Annotation of imach/src/imach.c, revision 1.222
1.222 ! brouard 1: /* $Id: imach.c,v 1.221 2016/02/15 23:35:36 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.222 ! brouard 4: Revision 1.221 2016/02/15 23:35:36 brouard
! 5: Summary: minor bug
! 6:
1.220 brouard 7: Revision 1.219 2016/02/15 00:48:12 brouard
8: *** empty log message ***
9:
1.219 brouard 10: Revision 1.218 2016/02/12 11:29:23 brouard
11: Summary: 0.99 Back projections
12:
1.218 brouard 13: Revision 1.217 2015/12/23 17:18:31 brouard
14: Summary: Experimental backcast
15:
1.217 brouard 16: Revision 1.216 2015/12/18 17:32:11 brouard
17: Summary: 0.98r4 Warning and status=-2
18:
19: Version 0.98r4 is now:
20: - displaying an error when status is -1, date of interview unknown and date of death known;
21: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
22: Older changes concerning s=-2, dating from 2005 have been supersed.
23:
1.216 brouard 24: Revision 1.215 2015/12/16 08:52:24 brouard
25: Summary: 0.98r4 working
26:
1.215 brouard 27: Revision 1.214 2015/12/16 06:57:54 brouard
28: Summary: temporary not working
29:
1.214 brouard 30: Revision 1.213 2015/12/11 18:22:17 brouard
31: Summary: 0.98r4
32:
1.213 brouard 33: Revision 1.212 2015/11/21 12:47:24 brouard
34: Summary: minor typo
35:
1.212 brouard 36: Revision 1.211 2015/11/21 12:41:11 brouard
37: Summary: 0.98r3 with some graph of projected cross-sectional
38:
39: Author: Nicolas Brouard
40:
1.211 brouard 41: Revision 1.210 2015/11/18 17:41:20 brouard
42: Summary: Start working on projected prevalences
43:
1.210 brouard 44: Revision 1.209 2015/11/17 22:12:03 brouard
45: Summary: Adding ftolpl parameter
46: Author: N Brouard
47:
48: We had difficulties to get smoothed confidence intervals. It was due
49: to the period prevalence which wasn't computed accurately. The inner
50: parameter ftolpl is now an outer parameter of the .imach parameter
51: file after estepm. If ftolpl is small 1.e-4 and estepm too,
52: computation are long.
53:
1.209 brouard 54: Revision 1.208 2015/11/17 14:31:57 brouard
55: Summary: temporary
56:
1.208 brouard 57: Revision 1.207 2015/10/27 17:36:57 brouard
58: *** empty log message ***
59:
1.207 brouard 60: Revision 1.206 2015/10/24 07:14:11 brouard
61: *** empty log message ***
62:
1.206 brouard 63: Revision 1.205 2015/10/23 15:50:53 brouard
64: Summary: 0.98r3 some clarification for graphs on likelihood contributions
65:
1.205 brouard 66: Revision 1.204 2015/10/01 16:20:26 brouard
67: Summary: Some new graphs of contribution to likelihood
68:
1.204 brouard 69: Revision 1.203 2015/09/30 17:45:14 brouard
70: Summary: looking at better estimation of the hessian
71:
72: Also a better criteria for convergence to the period prevalence And
73: therefore adding the number of years needed to converge. (The
74: prevalence in any alive state shold sum to one
75:
1.203 brouard 76: Revision 1.202 2015/09/22 19:45:16 brouard
77: Summary: Adding some overall graph on contribution to likelihood. Might change
78:
1.202 brouard 79: Revision 1.201 2015/09/15 17:34:58 brouard
80: Summary: 0.98r0
81:
82: - Some new graphs like suvival functions
83: - Some bugs fixed like model=1+age+V2.
84:
1.201 brouard 85: Revision 1.200 2015/09/09 16:53:55 brouard
86: Summary: Big bug thanks to Flavia
87:
88: Even model=1+age+V2. did not work anymore
89:
1.200 brouard 90: Revision 1.199 2015/09/07 14:09:23 brouard
91: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
92:
1.199 brouard 93: Revision 1.198 2015/09/03 07:14:39 brouard
94: Summary: 0.98q5 Flavia
95:
1.198 brouard 96: Revision 1.197 2015/09/01 18:24:39 brouard
97: *** empty log message ***
98:
1.197 brouard 99: Revision 1.196 2015/08/18 23:17:52 brouard
100: Summary: 0.98q5
101:
1.196 brouard 102: Revision 1.195 2015/08/18 16:28:39 brouard
103: Summary: Adding a hack for testing purpose
104:
105: After reading the title, ftol and model lines, if the comment line has
106: a q, starting with #q, the answer at the end of the run is quit. It
107: permits to run test files in batch with ctest. The former workaround was
108: $ echo q | imach foo.imach
109:
1.195 brouard 110: Revision 1.194 2015/08/18 13:32:00 brouard
111: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
112:
1.194 brouard 113: Revision 1.193 2015/08/04 07:17:42 brouard
114: Summary: 0.98q4
115:
1.193 brouard 116: Revision 1.192 2015/07/16 16:49:02 brouard
117: Summary: Fixing some outputs
118:
1.192 brouard 119: Revision 1.191 2015/07/14 10:00:33 brouard
120: Summary: Some fixes
121:
1.191 brouard 122: Revision 1.190 2015/05/05 08:51:13 brouard
123: Summary: Adding digits in output parameters (7 digits instead of 6)
124:
125: Fix 1+age+.
126:
1.190 brouard 127: Revision 1.189 2015/04/30 14:45:16 brouard
128: Summary: 0.98q2
129:
1.189 brouard 130: Revision 1.188 2015/04/30 08:27:53 brouard
131: *** empty log message ***
132:
1.188 brouard 133: Revision 1.187 2015/04/29 09:11:15 brouard
134: *** empty log message ***
135:
1.187 brouard 136: Revision 1.186 2015/04/23 12:01:52 brouard
137: Summary: V1*age is working now, version 0.98q1
138:
139: Some codes had been disabled in order to simplify and Vn*age was
140: working in the optimization phase, ie, giving correct MLE parameters,
141: but, as usual, outputs were not correct and program core dumped.
142:
1.186 brouard 143: Revision 1.185 2015/03/11 13:26:42 brouard
144: Summary: Inclusion of compile and links command line for Intel Compiler
145:
1.185 brouard 146: Revision 1.184 2015/03/11 11:52:39 brouard
147: Summary: Back from Windows 8. Intel Compiler
148:
1.184 brouard 149: Revision 1.183 2015/03/10 20:34:32 brouard
150: Summary: 0.98q0, trying with directest, mnbrak fixed
151:
152: We use directest instead of original Powell test; probably no
153: incidence on the results, but better justifications;
154: We fixed Numerical Recipes mnbrak routine which was wrong and gave
155: wrong results.
156:
1.183 brouard 157: Revision 1.182 2015/02/12 08:19:57 brouard
158: Summary: Trying to keep directest which seems simpler and more general
159: Author: Nicolas Brouard
160:
1.182 brouard 161: Revision 1.181 2015/02/11 23:22:24 brouard
162: Summary: Comments on Powell added
163:
164: Author:
165:
1.181 brouard 166: Revision 1.180 2015/02/11 17:33:45 brouard
167: Summary: Finishing move from main to function (hpijx and prevalence_limit)
168:
1.180 brouard 169: Revision 1.179 2015/01/04 09:57:06 brouard
170: Summary: back to OS/X
171:
1.179 brouard 172: Revision 1.178 2015/01/04 09:35:48 brouard
173: *** empty log message ***
174:
1.178 brouard 175: Revision 1.177 2015/01/03 18:40:56 brouard
176: Summary: Still testing ilc32 on OSX
177:
1.177 brouard 178: Revision 1.176 2015/01/03 16:45:04 brouard
179: *** empty log message ***
180:
1.176 brouard 181: Revision 1.175 2015/01/03 16:33:42 brouard
182: *** empty log message ***
183:
1.175 brouard 184: Revision 1.174 2015/01/03 16:15:49 brouard
185: Summary: Still in cross-compilation
186:
1.174 brouard 187: Revision 1.173 2015/01/03 12:06:26 brouard
188: Summary: trying to detect cross-compilation
189:
1.173 brouard 190: Revision 1.172 2014/12/27 12:07:47 brouard
191: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
192:
1.172 brouard 193: Revision 1.171 2014/12/23 13:26:59 brouard
194: Summary: Back from Visual C
195:
196: Still problem with utsname.h on Windows
197:
1.171 brouard 198: Revision 1.170 2014/12/23 11:17:12 brouard
199: Summary: Cleaning some \%% back to %%
200:
201: The escape was mandatory for a specific compiler (which one?), but too many warnings.
202:
1.170 brouard 203: Revision 1.169 2014/12/22 23:08:31 brouard
204: Summary: 0.98p
205:
206: Outputs some informations on compiler used, OS etc. Testing on different platforms.
207:
1.169 brouard 208: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 209: Summary: update
1.169 brouard 210:
1.168 brouard 211: Revision 1.167 2014/12/22 13:50:56 brouard
212: Summary: Testing uname and compiler version and if compiled 32 or 64
213:
214: Testing on Linux 64
215:
1.167 brouard 216: Revision 1.166 2014/12/22 11:40:47 brouard
217: *** empty log message ***
218:
1.166 brouard 219: Revision 1.165 2014/12/16 11:20:36 brouard
220: Summary: After compiling on Visual C
221:
222: * imach.c (Module): Merging 1.61 to 1.162
223:
1.165 brouard 224: Revision 1.164 2014/12/16 10:52:11 brouard
225: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
226:
227: * imach.c (Module): Merging 1.61 to 1.162
228:
1.164 brouard 229: Revision 1.163 2014/12/16 10:30:11 brouard
230: * imach.c (Module): Merging 1.61 to 1.162
231:
1.163 brouard 232: Revision 1.162 2014/09/25 11:43:39 brouard
233: Summary: temporary backup 0.99!
234:
1.162 brouard 235: Revision 1.1 2014/09/16 11:06:58 brouard
236: Summary: With some code (wrong) for nlopt
237:
238: Author:
239:
240: Revision 1.161 2014/09/15 20:41:41 brouard
241: Summary: Problem with macro SQR on Intel compiler
242:
1.161 brouard 243: Revision 1.160 2014/09/02 09:24:05 brouard
244: *** empty log message ***
245:
1.160 brouard 246: Revision 1.159 2014/09/01 10:34:10 brouard
247: Summary: WIN32
248: Author: Brouard
249:
1.159 brouard 250: Revision 1.158 2014/08/27 17:11:51 brouard
251: *** empty log message ***
252:
1.158 brouard 253: Revision 1.157 2014/08/27 16:26:55 brouard
254: Summary: Preparing windows Visual studio version
255: Author: Brouard
256:
257: In order to compile on Visual studio, time.h is now correct and time_t
258: and tm struct should be used. difftime should be used but sometimes I
259: just make the differences in raw time format (time(&now).
260: Trying to suppress #ifdef LINUX
261: Add xdg-open for __linux in order to open default browser.
262:
1.157 brouard 263: Revision 1.156 2014/08/25 20:10:10 brouard
264: *** empty log message ***
265:
1.156 brouard 266: Revision 1.155 2014/08/25 18:32:34 brouard
267: Summary: New compile, minor changes
268: Author: Brouard
269:
1.155 brouard 270: Revision 1.154 2014/06/20 17:32:08 brouard
271: Summary: Outputs now all graphs of convergence to period prevalence
272:
1.154 brouard 273: Revision 1.153 2014/06/20 16:45:46 brouard
274: Summary: If 3 live state, convergence to period prevalence on same graph
275: Author: Brouard
276:
1.153 brouard 277: Revision 1.152 2014/06/18 17:54:09 brouard
278: Summary: open browser, use gnuplot on same dir than imach if not found in the path
279:
1.152 brouard 280: Revision 1.151 2014/06/18 16:43:30 brouard
281: *** empty log message ***
282:
1.151 brouard 283: Revision 1.150 2014/06/18 16:42:35 brouard
284: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
285: Author: brouard
286:
1.150 brouard 287: Revision 1.149 2014/06/18 15:51:14 brouard
288: Summary: Some fixes in parameter files errors
289: Author: Nicolas Brouard
290:
1.149 brouard 291: Revision 1.148 2014/06/17 17:38:48 brouard
292: Summary: Nothing new
293: Author: Brouard
294:
295: Just a new packaging for OS/X version 0.98nS
296:
1.148 brouard 297: Revision 1.147 2014/06/16 10:33:11 brouard
298: *** empty log message ***
299:
1.147 brouard 300: Revision 1.146 2014/06/16 10:20:28 brouard
301: Summary: Merge
302: Author: Brouard
303:
304: Merge, before building revised version.
305:
1.146 brouard 306: Revision 1.145 2014/06/10 21:23:15 brouard
307: Summary: Debugging with valgrind
308: Author: Nicolas Brouard
309:
310: Lot of changes in order to output the results with some covariates
311: After the Edimburgh REVES conference 2014, it seems mandatory to
312: improve the code.
313: No more memory valgrind error but a lot has to be done in order to
314: continue the work of splitting the code into subroutines.
315: Also, decodemodel has been improved. Tricode is still not
316: optimal. nbcode should be improved. Documentation has been added in
317: the source code.
318:
1.144 brouard 319: Revision 1.143 2014/01/26 09:45:38 brouard
320: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
321:
322: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
323: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
324:
1.143 brouard 325: Revision 1.142 2014/01/26 03:57:36 brouard
326: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
327:
328: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
329:
1.142 brouard 330: Revision 1.141 2014/01/26 02:42:01 brouard
331: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
332:
1.141 brouard 333: Revision 1.140 2011/09/02 10:37:54 brouard
334: Summary: times.h is ok with mingw32 now.
335:
1.140 brouard 336: Revision 1.139 2010/06/14 07:50:17 brouard
337: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
338: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
339:
1.139 brouard 340: Revision 1.138 2010/04/30 18:19:40 brouard
341: *** empty log message ***
342:
1.138 brouard 343: Revision 1.137 2010/04/29 18:11:38 brouard
344: (Module): Checking covariates for more complex models
345: than V1+V2. A lot of change to be done. Unstable.
