;
8251:
8252: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
8253: // (HANDLE, PBOOL);
8254:
8255: //LPFN_ISWOW64PROCESS fnIsWow64Process;
8256:
8257: HMODULE module = GetModuleHandle(_T("kernel32"));
8258: const char funcName[] = "IsWow64Process";
8259: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
8260: GetProcAddress(module, funcName);
8261:
8262: if (NULL != fnIsWow64Process)
8263: {
8264: if (!fnIsWow64Process(GetCurrentProcess(),
8265: &bIsWow64))
8266: //throw std::exception("Unknown error");
8267: printf("Unknown error\n");
8268: }
8269: return bIsWow64 != FALSE;
8270: }
8271: #endif
1.177 brouard 8272:
1.191 brouard 8273: void syscompilerinfo(int logged)
1.167 brouard 8274: {
8275: /* #include "syscompilerinfo.h"*/
1.185 brouard 8276: /* command line Intel compiler 32bit windows, XP compatible:*/
8277: /* /GS /W3 /Gy
8278: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
8279: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
8280: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 8281: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
8282: */
8283: /* 64 bits */
1.185 brouard 8284: /*
8285: /GS /W3 /Gy
8286: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
8287: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
8288: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
8289: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
8290: /* Optimization are useless and O3 is slower than O2 */
8291: /*
8292: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
8293: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
8294: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
8295: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
8296: */
1.186 brouard 8297: /* Link is */ /* /OUT:"visual studio
1.185 brouard 8298: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
8299: /PDB:"visual studio
8300: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
8301: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
8302: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
8303: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
8304: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
8305: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
8306: uiAccess='false'"
8307: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
8308: /NOLOGO /TLBID:1
8309: */
1.177 brouard 8310: #if defined __INTEL_COMPILER
1.178 brouard 8311: #if defined(__GNUC__)
8312: struct utsname sysInfo; /* For Intel on Linux and OS/X */
8313: #endif
1.177 brouard 8314: #elif defined(__GNUC__)
1.179 brouard 8315: #ifndef __APPLE__
1.174 brouard 8316: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 8317: #endif
1.177 brouard 8318: struct utsname sysInfo;
1.178 brouard 8319: int cross = CROSS;
8320: if (cross){
8321: printf("Cross-");
1.191 brouard 8322: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 8323: }
1.174 brouard 8324: #endif
8325:
1.171 brouard 8326: #include <stdint.h>
1.178 brouard 8327:
1.191 brouard 8328: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 8329: #if defined(__clang__)
1.191 brouard 8330: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 8331: #endif
8332: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 8333: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 8334: #endif
8335: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 8336: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 8337: #endif
8338: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 8339: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 8340: #endif
8341: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 8342: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 8343: #endif
8344: #if defined(_MSC_VER)
1.191 brouard 8345: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 8346: #endif
8347: #if defined(__PGI)
1.191 brouard 8348: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 8349: #endif
8350: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 8351: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 8352: #endif
1.191 brouard 8353: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 8354:
1.167 brouard 8355: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
8356: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
8357: // Windows (x64 and x86)
1.191 brouard 8358: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 8359: #elif __unix__ // all unices, not all compilers
8360: // Unix
1.191 brouard 8361: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 8362: #elif __linux__
8363: // linux
1.191 brouard 8364: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 8365: #elif __APPLE__
1.174 brouard 8366: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 8367: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 8368: #endif
8369:
8370: /* __MINGW32__ */
8371: /* __CYGWIN__ */
8372: /* __MINGW64__ */
8373: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
8374: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
8375: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
8376: /* _WIN64 // Defined for applications for Win64. */
8377: /* _M_X64 // Defined for compilations that target x64 processors. */
8378: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 8379:
1.167 brouard 8380: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 8381: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 8382: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 8383: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 8384: #else
1.191 brouard 8385: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 8386: #endif
8387:
1.169 brouard 8388: #if defined(__GNUC__)
8389: # if defined(__GNUC_PATCHLEVEL__)
8390: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
8391: + __GNUC_MINOR__ * 100 \
8392: + __GNUC_PATCHLEVEL__)
8393: # else
8394: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
8395: + __GNUC_MINOR__ * 100)
8396: # endif
1.174 brouard 8397: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 8398: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 8399:
8400: if (uname(&sysInfo) != -1) {
8401: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 8402: 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 8403: }
8404: else
8405: perror("uname() error");
1.179 brouard 8406: //#ifndef __INTEL_COMPILER
8407: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 8408: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 8409: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 8410: #endif
1.169 brouard 8411: #endif
1.172 brouard 8412:
8413: // void main()
8414: // {
1.169 brouard 8415: #if defined(_MSC_VER)
1.174 brouard 8416: if (IsWow64()){
1.191 brouard 8417: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
8418: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 8419: }
8420: else{
1.191 brouard 8421: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
8422: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 8423: }
1.172 brouard 8424: // printf("\nPress Enter to continue...");
8425: // getchar();
8426: // }
8427:
1.169 brouard 8428: #endif
8429:
1.167 brouard 8430:
1.219 brouard 8431: }
1.136 brouard 8432:
1.219 brouard 8433: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.180 brouard 8434: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
8435: int i, j, k, i1 ;
1.202 brouard 8436: /* double ftolpl = 1.e-10; */
1.180 brouard 8437: double age, agebase, agelim;
1.203 brouard 8438: double tot;
1.180 brouard 8439:
1.202 brouard 8440: strcpy(filerespl,"PL_");
8441: strcat(filerespl,fileresu);
8442: if((ficrespl=fopen(filerespl,"w"))==NULL) {
8443: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
8444: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
8445: }
1.227 ! brouard 8446: printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
! 8447: fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
1.202 brouard 8448: pstamp(ficrespl);
1.203 brouard 8449: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 8450: fprintf(ficrespl,"#Age ");
8451: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
8452: fprintf(ficrespl,"\n");
1.180 brouard 8453:
1.219 brouard 8454: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180 brouard 8455:
1.219 brouard 8456: agebase=ageminpar;
8457: agelim=agemaxpar;
1.180 brouard 8458:
1.227 ! brouard 8459: /* i1=pow(2,ncoveff); */
! 8460: i1=pow(2,cptcoveff); /* Number of dummy covariates */
1.219 brouard 8461: if (cptcovn < 1){i1=1;}
1.180 brouard 8462:
1.220 brouard 8463: for(k=1; k<=i1;k++){
8464: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
1.180 brouard 8465: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
1.219 brouard 8466: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.220 brouard 8467: /* k=k+1; */
1.219 brouard 8468: /* to clean */
8469: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
8470: fprintf(ficrespl,"#******");
8471: printf("#******");
8472: fprintf(ficlog,"#******");
1.227 ! brouard 8473: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
! 8474: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
1.219 brouard 8475: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8476: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8477: }
8478: fprintf(ficrespl,"******\n");
8479: printf("******\n");
8480: fprintf(ficlog,"******\n");
1.227 ! brouard 8481: if(invalidvarcomb[k]){
! 8482: printf("\nCombination (%d) ignored because no case \n",k);
! 8483: fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
! 8484: fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
1.220 brouard 8485: continue;
1.227 ! brouard 8486: }
1.219 brouard 8487:
8488: fprintf(ficrespl,"#Age ");
1.227 ! brouard 8489: for(j=1;j<=cptcoveff;j++) {
1.219 brouard 8490: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8491: }
8492: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
8493: fprintf(ficrespl,"Total Years_to_converge\n");
1.227 ! brouard 8494:
1.219 brouard 8495: for (age=agebase; age<=agelim; age++){
8496: /* for (age=agebase; age<=agebase; age++){ */
8497: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
8498: fprintf(ficrespl,"%.0f ",age );
1.227 ! brouard 8499: for(j=1;j<=cptcoveff;j++)
! 8500: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.219 brouard 8501: tot=0.;
8502: for(i=1; i<=nlstate;i++){
1.227 ! brouard 8503: tot += prlim[i][i];
! 8504: fprintf(ficrespl," %.5f", prlim[i][i]);
1.219 brouard 8505: }
8506: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
8507: } /* Age */
8508: /* was end of cptcod */
8509: } /* cptcov */
8510: return 0;
1.180 brouard 8511: }
8512:
1.218 brouard 8513: 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){
8514: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
8515:
8516: /* Computes the back prevalence limit for any combination of covariate values
8517: * at any age between ageminpar and agemaxpar
8518: */
1.217 brouard 8519: int i, j, k, i1 ;
8520: /* double ftolpl = 1.e-10; */
8521: double age, agebase, agelim;
8522: double tot;
1.218 brouard 8523: /* double ***mobaverage; */
8524: /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
1.217 brouard 8525:
8526: strcpy(fileresplb,"PLB_");
8527: strcat(fileresplb,fileresu);
8528: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
8529: printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
8530: fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
8531: }
8532: printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
8533: fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
8534: pstamp(ficresplb);
8535: fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
8536: fprintf(ficresplb,"#Age ");
8537: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
8538: fprintf(ficresplb,"\n");
8539:
1.218 brouard 8540:
8541: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
8542:
8543: agebase=ageminpar;