346:
1.137 brouard 347: Revision 1.136 2010/04/26 20:30:53 brouard
348: (Module): merging some libgsl code. Fixing computation
349: of likelione (using inter/intrapolation if mle = 0) in order to
350: get same likelihood as if mle=1.
351: Some cleaning of code and comments added.
352:
1.136 brouard 353: Revision 1.135 2009/10/29 15:33:14 brouard
354: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
355:
1.135 brouard 356: Revision 1.134 2009/10/29 13:18:53 brouard
357: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
358:
1.134 brouard 359: Revision 1.133 2009/07/06 10:21:25 brouard
360: just nforces
361:
1.133 brouard 362: Revision 1.132 2009/07/06 08:22:05 brouard
363: Many tings
364:
1.132 brouard 365: Revision 1.131 2009/06/20 16:22:47 brouard
366: Some dimensions resccaled
367:
1.131 brouard 368: Revision 1.130 2009/05/26 06:44:34 brouard
369: (Module): Max Covariate is now set to 20 instead of 8. A
370: lot of cleaning with variables initialized to 0. Trying to make
371: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
372:
1.130 brouard 373: Revision 1.129 2007/08/31 13:49:27 lievre
374: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
375:
1.129 lievre 376: Revision 1.128 2006/06/30 13:02:05 brouard
377: (Module): Clarifications on computing e.j
378:
1.128 brouard 379: Revision 1.127 2006/04/28 18:11:50 brouard
380: (Module): Yes the sum of survivors was wrong since
381: imach-114 because nhstepm was no more computed in the age
382: loop. Now we define nhstepma in the age loop.
383: (Module): In order to speed up (in case of numerous covariates) we
384: compute health expectancies (without variances) in a first step
385: and then all the health expectancies with variances or standard
386: deviation (needs data from the Hessian matrices) which slows the
387: computation.
388: In the future we should be able to stop the program is only health
389: expectancies and graph are needed without standard deviations.
390:
1.127 brouard 391: Revision 1.126 2006/04/28 17:23:28 brouard
392: (Module): Yes the sum of survivors was wrong since
393: imach-114 because nhstepm was no more computed in the age
394: loop. Now we define nhstepma in the age loop.
395: Version 0.98h
396:
1.126 brouard 397: Revision 1.125 2006/04/04 15:20:31 lievre
398: Errors in calculation of health expectancies. Age was not initialized.
399: Forecasting file added.
400:
401: Revision 1.124 2006/03/22 17:13:53 lievre
402: Parameters are printed with %lf instead of %f (more numbers after the comma).
403: The log-likelihood is printed in the log file
404:
405: Revision 1.123 2006/03/20 10:52:43 brouard
406: * imach.c (Module): <title> changed, corresponds to .htm file
407: name. <head> headers where missing.
408:
409: * imach.c (Module): Weights can have a decimal point as for
410: English (a comma might work with a correct LC_NUMERIC environment,
411: otherwise the weight is truncated).
412: Modification of warning when the covariates values are not 0 or
413: 1.
414: Version 0.98g
415:
416: Revision 1.122 2006/03/20 09:45:41 brouard
417: (Module): Weights can have a decimal point as for
418: English (a comma might work with a correct LC_NUMERIC environment,
419: otherwise the weight is truncated).
420: Modification of warning when the covariates values are not 0 or
421: 1.
422: Version 0.98g
423:
424: Revision 1.121 2006/03/16 17:45:01 lievre
425: * imach.c (Module): Comments concerning covariates added
426:
427: * imach.c (Module): refinements in the computation of lli if
428: status=-2 in order to have more reliable computation if stepm is
429: not 1 month. Version 0.98f
430:
431: Revision 1.120 2006/03/16 15:10:38 lievre
432: (Module): refinements in the computation of lli if
433: status=-2 in order to have more reliable computation if stepm is
434: not 1 month. Version 0.98f
435:
436: Revision 1.119 2006/03/15 17:42:26 brouard
437: (Module): Bug if status = -2, the loglikelihood was
438: computed as likelihood omitting the logarithm. Version O.98e
439:
440: Revision 1.118 2006/03/14 18:20:07 brouard
441: (Module): varevsij Comments added explaining the second
442: table of variances if popbased=1 .
443: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
444: (Module): Function pstamp added
445: (Module): Version 0.98d
446:
447: Revision 1.117 2006/03/14 17:16:22 brouard
448: (Module): varevsij Comments added explaining the second
449: table of variances if popbased=1 .
450: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
451: (Module): Function pstamp added
452: (Module): Version 0.98d
453:
454: Revision 1.116 2006/03/06 10:29:27 brouard
455: (Module): Variance-covariance wrong links and
456: varian-covariance of ej. is needed (Saito).
457:
458: Revision 1.115 2006/02/27 12:17:45 brouard
459: (Module): One freematrix added in mlikeli! 0.98c
460:
461: Revision 1.114 2006/02/26 12:57:58 brouard
462: (Module): Some improvements in processing parameter
463: filename with strsep.
464:
465: Revision 1.113 2006/02/24 14:20:24 brouard
466: (Module): Memory leaks checks with valgrind and:
467: datafile was not closed, some imatrix were not freed and on matrix
468: allocation too.
469:
470: Revision 1.112 2006/01/30 09:55:26 brouard
471: (Module): Back to gnuplot.exe instead of wgnuplot.exe
472:
473: Revision 1.111 2006/01/25 20:38:18 brouard
474: (Module): Lots of cleaning and bugs added (Gompertz)
475: (Module): Comments can be added in data file. Missing date values
476: can be a simple dot '.'.
477:
478: Revision 1.110 2006/01/25 00:51:50 brouard
479: (Module): Lots of cleaning and bugs added (Gompertz)
480:
481: Revision 1.109 2006/01/24 19:37:15 brouard
482: (Module): Comments (lines starting with a #) are allowed in data.
483:
484: Revision 1.108 2006/01/19 18:05:42 lievre
485: Gnuplot problem appeared...
486: To be fixed
487:
488: Revision 1.107 2006/01/19 16:20:37 brouard
489: Test existence of gnuplot in imach path
490:
491: Revision 1.106 2006/01/19 13:24:36 brouard
492: Some cleaning and links added in html output
493:
494: Revision 1.105 2006/01/05 20:23:19 lievre
495: *** empty log message ***
496:
497: Revision 1.104 2005/09/30 16:11:43 lievre
498: (Module): sump fixed, loop imx fixed, and simplifications.
499: (Module): If the status is missing at the last wave but we know
500: that the person is alive, then we can code his/her status as -2
501: (instead of missing=-1 in earlier versions) and his/her
502: contributions to the likelihood is 1 - Prob of dying from last
503: health status (= 1-p13= p11+p12 in the easiest case of somebody in
504: the healthy state at last known wave). Version is 0.98
505:
506: Revision 1.103 2005/09/30 15:54:49 lievre
507: (Module): sump fixed, loop imx fixed, and simplifications.
508:
509: Revision 1.102 2004/09/15 17:31:30 brouard
510: Add the possibility to read data file including tab characters.
511:
512: Revision 1.101 2004/09/15 10:38:38 brouard
513: Fix on curr_time
514:
515: Revision 1.100 2004/07/12 18:29:06 brouard
516: Add version for Mac OS X. Just define UNIX in Makefile
517:
518: Revision 1.99 2004/06/05 08:57:40 brouard
519: *** empty log message ***
520:
521: Revision 1.98 2004/05/16 15:05:56 brouard
522: New version 0.97 . First attempt to estimate force of mortality
523: directly from the data i.e. without the need of knowing the health
524: state at each age, but using a Gompertz model: log u =a + b*age .
525: This is the basic analysis of mortality and should be done before any
526: other analysis, in order to test if the mortality estimated from the
527: cross-longitudinal survey is different from the mortality estimated
528: from other sources like vital statistic data.
529:
530: The same imach parameter file can be used but the option for mle should be -3.
531:
1.133 brouard 532: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 533: former routines in order to include the new code within the former code.
534:
535: The output is very simple: only an estimate of the intercept and of
536: the slope with 95% confident intervals.
537:
538: Current limitations:
539: A) Even if you enter covariates, i.e. with the
540: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
541: B) There is no computation of Life Expectancy nor Life Table.
542:
543: Revision 1.97 2004/02/20 13:25:42 lievre
544: Version 0.96d. Population forecasting command line is (temporarily)
545: suppressed.
546:
547: Revision 1.96 2003/07/15 15:38:55 brouard
548: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
549: rewritten within the same printf. Workaround: many printfs.
550:
551: Revision 1.95 2003/07/08 07:54:34 brouard
552: * imach.c (Repository):
553: (Repository): Using imachwizard code to output a more meaningful covariance
554: matrix (cov(a12,c31) instead of numbers.
555:
556: Revision 1.94 2003/06/27 13:00:02 brouard
557: Just cleaning
558:
559: Revision 1.93 2003/06/25 16:33:55 brouard
560: (Module): On windows (cygwin) function asctime_r doesn't
561: exist so I changed back to asctime which exists.
562: (Module): Version 0.96b
563:
564: Revision 1.92 2003/06/25 16:30:45 brouard
565: (Module): On windows (cygwin) function asctime_r doesn't
566: exist so I changed back to asctime which exists.
567:
568: Revision 1.91 2003/06/25 15:30:29 brouard
569: * imach.c (Repository): Duplicated warning errors corrected.
570: (Repository): Elapsed time after each iteration is now output. It
571: helps to forecast when convergence will be reached. Elapsed time
572: is stamped in powell. We created a new html file for the graphs
573: concerning matrix of covariance. It has extension -cov.htm.
574:
575: Revision 1.90 2003/06/24 12:34:15 brouard
576: (Module): Some bugs corrected for windows. Also, when
577: mle=-1 a template is output in file "or"mypar.txt with the design
578: of the covariance matrix to be input.
579:
580: Revision 1.89 2003/06/24 12:30:52 brouard
581: (Module): Some bugs corrected for windows. Also, when
582: mle=-1 a template is output in file "or"mypar.txt with the design
583: of the covariance matrix to be input.
584:
585: Revision 1.88 2003/06/23 17:54:56 brouard
586: * 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.
587:
588: Revision 1.87 2003/06/18 12:26:01 brouard
589: Version 0.96
590:
591: Revision 1.86 2003/06/17 20:04:08 brouard
592: (Module): Change position of html and gnuplot routines and added
593: routine fileappend.
594:
595: Revision 1.85 2003/06/17 13:12:43 brouard
596: * imach.c (Repository): Check when date of death was earlier that
597: current date of interview. It may happen when the death was just
598: prior to the death. In this case, dh was negative and likelihood
599: was wrong (infinity). We still send an "Error" but patch by
600: assuming that the date of death was just one stepm after the
601: interview.
602: (Repository): Because some people have very long ID (first column)
603: we changed int to long in num[] and we added a new lvector for
604: memory allocation. But we also truncated to 8 characters (left
605: truncation)
606: (Repository): No more line truncation errors.
607:
608: Revision 1.84 2003/06/13 21:44:43 brouard
609: * imach.c (Repository): Replace "freqsummary" at a correct
610: place. It differs from routine "prevalence" which may be called
611: many times. Probs is memory consuming and must be used with
612: parcimony.
613: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
614:
615: Revision 1.83 2003/06/10 13:39:11 lievre
616: *** empty log message ***
617:
618: Revision 1.82 2003/06/05 15:57:20 brouard
619: Add log in imach.c and fullversion number is now printed.
620:
621: */
622: /*
623: Interpolated Markov Chain
624:
625: Short summary of the programme:
626:
627: This program computes Healthy Life Expectancies from
628: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
629: first survey ("cross") where individuals from different ages are
630: interviewed on their health status or degree of disability (in the
631: case of a health survey which is our main interest) -2- at least a
632: second wave of interviews ("longitudinal") which measure each change
633: (if any) in individual health status. Health expectancies are
634: computed from the time spent in each health state according to a
635: model. More health states you consider, more time is necessary to reach the
636: Maximum Likelihood of the parameters involved in the model. The
637: simplest model is the multinomial logistic model where pij is the
638: probability to be observed in state j at the second wave
639: conditional to be observed in state i at the first wave. Therefore
640: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
641: 'age' is age and 'sex' is a covariate. If you want to have a more
642: complex model than "constant and age", you should modify the program
643: where the markup *Covariates have to be included here again* invites
644: you to do it. More covariates you add, slower the
645: convergence.
646:
647: The advantage of this computer programme, compared to a simple
648: multinomial logistic model, is clear when the delay between waves is not
649: identical for each individual. Also, if a individual missed an
650: intermediate interview, the information is lost, but taken into
651: account using an interpolation or extrapolation.
652:
653: hPijx is the probability to be observed in state i at age x+h
654: conditional to the observed state i at age x. The delay 'h' can be
655: split into an exact number (nh*stepm) of unobserved intermediate
656: states. This elementary transition (by month, quarter,
657: semester or year) is modelled as a multinomial logistic. The hPx
658: matrix is simply the matrix product of nh*stepm elementary matrices
659: and the contribution of each individual to the likelihood is simply
660: hPijx.
661:
662: Also this programme outputs the covariance matrix of the parameters but also
1.218 brouard 663: of the life expectancies. It also computes the period (stable) prevalence.
664:
665: Back prevalence and projections:
666: - 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)
667: Computes the back prevalence limit for any combination of covariate values k
668: at any age between ageminpar and agemaxpar and returns it in **bprlim. In the loops,
669: - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm, **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
670: - hBijx Back Probability to be in state i at age x-h being in j at x
671: Computes for any combination of covariates k and any age between bage and fage
672: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
673: oldm=oldms;savm=savms;
674: - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
675: Computes the transition matrix starting at age 'age' over
676: 'nhstepm*hstepm*stepm' months (i.e. until
677: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
678: nhstepm*hstepm matrices. Returns p3mat[i][j][h] after calling
679: p3mat[i][j][h]=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\
680: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
681:
1.133 brouard 682: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
683: Institut national d'études démographiques, Paris.