8544: agelim=agemaxpar;
8545:
8546:
1.227 ! brouard 8547: i1=pow(2,cptcoveff);
1.218 brouard 8548: if (cptcovn < 1){i1=1;}
1.227 ! brouard 8549:
! 8550: for(k=1; k<=i1;k++){
1.218 brouard 8551: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
8552: fprintf(ficresplb,"#******");
8553: printf("#******");
8554: fprintf(ficlog,"#******");
1.227 ! brouard 8555: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
1.218 brouard 8556: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8557: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8558: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8559: }
8560: fprintf(ficresplb,"******\n");
8561: printf("******\n");
8562: fprintf(ficlog,"******\n");
1.227 ! brouard 8563: if(invalidvarcomb[k]){
! 8564: printf("\nCombination (%d) ignored because no cases \n",k);
! 8565: fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
! 8566: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
! 8567: continue;
! 8568: }
1.218 brouard 8569:
8570: fprintf(ficresplb,"#Age ");
1.227 ! brouard 8571: for(j=1;j<=cptcoveff;j++) {
1.218 brouard 8572: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8573: }
8574: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
8575: fprintf(ficresplb,"Total Years_to_converge\n");
8576:
8577:
8578: for (age=agebase; age<=agelim; age++){
8579: /* for (age=agebase; age<=agebase; age++){ */
8580: if(mobilavproj > 0){
8581: /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
8582: /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.227 ! brouard 8583: bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);
1.218 brouard 8584: }else if (mobilavproj == 0){
1.227 ! brouard 8585: 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);
! 8586: 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);
! 8587: exit(1);
1.218 brouard 8588: }else{
1.227 ! brouard 8589: /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
! 8590: bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);
1.218 brouard 8591: }
8592: fprintf(ficresplb,"%.0f ",age );
1.227 ! brouard 8593: for(j=1;j<=cptcoveff;j++)
! 8594: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.218 brouard 8595: tot=0.;
8596: for(i=1; i<=nlstate;i++){
1.227 ! brouard 8597: tot += bprlim[i][i];
! 8598: fprintf(ficresplb," %.5f", bprlim[i][i]);
1.218 brouard 8599: }
8600: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
8601: } /* Age */
8602: /* was end of cptcod */
8603: } /* cptcov */
8604:
8605: /* hBijx(p, bage, fage); */
8606: /* fclose(ficrespijb); */
8607:
8608: return 0;
1.217 brouard 8609: }
1.218 brouard 8610:
1.180 brouard 8611: int hPijx(double *p, int bage, int fage){
8612: /*------------- h Pij x at various ages ------------*/
8613:
8614: int stepsize;
8615: int agelim;
8616: int hstepm;
8617: int nhstepm;
8618: int h, i, i1, j, k;
8619:
8620: double agedeb;
8621: double ***p3mat;
8622:
1.201 brouard 8623: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 8624: if((ficrespij=fopen(filerespij,"w"))==NULL) {
8625: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
8626: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
8627: }
8628: printf("Computing pij: result on file '%s' \n", filerespij);
8629: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
8630:
8631: stepsize=(int) (stepm+YEARM-1)/YEARM;
8632: /*if (stepm<=24) stepsize=2;*/
8633:
8634: agelim=AGESUP;
8635: hstepm=stepsize*YEARM; /* Every year of age */
8636: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.218 brouard 8637:
1.180 brouard 8638: /* hstepm=1; aff par mois*/
8639: pstamp(ficrespij);
8640: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.227 ! brouard 8641: i1= pow(2,cptcoveff);
1.218 brouard 8642: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
8643: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
8644: /* k=k+1; */
1.227 ! brouard 8645: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.183 brouard 8646: fprintf(ficrespij,"\n#****** ");
1.227 ! brouard 8647: for(j=1;j<=cptcoveff;j++)
1.198 brouard 8648: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.183 brouard 8649: fprintf(ficrespij,"******\n");
8650:
8651: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
8652: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
8653: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
8654:
8655: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 8656:
1.183 brouard 8657: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8658: oldm=oldms;savm=savms;
8659: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
8660: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
8661: for(i=1; i<=nlstate;i++)
8662: for(j=1; j<=nlstate+ndeath;j++)
8663: fprintf(ficrespij," %1d-%1d",i,j);
8664: fprintf(ficrespij,"\n");
8665: for (h=0; h<=nhstepm; h++){
8666: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
8667: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 8668: for(i=1; i<=nlstate;i++)
8669: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 8670: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 8671: fprintf(ficrespij,"\n");
8672: }
1.183 brouard 8673: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8674: fprintf(ficrespij,"\n");
8675: }
1.180 brouard 8676: /*}*/
8677: }
1.218 brouard 8678: return 0;
1.180 brouard 8679: }
1.218 brouard 8680:
8681: int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217 brouard 8682: /*------------- h Bij x at various ages ------------*/
8683:
8684: int stepsize;
1.218 brouard 8685: /* int agelim; */
8686: int ageminl;
1.217 brouard 8687: int hstepm;
8688: int nhstepm;
8689: int h, i, i1, j, k;
1.218 brouard 8690:
1.217 brouard 8691: double agedeb;
8692: double ***p3mat;
1.218 brouard 8693:
8694: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
8695: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
8696: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
8697: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
8698: }
8699: printf("Computing pij back: result on file '%s' \n", filerespijb);
8700: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
8701:
8702: stepsize=(int) (stepm+YEARM-1)/YEARM;
8703: /*if (stepm<=24) stepsize=2;*/
1.217 brouard 8704:
1.218 brouard 8705: /* agelim=AGESUP; */
8706: ageminl=30;
8707: hstepm=stepsize*YEARM; /* Every year of age */
8708: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
8709:
8710: /* hstepm=1; aff par mois*/
8711: pstamp(ficrespijb);
8712: fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");
1.227 ! brouard 8713: i1= pow(2,cptcoveff);
1.218 brouard 8714: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
8715: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
8716: /* k=k+1; */
1.227 ! brouard 8717: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.218 brouard 8718: fprintf(ficrespijb,"\n#****** ");
1.227 ! brouard 8719: for(j=1;j<=cptcoveff;j++)
1.218 brouard 8720: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8721: fprintf(ficrespijb,"******\n");
1.222 brouard 8722: if(invalidvarcomb[k]){
8723: fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
8724: continue;
8725: }
1.218 brouard 8726:
8727: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
8728: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
8729: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
8730: nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
8731: nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
8732:
8733: /* nhstepm=nhstepm*YEARM; aff par mois*/
8734:
8735: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8736: /* oldm=oldms;savm=savms; */
8737: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
8738: hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
8739: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
8740: fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
8741: for(i=1; i<=nlstate;i++)
8742: for(j=1; j<=nlstate+ndeath;j++)
8743: fprintf(ficrespijb," %1d-%1d",i,j);
8744: fprintf(ficrespijb,"\n");
8745: for (h=0; h<=nhstepm; h++){
8746: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
8747: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
8748: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
1.217 brouard 8749: for(i=1; i<=nlstate;i++)
8750: for(j=1; j<=nlstate+ndeath;j++)
1.218 brouard 8751: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
1.217 brouard 8752: fprintf(ficrespijb,"\n");
8753: }
1.218 brouard 8754: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8755: fprintf(ficrespijb,"\n");
1.217 brouard 8756: }
1.218 brouard 8757: /*}*/
8758: }
8759: return 0;
8760: } /* hBijx */
1.217 brouard 8761:
1.180 brouard 8762:
1.136 brouard 8763: /***********************************************/
8764: /**************** Main Program *****************/
8765: /***********************************************/
8766:
8767: int main(int argc, char *argv[])
8768: {
8769: #ifdef GSL
8770: const gsl_multimin_fminimizer_type *T;
8771: size_t iteri = 0, it;
8772: int rval = GSL_CONTINUE;
8773: int status = GSL_SUCCESS;
8774: double ssval;
8775: #endif
8776: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 8777: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.209 brouard 8778: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 8779: int jj, ll, li, lj, lk;
1.136 brouard 8780: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 8781: int num_filled;
1.136 brouard 8782: int itimes;
8783: int NDIM=2;
8784: int vpopbased=0;
8785:
1.164 brouard 8786: char ca[32], cb[32];
1.136 brouard 8787: /* FILE *fichtm; *//* Html File */
8788: /* FILE *ficgp;*/ /*Gnuplot File */
8789: struct stat info;
1.191 brouard 8790: double agedeb=0.;
1.194 brouard 8791:
8792: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219 brouard 8793: double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136 brouard 8794:
1.165 brouard 8795: double fret;
1.191 brouard 8796: double dum=0.; /* Dummy variable */
1.136 brouard 8797: double ***p3mat;
1.218 brouard 8798: /* double ***mobaverage; */
1.164 brouard 8799:
8800: char line[MAXLINE];
1.197 brouard 8801: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
8802:
8803: char model[MAXLINE], modeltemp[MAXLINE];
1.136 brouard 8804: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 8805: char *tok, *val; /* pathtot */
1.136 brouard 8806: int firstobs=1, lastobs=10;
1.195 brouard 8807: int c, h , cpt, c2;
1.191 brouard 8808: int jl=0;
8809: int i1, j1, jk, stepsize=0;
1.194 brouard 8810: int count=0;
8811:
1.164 brouard 8812: int *tab;
1.136 brouard 8813: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.217 brouard 8814: int backcast=0;
1.136 brouard 8815: int mobilav=0,popforecast=0;
1.191 brouard 8816: int hstepm=0, nhstepm=0;
1.136 brouard 8817: int agemortsup;
8818: float sumlpop=0.;
8819: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
8820: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
8821:
1.191 brouard 8822: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 8823: double ftolpl=FTOL;
8824: double **prlim;
1.217 brouard 8825: double **bprlim;
1.136 brouard 8826: double ***param; /* Matrix of parameters */
8827: double *p;
8828: double **matcov; /* Matrix of covariance */
1.203 brouard 8829: double **hess; /* Hessian matrix */
1.136 brouard 8830: double ***delti3; /* Scale */
8831: double *delti; /* Scale */
8832: double ***eij, ***vareij;
8833: double **varpl; /* Variances of prevalence limits by age */
8834: double *epj, vepp;
1.164 brouard 8835:
1.136 brouard 8836: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.217 brouard 8837: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;
8838:
1.136 brouard 8839: double **ximort;
1.145 brouard 8840: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 8841: int *dcwave;
8842:
1.164 brouard 8843: char z[1]="c";
1.136 brouard 8844:
8845: /*char *strt;*/
8846: char strtend[80];
1.126 brouard 8847:
1.164 brouard 8848:
1.126 brouard 8849: /* setlocale (LC_ALL, ""); */
8850: /* bindtextdomain (PACKAGE, LOCALEDIR); */
8851: /* textdomain (PACKAGE); */
8852: /* setlocale (LC_CTYPE, ""); */
8853: /* setlocale (LC_MESSAGES, ""); */
8854:
8855: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 8856: rstart_time = time(NULL);
8857: /* (void) gettimeofday(&start_time,&tzp);*/
8858: start_time = *localtime(&rstart_time);
1.126 brouard 8859: curr_time=start_time;
1.157 brouard 8860: /*tml = *localtime(&start_time.tm_sec);*/
8861: /* strcpy(strstart,asctime(&tml)); */
8862: strcpy(strstart,asctime(&start_time));
1.126 brouard 8863:
8864: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 8865: /* tp.tm_sec = tp.tm_sec +86400; */
8866: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 8867: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
8868: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
8869: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 8870: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 8871: /* strt=asctime(&tmg); */
8872: /* printf("Time(after) =%s",strstart); */
8873: /* (void) time (&time_value);
8874: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
8875: * tm = *localtime(&time_value);
8876: * strstart=asctime(&tm);
8877: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
8878: */
8879:
8880: nberr=0; /* Number of errors and warnings */
8881: nbwarn=0;
1.184 brouard 8882: #ifdef WIN32
8883: _getcwd(pathcd, size);
8884: #else
1.126 brouard 8885: getcwd(pathcd, size);
1.184 brouard 8886: #endif
1.191 brouard 8887: syscompilerinfo(0);
1.196 brouard 8888: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 8889: if(argc <=1){
8890: printf("\nEnter the parameter file name: ");
1.205 brouard 8891: if(!fgets(pathr,FILENAMELENGTH,stdin)){
8892: printf("ERROR Empty parameter file name\n");
8893: goto end;
8894: }
1.126 brouard 8895: i=strlen(pathr);
8896: if(pathr[i-1]=='\n')
8897: pathr[i-1]='\0';
1.156 brouard 8898: i=strlen(pathr);
1.205 brouard 8899: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 8900: pathr[i-1]='\0';
1.205 brouard 8901: }
8902: i=strlen(pathr);
8903: if( i==0 ){
8904: printf("ERROR Empty parameter file name\n");
8905: goto end;
8906: }
8907: for (tok = pathr; tok != NULL; ){
1.126 brouard 8908: printf("Pathr |%s|\n",pathr);
8909: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
8910: printf("val= |%s| pathr=%s\n",val,pathr);
8911: strcpy (pathtot, val);
8912: if(pathr[0] == '\0') break; /* Dirty */
8913: }
8914: }
8915: else{
8916: strcpy(pathtot,argv[1]);
8917: }
8918: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
8919: /*cygwin_split_path(pathtot,path,optionfile);
8920: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
8921: /* cutv(path,optionfile,pathtot,'\\');*/
8922:
8923: /* Split argv[0], imach program to get pathimach */
8924: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
8925: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
8926: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
8927: /* strcpy(pathimach,argv[0]); */
8928: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
8929: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
8930: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 8931: #ifdef WIN32
8932: _chdir(path); /* Can be a relative path */
8933: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
8934: #else
1.126 brouard 8935: chdir(path); /* Can be a relative path */
1.184 brouard 8936: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
8937: #endif
8938: printf("Current directory %s!\n",pathcd);
1.126 brouard 8939: strcpy(command,"mkdir ");
8940: strcat(command,optionfilefiname);
8941: if((outcmd=system(command)) != 0){
1.169 brouard 8942: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 8943: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
8944: /* fclose(ficlog); */
8945: /* exit(1); */
8946: }
8947: /* if((imk=mkdir(optionfilefiname))<0){ */
8948: /* perror("mkdir"); */
8949: /* } */
8950:
8951: /*-------- arguments in the command line --------*/
8952:
1.186 brouard 8953: /* Main Log file */
1.126 brouard 8954: strcat(filelog, optionfilefiname);
8955: strcat(filelog,".log"); /* */
8956: if((ficlog=fopen(filelog,"w"))==NULL) {
8957: printf("Problem with logfile %s\n",filelog);
8958: goto end;
8959: }
8960: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 8961: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 8962: fprintf(ficlog,"\nEnter the parameter file name: \n");
8963: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
8964: path=%s \n\
8965: optionfile=%s\n\
8966: optionfilext=%s\n\
1.156 brouard 8967: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 8968:
1.197 brouard 8969: syscompilerinfo(1);
1.167 brouard 8970:
1.126 brouard 8971: printf("Local time (at start):%s",strstart);
8972: fprintf(ficlog,"Local time (at start): %s",strstart);
8973: fflush(ficlog);
8974: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 8975: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 8976:
8977: /* */
8978: strcpy(fileres,"r");
8979: strcat(fileres, optionfilefiname);
1.201 brouard 8980: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 8981: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 8982: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 8983:
1.186 brouard 8984: /* Main ---------arguments file --------*/
1.126 brouard 8985:
8986: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 8987: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
8988: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 8989: fflush(ficlog);
1.149 brouard 8990: /* goto end; */
8991: exit(70);
1.126 brouard 8992: }
8993:
8994:
8995:
8996: strcpy(filereso,"o");
1.201 brouard 8997: strcat(filereso,fileresu);
1.126 brouard 8998: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
8999: printf("Problem with Output resultfile: %s\n", filereso);
9000: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
9001: fflush(ficlog);
9002: goto end;
9003: }
9004:
9005: /* Reads comments: lines beginning with '#' */
9006: numlinepar=0;
1.197 brouard 9007:
9008: /* First parameter line */
9009: while(fgets(line, MAXLINE, ficpar)) {
9010: /* If line starts with a # it is a comment */
9011: if (line[0] == '#') {
9012: numlinepar++;
9013: fputs(line,stdout);
9014: fputs(line,ficparo);
9015: fputs(line,ficlog);
9016: continue;
9017: }else
9018: break;
9019: }
9020: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
9021: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
9022: if (num_filled != 5) {
9023: printf("Should be 5 parameters\n");
9024: }
1.126 brouard 9025: numlinepar++;
1.197 brouard 9026: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
9027: }
9028: /* Second parameter line */
9029: while(fgets(line, MAXLINE, ficpar)) {
9030: /* If line starts with a # it is a comment */
9031: if (line[0] == '#') {
9032: numlinepar++;
9033: fputs(line,stdout);
9034: fputs(line,ficparo);
9035: fputs(line,ficlog);
9036: continue;
9037: }else
9038: break;
9039: }
1.223 brouard 9040: 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", \
9041: &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
9042: if (num_filled != 11) {
9043: 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 9044: printf("but line=%s\n",line);
1.197 brouard 9045: }
1.223 brouard 9046: 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 9047: }
1.203 brouard 9048: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 9049: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 9050: /* Third parameter line */
9051: while(fgets(line, MAXLINE, ficpar)) {
9052: /* If line starts with a # it is a comment */
9053: if (line[0] == '#') {
9054: numlinepar++;
9055: fputs(line,stdout);
9056: fputs(line,ficparo);
9057: fputs(line,ficlog);
9058: continue;
9059: }else
9060: break;
9061: }
1.201 brouard 9062: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
9063: if (num_filled == 0)
9064: model[0]='\0';
9065: else if (num_filled != 1){
1.197 brouard 9066: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
9067: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
9068: model[0]='\0';
9069: goto end;
9070: }
9071: else{
9072: if (model[0]=='+'){
9073: for(i=1; i<=strlen(model);i++)
9074: modeltemp[i-1]=model[i];
1.201 brouard 9075: strcpy(model,modeltemp);
1.197 brouard 9076: }
9077: }
1.199 brouard 9078: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 9079: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 9080: }
9081: /* 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); */
9082: /* numlinepar=numlinepar+3; /\* In general *\/ */
9083: /* 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 9084: 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);
9085: 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 9086: fflush(ficlog);
1.190 brouard 9087: /* if(model[0]=='#'|| model[0]== '\0'){ */
9088: if(model[0]=='#'){
1.187 brouard 9089: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
9090: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
9091: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
9092: if(mle != -1){
9093: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
9094: exit(1);
9095: }
9096: }
1.126 brouard 9097: while((c=getc(ficpar))=='#' && c!= EOF){
9098: ungetc(c,ficpar);
9099: fgets(line, MAXLINE, ficpar);
9100: numlinepar++;
1.195 brouard 9101: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
9102: z[0]=line[1];
9103: }
9104: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 9105: fputs(line, stdout);
9106: //puts(line);
1.126 brouard 9107: fputs(line,ficparo);
9108: fputs(line,ficlog);
9109: }
9110: ungetc(c,ficpar);
9111:
9112:
1.145 brouard 9113: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.225 brouard 9114: coqvar=matrix(1,nqv,1,n); /**< Fixed quantitative covariate */
9115: cotvar=ma3x(1,maxwav,1,ntv,1,n); /**< Time varying covariate */
9116: cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /**< Time varying quantitative covariate */
1.136 brouard 9117: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
9118: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
9119: v1+v2*age+v2*v3 makes cptcovn = 3
9120: */
9121: if (strlen(model)>1)
1.187 brouard 9122: 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 9123: else
1.187 brouard 9124: ncovmodel=2; /* Constant and age */
1.133 brouard 9125: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
9126: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 9127: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
9128: 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);
9129: 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);
9130: fflush(stdout);
9131: fclose (ficlog);
9132: goto end;
9133: }
1.126 brouard 9134: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
9135: delti=delti3[1][1];
9136: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
9137: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
9138: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 9139: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
9140: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 9141: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
9142: fclose (ficparo);
9143: fclose (ficlog);
9144: goto end;
9145: exit(0);
1.220 brouard 9146: } else if(mle==-5) { /* Main Wizard */
1.126 brouard 9147: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 9148: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
9149: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 9150: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
9151: matcov=matrix(1,npar,1,npar);
1.203 brouard 9152: hess=matrix(1,npar,1,npar);
1.220 brouard 9153: } else{ /* Begin of mle != -1 or -5 */
1.145 brouard 9154: /* Read guessed parameters */