1.126 brouard 684: This software have been partly granted by Euro-REVES, a concerted action
685: from the European Union.
686: It is copyrighted identically to a GNU software product, ie programme and
687: software can be distributed freely for non commercial use. Latest version
688: can be accessed at http://euroreves.ined.fr/imach .
689:
690: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
691: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
692:
693: **********************************************************************/
694: /*
695: main
696: read parameterfile
697: read datafile
698: concatwav
699: freqsummary
700: if (mle >= 1)
701: mlikeli
702: print results files
703: if mle==1
704: computes hessian
705: read end of parameter file: agemin, agemax, bage, fage, estepm
706: begin-prev-date,...
707: open gnuplot file
708: open html file
1.145 brouard 709: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
710: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
711: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
712: freexexit2 possible for memory heap.
713:
714: h Pij x | pij_nom ficrestpij
715: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
716: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
717: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
718:
719: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
720: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
721: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
722: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
723: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
724:
1.126 brouard 725: forecasting if prevfcast==1 prevforecast call prevalence()
726: health expectancies
727: Variance-covariance of DFLE
728: prevalence()
729: movingaverage()
730: varevsij()
731: if popbased==1 varevsij(,popbased)
732: total life expectancies
733: Variance of period (stable) prevalence
734: end
735: */
736:
1.187 brouard 737: /* #define DEBUG */
738: /* #define DEBUGBRENT */
1.203 brouard 739: /* #define DEBUGLINMIN */
740: /* #define DEBUGHESS */
741: #define DEBUGHESSIJ
1.220 brouard 742: #define LINMINORIGINAL /* Don't use loop on scale in linmin (accepting nan)*/
1.165 brouard 743: #define POWELL /* Instead of NLOPT */
1.192 brouard 744: #define POWELLF1F3 /* Skip test */
1.186 brouard 745: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
746: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 747:
748: #include <math.h>
749: #include <stdio.h>
750: #include <stdlib.h>
751: #include <string.h>
1.159 brouard 752:
753: #ifdef _WIN32
754: #include <io.h>
1.172 brouard 755: #include <windows.h>
756: #include <tchar.h>
1.159 brouard 757: #else
1.126 brouard 758: #include <unistd.h>
1.159 brouard 759: #endif
1.126 brouard 760:
761: #include <limits.h>
762: #include <sys/types.h>
1.171 brouard 763:
764: #if defined(__GNUC__)
765: #include <sys/utsname.h> /* Doesn't work on Windows */
766: #endif
767:
1.126 brouard 768: #include <sys/stat.h>
769: #include <errno.h>
1.159 brouard 770: /* extern int errno; */
1.126 brouard 771:
1.157 brouard 772: /* #ifdef LINUX */
773: /* #include <time.h> */
774: /* #include "timeval.h" */
775: /* #else */
776: /* #include <sys/time.h> */
777: /* #endif */
778:
1.126 brouard 779: #include <time.h>
780:
1.136 brouard 781: #ifdef GSL
782: #include <gsl/gsl_errno.h>
783: #include <gsl/gsl_multimin.h>
784: #endif
785:
1.167 brouard 786:
1.162 brouard 787: #ifdef NLOPT
788: #include <nlopt.h>
789: typedef struct {
790: double (* function)(double [] );
791: } myfunc_data ;
792: #endif
793:
1.126 brouard 794: /* #include <libintl.h> */
795: /* #define _(String) gettext (String) */
796:
1.141 brouard 797: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 798:
799: #define GNUPLOTPROGRAM "gnuplot"
800: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
801: #define FILENAMELENGTH 132
802:
803: #define GLOCK_ERROR_NOPATH -1 /* empty path */
804: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
805:
1.144 brouard 806: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
807: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 808:
809: #define NINTERVMAX 8
1.144 brouard 810: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
811: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
812: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 813: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 814: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
815: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.126 brouard 816: #define MAXN 20000
1.144 brouard 817: #define YEARM 12. /**< Number of months per year */
1.218 brouard 818: /* #define AGESUP 130 */
819: #define AGESUP 150
820: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126 brouard 821: #define AGEBASE 40
1.194 brouard 822: #define AGEOVERFLOW 1.e20
1.164 brouard 823: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 824: #ifdef _WIN32
825: #define DIRSEPARATOR '\\'
826: #define CHARSEPARATOR "\\"
827: #define ODIRSEPARATOR '/'
828: #else
1.126 brouard 829: #define DIRSEPARATOR '/'
830: #define CHARSEPARATOR "/"
831: #define ODIRSEPARATOR '\\'
832: #endif
833:
1.222 ! brouard 834: /* $Id: imach.c,v 1.221 2016/02/15 23:35:36 brouard Exp $ */
1.126 brouard 835: /* $State: Exp $ */
1.196 brouard 836: #include "version.h"
837: char version[]=__IMACH_VERSION__;
1.204 brouard 838: char copyright[]="October 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
1.222 ! brouard 839: char fullversion[]="$Revision: 1.221 $ $Date: 2016/02/15 23:35:36 $";
1.126 brouard 840: char strstart[80];
841: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 842: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 843: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 844: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
845: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
846: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
847: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
848: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
849: int cptcovprodnoage=0; /**< Number of covariate products without age */
850: int cptcoveff=0; /* Total number of covariates to vary for printing results */
851: int cptcov=0; /* Working variable */
1.218 brouard 852: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.126 brouard 853: int npar=NPARMAX;
854: int nlstate=2; /* Number of live states */
855: int ndeath=1; /* Number of dead states */
1.130 brouard 856: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 857: int popbased=0;
858:
859: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 860: int maxwav=0; /* Maxim number of waves */
861: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
862: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
863: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 864: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 865: int mle=1, weightopt=0;
1.126 brouard 866: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
867: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
868: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
869: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 870: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 871: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 872: double **matprod2(); /* test */
1.126 brouard 873: double **oldm, **newm, **savm; /* Working pointers to matrices */
874: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218 brouard 875: double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
876:
1.136 brouard 877: /*FILE *fic ; */ /* Used in readdata only */
1.217 brouard 878: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 879: FILE *ficlog, *ficrespow;
1.130 brouard 880: int globpr=0; /* Global variable for printing or not */
1.126 brouard 881: double fretone; /* Only one call to likelihood */
1.130 brouard 882: long ipmx=0; /* Number of contributions */
1.126 brouard 883: double sw; /* Sum of weights */
884: char filerespow[FILENAMELENGTH];
885: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
886: FILE *ficresilk;
887: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
888: FILE *ficresprobmorprev;
889: FILE *fichtm, *fichtmcov; /* Html File */
890: FILE *ficreseij;
891: char filerese[FILENAMELENGTH];
892: FILE *ficresstdeij;
893: char fileresstde[FILENAMELENGTH];
894: FILE *ficrescveij;
895: char filerescve[FILENAMELENGTH];
896: FILE *ficresvij;
897: char fileresv[FILENAMELENGTH];
898: FILE *ficresvpl;
899: char fileresvpl[FILENAMELENGTH];
900: char title[MAXLINE];
1.217 brouard 901: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 902: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
903: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
904: char command[FILENAMELENGTH];
905: int outcmd=0;
906:
1.217 brouard 907: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 908: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 909: char filelog[FILENAMELENGTH]; /* Log file */
910: char filerest[FILENAMELENGTH];
911: char fileregp[FILENAMELENGTH];
912: char popfile[FILENAMELENGTH];
913:
914: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
915:
1.157 brouard 916: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
917: /* struct timezone tzp; */
918: /* extern int gettimeofday(); */
919: struct tm tml, *gmtime(), *localtime();
920:
921: extern time_t time();
922:
923: struct tm start_time, end_time, curr_time, last_time, forecast_time;
924: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
925: struct tm tm;
926:
1.126 brouard 927: char strcurr[80], strfor[80];
928:
929: char *endptr;
930: long lval;
931: double dval;
932:
933: #define NR_END 1
934: #define FREE_ARG char*
935: #define FTOL 1.0e-10
936:
937: #define NRANSI
938: #define ITMAX 200
939:
940: #define TOL 2.0e-4
941:
942: #define CGOLD 0.3819660
943: #define ZEPS 1.0e-10
944: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
945:
946: #define GOLD 1.618034
947: #define GLIMIT 100.0
948: #define TINY 1.0e-20
949:
950: static double maxarg1,maxarg2;
951: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
952: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
953:
954: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
955: #define rint(a) floor(a+0.5)
1.166 brouard 956: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 957: #define mytinydouble 1.0e-16
1.166 brouard 958: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
959: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
960: /* static double dsqrarg; */
961: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 962: static double sqrarg;
963: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
964: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
965: int agegomp= AGEGOMP;
966:
967: int imx;
968: int stepm=1;
969: /* Stepm, step in month: minimum step interpolation*/
970:
971: int estepm;
972: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
973:
974: int m,nb;
975: long *num;
1.197 brouard 976: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 977: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
978: covariate for which somebody answered excluding
979: undefined. Usually 2: 0 and 1. */
980: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
981: covariate for which somebody answered including
982: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 983: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218 brouard 984: double **pmmij, ***probs; /* Global pointer */
1.219 brouard 985: double ***mobaverage, ***mobaverages; /* New global variable */
1.126 brouard 986: double *ageexmed,*agecens;
987: double dateintmean=0;
988:
989: double *weight;
990: int **s; /* Status */
1.141 brouard 991: double *agedc;
1.145 brouard 992: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 993: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 994: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 995: double idx;
996: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.197 brouard 997: int *Tage;
1.145 brouard 998: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 999: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.220 brouard 1000: int **Tvard, *Tprod, cptcovprod, *Tvaraff, *invalidvarcomb;
1.126 brouard 1001: double *lsurv, *lpop, *tpop;
1002:
1.143 brouard 1003: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
1004: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 1005:
1006: /**************** split *************************/
1007: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1008: {
1009: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1010: the name of the file (name), its extension only (ext) and its first part of the name (finame)
1011: */
1012: char *ss; /* pointer */
1.186 brouard 1013: int l1=0, l2=0; /* length counters */
1.126 brouard 1014:
1015: l1 = strlen(path ); /* length of path */
1016: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1017: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1018: if ( ss == NULL ) { /* no directory, so determine current directory */
1019: strcpy( name, path ); /* we got the fullname name because no directory */
1020: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
1021: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1022: /* get current working directory */
1023: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 1024: #ifdef WIN32
1025: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
1026: #else
1027: if (getcwd(dirc, FILENAME_MAX) == NULL) {
1028: #endif
1.126 brouard 1029: return( GLOCK_ERROR_GETCWD );
1030: }
1031: /* got dirc from getcwd*/
1032: printf(" DIRC = %s \n",dirc);
1.205 brouard 1033: } else { /* strip directory from path */
1.126 brouard 1034: ss++; /* after this, the filename */
1035: l2 = strlen( ss ); /* length of filename */
1036: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1037: strcpy( name, ss ); /* save file name */
1038: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1039: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1040: printf(" DIRC2 = %s \n",dirc);
1041: }
1042: /* We add a separator at the end of dirc if not exists */
1043: l1 = strlen( dirc ); /* length of directory */
1044: if( dirc[l1-1] != DIRSEPARATOR ){
1045: dirc[l1] = DIRSEPARATOR;
1046: dirc[l1+1] = 0;
1047: printf(" DIRC3 = %s \n",dirc);
1048: }
1049: ss = strrchr( name, '.' ); /* find last / */
1050: if (ss >0){
1051: ss++;
1052: strcpy(ext,ss); /* save extension */
1053: l1= strlen( name);
1054: l2= strlen(ss)+1;
1055: strncpy( finame, name, l1-l2);
1056: finame[l1-l2]= 0;
1057: }
1058:
1059: return( 0 ); /* we're done */
1060: }
1061:
1062:
1063: /******************************************/
1064:
1065: void replace_back_to_slash(char *s, char*t)
1066: {
1067: int i;
1068: int lg=0;
1069: i=0;
1070: lg=strlen(t);
1071: for(i=0; i<= lg; i++) {
1072: (s[i] = t[i]);
1073: if (t[i]== '\\') s[i]='/';
1074: }
1075: }
1076:
1.132 brouard 1077: char *trimbb(char *out, char *in)
1.137 brouard 1078: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1079: char *s;
1080: s=out;
1081: while (*in != '\0'){
1.137 brouard 1082: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1083: in++;
1084: }
1085: *out++ = *in++;
1086: }
1087: *out='\0';
1088: return s;
1089: }
1090:
1.187 brouard 1091: /* char *substrchaine(char *out, char *in, char *chain) */
1092: /* { */
1093: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1094: /* char *s, *t; */
1095: /* t=in;s=out; */
1096: /* while ((*in != *chain) && (*in != '\0')){ */
1097: /* *out++ = *in++; */
1098: /* } */
1099:
1100: /* /\* *in matches *chain *\/ */
1101: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1102: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1103: /* } */
1104: /* in--; chain--; */
1105: /* while ( (*in != '\0')){ */
1106: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1107: /* *out++ = *in++; */
1108: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1109: /* } */
1110: /* *out='\0'; */
1111: /* out=s; */
1112: /* return out; */
1113: /* } */
1114: char *substrchaine(char *out, char *in, char *chain)
1115: {
1116: /* Substract chain 'chain' from 'in', return and output 'out' */
1117: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1118:
1119: char *strloc;
1120:
1121: strcpy (out, in);
1122: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1123: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1124: if(strloc != NULL){
1125: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1126: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1127: /* strcpy (strloc, strloc +strlen(chain));*/
1128: }
1129: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1130: return out;
1131: }
1132:
1133:
1.145 brouard 1134: char *cutl(char *blocc, char *alocc, char *in, char occ)
1135: {
1.187 brouard 1136: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1137: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1138: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1139: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1140: */
1.160 brouard 1141: char *s, *t;
1.145 brouard 1142: t=in;s=in;
1143: while ((*in != occ) && (*in != '\0')){
1144: *alocc++ = *in++;
1145: }
1146: if( *in == occ){
1147: *(alocc)='\0';
1148: s=++in;
1149: }
1150:
1151: if (s == t) {/* occ not found */
1152: *(alocc-(in-s))='\0';
1153: in=s;
1154: }
1155: while ( *in != '\0'){
1156: *blocc++ = *in++;
1157: }
1158:
1159: *blocc='\0';
1160: return t;
1161: }
1.137 brouard 1162: char *cutv(char *blocc, char *alocc, char *in, char occ)
1163: {
1.187 brouard 1164: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1165: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1166: gives blocc="abcdef2ghi" and alocc="j".