1.126 brouard 9155: /* Reads comments: lines beginning with '#' */
9156: while((c=getc(ficpar))=='#' && c!= EOF){
9157: ungetc(c,ficpar);
9158: fgets(line, MAXLINE, ficpar);
9159: numlinepar++;
1.141 brouard 9160: fputs(line,stdout);
1.126 brouard 9161: fputs(line,ficparo);
9162: fputs(line,ficlog);
9163: }
9164: ungetc(c,ficpar);
9165:
9166: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
9167: for(i=1; i <=nlstate; i++){
1.220 brouard 9168: j=0;
1.126 brouard 9169: for(jj=1; jj <=nlstate+ndeath; jj++){
1.220 brouard 9170: if(jj==i) continue;
9171: j++;
9172: fscanf(ficpar,"%1d%1d",&i1,&j1);
9173: if ((i1 != i) || (j1 != jj)){
9174: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126 brouard 9175: It might be a problem of design; if ncovcol and the model are correct\n \
9176: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.220 brouard 9177: exit(1);
9178: }
9179: fprintf(ficparo,"%1d%1d",i1,j1);
9180: if(mle==1)
9181: printf("%1d%1d",i,jj);
9182: fprintf(ficlog,"%1d%1d",i,jj);
9183: for(k=1; k<=ncovmodel;k++){
9184: fscanf(ficpar," %lf",¶m[i][j][k]);
9185: if(mle==1){
9186: printf(" %lf",param[i][j][k]);
9187: fprintf(ficlog," %lf",param[i][j][k]);
9188: }
9189: else
9190: fprintf(ficlog," %lf",param[i][j][k]);
9191: fprintf(ficparo," %lf",param[i][j][k]);
9192: }
9193: fscanf(ficpar,"\n");
9194: numlinepar++;
9195: if(mle==1)
9196: printf("\n");
9197: fprintf(ficlog,"\n");
9198: fprintf(ficparo,"\n");
1.126 brouard 9199: }
9200: }
9201: fflush(ficlog);
9202:
1.145 brouard 9203: /* Reads scales values */
1.126 brouard 9204: p=param[1][1];
9205:
9206: /* Reads comments: lines beginning with '#' */
9207: while((c=getc(ficpar))=='#' && c!= EOF){
9208: ungetc(c,ficpar);
9209: fgets(line, MAXLINE, ficpar);
9210: numlinepar++;
1.141 brouard 9211: fputs(line,stdout);
1.126 brouard 9212: fputs(line,ficparo);
9213: fputs(line,ficlog);
9214: }
9215: ungetc(c,ficpar);
9216:
9217: for(i=1; i <=nlstate; i++){
9218: for(j=1; j <=nlstate+ndeath-1; j++){
1.220 brouard 9219: fscanf(ficpar,"%1d%1d",&i1,&j1);
9220: if ( (i1-i) * (j1-j) != 0){
9221: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
9222: exit(1);
9223: }
9224: printf("%1d%1d",i,j);
9225: fprintf(ficparo,"%1d%1d",i1,j1);
9226: fprintf(ficlog,"%1d%1d",i1,j1);
9227: for(k=1; k<=ncovmodel;k++){
9228: fscanf(ficpar,"%le",&delti3[i][j][k]);
9229: printf(" %le",delti3[i][j][k]);
9230: fprintf(ficparo," %le",delti3[i][j][k]);
9231: fprintf(ficlog," %le",delti3[i][j][k]);
9232: }
9233: fscanf(ficpar,"\n");
9234: numlinepar++;
9235: printf("\n");
9236: fprintf(ficparo,"\n");
9237: fprintf(ficlog,"\n");
1.126 brouard 9238: }
9239: }
9240: fflush(ficlog);
1.220 brouard 9241:
1.145 brouard 9242: /* Reads covariance matrix */
1.126 brouard 9243: delti=delti3[1][1];
1.220 brouard 9244:
9245:
1.126 brouard 9246: /* 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 9247:
1.126 brouard 9248: /* Reads comments: lines beginning with '#' */
9249: while((c=getc(ficpar))=='#' && c!= EOF){
9250: ungetc(c,ficpar);
9251: fgets(line, MAXLINE, ficpar);
9252: numlinepar++;
1.141 brouard 9253: fputs(line,stdout);
1.126 brouard 9254: fputs(line,ficparo);
9255: fputs(line,ficlog);
9256: }
9257: ungetc(c,ficpar);
1.220 brouard 9258:
1.126 brouard 9259: matcov=matrix(1,npar,1,npar);
1.203 brouard 9260: hess=matrix(1,npar,1,npar);
1.131 brouard 9261: for(i=1; i <=npar; i++)
9262: for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220 brouard 9263:
1.194 brouard 9264: /* Scans npar lines */
1.126 brouard 9265: for(i=1; i <=npar; i++){
1.226 brouard 9266: count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
1.194 brouard 9267: if(count != 3){
1.226 brouard 9268: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 9269: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
9270: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 9271: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 9272: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
9273: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 9274: exit(1);
1.220 brouard 9275: }else{
1.226 brouard 9276: if(mle==1)
9277: printf("%1d%1d%d",i1,j1,jk);
9278: }
9279: fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
9280: fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
1.126 brouard 9281: for(j=1; j <=i; j++){
1.226 brouard 9282: fscanf(ficpar," %le",&matcov[i][j]);
9283: if(mle==1){
9284: printf(" %.5le",matcov[i][j]);
9285: }
9286: fprintf(ficlog," %.5le",matcov[i][j]);
9287: fprintf(ficparo," %.5le",matcov[i][j]);
1.126 brouard 9288: }
9289: fscanf(ficpar,"\n");
9290: numlinepar++;
9291: if(mle==1)
1.220 brouard 9292: printf("\n");
1.126 brouard 9293: fprintf(ficlog,"\n");
9294: fprintf(ficparo,"\n");
9295: }
1.194 brouard 9296: /* End of read covariance matrix npar lines */
1.126 brouard 9297: for(i=1; i <=npar; i++)
9298: for(j=i+1;j<=npar;j++)
1.226 brouard 9299: matcov[i][j]=matcov[j][i];
1.126 brouard 9300:
9301: if(mle==1)
9302: printf("\n");
9303: fprintf(ficlog,"\n");
9304:
9305: fflush(ficlog);
9306:
9307: /*-------- Rewriting parameter file ----------*/
9308: strcpy(rfileres,"r"); /* "Rparameterfile */
9309: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
9310: strcat(rfileres,"."); /* */
9311: strcat(rfileres,optionfilext); /* Other files have txt extension */
9312: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 9313: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
9314: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 9315: }
9316: fprintf(ficres,"#%s\n",version);
9317: } /* End of mle != -3 */
1.218 brouard 9318:
1.186 brouard 9319: /* Main data
9320: */
1.126 brouard 9321: n= lastobs;
9322: num=lvector(1,n);
9323: moisnais=vector(1,n);
9324: annais=vector(1,n);
9325: moisdc=vector(1,n);
9326: andc=vector(1,n);
1.220 brouard 9327: weight=vector(1,n);
1.126 brouard 9328: agedc=vector(1,n);
9329: cod=ivector(1,n);
1.220 brouard 9330: for(i=1;i<=n;i++){
9331: num[i]=0;
9332: moisnais[i]=0;
9333: annais[i]=0;
9334: moisdc[i]=0;
9335: andc[i]=0;
9336: agedc[i]=0;
9337: cod[i]=0;
9338: weight[i]=1.0; /* Equal weights, 1 by default */
9339: }
1.126 brouard 9340: mint=matrix(1,maxwav,1,n);
9341: anint=matrix(1,maxwav,1,n);
1.131 brouard 9342: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 9343: tab=ivector(1,NCOVMAX);
1.144 brouard 9344: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 9345: 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 9346:
1.136 brouard 9347: /* Reads data from file datafile */
9348: if (readdata(datafile, firstobs, lastobs, &imx)==1)
9349: goto end;
9350:
9351: /* Calculation of the number of parameters from char model */
1.137 brouard 9352: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
9353: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
9354: k=3 V4 Tvar[k=3]= 4 (from V4)
9355: k=2 V1 Tvar[k=2]= 1 (from V1)
9356: k=1 Tvar[1]=2 (from V2)
9357: */
9358: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
1.226 brouard 9359: Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
9360: Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
9361: Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
1.137 brouard 9362: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
9363: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
9364: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
9365: */
9366: /* For model-covariate k tells which data-covariate to use but
9367: because this model-covariate is a construction we invent a new column
9368: ncovcol + k1
9369: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
9370: Tvar[3=V1*V4]=4+1 etc */
1.227 ! brouard 9371: Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
! 9372: Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
1.137 brouard 9373: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
9374: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
1.227 ! brouard 9375: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
1.137 brouard 9376: */
1.145 brouard 9377: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
9378: 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 9379: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
9380: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 9381: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 9382: 4 covariates (3 plus signs)
9383: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
9384: */
1.227 ! brouard 9385: Tmodelind=ivector(1,NCOVMAX);/** five the k model position of an
! 9386: * individual dummy, fixed or varying:
! 9387: * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
! 9388: * 3, 1, 0, 0, 0, 0, 0, 0},
! 9389: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.186 brouard 9390: /* Main decodemodel */
9391:
1.187 brouard 9392:
1.223 brouard 9393: if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/
1.136 brouard 9394: goto end;
9395:
1.137 brouard 9396: if((double)(lastobs-imx)/(double)imx > 1.10){
9397: nbwarn++;
9398: 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);
9399: 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);
9400: }
1.136 brouard 9401: /* if(mle==1){*/
1.137 brouard 9402: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
9403: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 9404: }
9405:
9406: /*-calculation of age at interview from date of interview and age at death -*/
9407: agev=matrix(1,maxwav,1,imx);
9408:
9409: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
9410: goto end;
9411:
1.126 brouard 9412:
1.136 brouard 9413: agegomp=(int)agemin;
9414: free_vector(moisnais,1,n);
9415: free_vector(annais,1,n);
1.126 brouard 9416: /* free_matrix(mint,1,maxwav,1,n);
9417: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 9418: /* free_vector(moisdc,1,n); */
9419: /* free_vector(andc,1,n); */
1.145 brouard 9420: /* */
9421:
1.126 brouard 9422: wav=ivector(1,imx);
1.214 brouard 9423: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
9424: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
9425: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
9426: 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.*/
9427: bh=imatrix(1,lastpass-firstpass+2,1,imx);
9428: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 9429:
9430: /* Concatenates waves */
1.214 brouard 9431: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
9432: Death is a valid wave (if date is known).
9433: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
9434: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
9435: and mw[mi+1][i]. dh depends on stepm.
9436: */
9437:
1.126 brouard 9438: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 9439: /* */
9440:
1.215 brouard 9441: free_vector(moisdc,1,n);
9442: free_vector(andc,1,n);
9443:
1.126 brouard 9444: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
9445: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
9446: ncodemax[1]=1;
1.145 brouard 9447: Ndum =ivector(-1,NCOVMAX);
1.225 brouard 9448: cptcoveff=0;
1.220 brouard 9449: if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
9450: tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.227 ! brouard 9451: }
! 9452:
! 9453: ncovcombmax=pow(2,cptcoveff);
! 9454: invalidvarcomb=ivector(1, ncovcombmax);
! 9455: for(i=1;i<ncovcombmax;i++)
! 9456: invalidvarcomb[i]=0;
! 9457:
1.211 brouard 9458: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 9459: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 9460: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.227 ! brouard 9461:
1.200 brouard 9462: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 9463: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 9464: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 9465: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
9466: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
9467: * (currently 0 or 1) in the data.