1167: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1168: */
1169: char *s, *t;
1170: t=in;s=in;
1171: while (*in != '\0'){
1172: while( *in == occ){
1173: *blocc++ = *in++;
1174: s=in;
1175: }
1176: *blocc++ = *in++;
1177: }
1178: if (s == t) /* occ not found */
1179: *(blocc-(in-s))='\0';
1180: else
1181: *(blocc-(in-s)-1)='\0';
1182: in=s;
1183: while ( *in != '\0'){
1184: *alocc++ = *in++;
1185: }
1186:
1187: *alocc='\0';
1188: return s;
1189: }
1190:
1.126 brouard 1191: int nbocc(char *s, char occ)
1192: {
1193: int i,j=0;
1194: int lg=20;
1195: i=0;
1196: lg=strlen(s);
1197: for(i=0; i<= lg; i++) {
1198: if (s[i] == occ ) j++;
1199: }
1200: return j;
1201: }
1202:
1.137 brouard 1203: /* void cutv(char *u,char *v, char*t, char occ) */
1204: /* { */
1205: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1206: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1207: /* gives u="abcdef2ghi" and v="j" *\/ */
1208: /* int i,lg,j,p=0; */
1209: /* i=0; */
1210: /* lg=strlen(t); */
1211: /* for(j=0; j<=lg-1; j++) { */
1212: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1213: /* } */
1.126 brouard 1214:
1.137 brouard 1215: /* for(j=0; j<p; j++) { */
1216: /* (u[j] = t[j]); */
1217: /* } */
1218: /* u[p]='\0'; */
1.126 brouard 1219:
1.137 brouard 1220: /* for(j=0; j<= lg; j++) { */
1221: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1222: /* } */
1223: /* } */
1.126 brouard 1224:
1.160 brouard 1225: #ifdef _WIN32
1226: char * strsep(char **pp, const char *delim)
1227: {
1228: char *p, *q;
1229:
1230: if ((p = *pp) == NULL)
1231: return 0;
1232: if ((q = strpbrk (p, delim)) != NULL)
1233: {
1234: *pp = q + 1;
1235: *q = '\0';
1236: }
1237: else
1238: *pp = 0;
1239: return p;
1240: }
1241: #endif
1242:
1.126 brouard 1243: /********************** nrerror ********************/
1244:
1245: void nrerror(char error_text[])
1246: {
1247: fprintf(stderr,"ERREUR ...\n");
1248: fprintf(stderr,"%s\n",error_text);
1249: exit(EXIT_FAILURE);
1250: }
1251: /*********************** vector *******************/
1252: double *vector(int nl, int nh)
1253: {
1254: double *v;
1255: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1256: if (!v) nrerror("allocation failure in vector");
1257: return v-nl+NR_END;
1258: }
1259:
1260: /************************ free vector ******************/
1261: void free_vector(double*v, int nl, int nh)
1262: {
1263: free((FREE_ARG)(v+nl-NR_END));
1264: }
1265:
1266: /************************ivector *******************************/
1267: int *ivector(long nl,long nh)
1268: {
1269: int *v;
1270: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1271: if (!v) nrerror("allocation failure in ivector");
1272: return v-nl+NR_END;
1273: }
1274:
1275: /******************free ivector **************************/
1276: void free_ivector(int *v, long nl, long nh)
1277: {
1278: free((FREE_ARG)(v+nl-NR_END));
1279: }
1280:
1281: /************************lvector *******************************/
1282: long *lvector(long nl,long nh)
1283: {
1284: long *v;
1285: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1286: if (!v) nrerror("allocation failure in ivector");
1287: return v-nl+NR_END;
1288: }
1289:
1290: /******************free lvector **************************/
1291: void free_lvector(long *v, long nl, long nh)
1292: {
1293: free((FREE_ARG)(v+nl-NR_END));
1294: }
1295:
1296: /******************* imatrix *******************************/
1297: int **imatrix(long nrl, long nrh, long ncl, long nch)
1298: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1299: {
1300: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1301: int **m;
1302:
1303: /* allocate pointers to rows */
1304: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1305: if (!m) nrerror("allocation failure 1 in matrix()");
1306: m += NR_END;
1307: m -= nrl;
1308:
1309:
1310: /* allocate rows and set pointers to them */
1311: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1312: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1313: m[nrl] += NR_END;
1314: m[nrl] -= ncl;
1315:
1316: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1317:
1318: /* return pointer to array of pointers to rows */
1319: return m;
1320: }
1321:
1322: /****************** free_imatrix *************************/
1323: void free_imatrix(m,nrl,nrh,ncl,nch)
1324: int **m;
1325: long nch,ncl,nrh,nrl;
1326: /* free an int matrix allocated by imatrix() */
1327: {
1328: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1329: free((FREE_ARG) (m+nrl-NR_END));
1330: }
1331:
1332: /******************* matrix *******************************/
1333: double **matrix(long nrl, long nrh, long ncl, long nch)
1334: {
1335: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1336: double **m;
1337:
1338: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1339: if (!m) nrerror("allocation failure 1 in matrix()");
1340: m += NR_END;
1341: m -= nrl;
1342:
1343: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1344: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1345: m[nrl] += NR_END;
1346: m[nrl] -= ncl;
1347:
1348: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1349: return m;
1.145 brouard 1350: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1351: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1352: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1353: */
1354: }
1355:
1356: /*************************free matrix ************************/
1357: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1358: {
1359: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1360: free((FREE_ARG)(m+nrl-NR_END));
1361: }
1362:
1363: /******************* ma3x *******************************/
1364: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1365: {
1366: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1367: double ***m;
1368:
1369: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1370: if (!m) nrerror("allocation failure 1 in matrix()");
1371: m += NR_END;
1372: m -= nrl;
1373:
1374: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1375: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1376: m[nrl] += NR_END;
1377: m[nrl] -= ncl;
1378:
1379: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1380:
1381: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1382: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1383: m[nrl][ncl] += NR_END;
1384: m[nrl][ncl] -= nll;
1385: for (j=ncl+1; j<=nch; j++)
1386: m[nrl][j]=m[nrl][j-1]+nlay;
1387:
1388: for (i=nrl+1; i<=nrh; i++) {
1389: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1390: for (j=ncl+1; j<=nch; j++)
1391: m[i][j]=m[i][j-1]+nlay;
1392: }
1393: return m;
1394: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1395: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1396: */
1397: }
1398:
1399: /*************************free ma3x ************************/
1400: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1401: {
1402: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1403: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1404: free((FREE_ARG)(m+nrl-NR_END));
1405: }
1406:
1407: /*************** function subdirf ***********/
1408: char *subdirf(char fileres[])
1409: {
1410: /* Caution optionfilefiname is hidden */
1411: strcpy(tmpout,optionfilefiname);
1412: strcat(tmpout,"/"); /* Add to the right */
1413: strcat(tmpout,fileres);
1414: return tmpout;
1415: }
1416:
1417: /*************** function subdirf2 ***********/
1418: char *subdirf2(char fileres[], char *preop)
1419: {
1420:
1421: /* Caution optionfilefiname is hidden */
1422: strcpy(tmpout,optionfilefiname);
1423: strcat(tmpout,"/");
1424: strcat(tmpout,preop);
1425: strcat(tmpout,fileres);
1426: return tmpout;
1427: }
1428:
1429: /*************** function subdirf3 ***********/
1430: char *subdirf3(char fileres[], char *preop, char *preop2)
1431: {
1432:
1433: /* Caution optionfilefiname is hidden */
1434: strcpy(tmpout,optionfilefiname);
1435: strcat(tmpout,"/");
1436: strcat(tmpout,preop);
1437: strcat(tmpout,preop2);
1438: strcat(tmpout,fileres);
1439: return tmpout;
1440: }
1.213 brouard 1441:
1442: /*************** function subdirfext ***********/
1443: char *subdirfext(char fileres[], char *preop, char *postop)
1444: {
1445:
1446: strcpy(tmpout,preop);
1447: strcat(tmpout,fileres);
1448: strcat(tmpout,postop);
1449: return tmpout;
1450: }
1.126 brouard 1451:
1.213 brouard 1452: /*************** function subdirfext3 ***********/
1453: char *subdirfext3(char fileres[], char *preop, char *postop)
1454: {
1455:
1456: /* Caution optionfilefiname is hidden */
1457: strcpy(tmpout,optionfilefiname);
1458: strcat(tmpout,"/");
1459: strcat(tmpout,preop);
1460: strcat(tmpout,fileres);
1461: strcat(tmpout,postop);
1462: return tmpout;
1463: }
1464:
1.162 brouard 1465: char *asc_diff_time(long time_sec, char ascdiff[])
1466: {
1467: long sec_left, days, hours, minutes;
1468: days = (time_sec) / (60*60*24);
1469: sec_left = (time_sec) % (60*60*24);
1470: hours = (sec_left) / (60*60) ;
1471: sec_left = (sec_left) %(60*60);
1472: minutes = (sec_left) /60;
1473: sec_left = (sec_left) % (60);
1474: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1475: return ascdiff;
1476: }
1477:
1.126 brouard 1478: /***************** f1dim *************************/
1479: extern int ncom;
1480: extern double *pcom,*xicom;
1481: extern double (*nrfunc)(double []);
1482:
1483: double f1dim(double x)
1484: {
1485: int j;
1486: double f;
1487: double *xt;
1488:
1489: xt=vector(1,ncom);
1490: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1491: f=(*nrfunc)(xt);
1492: free_vector(xt,1,ncom);
1493: return f;
1494: }
1495:
1496: /*****************brent *************************/
1497: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1498: {
1499: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1500: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1501: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1502: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1503: * returned function value.