9468: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
9469: * corresponding modality (h,j).
9470: */
9471:
1.145 brouard 9472: h=0;
9473: /*if (cptcovn > 0) */
1.126 brouard 9474: m=pow(2,cptcoveff);
9475:
1.144 brouard 9476: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 9477: * For k=4 covariates, h goes from 1 to m=2**k
9478: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
9479: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 9480: * h\k 1 2 3 4
1.143 brouard 9481: *______________________________
9482: * 1 i=1 1 i=1 1 i=1 1 i=1 1
9483: * 2 2 1 1 1
9484: * 3 i=2 1 2 1 1
9485: * 4 2 2 1 1
9486: * 5 i=3 1 i=2 1 2 1
9487: * 6 2 1 2 1
9488: * 7 i=4 1 2 2 1
9489: * 8 2 2 2 1
1.197 brouard 9490: * 9 i=5 1 i=3 1 i=2 1 2
9491: * 10 2 1 1 2
9492: * 11 i=6 1 2 1 2
9493: * 12 2 2 1 2
9494: * 13 i=7 1 i=4 1 2 2
9495: * 14 2 1 2 2
9496: * 15 i=8 1 2 2 2
9497: * 16 2 2 2 2
1.143 brouard 9498: */
1.212 brouard 9499: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 9500: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
9501: * and the value of each covariate?
9502: * V1=1, V2=1, V3=2, V4=1 ?
9503: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
9504: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
9505: * In order to get the real value in the data, we use nbcode
9506: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
9507: * We are keeping this crazy system in order to be able (in the future?)
9508: * to have more than 2 values (0 or 1) for a covariate.
9509: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
9510: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
9511: * bbbbbbbb
9512: * 76543210
9513: * h-1 00000101 (6-1=5)
1.219 brouard 9514: *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211 brouard 9515: * &
9516: * 1 00000001 (1)
1.219 brouard 9517: * 00000000 = 1 & ((h-1) >> (k-1))
9518: * +1= 00000001 =1
1.211 brouard 9519: *
9520: * h=14, k=3 => h'=h-1=13, k'=k-1=2
9521: * h' 1101 =2^3+2^2+0x2^1+2^0
9522: * >>k' 11
9523: * & 00000001
9524: * = 00000001
9525: * +1 = 00000010=2 = codtabm(14,3)
9526: * Reverse h=6 and m=16?
9527: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
9528: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
9529: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
9530: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
9531: * V3=decodtabm(14,3,2**4)=2
9532: * h'=13 1101 =2^3+2^2+0x2^1+2^0
9533: *(h-1) >> (j-1) 0011 =13 >> 2
9534: * &1 000000001
9535: * = 000000001
9536: * +1= 000000010 =2
9537: * 2211
9538: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
9539: * V3=2
1.220 brouard 9540: * codtabm and decodtabm are identical
1.211 brouard 9541: */
9542:
1.145 brouard 9543:
9544: free_ivector(Ndum,-1,NCOVMAX);
9545:
9546:
1.126 brouard 9547:
1.186 brouard 9548: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 9549: strcpy(optionfilegnuplot,optionfilefiname);
9550: if(mle==-3)
1.201 brouard 9551: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 9552: strcat(optionfilegnuplot,".gp");
9553:
9554: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
9555: printf("Problem with file %s",optionfilegnuplot);
9556: }
9557: else{
1.204 brouard 9558: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 9559: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 9560: //fprintf(ficgp,"set missing 'NaNq'\n");
9561: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 9562: }
9563: /* fclose(ficgp);*/
1.186 brouard 9564:
9565:
9566: /* Initialisation of --------- index.htm --------*/
1.126 brouard 9567:
9568: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
9569: if(mle==-3)
1.201 brouard 9570: strcat(optionfilehtm,"-MORT_");
1.126 brouard 9571: strcat(optionfilehtm,".htm");
9572: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 9573: printf("Problem with %s \n",optionfilehtm);
9574: exit(0);
1.126 brouard 9575: }
9576:
9577: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
9578: strcat(optionfilehtmcov,"-cov.htm");
9579: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
9580: printf("Problem with %s \n",optionfilehtmcov), exit(0);
9581: }
9582: else{
9583: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
9584: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 9585: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 9586: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
9587: }
9588:
1.213 brouard 9589: 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 9590: <hr size=\"2\" color=\"#EC5E5E\"> \n\
9591: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 9592: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 9593: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 9594: \n\
9595: <hr size=\"2\" color=\"#EC5E5E\">\
9596: <ul><li><h4>Parameter files</h4>\n\
9597: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
9598: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
9599: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
9600: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
9601: - Date and time at start: %s</ul>\n",\
9602: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
9603: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
9604: fileres,fileres,\
9605: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
9606: fflush(fichtm);
9607:
9608: strcpy(pathr,path);
9609: strcat(pathr,optionfilefiname);
1.184 brouard 9610: #ifdef WIN32
9611: _chdir(optionfilefiname); /* Move to directory named optionfile */
9612: #else
1.126 brouard 9613: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 9614: #endif
9615:
1.126 brouard 9616:
1.220 brouard 9617: /* Calculates basic frequencies. Computes observed prevalence at single age
9618: and for any valid combination of covariates
1.126 brouard 9619: and prints on file fileres'p'. */
1.227 ! brouard 9620: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
! 9621: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 9622:
9623: fprintf(fichtm,"\n");
9624: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
9625: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
9626: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
9627: imx,agemin,agemax,jmin,jmax,jmean);
9628: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.220 brouard 9629: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9630: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9631: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9632: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218 brouard 9633:
1.126 brouard 9634: /* For Powell, parameters are in a vector p[] starting at p[1]
9635: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
9636: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
9637:
9638: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 9639: /* For mortality only */
1.126 brouard 9640: if (mle==-3){
1.136 brouard 9641: ximort=matrix(1,NDIM,1,NDIM);
1.220 brouard 9642: for(i=1;i<=NDIM;i++)
9643: for(j=1;j<=NDIM;j++)
9644: ximort[i][j]=0.;
1.186 brouard 9645: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 9646: cens=ivector(1,n);
9647: ageexmed=vector(1,n);
9648: agecens=vector(1,n);
9649: dcwave=ivector(1,n);
1.223 brouard 9650:
1.126 brouard 9651: for (i=1; i<=imx; i++){
9652: dcwave[i]=-1;
9653: for (m=firstpass; m<=lastpass; m++)
1.226 brouard 9654: if (s[m][i]>nlstate) {
9655: dcwave[i]=m;
9656: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
9657: break;
9658: }
1.126 brouard 9659: }
1.226 brouard 9660:
1.126 brouard 9661: for (i=1; i<=imx; i++) {
9662: if (wav[i]>0){
1.226 brouard 9663: ageexmed[i]=agev[mw[1][i]][i];
9664: j=wav[i];
9665: agecens[i]=1.;
9666:
9667: if (ageexmed[i]> 1 && wav[i] > 0){
9668: agecens[i]=agev[mw[j][i]][i];
9669: cens[i]= 1;
9670: }else if (ageexmed[i]< 1)
9671: cens[i]= -1;
9672: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
9673: cens[i]=0 ;
1.126 brouard 9674: }
9675: else cens[i]=-1;
9676: }
9677:
9678: for (i=1;i<=NDIM;i++) {
9679: for (j=1;j<=NDIM;j++)
1.226 brouard 9680: ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126 brouard 9681: }
9682:
1.145 brouard 9683: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 9684: /*printf("%lf %lf", p[1], p[2]);*/
9685:
9686:
1.136 brouard 9687: #ifdef GSL
9688: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 9689: #else
1.126 brouard 9690: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 9691: #endif
1.201 brouard 9692: strcpy(filerespow,"POW-MORT_");
9693: strcat(filerespow,fileresu);
1.126 brouard 9694: if((ficrespow=fopen(filerespow,"w"))==NULL) {
9695: printf("Problem with resultfile: %s\n", filerespow);
9696: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
9697: }
1.136 brouard 9698: #ifdef GSL
9699: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 9700: #else
1.126 brouard 9701: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 9702: #endif
1.126 brouard 9703: /* for (i=1;i<=nlstate;i++)
9704: for(j=1;j<=nlstate+ndeath;j++)
9705: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
9706: */
9707: fprintf(ficrespow,"\n");
1.136 brouard 9708: #ifdef GSL
9709: /* gsl starts here */
9710: T = gsl_multimin_fminimizer_nmsimplex;
9711: gsl_multimin_fminimizer *sfm = NULL;
9712: gsl_vector *ss, *x;
9713: gsl_multimin_function minex_func;
9714:
9715: /* Initial vertex size vector */
9716: ss = gsl_vector_alloc (NDIM);
9717:
9718: if (ss == NULL){
9719: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
9720: }
9721: /* Set all step sizes to 1 */
9722: gsl_vector_set_all (ss, 0.001);
9723:
9724: /* Starting point */
1.126 brouard 9725:
1.136 brouard 9726: x = gsl_vector_alloc (NDIM);
9727:
9728: if (x == NULL){
9729: gsl_vector_free(ss);
9730: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
9731: }
9732:
9733: /* Initialize method and iterate */
9734: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 9735: /* gsl_vector_set(x, 0, 0.0268); */
9736: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 9737: gsl_vector_set(x, 0, p[1]);
9738: gsl_vector_set(x, 1, p[2]);
9739:
9740: minex_func.f = &gompertz_f;
9741: minex_func.n = NDIM;
9742: minex_func.params = (void *)&p; /* ??? */
9743:
9744: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
9745: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
9746:
9747: printf("Iterations beginning .....\n\n");
9748: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
9749:
9750: iteri=0;
9751: while (rval == GSL_CONTINUE){
9752: iteri++;
9753: status = gsl_multimin_fminimizer_iterate(sfm);
9754:
9755: if (status) printf("error: %s\n", gsl_strerror (status));
9756: fflush(0);
9757:
9758: if (status)
9759: break;
9760:
9761: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
9762: ssval = gsl_multimin_fminimizer_size (sfm);
9763:
9764: if (rval == GSL_SUCCESS)
9765: printf ("converged to a local maximum at\n");
9766:
9767: printf("%5d ", iteri);
9768: for (it = 0; it < NDIM; it++){
9769: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
9770: }
9771: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
9772: }
9773:
9774: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
9775:
9776: gsl_vector_free(x); /* initial values */
9777: gsl_vector_free(ss); /* inital step size */
9778: for (it=0; it<NDIM; it++){
9779: p[it+1]=gsl_vector_get(sfm->x,it);
9780: fprintf(ficrespow," %.12lf", p[it]);
9781: }
9782: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
9783: #endif
9784: #ifdef POWELL
9785: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
9786: #endif
1.126 brouard 9787: fclose(ficrespow);
9788:
1.203 brouard 9789: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 9790:
9791: for(i=1; i <=NDIM; i++)
9792: for(j=i+1;j<=NDIM;j++)
1.220 brouard 9793: matcov[i][j]=matcov[j][i];
1.126 brouard 9794:
9795: printf("\nCovariance matrix\n ");
1.203 brouard 9796: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 9797: for(i=1; i <=NDIM; i++) {
9798: for(j=1;j<=NDIM;j++){
1.220 brouard 9799: printf("%f ",matcov[i][j]);
9800: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 9801: }
1.203 brouard 9802: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 9803: }
9804:
9805: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 9806: for (i=1;i<=NDIM;i++) {
1.126 brouard 9807: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 9808: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
9809: }
1.126 brouard 9810: lsurv=vector(1,AGESUP);
9811: lpop=vector(1,AGESUP);
9812: tpop=vector(1,AGESUP);
9813: lsurv[agegomp]=100000;
9814:
9815: for (k=agegomp;k<=AGESUP;k++) {
9816: agemortsup=k;
9817: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
9818: }
9819:
9820: for (k=agegomp;k<agemortsup;k++)
9821: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
9822:
9823: for (k=agegomp;k<agemortsup;k++){
9824: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
9825: sumlpop=sumlpop+lpop[k];
9826: }
9827:
9828: tpop[agegomp]=sumlpop;
9829: for (k=agegomp;k<(agemortsup-3);k++){
9830: /* tpop[k+1]=2;*/
9831: tpop[k+1]=tpop[k]-lpop[k];
9832: }
9833:
9834:
9835: printf("\nAge lx qx dx Lx Tx e(x)\n");
9836: for (k=agegomp;k<(agemortsup-2);k++)
9837: 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]);
9838:
9839:
9840: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220 brouard 9841: ageminpar=50;
9842: agemaxpar=100;
1.194 brouard 9843: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
9844: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
9845: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9846: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
9847: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
9848: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9849: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 9850: }else{
9851: printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
9852: 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 9853: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220 brouard 9854: }
1.201 brouard 9855: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 9856: stepm, weightopt,\
9857: model,imx,p,matcov,agemortsup);
9858:
9859: free_vector(lsurv,1,AGESUP);
9860: free_vector(lpop,1,AGESUP);
9861: free_vector(tpop,1,AGESUP);
1.220 brouard 9862: free_matrix(ximort,1,NDIM,1,NDIM);
1.136 brouard 9863: free_ivector(cens,1,n);
9864: free_vector(agecens,1,n);
9865: free_ivector(dcwave,1,n);
1.220 brouard 9866: #ifdef GSL
1.136 brouard 9867: #endif
1.186 brouard 9868: } /* Endof if mle==-3 mortality only */
1.205 brouard 9869: /* Standard */
9870: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
9871: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
9872: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 9873: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 9874: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
9875: for (k=1; k<=npar;k++)
9876: printf(" %d %8.5f",k,p[k]);
9877: printf("\n");
1.205 brouard 9878: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
9879: /* mlikeli uses func not funcone */
9880: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
9881: }
9882: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
9883: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
9884: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
9885: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
9886: }
9887: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 9888: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
9889: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
9890: for (k=1; k<=npar;k++)
9891: printf(" %d %8.5f",k,p[k]);
9892: printf("\n");
9893:
9894: /*--------- results files --------------*/
1.224 brouard 9895: 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 9896:
9897:
9898: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9899: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9900: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9901: for(i=1,jk=1; i <=nlstate; i++){
9902: for(k=1; k <=(nlstate+ndeath); k++){
1.225 brouard 9903: if (k != i) {
9904: printf("%d%d ",i,k);
9905: fprintf(ficlog,"%d%d ",i,k);
9906: fprintf(ficres,"%1d%1d ",i,k);
9907: for(j=1; j <=ncovmodel; j++){
9908: printf("%12.7f ",p[jk]);
9909: fprintf(ficlog,"%12.7f ",p[jk]);
9910: fprintf(ficres,"%12.7f ",p[jk]);
9911: jk++;
9912: }
9913: printf("\n");
9914: fprintf(ficlog,"\n");
9915: fprintf(ficres,"\n");
9916: }
1.126 brouard 9917: }
9918: }
1.203 brouard 9919: if(mle != 0){
9920: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 9921: ftolhess=ftol; /* Usually correct */
1.203 brouard 9922: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
9923: 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");
9924: 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");
9925: for(i=1,jk=1; i <=nlstate; i++){
1.225 brouard 9926: for(k=1; k <=(nlstate+ndeath); k++){
9927: if (k != i) {
9928: printf("%d%d ",i,k);
9929: fprintf(ficlog,"%d%d ",i,k);
9930: for(j=1; j <=ncovmodel; j++){
9931: 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]));
9932: 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]));
9933: jk++;
9934: }
9935: printf("\n");
9936: fprintf(ficlog,"\n");
9937: }
9938: }
1.193 brouard 9939: }
1.203 brouard 9940: } /* end of hesscov and Wald tests */
1.225 brouard 9941:
1.203 brouard 9942: /* */
1.126 brouard 9943: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
9944: printf("# Scales (for hessian or gradient estimation)\n");
9945: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
9946: for(i=1,jk=1; i <=nlstate; i++){
9947: for(j=1; j <=nlstate+ndeath; j++){
1.225 brouard 9948: if (j!=i) {
9949: fprintf(ficres,"%1d%1d",i,j);
9950: printf("%1d%1d",i,j);
9951: fprintf(ficlog,"%1d%1d",i,j);
9952: for(k=1; k<=ncovmodel;k++){
9953: printf(" %.5e",delti[jk]);
9954: fprintf(ficlog," %.5e",delti[jk]);
9955: fprintf(ficres," %.5e",delti[jk]);
9956: jk++;
9957: }
9958: printf("\n");
9959: fprintf(ficlog,"\n");
9960: fprintf(ficres,"\n");
9961: }
1.126 brouard 9962: }
9963: }
9964:
9965: 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 9966: if(mle >= 1) /* To big for the screen */
1.126 brouard 9967: 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");
9968: 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");
9969: /* # 121 Var(a12)\n\ */
9970: /* # 122 Cov(b12,a12) Var(b12)\n\ */
9971: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
9972: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
9973: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
9974: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
9975: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
9976: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
9977:
9978:
9979: /* Just to have a covariance matrix which will be more understandable
9980: even is we still don't want to manage dictionary of variables
9981: */
9982: for(itimes=1;itimes<=2;itimes++){
9983: jj=0;
9984: for(i=1; i <=nlstate; i++){
1.225 brouard 9985: for(j=1; j <=nlstate+ndeath; j++){
9986: if(j==i) continue;
9987: for(k=1; k<=ncovmodel;k++){
9988: jj++;
9989: ca[0]= k+'a'-1;ca[1]='\0';
9990: if(itimes==1){
9991: if(mle>=1)
9992: printf("#%1d%1d%d",i,j,k);
9993: fprintf(ficlog,"#%1d%1d%d",i,j,k);
9994: fprintf(ficres,"#%1d%1d%d",i,j,k);
9995: }else{
9996: if(mle>=1)
9997: printf("%1d%1d%d",i,j,k);
9998: fprintf(ficlog,"%1d%1d%d",i,j,k);
9999: fprintf(ficres,"%1d%1d%d",i,j,k);
10000: }
10001: ll=0;
10002: for(li=1;li <=nlstate; li++){
10003: for(lj=1;lj <=nlstate+ndeath; lj++){
10004: if(lj==li) continue;
10005: for(lk=1;lk<=ncovmodel;lk++){
10006: ll++;
10007: if(ll<=jj){
10008: cb[0]= lk +'a'-1;cb[1]='\0';
10009: if(ll<jj){
10010: if(itimes==1){
10011: if(mle>=1)
10012: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
10013: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
10014: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
10015: }else{
10016: if(mle>=1)
10017: printf(" %.5e",matcov[jj][ll]);
10018: fprintf(ficlog," %.5e",matcov[jj][ll]);
10019: fprintf(ficres," %.5e",matcov[jj][ll]);
10020: }
10021: }else{
10022: if(itimes==1){
10023: if(mle>=1)
10024: printf(" Var(%s%1d%1d)",ca,i,j);
10025: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
10026: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
10027: }else{
10028: if(mle>=1)
10029: printf(" %.7e",matcov[jj][ll]);
10030: fprintf(ficlog," %.7e",matcov[jj][ll]);
10031: fprintf(ficres," %.7e",matcov[jj][ll]);
10032: }
10033: }
10034: }
10035: } /* end lk */
10036: } /* end lj */
10037: } /* end li */
10038: if(mle>=1)
10039: printf("\n");
10040: fprintf(ficlog,"\n");
10041: fprintf(ficres,"\n");
10042: numlinepar++;
10043: } /* end k*/
10044: } /*end j */
1.126 brouard 10045: } /* end i */
10046: } /* end itimes */
10047:
10048: fflush(ficlog);
10049: fflush(ficres);
1.225 brouard 10050: while(fgets(line, MAXLINE, ficpar)) {
10051: /* If line starts with a # it is a comment */
10052: if (line[0] == '#') {
10053: numlinepar++;
10054: fputs(line,stdout);
10055: fputs(line,ficparo);
10056: fputs(line,ficlog);
10057: continue;
10058: }else
10059: break;
10060: }
10061:
1.209 brouard 10062: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
10063: /* ungetc(c,ficpar); */
10064: /* fgets(line, MAXLINE, ficpar); */
10065: /* fputs(line,stdout); */
10066: /* fputs(line,ficparo); */
10067: /* } */
10068: /* ungetc(c,ficpar); */
1.126 brouard 10069:
10070: estepm=0;
1.209 brouard 10071: 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 10072:
10073: if (num_filled != 6) {
10074: 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);
10075: 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);
10076: goto end;
10077: }
10078: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
10079: }
10080: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
10081: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
10082:
1.209 brouard 10083: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 10084: if (estepm==0 || estepm < stepm) estepm=stepm;
10085: if (fage <= 2) {
10086: bage = ageminpar;
10087: fage = agemaxpar;
10088: }
10089:
10090: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 10091: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
10092: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220 brouard 10093:
1.186 brouard 10094: /* Other stuffs, more or less useful */
1.126 brouard 10095: while((c=getc(ficpar))=='#' && c!= EOF){
10096: ungetc(c,ficpar);
10097: fgets(line, MAXLINE, ficpar);
1.141 brouard 10098: fputs(line,stdout);
1.126 brouard 10099: fputs(line,ficparo);
10100: }
10101: ungetc(c,ficpar);
10102:
10103: 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);
10104: 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);
10105: 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);
10106: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
10107: 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);
10108:
10109: while((c=getc(ficpar))=='#' && c!= EOF){
10110: ungetc(c,ficpar);
10111: fgets(line, MAXLINE, ficpar);
1.141 brouard 10112: fputs(line,stdout);
1.126 brouard 10113: fputs(line,ficparo);
10114: }
10115: ungetc(c,ficpar);
10116:
10117:
10118: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
10119: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
10120:
10121: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 10122: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 10123: fprintf(ficparo,"pop_based=%d\n",popbased);
10124: fprintf(ficres,"pop_based=%d\n",popbased);
10125:
10126: while((c=getc(ficpar))=='#' && c!= EOF){
10127: ungetc(c,ficpar);
10128: fgets(line, MAXLINE, ficpar);
1.141 brouard 10129: fputs(line,stdout);
1.126 brouard 10130: fputs(line,ficparo);
10131: }
10132: ungetc(c,ficpar);
10133:
10134: 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);
10135: 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);
10136: 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);
10137: 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);
10138: 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);
10139: /* day and month of proj2 are not used but only year anproj2.*/
10140:
1.217 brouard 10141: while((c=getc(ficpar))=='#' && c!= EOF){
10142: ungetc(c,ficpar);
10143: fgets(line, MAXLINE, ficpar);
10144: fputs(line,stdout);
10145: fputs(line,ficparo);
10146: }
10147: ungetc(c,ficpar);
10148:
10149: 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 10150: 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);
10151: 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);
10152: 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 10153: /* day and month of proj2 are not used but only year anproj2.*/
1.126 brouard 10154:
10155:
1.220 brouard 10156: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145 brouard 10157: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 10158:
10159: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 10160: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.220 brouard 10161: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 10162: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
10163: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 10164: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 10165: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
10166: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 10167: }else{
1.218 brouard 10168: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
1.220 brouard 10169: }
10170: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
1.225 brouard 10171: model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
10172: jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
1.220 brouard 10173:
1.225 brouard 10174: /*------------ free_vector -------------*/
10175: /* chdir(path); */
1.220 brouard 10176:
1.215 brouard 10177: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
10178: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
10179: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
10180: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.126 brouard 10181: free_lvector(num,1,n);
10182: free_vector(agedc,1,n);
10183: /*free_matrix(covar,0,NCOVMAX,1,n);*/
10184: /*free_matrix(covar,1,NCOVMAX,1,n);*/
10185: fclose(ficparo);
10186: fclose(ficres);
1.220 brouard 10187:
10188:
1.186 brouard 10189: /* Other results (useful)*/
1.220 brouard 10190:
10191:
1.126 brouard 10192: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 10193: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
10194: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 10195: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 10196: fclose(ficrespl);
10197:
10198: /*------------- h Pij x at various ages ------------*/
1.180 brouard 10199: /*#include "hpijx.h"*/
10200: hPijx(p, bage, fage);
1.145 brouard 10201: fclose(ficrespij);
1.227 ! brouard 10202:
1.220 brouard 10203: /* ncovcombmax= pow(2,cptcoveff); */
1.219 brouard 10204: /*-------------- Variance of one-step probabilities---*/
1.145 brouard 10205: k=1;
1.126 brouard 10206: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.227 ! brouard 10207:
1.219 brouard 10208: /* Prevalence for each covariates in probs[age][status][cov] */
1.218 brouard 10209: probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.126 brouard 10210: for(i=1;i<=AGESUP;i++)
1.219 brouard 10211: for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.225 brouard 10212: for(k=1;k<=ncovcombmax;k++)
10213: probs[i][j][k]=0.;
1.219 brouard 10214: prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
10215: if (mobilav!=0 ||mobilavproj !=0 ) {
10216: mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.227 ! brouard 10217: for(i=1;i<=AGESUP;i++)
! 10218: for(j=1;j<=nlstate;j++)
! 10219: for(k=1;k<=ncovcombmax;k++)
! 10220: mobaverages[i][j][k]=0.;
1.219 brouard 10221: mobaverage=mobaverages;
10222: if (mobilav!=0) {
1.227 ! brouard 10223: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
! 10224: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
! 10225: printf(" Error in movingaverage mobilav=%d\n",mobilav);
! 10226: }
1.219 brouard 10227: }
10228: /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
10229: /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
10230: else if (mobilavproj !=0) {
1.227 ! brouard 10231: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
! 10232: fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
! 10233: printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
! 10234: }
1.219 brouard 10235: }
10236: }/* end if moving average */
1.227 ! brouard 10237:
1.126 brouard 10238: /*---------- Forecasting ------------------*/
10239: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
10240: if(prevfcast==1){
10241: /* if(stepm ==1){*/
1.225 brouard 10242: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 10243: }
1.217 brouard 10244: if(backcast==1){
1.219 brouard 10245: ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
10246: ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
10247: ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
10248:
10249: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
10250:
10251: bprlim=matrix(1,nlstate,1,nlstate);
10252: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
10253: fclose(ficresplb);
10254:
1.222 brouard 10255: hBijx(p, bage, fage, mobaverage);
10256: fclose(ficrespijb);
1.219 brouard 10257: free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
10258:
10259: /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
1.225 brouard 10260: bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
1.219 brouard 10261: free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
10262: free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
10263: free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
10264: }
1.217 brouard 10265:
1.186 brouard 10266:
10267: /* ------ Other prevalence ratios------------ */
1.126 brouard 10268:
1.215 brouard 10269: free_ivector(wav,1,imx);
10270: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
10271: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
10272: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.218 brouard 10273:
10274:
1.127 brouard 10275: /*---------- Health expectancies, no variances ------------*/
1.218 brouard 10276:
1.201 brouard 10277: strcpy(filerese,"E_");
10278: strcat(filerese,fileresu);
1.126 brouard 10279: if((ficreseij=fopen(filerese,"w"))==NULL) {
10280: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
10281: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
10282: }
1.208 brouard 10283: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
10284: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.219 brouard 10285:
1.227 ! brouard 10286: for (k=1; k <= (int) pow(2,cptcoveff); k++){ /* For any combination of dummy covariates, fixed and varying */
1.219 brouard 10287: fprintf(ficreseij,"\n#****** ");
1.225 brouard 10288: for(j=1;j<=cptcoveff;j++) {
1.227 ! brouard 10289: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.219 brouard 10290: }
10291: fprintf(ficreseij,"******\n");
10292:
10293: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
10294: oldm=oldms;savm=savms;
10295: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
1.127 brouard 10296:
1.219 brouard 10297: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127 brouard 10298: }
10299: fclose(ficreseij);
1.208 brouard 10300: printf("done evsij\n");fflush(stdout);
10301: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.218 brouard 10302:
1.227 ! brouard 10303: /*---------- State-specific expectancies and variances ------------*/
1.218 brouard 10304:
10305:
1.201 brouard 10306: strcpy(filerest,"T_");
10307: strcat(filerest,fileresu);
1.127 brouard 10308: if((ficrest=fopen(filerest,"w"))==NULL) {
10309: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
10310: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
10311: }
1.208 brouard 10312: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
10313: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.218 brouard 10314:
1.126 brouard 10315:
1.201 brouard 10316: strcpy(fileresstde,"STDE_");
10317: strcat(fileresstde,fileresu);
1.126 brouard 10318: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
1.227 ! brouard 10319: printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
! 10320: fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
1.126 brouard 10321: }
1.227 ! brouard 10322: printf(" Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
! 10323: fprintf(ficlog," Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 10324:
1.201 brouard 10325: strcpy(filerescve,"CVE_");
10326: strcat(filerescve,fileresu);
1.126 brouard 10327: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
1.227 ! brouard 10328: printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
! 10329: fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
1.126 brouard 10330: }
1.227 ! brouard 10331: printf(" Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
! 10332: fprintf(ficlog," Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 10333:
1.201 brouard 10334: strcpy(fileresv,"V_");
10335: strcat(fileresv,fileresu);
1.126 brouard 10336: if((ficresvij=fopen(fileresv,"w"))==NULL) {
10337: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
10338: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
10339: }
1.227 ! brouard 10340: printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
! 10341: fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 10342:
1.145 brouard 10343: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
10344: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
10345:
1.225 brouard 10346: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.227 ! brouard 10347: printf("\n#****** ");
1.208 brouard 10348: fprintf(ficrest,"\n#****** ");
1.227 ! brouard 10349: fprintf(ficlog,"\n#****** ");
! 10350: for(j=1;j<=cptcoveff;j++){
! 10351: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 10352: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 10353: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 10354: }
1.208 brouard 10355: fprintf(ficrest,"******\n");
1.227 ! brouard 10356: fprintf(ficlog,"******\n");
! 10357: printf("******\n");
1.208 brouard 10358:
10359: fprintf(ficresstdeij,"\n#****** ");
10360: fprintf(ficrescveij,"\n#****** ");
1.225 brouard 10361: for(j=1;j<=cptcoveff;j++) {
1.227 ! brouard 10362: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 10363: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 10364: }
10365: fprintf(ficresstdeij,"******\n");
10366: fprintf(ficrescveij,"******\n");
10367:
10368: fprintf(ficresvij,"\n#****** ");
1.225 brouard 10369: for(j=1;j<=cptcoveff;j++)
1.227 ! brouard 10370: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 10371: fprintf(ficresvij,"******\n");
10372:
10373: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