1504: */
1.126 brouard 1505: int iter;
1506: double a,b,d,etemp;
1.159 brouard 1507: double fu=0,fv,fw,fx;
1.164 brouard 1508: double ftemp=0.;
1.126 brouard 1509: double p,q,r,tol1,tol2,u,v,w,x,xm;
1510: double e=0.0;
1511:
1512: a=(ax < cx ? ax : cx);
1513: b=(ax > cx ? ax : cx);
1514: x=w=v=bx;
1515: fw=fv=fx=(*f)(x);
1516: for (iter=1;iter<=ITMAX;iter++) {
1517: xm=0.5*(a+b);
1518: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1519: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1520: printf(".");fflush(stdout);
1521: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1522: #ifdef DEBUGBRENT
1.126 brouard 1523: 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);
1524: 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);
1525: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1526: #endif
1527: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1528: *xmin=x;
1529: return fx;
1530: }
1531: ftemp=fu;
1532: if (fabs(e) > tol1) {
1533: r=(x-w)*(fx-fv);
1534: q=(x-v)*(fx-fw);
1535: p=(x-v)*q-(x-w)*r;
1536: q=2.0*(q-r);
1537: if (q > 0.0) p = -p;
1538: q=fabs(q);
1539: etemp=e;
1540: e=d;
1541: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1542: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1543: else {
1544: d=p/q;
1545: u=x+d;
1546: if (u-a < tol2 || b-u < tol2)
1547: d=SIGN(tol1,xm-x);
1548: }
1549: } else {
1550: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1551: }
1552: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1553: fu=(*f)(u);
1554: if (fu <= fx) {
1555: if (u >= x) a=x; else b=x;
1556: SHFT(v,w,x,u)
1.183 brouard 1557: SHFT(fv,fw,fx,fu)
1558: } else {
1559: if (u < x) a=u; else b=u;
1560: if (fu <= fw || w == x) {
1561: v=w;
1562: w=u;
1563: fv=fw;
1564: fw=fu;
1565: } else if (fu <= fv || v == x || v == w) {
1566: v=u;
1567: fv=fu;
1568: }
1569: }
1.126 brouard 1570: }
1571: nrerror("Too many iterations in brent");
1572: *xmin=x;
1573: return fx;
1574: }
1575:
1576: /****************** mnbrak ***********************/
1577:
1578: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1579: double (*func)(double))
1.183 brouard 1580: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1581: the downhill direction (defined by the function as evaluated at the initial points) and returns
1582: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1583: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1584: */
1.126 brouard 1585: double ulim,u,r,q, dum;
1586: double fu;
1.187 brouard 1587:
1588: double scale=10.;
1589: int iterscale=0;
1590:
1591: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1592: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1593:
1594:
1595: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1596: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1597: /* *bx = *ax - (*ax - *bx)/scale; */
1598: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1599: /* } */
1600:
1.126 brouard 1601: if (*fb > *fa) {
1602: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1603: SHFT(dum,*fb,*fa,dum)
1604: }
1.126 brouard 1605: *cx=(*bx)+GOLD*(*bx-*ax);
1606: *fc=(*func)(*cx);
1.183 brouard 1607: #ifdef DEBUG
1608: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1609: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1610: #endif
1611: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1612: r=(*bx-*ax)*(*fb-*fc);
1613: q=(*bx-*cx)*(*fb-*fa);
1614: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1615: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1616: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1617: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1618: fu=(*func)(u);
1.163 brouard 1619: #ifdef DEBUG
1620: /* f(x)=A(x-u)**2+f(u) */
1621: double A, fparabu;
1622: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1623: fparabu= *fa - A*(*ax-u)*(*ax-u);
1624: printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
1625: fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
1.183 brouard 1626: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1627: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1628: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1629: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1630: #endif
1.184 brouard 1631: #ifdef MNBRAKORIGINAL
1.183 brouard 1632: #else
1.191 brouard 1633: /* if (fu > *fc) { */
1634: /* #ifdef DEBUG */
1635: /* printf("mnbrak4 fu > fc \n"); */
1636: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1637: /* #endif */
1638: /* /\* 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 *\\/ *\/ */
1639: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1640: /* dum=u; /\* Shifting c and u *\/ */
1641: /* u = *cx; */
1642: /* *cx = dum; */
1643: /* dum = fu; */
1644: /* fu = *fc; */
1645: /* *fc =dum; */
1646: /* } else { /\* end *\/ */
1647: /* #ifdef DEBUG */
1648: /* printf("mnbrak3 fu < fc \n"); */
1649: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1650: /* #endif */
1651: /* dum=u; /\* Shifting c and u *\/ */
1652: /* u = *cx; */
1653: /* *cx = dum; */
1654: /* dum = fu; */
1655: /* fu = *fc; */
1656: /* *fc =dum; */
1657: /* } */
1.183 brouard 1658: #ifdef DEBUG
1.191 brouard 1659: printf("mnbrak34 fu < or >= fc \n");
1660: fprintf(ficlog, "mnbrak34 fu < fc\n");
1.183 brouard 1661: #endif
1.191 brouard 1662: dum=u; /* Shifting c and u */
1663: u = *cx;
1664: *cx = dum;
1665: dum = fu;
1666: fu = *fc;
1667: *fc =dum;
1.183 brouard 1668: #endif
1.162 brouard 1669: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1670: #ifdef DEBUG
1671: printf("mnbrak2 u after c but before ulim\n");
1672: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1673: #endif
1.126 brouard 1674: fu=(*func)(u);
1675: if (fu < *fc) {
1.183 brouard 1676: #ifdef DEBUG
1677: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1678: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1679: #endif
1.126 brouard 1680: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1681: SHFT(*fb,*fc,fu,(*func)(u))
1682: }
1.162 brouard 1683: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1684: #ifdef DEBUG
1685: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1686: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1687: #endif
1.126 brouard 1688: u=ulim;
1689: fu=(*func)(u);
1.183 brouard 1690: } else { /* u could be left to b (if r > q parabola has a maximum) */
1691: #ifdef DEBUG
1692: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1693: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1694: #endif
1.126 brouard 1695: u=(*cx)+GOLD*(*cx-*bx);
1696: fu=(*func)(u);
1.183 brouard 1697: } /* end tests */
1.126 brouard 1698: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1699: SHFT(*fa,*fb,*fc,fu)
1700: #ifdef DEBUG
1701: printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
1702: fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
1703: #endif
1704: } /* 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 1705: }
1706:
1707: /*************** linmin ************************/
1.162 brouard 1708: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1709: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1710: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1711: the value of func at the returned location p . This is actually all accomplished by calling the
1712: routines mnbrak and brent .*/
1.126 brouard 1713: int ncom;
1714: double *pcom,*xicom;
1715: double (*nrfunc)(double []);
1716:
1717: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1718: {
1719: double brent(double ax, double bx, double cx,
1720: double (*f)(double), double tol, double *xmin);
1721: double f1dim(double x);
1722: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1723: double *fc, double (*func)(double));
1724: int j;
1725: double xx,xmin,bx,ax;
1726: double fx,fb,fa;
1.187 brouard 1727:
1.203 brouard 1728: #ifdef LINMINORIGINAL
1729: #else
1730: double scale=10., axs, xxs; /* Scale added for infinity */
1731: #endif
1732:
1.126 brouard 1733: ncom=n;
1734: pcom=vector(1,n);
1735: xicom=vector(1,n);
1736: nrfunc=func;
1737: for (j=1;j<=n;j++) {
1738: pcom[j]=p[j];
1.202 brouard 1739: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1740: }
1.187 brouard 1741:
1.203 brouard 1742: #ifdef LINMINORIGINAL
1743: xx=1.;
1744: #else
1745: axs=0.0;
1746: xxs=1.;
1747: do{
1748: xx= xxs;
1749: #endif
1.187 brouard 1750: ax=0.;
1751: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1752: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1753: /* 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)) */
1754: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1755: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1756: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1757: /* 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 1758: #ifdef LINMINORIGINAL
1759: #else
1760: if (fx != fx){
1761: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1762: printf("|");
1763: fprintf(ficlog,"|");
1764: #ifdef DEBUGLINMIN
1765: 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);
1766: #endif
1767: }
1768: }while(fx != fx);
1769: #endif
1770:
1.191 brouard 1771: #ifdef DEBUGLINMIN
1772: 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 1773: 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 1774: #endif
1.187 brouard 1775: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1776: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1777: /* fmin = f(p[j] + xmin * xi[j]) */
1778: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1779: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1780: #ifdef DEBUG
1781: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1782: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1783: #endif
1.191 brouard 1784: #ifdef DEBUGLINMIN
1785: printf("linmin end ");
1.202 brouard 1786: fprintf(ficlog,"linmin end ");
1.191 brouard 1787: #endif
1.126 brouard 1788: for (j=1;j<=n;j++) {
1.203 brouard 1789: #ifdef LINMINORIGINAL
1790: xi[j] *= xmin;
1791: #else
1792: #ifdef DEBUGLINMIN
1793: if(xxs <1.0)
1794: printf(" before xi[%d]=%12.8f", j,xi[j]);
1795: #endif
1796: 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) */
1797: #ifdef DEBUGLINMIN
1798: if(xxs <1.0)
1799: 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 );
1800: #endif
1801: #endif
1.187 brouard 1802: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1803: }
1.191 brouard 1804: #ifdef DEBUGLINMIN
1.203 brouard 1805: printf("\n");
1.191 brouard 1806: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 1807: 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 1808: for (j=1;j<=n;j++) {
1.202 brouard 1809: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1810: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1811: if(j % ncovmodel == 0){
1.191 brouard 1812: printf("\n");
1.202 brouard 1813: fprintf(ficlog,"\n");
1814: }
1.191 brouard 1815: }
1.203 brouard 1816: #else
1.191 brouard 1817: #endif
1.126 brouard 1818: free_vector(xicom,1,n);
1819: free_vector(pcom,1,n);
1820: }
1821:
1822:
1823: /*************** powell ************************/
1.162 brouard 1824: /*
1825: Minimization of a function func of n variables. Input consists of an initial starting point
1826: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1827: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1828: such that failure to decrease by more than this amount on one iteration signals doneness. On
1829: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1830: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1831: */
1.126 brouard 1832: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1833: double (*func)(double []))
1834: {
1835: void linmin(double p[], double xi[], int n, double *fret,
1836: double (*func)(double []));
1837: int i,ibig,j;
1838: double del,t,*pt,*ptt,*xit;
1.181 brouard 1839: double directest;
1.126 brouard 1840: double fp,fptt;
1841: double *xits;
1842: int niterf, itmp;
1843:
1844: pt=vector(1,n);
1845: ptt=vector(1,n);
1846: xit=vector(1,n);
1847: xits=vector(1,n);
1848: *fret=(*func)(p);
1849: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 1850: rcurr_time = time(NULL);
1.126 brouard 1851: for (*iter=1;;++(*iter)) {
1.187 brouard 1852: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1853: ibig=0;
1854: del=0.0;
1.157 brouard 1855: rlast_time=rcurr_time;
1856: /* (void) gettimeofday(&curr_time,&tzp); */
1857: rcurr_time = time(NULL);
1858: curr_time = *localtime(&rcurr_time);
1859: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1860: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1861: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1862: for (i=1;i<=n;i++) {
1.126 brouard 1863: printf(" %d %.12f",i, p[i]);
1864: fprintf(ficlog," %d %.12lf",i, p[i]);
1865: fprintf(ficrespow," %.12lf", p[i]);
1866: }
1867: printf("\n");
1868: fprintf(ficlog,"\n");
1869: fprintf(ficrespow,"\n");fflush(ficrespow);
1870: if(*iter <=3){
1.157 brouard 1871: tml = *localtime(&rcurr_time);
1872: strcpy(strcurr,asctime(&tml));
1873: rforecast_time=rcurr_time;
1.126 brouard 1874: itmp = strlen(strcurr);
1875: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1876: strcurr[itmp-1]='\0';
1.162 brouard 1877: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1878: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1879: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1880: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1881: forecast_time = *localtime(&rforecast_time);
1882: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1883: itmp = strlen(strfor);
1884: if(strfor[itmp-1]=='\n')
1885: strfor[itmp-1]='\0';
1.157 brouard 1886: 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);
1887: 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 1888: }
1889: }
1.187 brouard 1890: for (i=1;i<=n;i++) { /* For each direction i */
1891: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1892: fptt=(*fret);
1893: #ifdef DEBUG
1.203 brouard 1894: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1895: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1896: #endif
1.203 brouard 1897: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1898: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 brouard 1899: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1900: /* Outputs are fret(new point p) p is updated and xit rescaled */
1901: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1902: /* because that direction will be replaced unless the gain del is small */
1903: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1904: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1905: /* with the new direction. */
1.126 brouard 1906: del=fabs(fptt-(*fret));
1907: ibig=i;
1908: }
1909: #ifdef DEBUG
1910: printf("%d %.12e",i,(*fret));
1911: fprintf(ficlog,"%d %.12e",i,(*fret));
1912: for (j=1;j<=n;j++) {
1913: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1914: printf(" x(%d)=%.12e",j,xit[j]);
1915: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1916: }
1917: for(j=1;j<=n;j++) {
1.162 brouard 1918: printf(" p(%d)=%.12e",j,p[j]);
1919: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1920: }
1921: printf("\n");
1922: fprintf(ficlog,"\n");
1923: #endif
1.187 brouard 1924: } /* end loop on each direction i */
1925: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1926: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1927: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1928: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1929: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1930: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1931: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1932: /* decreased of more than 3.84 */
1933: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1934: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1935: /* By adding 10 parameters more the gain should be 18.31 */
1936:
1937: /* Starting the program with initial values given by a former maximization will simply change */
1938: /* the scales of the directions and the directions, because the are reset to canonical directions */
1939: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1940: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1941: #ifdef DEBUG
1942: int k[2],l;
1943: k[0]=1;
1944: k[1]=-1;
1945: printf("Max: %.12e",(*func)(p));
1946: fprintf(ficlog,"Max: %.12e",(*func)(p));
1947: for (j=1;j<=n;j++) {
1948: printf(" %.12e",p[j]);
1949: fprintf(ficlog," %.12e",p[j]);
1950: }
1951: printf("\n");
1952: fprintf(ficlog,"\n");
1953: for(l=0;l<=1;l++) {
1954: for (j=1;j<=n;j++) {
1955: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1956: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1957: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1958: }
1959: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1960: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1961: }
1962: #endif
1963:
1964:
1965: free_vector(xit,1,n);
1966: free_vector(xits,1,n);
1967: free_vector(ptt,1,n);
1968: free_vector(pt,1,n);
1969: return;
1.192 brouard 1970: } /* enough precision */
1.126 brouard 1971: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1972: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1973: ptt[j]=2.0*p[j]-pt[j];
1974: xit[j]=p[j]-pt[j];
1975: pt[j]=p[j];
1976: }
1.181 brouard 1977: fptt=(*func)(ptt); /* f_3 */
1.192 brouard 1978: #ifdef POWELLF1F3
1979: #else
1.161 brouard 1980: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 1981: #endif
1.162 brouard 1982: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1983: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1984: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1985: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1986: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1987: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1988: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1989: #ifdef NRCORIGINAL
1990: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1991: #else
1992: 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 1993: t= t- del*SQR(fp-fptt);
1.183 brouard 1994: #endif
1.202 brouard 1995: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 1996: #ifdef DEBUG
1.181 brouard 1997: 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);
1998: 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 1999: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2000: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2001: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2002: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2003: 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);
2004: 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);
2005: #endif
1.183 brouard 2006: #ifdef POWELLORIGINAL
2007: if (t < 0.0) { /* Then we use it for new direction */
2008: #else
1.182 brouard 2009: if (directest*t < 0.0) { /* Contradiction between both tests */
1.202 brouard 2010: 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 2011: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1.202 brouard 2012: fprintf(ficlog,"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 2013: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
2014: }
1.181 brouard 2015: if (directest < 0.0) { /* Then we use it for new direction */
2016: #endif
1.191 brouard 2017: #ifdef DEBUGLINMIN
2018: printf("Before linmin in direction P%d-P0\n",n);
2019: for (j=1;j<=n;j++) {
1.202 brouard 2020: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2021: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2022: if(j % ncovmodel == 0){
1.191 brouard 2023: printf("\n");
1.202 brouard 2024: fprintf(ficlog,"\n");
2025: }
1.191 brouard 2026: }
2027: #endif
1.187 brouard 2028: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.191 brouard 2029: #ifdef DEBUGLINMIN
2030: for (j=1;j<=n;j++) {
2031: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1.202 brouard 2032: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2033: if(j % ncovmodel == 0){
1.191 brouard 2034: printf("\n");
1.202 brouard 2035: fprintf(ficlog,"\n");
2036: }
1.191 brouard 2037: }
2038: #endif
1.126 brouard 2039: for (j=1;j<=n;j++) {
1.181 brouard 2040: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
2041: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 2042: }
1.181 brouard 2043: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2044: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 2045:
1.126 brouard 2046: #ifdef DEBUG
1.164 brouard 2047: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2048: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 2049: for(j=1;j<=n;j++){
2050: printf(" %.12e",xit[j]);
2051: fprintf(ficlog," %.12e",xit[j]);
2052: }
2053: printf("\n");
2054: fprintf(ficlog,"\n");
2055: #endif
1.192 brouard 2056: } /* end of t or directest negative */
2057: #ifdef POWELLF1F3
2058: #else
1.162 brouard 2059: } /* end if (fptt < fp) */
1.192 brouard 2060: #endif
2061: } /* loop iteration */
1.126 brouard 2062: }
2063:
2064: /**** Prevalence limit (stable or period prevalence) ****************/
2065:
1.203 brouard 2066: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
1.126 brouard 2067: {
1.218 brouard 2068: /* Computes the prevalence limit in each live state at age x and for covariate ij by left multiplying the unit
1.203 brouard 2069: matrix by transitions matrix until convergence is reached with precision ftolpl */
1.206 brouard 2070: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2071: /* Wx is row vector: population in state 1, population in state 2, population dead */
2072: /* or prevalence in state 1, prevalence in state 2, 0 */
2073: /* newm is the matrix after multiplications, its rows are identical at a factor */
2074: /* Initial matrix pimij */
2075: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2076: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2077: /* 0, 0 , 1} */
2078: /*
2079: * and after some iteration: */
2080: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2081: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2082: /* 0, 0 , 1} */
2083: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2084: /* {0.51571254859325999, 0.4842874514067399, */
2085: /* 0.51326036147820708, 0.48673963852179264} */
2086: /* If we start from prlim again, prlim tends to a constant matrix */
2087:
1.126 brouard 2088: int i, ii,j,k;
1.209 brouard 2089: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2090: /* double **matprod2(); */ /* test */
1.218 brouard 2091: double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126 brouard 2092: double **newm;
1.209 brouard 2093: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2094: int ncvloop=0;
1.169 brouard 2095:
1.209 brouard 2096: min=vector(1,nlstate);
2097: max=vector(1,nlstate);
2098: meandiff=vector(1,nlstate);
2099:
1.218 brouard 2100: /* Starting with matrix unity */
1.126 brouard 2101: for (ii=1;ii<=nlstate+ndeath;ii++)
2102: for (j=1;j<=nlstate+ndeath;j++){
2103: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2104: }
1.169 brouard 2105:
2106: cov[1]=1.;
2107:
2108: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2109: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2110: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2111: ncvloop++;
1.126 brouard 2112: newm=savm;
2113: /* Covariates have to be included here again */
1.138 brouard 2114: cov[2]=agefin;
1.187 brouard 2115: if(nagesqr==1)
2116: cov[3]= agefin*agefin;;
1.138 brouard 2117: for (k=1; k<=cptcovn;k++) {
1.200 brouard 2118: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.218 brouard 2119: /* Here comes the value of the covariate 'ij' */
1.200 brouard 2120: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
1.198 brouard 2121: /* 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 2122: }
1.186 brouard 2123: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2124: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2125: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
1.186 brouard 2126: for (k=1; k<=cptcovprod;k++) /* Useless */
1.200 brouard 2127: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2128: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.138 brouard 2129:
2130: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2131: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2132: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2133: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2134: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2135: /* age and covariate values of ij are in 'cov' */
1.142 brouard 2136: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2137:
1.126 brouard 2138: savm=oldm;
2139: oldm=newm;
1.209 brouard 2140:
2141: for(j=1; j<=nlstate; j++){
2142: max[j]=0.;
2143: min[j]=1.;
2144: }
2145: for(i=1;i<=nlstate;i++){
2146: sumnew=0;
2147: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2148: for(j=1; j<=nlstate; j++){
2149: prlim[i][j]= newm[i][j]/(1-sumnew);
2150: max[j]=FMAX(max[j],prlim[i][j]);
2151: min[j]=FMIN(min[j],prlim[i][j]);
2152: }
2153: }
2154:
1.126 brouard 2155: maxmax=0.;
1.209 brouard 2156: for(j=1; j<=nlstate; j++){
2157: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2158: maxmax=FMAX(maxmax,meandiff[j]);
2159: /* 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 2160: } /* j loop */
1.203 brouard 2161: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2162: /* 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 2163: if(maxmax < ftolpl){
1.209 brouard 2164: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2165: free_vector(min,1,nlstate);
2166: free_vector(max,1,nlstate);
2167: free_vector(meandiff,1,nlstate);
1.126 brouard 2168: return prlim;
2169: }
1.169 brouard 2170: } /* age loop */
1.208 brouard 2171: /* After some age loop it doesn't converge */
1.209 brouard 2172: 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 2173: 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 2174: /* 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); */
2175: free_vector(min,1,nlstate);
2176: free_vector(max,1,nlstate);
2177: free_vector(meandiff,1,nlstate);
1.208 brouard 2178:
1.169 brouard 2179: return prlim; /* should not reach here */
1.126 brouard 2180: }
2181:
1.217 brouard 2182:
2183: /**** Back Prevalence limit (stable or period prevalence) ****************/
2184:
1.218 brouard 2185: /* 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) */
2186: /* 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) */
2187: double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij)
1.217 brouard 2188: {
1.218 brouard 2189: /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit
1.217 brouard 2190: matrix by transitions matrix until convergence is reached with precision ftolpl */
2191: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2192: /* Wx is row vector: population in state 1, population in state 2, population dead */
2193: /* or prevalence in state 1, prevalence in state 2, 0 */
2194: /* newm is the matrix after multiplications, its rows are identical at a factor */
2195: /* Initial matrix pimij */
2196: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2197: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2198: /* 0, 0 , 1} */
2199: /*
2200: * and after some iteration: */
2201: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2202: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2203: /* 0, 0 , 1} */
2204: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2205: /* {0.51571254859325999, 0.4842874514067399, */
2206: /* 0.51326036147820708, 0.48673963852179264} */
2207: /* If we start from prlim again, prlim tends to a constant matrix */
2208:
2209: int i, ii,j,k;
2210: double *min, *max, *meandiff, maxmax,sumnew=0.;
2211: /* double **matprod2(); */ /* test */
2212: double **out, cov[NCOVMAX+1], **bmij();
2213: double **newm;
1.218 brouard 2214: double **dnewm, **doldm, **dsavm; /* for use */
2215: double **oldm, **savm; /* for use */
2216:
1.217 brouard 2217: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
2218: int ncvloop=0;
2219:
2220: min=vector(1,nlstate);
2221: max=vector(1,nlstate);
2222: meandiff=vector(1,nlstate);
2223:
1.218 brouard 2224: dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
2225: oldm=oldms; savm=savms;
2226:
2227: /* Starting with matrix unity */
2228: for (ii=1;ii<=nlstate+ndeath;ii++)
2229: for (j=1;j<=nlstate+ndeath;j++){
1.217 brouard 2230: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2231: }
2232:
2233: cov[1]=1.;
2234:
2235: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2236: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218 brouard 2237: /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
2238: for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217 brouard 2239: ncvloop++;
1.218 brouard 2240: newm=savm; /* oldm should be kept from previous iteration or unity at start */
2241: /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217 brouard 2242: /* Covariates have to be included here again */
2243: cov[2]=agefin;
2244: if(nagesqr==1)
2245: cov[3]= agefin*agefin;;
2246: for (k=1; k<=cptcovn;k++) {
2247: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
2248: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2249: /* 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])]); */
2250: }
2251: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2252: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2253: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
2254: for (k=1; k<=cptcovprod;k++) /* Useless */
2255: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2256: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2257:
2258: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2259: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2260: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
2261: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2262: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2263: /* ij should be linked to the correct index of cov */
2264: /* age and covariate values ij are in 'cov', but we need to pass
2265: * ij for the observed prevalence at age and status and covariate
2266: * number: prevacurrent[(int)agefin][ii][ij]
2267: */
2268: /* 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 *\/ */
2269: /* 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 *\/ */
2270: 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 2271: savm=oldm;
2272: oldm=newm;
2273: for(j=1; j<=nlstate; j++){
2274: max[j]=0.;
2275: min[j]=1.;
2276: }
2277: for(j=1; j<=nlstate; j++){
2278: for(i=1;i<=nlstate;i++){
1.218 brouard 2279: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
2280: bprlim[i][j]= newm[i][j];
2281: max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
2282: min[i]=FMIN(min[i],bprlim[i][j]);
1.217 brouard 2283: }
2284: }
1.218 brouard 2285:
1.217 brouard 2286: maxmax=0.;
2287: for(i=1; i<=nlstate; i++){
2288: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
2289: maxmax=FMAX(maxmax,meandiff[i]);
2290: /* 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); */
2291: } /* j loop */
2292: *ncvyear= -( (int)age- (int)agefin);
1.218 brouard 2293: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/
1.217 brouard 2294: if(maxmax < ftolpl){
1.220 brouard 2295: /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2296: free_vector(min,1,nlstate);
2297: free_vector(max,1,nlstate);
2298: free_vector(meandiff,1,nlstate);
2299: return bprlim;
2300: }
2301: } /* age loop */
2302: /* After some age loop it doesn't converge */
2303: 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\
2304: 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);
2305: /* 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); */
2306: free_vector(min,1,nlstate);
2307: free_vector(max,1,nlstate);
2308: free_vector(meandiff,1,nlstate);
2309:
2310: return bprlim; /* should not reach here */
2311: }
2312:
1.126 brouard 2313: /*************** transition probabilities ***************/
2314:
2315: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2316: {
1.138 brouard 2317: /* According to parameters values stored in x and the covariate's values stored in cov,
2318: computes the probability to be observed in state j being in state i by appying the
2319: model to the ncovmodel covariates (including constant and age).
2320: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2321: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2322: ncth covariate in the global vector x is given by the formula:
2323: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2324: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2325: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2326: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2327: Outputs ps[i][j] the probability to be observed in j being in j according to
2328: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2329: */
2330: double s1, lnpijopii;
1.126 brouard 2331: /*double t34;*/
1.164 brouard 2332: int i,j, nc, ii, jj;
1.126 brouard 2333:
1.218 brouard 2334: for(i=1; i<= nlstate; i++){
2335: for(j=1; j<i;j++){
2336: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2337: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2338: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2339: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2340: }
2341: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2342: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2343: }
2344: for(j=i+1; j<=nlstate+ndeath;j++){
2345: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2346: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2347: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2348: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2349: }
2350: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2351: }
2352: }
2353:
2354: for(i=1; i<= nlstate; i++){
2355: s1=0;
2356: for(j=1; j<i; j++){
2357: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2358: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2359: }
2360: for(j=i+1; j<=nlstate+ndeath; j++){
2361: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2362: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2363: }
2364: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2365: ps[i][i]=1./(s1+1.);
2366: /* Computing other pijs */
2367: for(j=1; j<i; j++)
2368: ps[i][j]= exp(ps[i][j])*ps[i][i];
2369: for(j=i+1; j<=nlstate+ndeath; j++)
2370: ps[i][j]= exp(ps[i][j])*ps[i][i];
2371: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2372: } /* end i */
2373:
2374: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2375: for(jj=1; jj<= nlstate+ndeath; jj++){
2376: ps[ii][jj]=0;
2377: ps[ii][ii]=1;
2378: }
2379: }
2380:
2381:
2382: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2383: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2384: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2385: /* } */
2386: /* printf("\n "); */
2387: /* } */
2388: /* printf("\n ");printf("%lf ",cov[2]);*/
2389: /*
2390: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2391: goto end;*/
2392: return ps;
1.126 brouard 2393: }
2394:
1.218 brouard 2395: /*************** backward transition probabilities ***************/
2396:
2397: /* 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 ) */
2398: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
2399: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij )
2400: {
1.222 ! brouard 2401: /* Computes the backward probability at age agefin and covariate ij
! 2402: * and returns in **ps as well as **bmij.
! 2403: */
1.218 brouard 2404: int i, ii, j,k;
1.222 ! brouard 2405:
! 2406: double **out, **pmij();
! 2407: double sumnew=0.;
1.218 brouard 2408: double agefin;
1.222 ! brouard 2409:
! 2410: double **dnewm, **dsavm, **doldm;
! 2411: double **bbmij;
! 2412:
1.218 brouard 2413: doldm=ddoldms; /* global pointers */
1.222 ! brouard 2414: dnewm=ddnewms;
! 2415: dsavm=ddsavms;
! 2416:
! 2417: agefin=cov[2];
! 2418: /* bmij *//* age is cov[2], ij is included in cov, but we need for
! 2419: the observed prevalence (with this covariate ij) */
! 2420: dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
! 2421: /* We do have the matrix Px in savm and we need pij */
! 2422: for (j=1;j<=nlstate+ndeath;j++){
! 2423: sumnew=0.; /* w1 p11 + w2 p21 only on live states */
! 2424: for (ii=1;ii<=nlstate;ii++){
! 2425: sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
! 2426: } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
! 2427: for (ii=1;ii<=nlstate+ndeath;ii++){
! 2428: if(sumnew >= 1.e-10){
! 2429: /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
! 2430: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
! 2431: /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
! 2432: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
! 2433: /* }else */
! 2434: doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
! 2435: }else{
! 2436: 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);
! 2437: }
! 2438: } /*End ii */
! 2439: } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
! 2440: /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
! 2441: bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
! 2442: /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
! 2443: /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
! 2444: /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
! 2445: /* left Product of this matrix by diag matrix of prevalences (savm) */
! 2446: for (j=1;j<=nlstate+ndeath;j++){
! 2447: for (ii=1;ii<=nlstate+ndeath;ii++){
! 2448: dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
! 2449: }
! 2450: } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
! 2451: ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
! 2452: /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
! 2453: /* end bmij */
! 2454: return ps;
1.218 brouard 2455: }
1.217 brouard 2456: /*************** transition probabilities ***************/
2457:
1.218 brouard 2458: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217 brouard 2459: {
2460: /* According to parameters values stored in x and the covariate's values stored in cov,
2461: computes the probability to be observed in state j being in state i by appying the
2462: model to the ncovmodel covariates (including constant and age).