10374: oldm=oldms;savm=savms;
1.227 ! brouard 10375: printf(" cvevsij combination#=%d, ",k);
! 10376: fprintf(ficlog, " cvevsij combination#=%d, ",k);
1.208 brouard 10377: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
10378: printf(" end cvevsij \n ");
10379: fprintf(ficlog, " end cvevsij \n ");
10380:
10381: /*
10382: */
10383: /* goto endfree; */
10384:
10385: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
10386: pstamp(ficrest);
10387:
10388:
10389: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.227 ! brouard 10390: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
! 10391: cptcod= 0; /* To be deleted */
! 10392: printf("varevsij vpopbased=%d \n",vpopbased);
! 10393: fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
! 10394: 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 */
! 10395: 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 ");
! 10396: if(vpopbased==1)
! 10397: 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);
! 10398: else
! 10399: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
! 10400: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
! 10401: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
! 10402: fprintf(ficrest,"\n");
! 10403: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
! 10404: epj=vector(1,nlstate+1);
! 10405: printf("Computing age specific period (stable) prevalences in each health state \n");
! 10406: fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
! 10407: for(age=bage; age <=fage ;age++){
! 10408: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
! 10409: if (vpopbased==1) {
! 10410: if(mobilav ==0){
! 10411: for(i=1; i<=nlstate;i++)
! 10412: prlim[i][i]=probs[(int)age][i][k];
! 10413: }else{ /* mobilav */
! 10414: for(i=1; i<=nlstate;i++)
! 10415: prlim[i][i]=mobaverage[(int)age][i][k];
! 10416: }
! 10417: }
1.219 brouard 10418:
1.227 ! brouard 10419: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
! 10420: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
! 10421: /* printf(" age %4.0f ",age); */
! 10422: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
! 10423: for(i=1, epj[j]=0.;i <=nlstate;i++) {
! 10424: epj[j] += prlim[i][i]*eij[i][j][(int)age];
! 10425: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
! 10426: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
! 10427: }
! 10428: epj[nlstate+1] +=epj[j];
! 10429: }
! 10430: /* printf(" age %4.0f \n",age); */
1.219 brouard 10431:
1.227 ! brouard 10432: for(i=1, vepp=0.;i <=nlstate;i++)
! 10433: for(j=1;j <=nlstate;j++)
! 10434: vepp += vareij[i][j][(int)age];
! 10435: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
! 10436: for(j=1;j <=nlstate;j++){
! 10437: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
! 10438: }
! 10439: fprintf(ficrest,"\n");
! 10440: }
1.208 brouard 10441: } /* End vpopbased */
10442: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
10443: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
10444: free_vector(epj,1,nlstate+1);
10445: printf("done \n");fflush(stdout);
10446: fprintf(ficlog,"done\n");fflush(ficlog);
10447:
1.145 brouard 10448: /*}*/
1.208 brouard 10449: } /* End k */
1.227 ! brouard 10450:
! 10451: printf("done State-specific expectancies\n");fflush(stdout);
! 10452: fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
! 10453:
1.126 brouard 10454: /*------- Variance of period (stable) prevalence------*/
1.227 ! brouard 10455:
1.201 brouard 10456: strcpy(fileresvpl,"VPL_");
10457: strcat(fileresvpl,fileresu);
1.126 brouard 10458: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
10459: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
10460: exit(0);
10461: }
1.208 brouard 10462: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
10463: fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.227 ! brouard 10464:
1.145 brouard 10465: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
10466: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
1.227 ! brouard 10467:
1.225 brouard 10468: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.227 ! brouard 10469: fprintf(ficresvpl,"\n#****** ");
! 10470: printf("\n#****** ");
! 10471: fprintf(ficlog,"\n#****** ");
! 10472: for(j=1;j<=cptcoveff;j++) {
! 10473: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 10474: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 10475: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 10476: }
! 10477: fprintf(ficresvpl,"******\n");
! 10478: printf("******\n");
! 10479: fprintf(ficlog,"******\n");
! 10480:
! 10481: varpl=matrix(1,nlstate,(int) bage, (int) fage);
! 10482: oldm=oldms;savm=savms;
! 10483: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
! 10484: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 10485: /*}*/
1.126 brouard 10486: }
1.227 ! brouard 10487:
1.126 brouard 10488: fclose(ficresvpl);
1.208 brouard 10489: printf("done variance-covariance of period prevalence\n");fflush(stdout);
10490: fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
1.227 ! brouard 10491:
! 10492: free_vector(weight,1,n);
! 10493: free_imatrix(Tvard,1,NCOVMAX,1,2);
! 10494: free_imatrix(s,1,maxwav+1,1,n);
! 10495: free_matrix(anint,1,maxwav,1,n);
! 10496: free_matrix(mint,1,maxwav,1,n);
! 10497: free_ivector(cod,1,n);
! 10498: free_ivector(tab,1,NCOVMAX);
! 10499: fclose(ficresstdeij);
! 10500: fclose(ficrescveij);
! 10501: fclose(ficresvij);
! 10502: fclose(ficrest);
! 10503: fclose(ficpar);
! 10504:
! 10505:
1.126 brouard 10506: /*---------- End : free ----------------*/
1.219 brouard 10507: if (mobilav!=0 ||mobilavproj !=0)
10508: 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 10509: free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220 brouard 10510: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
10511: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126 brouard 10512: } /* mle==-3 arrives here for freeing */
1.227 ! brouard 10513: /* endfree:*/
! 10514: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
! 10515: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
! 10516: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
! 10517: free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
! 10518: free_ma3x(cotvar,1,maxwav,1,ntv,1,n);
! 10519: free_matrix(coqvar,1,maxwav,1,n);
! 10520: free_matrix(covar,0,NCOVMAX,1,n);
! 10521: free_matrix(matcov,1,npar,1,npar);
! 10522: free_matrix(hess,1,npar,1,npar);
! 10523: /*free_vector(delti,1,npar);*/
! 10524: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
! 10525: free_matrix(agev,1,maxwav,1,imx);
! 10526: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
! 10527:
! 10528: free_ivector(ncodemax,1,NCOVMAX);
! 10529: free_ivector(ncodemaxwundef,1,NCOVMAX);
! 10530: free_ivector(Dummy,-1,NCOVMAX);
! 10531: free_ivector(Fixed,-1,NCOVMAX);
! 10532: free_ivector(Typevar,-1,NCOVMAX);
! 10533: free_ivector(Tvar,1,NCOVMAX);
! 10534: free_ivector(Tposprod,1,NCOVMAX);
! 10535: free_ivector(Tprod,1,NCOVMAX);
! 10536: free_ivector(Tvaraff,1,NCOVMAX);
! 10537: free_ivector(invalidvarcomb,1,ncovcombmax);
! 10538: free_ivector(Tage,1,NCOVMAX);
! 10539: free_ivector(Tmodelind,1,NCOVMAX);
! 10540:
! 10541: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
! 10542: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 10543: fflush(fichtm);
10544: fflush(ficgp);
10545:
1.227 ! brouard 10546:
1.126 brouard 10547: if((nberr >0) || (nbwarn>0)){
1.216 brouard 10548: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
10549: 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 10550: }else{
10551: printf("End of Imach\n");
10552: fprintf(ficlog,"End of Imach\n");
10553: }
10554: printf("See log file on %s\n",filelog);
10555: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 10556: /*(void) gettimeofday(&end_time,&tzp);*/
10557: rend_time = time(NULL);
10558: end_time = *localtime(&rend_time);
10559: /* tml = *localtime(&end_time.tm_sec); */
10560: strcpy(strtend,asctime(&end_time));
1.126 brouard 10561: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
10562: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 10563: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.227 ! brouard 10564:
1.157 brouard 10565: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
10566: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
10567: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 10568: /* printf("Total time was %d uSec.\n", total_usecs);*/
10569: /* if(fileappend(fichtm,optionfilehtm)){ */
10570: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
10571: fclose(fichtm);
10572: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
10573: fclose(fichtmcov);
10574: fclose(ficgp);
10575: fclose(ficlog);
10576: /*------ End -----------*/
1.227 ! brouard 10577:
! 10578:
! 10579: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 10580: #ifdef WIN32
1.227 ! brouard 10581: if (_chdir(pathcd) != 0)
! 10582: printf("Can't move to directory %s!\n",path);
! 10583: if(_getcwd(pathcd,MAXLINE) > 0)
1.184 brouard 10584: #else
1.227 ! brouard 10585: if(chdir(pathcd) != 0)
! 10586: printf("Can't move to directory %s!\n", path);
! 10587: if (getcwd(pathcd, MAXLINE) > 0)
1.184 brouard 10588: #endif
1.126 brouard 10589: printf("Current directory %s!\n",pathcd);
10590: /*strcat(plotcmd,CHARSEPARATOR);*/
10591: sprintf(plotcmd,"gnuplot");
1.157 brouard 10592: #ifdef _WIN32
1.126 brouard 10593: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
10594: #endif
10595: if(!stat(plotcmd,&info)){
1.158 brouard 10596: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 10597: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 10598: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 10599: }else
10600: strcpy(pplotcmd,plotcmd);
1.157 brouard 10601: #ifdef __unix
1.126 brouard 10602: strcpy(plotcmd,GNUPLOTPROGRAM);
10603: if(!stat(plotcmd,&info)){
1.158 brouard 10604: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 10605: }else
10606: strcpy(pplotcmd,plotcmd);
10607: #endif
10608: }else
10609: strcpy(pplotcmd,plotcmd);
10610:
10611: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 10612: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.227 ! brouard 10613:
1.126 brouard 10614: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 10615: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 10616: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 10617: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 10618: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 10619: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 10620: }
1.158 brouard 10621: printf(" Successful, please wait...");
1.126 brouard 10622: while (z[0] != 'q') {
10623: /* chdir(path); */
1.154 brouard 10624: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 10625: scanf("%s",z);
10626: /* if (z[0] == 'c') system("./imach"); */
10627: if (z[0] == 'e') {
1.158 brouard 10628: #ifdef __APPLE__
1.152 brouard 10629: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 10630: #elif __linux
10631: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 10632: #else
1.152 brouard 10633: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 10634: #endif
10635: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
10636: system(pplotcmd);
1.126 brouard 10637: }
10638: else if (z[0] == 'g') system(plotcmd);
10639: else if (z[0] == 'q') exit(0);
10640: }
1.227 ! brouard 10641: end:
1.126 brouard 10642: while (z[0] != 'q') {
1.195 brouard 10643: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 10644: scanf("%s",z);
10645: }
10646: }
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