2463: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2464: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2465: ncth covariate in the global vector x is given by the formula:
2466: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2467: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2468: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2469: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2470: Outputs ps[i][j] the probability to be observed in j being in j according to
2471: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2472: */
2473: double s1, lnpijopii;
2474: /*double t34;*/
2475: int i,j, nc, ii, jj;
2476:
1.218 brouard 2477: for(i=1; i<= nlstate; i++){
2478: for(j=1; j<i;j++){
2479: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2480: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2481: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2482: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2483: }
2484: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2485: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2486: }
2487: for(j=i+1; j<=nlstate+ndeath;j++){
2488: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2489: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2490: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2491: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2492: }
2493: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2494: }
2495: }
2496:
2497: for(i=1; i<= nlstate; i++){
2498: s1=0;
2499: for(j=1; j<i; j++){
2500: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2501: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2502: }
2503: for(j=i+1; j<=nlstate+ndeath; j++){
2504: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2505: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2506: }
2507: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2508: ps[i][i]=1./(s1+1.);
2509: /* Computing other pijs */
2510: for(j=1; j<i; j++)
2511: ps[i][j]= exp(ps[i][j])*ps[i][i];
2512: for(j=i+1; j<=nlstate+ndeath; j++)
2513: ps[i][j]= exp(ps[i][j])*ps[i][i];
2514: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2515: } /* end i */
2516:
2517: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2518: for(jj=1; jj<= nlstate+ndeath; jj++){
2519: ps[ii][jj]=0;
2520: ps[ii][ii]=1;
2521: }
2522: }
2523: /* Added for backcast */ /* Transposed matrix too */
2524: for(jj=1; jj<= nlstate+ndeath; jj++){
2525: s1=0.;
2526: for(ii=1; ii<= nlstate+ndeath; ii++){
2527: s1+=ps[ii][jj];
2528: }
2529: for(ii=1; ii<= nlstate; ii++){
2530: ps[ii][jj]=ps[ii][jj]/s1;
2531: }
2532: }
2533: /* Transposition */
2534: for(jj=1; jj<= nlstate+ndeath; jj++){
2535: for(ii=jj; ii<= nlstate+ndeath; ii++){
2536: s1=ps[ii][jj];
2537: ps[ii][jj]=ps[jj][ii];
2538: ps[jj][ii]=s1;
2539: }
2540: }
2541: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2542: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2543: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2544: /* } */
2545: /* printf("\n "); */
2546: /* } */
2547: /* printf("\n ");printf("%lf ",cov[2]);*/
2548: /*
2549: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2550: goto end;*/
2551: return ps;
1.217 brouard 2552: }
2553:
2554:
1.126 brouard 2555: /**************** Product of 2 matrices ******************/
2556:
1.145 brouard 2557: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2558: {
2559: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2560: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2561: /* in, b, out are matrice of pointers which should have been initialized
2562: before: only the contents of out is modified. The function returns
2563: a pointer to pointers identical to out */
1.145 brouard 2564: int i, j, k;
1.126 brouard 2565: for(i=nrl; i<= nrh; i++)
1.145 brouard 2566: for(k=ncolol; k<=ncoloh; k++){
2567: out[i][k]=0.;
2568: for(j=ncl; j<=nch; j++)
2569: out[i][k] +=in[i][j]*b[j][k];
2570: }
1.126 brouard 2571: return out;
2572: }
2573:
2574:
2575: /************* Higher Matrix Product ***************/
2576:
2577: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2578: {
1.218 brouard 2579: /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
1.126 brouard 2580: 'nhstepm*hstepm*stepm' months (i.e. until
2581: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2582: nhstepm*hstepm matrices.
2583: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2584: (typically every 2 years instead of every month which is too big
2585: for the memory).
2586: Model is determined by parameters x and covariates have to be
2587: included manually here.
2588:
2589: */
2590:
2591: int i, j, d, h, k;
1.131 brouard 2592: double **out, cov[NCOVMAX+1];
1.126 brouard 2593: double **newm;
1.187 brouard 2594: double agexact;
1.214 brouard 2595: double agebegin, ageend;
1.126 brouard 2596:
2597: /* Hstepm could be zero and should return the unit matrix */
2598: for (i=1;i<=nlstate+ndeath;i++)
2599: for (j=1;j<=nlstate+ndeath;j++){
2600: oldm[i][j]=(i==j ? 1.0 : 0.0);
2601: po[i][j][0]=(i==j ? 1.0 : 0.0);
2602: }
2603: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2604: for(h=1; h <=nhstepm; h++){
2605: for(d=1; d <=hstepm; d++){
2606: newm=savm;
2607: /* Covariates have to be included here again */
2608: cov[1]=1.;
1.214 brouard 2609: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 2610: cov[2]=agexact;
2611: if(nagesqr==1)
1.218 brouard 2612: cov[3]= agexact*agexact;
1.131 brouard 2613: for (k=1; k<=cptcovn;k++)
1.218 brouard 2614: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2615: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.186 brouard 2616: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1.218 brouard 2617: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2618: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2619: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.145 brouard 2620: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.218 brouard 2621: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2622: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
1.126 brouard 2623:
2624:
2625: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2626: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 2627: /* right multiplication of oldm by the current matrix */
1.126 brouard 2628: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2629: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 brouard 2630: /* if((int)age == 70){ */
2631: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
2632: /* for(i=1; i<=nlstate+ndeath; i++) { */
2633: /* printf("%d pmmij ",i); */
2634: /* for(j=1;j<=nlstate+ndeath;j++) { */
2635: /* printf("%f ",pmmij[i][j]); */
2636: /* } */
2637: /* printf(" oldm "); */
2638: /* for(j=1;j<=nlstate+ndeath;j++) { */
2639: /* printf("%f ",oldm[i][j]); */
2640: /* } */
2641: /* printf("\n"); */
2642: /* } */
2643: /* } */
1.126 brouard 2644: savm=oldm;
2645: oldm=newm;
2646: }
2647: for(i=1; i<=nlstate+ndeath; i++)
2648: for(j=1;j<=nlstate+ndeath;j++) {
1.218 brouard 2649: po[i][j][h]=newm[i][j];
2650: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2651: }
1.128 brouard 2652: /*printf("h=%d ",h);*/
1.126 brouard 2653: } /* end h */
1.218 brouard 2654: /* printf("\n H=%d \n",h); */
1.126 brouard 2655: return po;
2656: }
2657:
1.217 brouard 2658: /************* Higher Back Matrix Product ***************/
1.218 brouard 2659: /* 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 2660: double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )
1.217 brouard 2661: {
1.218 brouard 2662: /* Computes the transition matrix starting at age 'age' over
1.217 brouard 2663: 'nhstepm*hstepm*stepm' months (i.e. until
1.218 brouard 2664: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2665: nhstepm*hstepm matrices.
2666: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2667: (typically every 2 years instead of every month which is too big
1.217 brouard 2668: for the memory).
1.218 brouard 2669: Model is determined by parameters x and covariates have to be
2670: included manually here.
1.217 brouard 2671:
1.222 ! brouard 2672: */
1.217 brouard 2673:
2674: int i, j, d, h, k;
2675: double **out, cov[NCOVMAX+1];
2676: double **newm;
2677: double agexact;
2678: double agebegin, ageend;
1.222 ! brouard 2679: double **oldm, **savm;
1.217 brouard 2680:
1.222 ! brouard 2681: oldm=oldms;savm=savms;
1.217 brouard 2682: /* Hstepm could be zero and should return the unit matrix */
2683: for (i=1;i<=nlstate+ndeath;i++)
2684: for (j=1;j<=nlstate+ndeath;j++){
2685: oldm[i][j]=(i==j ? 1.0 : 0.0);
2686: po[i][j][0]=(i==j ? 1.0 : 0.0);
2687: }
2688: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2689: for(h=1; h <=nhstepm; h++){
2690: for(d=1; d <=hstepm; d++){
2691: newm=savm;
2692: /* Covariates have to be included here again */
2693: cov[1]=1.;
2694: agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
2695: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
2696: cov[2]=agexact;
2697: if(nagesqr==1)
1.222 ! brouard 2698: cov[3]= agexact*agexact;
1.218 brouard 2699: for (k=1; k<=cptcovn;k++)
1.222 ! brouard 2700: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
! 2701: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.217 brouard 2702: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1.222 ! brouard 2703: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
! 2704: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
! 2705: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.217 brouard 2706: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.222 ! brouard 2707: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
! 2708: /* 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 2709:
2710:
1.217 brouard 2711: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2712: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 2713: /* Careful transposed matrix */
1.222 ! brouard 2714: /* age is in cov[2] */
1.218 brouard 2715: /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
1.222 ! brouard 2716: /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
1.218 brouard 2717: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1.222 ! brouard 2718: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217 brouard 2719: /* if((int)age == 70){ */
2720: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
2721: /* for(i=1; i<=nlstate+ndeath; i++) { */
2722: /* printf("%d pmmij ",i); */
2723: /* for(j=1;j<=nlstate+ndeath;j++) { */
2724: /* printf("%f ",pmmij[i][j]); */
2725: /* } */
2726: /* printf(" oldm "); */
2727: /* for(j=1;j<=nlstate+ndeath;j++) { */
2728: /* printf("%f ",oldm[i][j]); */
2729: /* } */
2730: /* printf("\n"); */
2731: /* } */
2732: /* } */
2733: savm=oldm;
2734: oldm=newm;
2735: }
2736: for(i=1; i<=nlstate+ndeath; i++)
2737: for(j=1;j<=nlstate+ndeath;j++) {
1.222 ! brouard 2738: po[i][j][h]=newm[i][j];
! 2739: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.217 brouard 2740: }
2741: /*printf("h=%d ",h);*/
2742: } /* end h */
1.222 ! brouard 2743: /* printf("\n H=%d \n",h); */
1.217 brouard 2744: return po;
2745: }
2746:
2747:
1.162 brouard 2748: #ifdef NLOPT
2749: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2750: double fret;
2751: double *xt;
2752: int j;
2753: myfunc_data *d2 = (myfunc_data *) pd;
2754: /* xt = (p1-1); */
2755: xt=vector(1,n);
2756: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2757:
2758: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2759: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2760: printf("Function = %.12lf ",fret);
2761: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2762: printf("\n");
2763: free_vector(xt,1,n);
2764: return fret;
2765: }
2766: #endif
1.126 brouard 2767:
2768: /*************** log-likelihood *************/
2769: double func( double *x)
2770: {
2771: int i, ii, j, k, mi, d, kk;
1.131 brouard 2772: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2773: double **out;
2774: double sw; /* Sum of weights */
2775: double lli; /* Individual log likelihood */
2776: int s1, s2;
2777: double bbh, survp;
2778: long ipmx;
1.187 brouard 2779: double agexact;
1.126 brouard 2780: /*extern weight */
2781: /* We are differentiating ll according to initial status */
2782: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2783: /*for(i=1;i<imx;i++)
2784: printf(" %d\n",s[4][i]);
2785: */
1.162 brouard 2786:
2787: ++countcallfunc;
2788:
1.126 brouard 2789: cov[1]=1.;
2790:
2791: for(k=1; k<=nlstate; k++) ll[k]=0.;
2792:
2793: if(mle==1){
2794: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2795: /* Computes the values of the ncovmodel covariates of the model
2796: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2797: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2798: to be observed in j being in i according to the model.
2799: */
1.145 brouard 2800: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 brouard 2801: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2802: }
1.137 brouard 2803: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2804: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2805: has been calculated etc */
1.126 brouard 2806: for(mi=1; mi<= wav[i]-1; mi++){
2807: for (ii=1;ii<=nlstate+ndeath;ii++)
2808: for (j=1;j<=nlstate+ndeath;j++){
2809: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2810: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2811: }
2812: for(d=0; d<dh[mi][i]; d++){
2813: newm=savm;
1.187 brouard 2814: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2815: cov[2]=agexact;
2816: if(nagesqr==1)
2817: cov[3]= agexact*agexact;
1.126 brouard 2818: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2819: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2820: }
2821: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2822: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2823: savm=oldm;
2824: oldm=newm;
2825: } /* end mult */
2826:
2827: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2828: /* But now since version 0.9 we anticipate for bias at large stepm.
2829: * If stepm is larger than one month (smallest stepm) and if the exact delay
2830: * (in months) between two waves is not a multiple of stepm, we rounded to
2831: * the nearest (and in case of equal distance, to the lowest) interval but now
2832: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2833: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2834: * probability in order to take into account the bias as a fraction of the way
2835: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2836: * -stepm/2 to stepm/2 .
2837: * For stepm=1 the results are the same as for previous versions of Imach.
2838: * For stepm > 1 the results are less biased than in previous versions.
2839: */
2840: s1=s[mw[mi][i]][i];
2841: s2=s[mw[mi+1][i]][i];
2842: bbh=(double)bh[mi][i]/(double)stepm;
2843: /* bias bh is positive if real duration
2844: * is higher than the multiple of stepm and negative otherwise.
2845: */
2846: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2847: if( s2 > nlstate){
2848: /* i.e. if s2 is a death state and if the date of death is known
2849: then the contribution to the likelihood is the probability to
2850: die between last step unit time and current step unit time,
2851: which is also equal to probability to die before dh
2852: minus probability to die before dh-stepm .
2853: In version up to 0.92 likelihood was computed
2854: as if date of death was unknown. Death was treated as any other
2855: health state: the date of the interview describes the actual state
2856: and not the date of a change in health state. The former idea was
2857: to consider that at each interview the state was recorded
2858: (healthy, disable or death) and IMaCh was corrected; but when we
2859: introduced the exact date of death then we should have modified
2860: the contribution of an exact death to the likelihood. This new
2861: contribution is smaller and very dependent of the step unit
2862: stepm. It is no more the probability to die between last interview
2863: and month of death but the probability to survive from last
2864: interview up to one month before death multiplied by the
2865: probability to die within a month. Thanks to Chris
2866: Jackson for correcting this bug. Former versions increased
2867: mortality artificially. The bad side is that we add another loop
2868: which slows down the processing. The difference can be up to 10%
2869: lower mortality.
2870: */
1.183 brouard 2871: /* If, at the beginning of the maximization mostly, the
2872: cumulative probability or probability to be dead is
2873: constant (ie = 1) over time d, the difference is equal to
2874: 0. out[s1][3] = savm[s1][3]: probability, being at state
2875: s1 at precedent wave, to be dead a month before current
2876: wave is equal to probability, being at state s1 at
2877: precedent wave, to be dead at mont of the current
2878: wave. Then the observed probability (that this person died)
2879: is null according to current estimated parameter. In fact,
2880: it should be very low but not zero otherwise the log go to
2881: infinity.
2882: */
2883: /* #ifdef INFINITYORIGINAL */
2884: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2885: /* #else */
2886: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2887: /* lli=log(mytinydouble); */
2888: /* else */
2889: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2890: /* #endif */
1.216 brouard 2891: lli=log(out[s1][s2] - savm[s1][s2]);
2892:
2893: } else if ( s2==-1 ) { /* alive */
1.126 brouard 2894: for (j=1,survp=0. ; j<=nlstate; j++)
2895: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2896: /*survp += out[s1][j]; */
2897: lli= log(survp);
2898: }
2899: else if (s2==-4) {
2900: for (j=3,survp=0. ; j<=nlstate; j++)
2901: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2902: lli= log(survp);
2903: }
2904: else if (s2==-5) {
2905: for (j=1,survp=0. ; j<=2; j++)
2906: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2907: lli= log(survp);
2908: }
2909: else{
2910: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2911: /* 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 */
2912: }
2913: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2914: /*if(lli ==000.0)*/
2915: /*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); */
2916: ipmx +=1;
2917: sw += weight[i];
2918: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2919: /* if (lli < log(mytinydouble)){ */
2920: /* 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); */
2921: /* 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]); */
2922: /* } */
1.126 brouard 2923: } /* end of wave */
2924: } /* end of individual */
2925: } else if(mle==2){
2926: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2927: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2928: for(mi=1; mi<= wav[i]-1; mi++){
2929: for (ii=1;ii<=nlstate+ndeath;ii++)
2930: for (j=1;j<=nlstate+ndeath;j++){
2931: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2932: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2933: }
2934: for(d=0; d<=dh[mi][i]; d++){
2935: newm=savm;
1.187 brouard 2936: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2937: cov[2]=agexact;
2938: if(nagesqr==1)
2939: cov[3]= agexact*agexact;
1.126 brouard 2940: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2941: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2942: }
2943: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2944: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2945: savm=oldm;
2946: oldm=newm;
2947: } /* end mult */
2948:
2949: s1=s[mw[mi][i]][i];
2950: s2=s[mw[mi+1][i]][i];
2951: bbh=(double)bh[mi][i]/(double)stepm;
2952: 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 */
2953: ipmx +=1;
2954: sw += weight[i];
2955: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2956: } /* end of wave */
2957: } /* end of individual */
2958: } else if(mle==3){ /* exponential inter-extrapolation */
2959: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2960: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2961: for(mi=1; mi<= wav[i]-1; mi++){
2962: for (ii=1;ii<=nlstate+ndeath;ii++)
2963: for (j=1;j<=nlstate+ndeath;j++){
2964: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2965: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2966: }
2967: for(d=0; d<dh[mi][i]; d++){
2968: newm=savm;
1.187 brouard 2969: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2970: cov[2]=agexact;
2971: if(nagesqr==1)
2972: cov[3]= agexact*agexact;
1.126 brouard 2973: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2974: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2975: }
2976: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2977: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2978: savm=oldm;
2979: oldm=newm;
2980: } /* end mult */
2981:
2982: s1=s[mw[mi][i]][i];
2983: s2=s[mw[mi+1][i]][i];
2984: bbh=(double)bh[mi][i]/(double)stepm;
2985: 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 */
2986: ipmx +=1;
2987: sw += weight[i];
2988: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2989: } /* end of wave */
2990: } /* end of individual */
2991: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2992: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2993: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2994: for(mi=1; mi<= wav[i]-1; mi++){
2995: for (ii=1;ii<=nlstate+ndeath;ii++)
2996: for (j=1;j<=nlstate+ndeath;j++){
2997: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2998: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2999: }
3000: for(d=0; d<dh[mi][i]; d++){
3001: newm=savm;
1.187 brouard 3002: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3003: cov[2]=agexact;
3004: if(nagesqr==1)
3005: cov[3]= agexact*agexact;
1.126 brouard 3006: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 3007: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 3008: }
3009:
3010: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3011: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3012: savm=oldm;
3013: oldm=newm;
3014: } /* end mult */
3015:
3016: s1=s[mw[mi][i]][i];
3017: s2=s[mw[mi+1][i]][i];
3018: if( s2 > nlstate){
3019: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3020: } else if ( s2==-1 ) { /* alive */
3021: for (j=1,survp=0. ; j<=nlstate; j++)
3022: survp += out[s1][j];
3023: lli= log(survp);
1.126 brouard 3024: }else{
3025: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3026: }
3027: ipmx +=1;
3028: sw += weight[i];
3029: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3030: /* 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]); */
3031: } /* end of wave */
3032: } /* end of individual */
3033: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
3034: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 3035: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 3036: for(mi=1; mi<= wav[i]-1; mi++){
3037: for (ii=1;ii<=nlstate+ndeath;ii++)
3038: for (j=1;j<=nlstate+ndeath;j++){
3039: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3040: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3041: }
3042: for(d=0; d<dh[mi][i]; d++){
3043: newm=savm;
1.187 brouard 3044: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3045: cov[2]=agexact;
3046: if(nagesqr==1)
3047: cov[3]= agexact*agexact;
1.126 brouard 3048: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 3049: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 3050: }
3051:
3052: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3053: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3054: savm=oldm;
3055: oldm=newm;
3056: } /* end mult */
3057:
3058: s1=s[mw[mi][i]][i];
3059: s2=s[mw[mi+1][i]][i];
3060: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3061: ipmx +=1;
3062: sw += weight[i];
3063: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3064: /*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]);*/
3065: } /* end of wave */
3066: } /* end of individual */
3067: } /* End of if */
3068: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3069: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3070: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3071: return -l;
3072: }
3073:
3074: /*************** log-likelihood *************/
3075: double funcone( double *x)
3076: {
3077: /* Same as likeli but slower because of a lot of printf and if */
3078: int i, ii, j, k, mi, d, kk;
1.131 brouard 3079: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 3080: double **out;
3081: double lli; /* Individual log likelihood */
3082: double llt;
3083: int s1, s2;
3084: double bbh, survp;
1.187 brouard 3085: double agexact;
1.214 brouard 3086: double agebegin, ageend;
1.126 brouard 3087: /*extern weight */
3088: /* We are differentiating ll according to initial status */
3089: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3090: /*for(i=1;i<imx;i++)
3091: printf(" %d\n",s[4][i]);
3092: */
3093: cov[1]=1.;
3094:
3095: for(k=1; k<=nlstate; k++) ll[k]=0.;
3096:
3097: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 3098: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 3099: for(mi=1; mi<= wav[i]-1; mi++){
3100: for (ii=1;ii<=nlstate+ndeath;ii++)
3101: for (j=1;j<=nlstate+ndeath;j++){
3102: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3103: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3104: }
1.214 brouard 3105:
3106: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
3107: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
3108: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
3109: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3110: and mw[mi+1][i]. dh depends on stepm.*/
1.126 brouard 3111: newm=savm;
1.187 brouard 3112: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3113: cov[2]=agexact;
3114: if(nagesqr==1)
3115: cov[3]= agexact*agexact;
1.126 brouard 3116: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 3117: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 3118: }
1.187 brouard 3119:
1.145 brouard 3120: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 3121: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3122: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 3123: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
3124: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 3125: savm=oldm;
3126: oldm=newm;
3127: } /* end mult */
3128:
3129: s1=s[mw[mi][i]][i];
3130: s2=s[mw[mi+1][i]][i];
1.217 brouard 3131: /* if(s2==-1){ */
3132: /* printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */
3133: /* /\* exit(1); *\/ */
3134: /* } */
1.126 brouard 3135: bbh=(double)bh[mi][i]/(double)stepm;
3136: /* bias is positive if real duration
3137: * is higher than the multiple of stepm and negative otherwise.
3138: */
3139: if( s2 > nlstate && (mle <5) ){ /* Jackson */
3140: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3141: } else if ( s2==-1 ) { /* alive */
1.126 brouard 3142: for (j=1,survp=0. ; j<=nlstate; j++)
3143: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3144: lli= log(survp);
3145: }else if (mle==1){
3146: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3147: } else if(mle==2){
3148: 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 */
3149: } else if(mle==3){ /* exponential inter-extrapolation */
3150: 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 */
3151: } else if (mle==4){ /* mle=4 no inter-extrapolation */
3152: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 3153: } else{ /* mle=0 back to 1 */
3154: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3155: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 3156: } /* End of if */
3157: ipmx +=1;
3158: sw += weight[i];
3159: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 3160: /*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 3161: if(globpr){
1.214 brouard 3162: fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\
1.126 brouard 3163: %11.6f %11.6f %11.6f ", \
1.214 brouard 3164: num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
1.126 brouard 3165: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
3166: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
3167: llt +=ll[k]*gipmx/gsw;
3168: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
3169: }
3170: fprintf(ficresilk," %10.6f\n", -llt);
3171: }
3172: } /* end of wave */
3173: } /* end of individual */
3174: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3175: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3176: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3177: if(globpr==0){ /* First time we count the contributions and weights */
3178: gipmx=ipmx;
3179: gsw=sw;
3180: }
3181: return -l;
3182: }
3183:
3184:
3185: /*************** function likelione ***********/
3186: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
3187: {
3188: /* This routine should help understanding what is done with
3189: the selection of individuals/waves and
3190: to check the exact contribution to the likelihood.
3191: Plotting could be done.
3192: */
3193: int k;
3194:
3195: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 3196: strcpy(fileresilk,"ILK_");
1.202 brouard 3197: strcat(fileresilk,fileresu);
1.126 brouard 3198: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
3199: printf("Problem with resultfile: %s\n", fileresilk);
3200: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
3201: }
1.214 brouard 3202: 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");
3203: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 3204: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
3205: for(k=1; k<=nlstate; k++)
3206: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
3207: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
3208: }
3209:
3210: *fretone=(*funcone)(p);
3211: if(*globpri !=0){
3212: fclose(ficresilk);
1.205 brouard 3213: if (mle ==0)
3214: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
3215: else if(mle >=1)
3216: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
3217: 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 3218:
1.208 brouard 3219:
3220: for (k=1; k<= nlstate ; k++) {
1.211 brouard 3221: 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 3222: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
3223: }
1.207 brouard 3224: 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 3225: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3226: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 3227: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3228: fflush(fichtm);
1.205 brouard 3229: }
1.126 brouard 3230: return;
3231: }
3232:
3233:
3234: /*********** Maximum Likelihood Estimation ***************/
3235:
3236: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
3237: {
1.165 brouard 3238: int i,j, iter=0;
1.126 brouard 3239: double **xi;
3240: double fret;
3241: double fretone; /* Only one call to likelihood */
3242: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 3243:
3244: #ifdef NLOPT
3245: int creturn;
3246: nlopt_opt opt;
3247: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
3248: double *lb;
3249: double minf; /* the minimum objective value, upon return */
3250: double * p1; /* Shifted parameters from 0 instead of 1 */
3251: myfunc_data dinst, *d = &dinst;
3252: #endif
3253:
3254:
1.126 brouard 3255: xi=matrix(1,npar,1,npar);
3256: for (i=1;i<=npar;i++)
3257: for (j=1;j<=npar;j++)
3258: xi[i][j]=(i==j ? 1.0 : 0.0);
3259: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 3260: strcpy(filerespow,"POW_");
1.126 brouard 3261: strcat(filerespow,fileres);
3262: if((ficrespow=fopen(filerespow,"w"))==NULL) {
3263: printf("Problem with resultfile: %s\n", filerespow);
3264: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
3265: }
3266: fprintf(ficrespow,"# Powell\n# iter -2*LL");
3267: for (i=1;i<=nlstate;i++)
3268: for(j=1;j<=nlstate+ndeath;j++)
3269: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
3270: fprintf(ficrespow,"\n");
1.162 brouard 3271: #ifdef POWELL
1.126 brouard 3272: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 3273: #endif
1.126 brouard 3274:
1.162 brouard 3275: #ifdef NLOPT
3276: #ifdef NEWUOA
3277: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
3278: #else
3279: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
3280: #endif
3281: lb=vector(0,npar-1);
3282: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
3283: nlopt_set_lower_bounds(opt, lb);
3284: nlopt_set_initial_step1(opt, 0.1);
3285:
3286: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
3287: d->function = func;
3288: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
3289: nlopt_set_min_objective(opt, myfunc, d);
3290: nlopt_set_xtol_rel(opt, ftol);
3291: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
3292: printf("nlopt failed! %d\n",creturn);
3293: }
3294: else {
3295: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
3296: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
3297: iter=1; /* not equal */
3298: }
3299: nlopt_destroy(opt);
3300: #endif
1.126 brouard 3301: free_matrix(xi,1,npar,1,npar);
3302: fclose(ficrespow);
1.203 brouard 3303: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
3304: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 3305: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 3306:
3307: }
3308:
3309: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 3310: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 3311: {
3312: double **a,**y,*x,pd;
1.203 brouard 3313: /* double **hess; */
1.164 brouard 3314: int i, j;
1.126 brouard 3315: int *indx;
3316:
3317: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 3318: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 3319: void lubksb(double **a, int npar, int *indx, double b[]) ;
3320: void ludcmp(double **a, int npar, int *indx, double *d) ;
3321: double gompertz(double p[]);
1.203 brouard 3322: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 3323:
3324: printf("\nCalculation of the hessian matrix. Wait...\n");
3325: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
3326: for (i=1;i<=npar;i++){
1.203 brouard 3327: printf("%d-",i);fflush(stdout);
3328: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 3329:
3330: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
3331:
3332: /* printf(" %f ",p[i]);
3333: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
3334: }
3335:
3336: for (i=1;i<=npar;i++) {
3337: for (j=1;j<=npar;j++) {
3338: if (j>i) {
1.203 brouard 3339: printf(".%d-%d",i,j);fflush(stdout);
3340: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
3341: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 3342:
3343: hess[j][i]=hess[i][j];
3344: /*printf(" %lf ",hess[i][j]);*/
3345: }
3346: }
3347: }
3348: printf("\n");
3349: fprintf(ficlog,"\n");
3350:
3351: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
3352: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
3353:
3354: a=matrix(1,npar,1,npar);
3355: y=matrix(1,npar,1,npar);
3356: x=vector(1,npar);
3357: indx=ivector(1,npar);
3358: for (i=1;i<=npar;i++)
3359: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
3360: ludcmp(a,npar,indx,&pd);
3361:
3362: for (j=1;j<=npar;j++) {
3363: for (i=1;i<=npar;i++) x[i]=0;
3364: x[j]=1;
3365: lubksb(a,npar,indx,x);
3366: for (i=1;i<=npar;i++){
3367: matcov[i][j]=x[i];
3368: }
3369: }
3370:
3371: printf("\n#Hessian matrix#\n");
3372: fprintf(ficlog,"\n#Hessian matrix#\n");
3373: for (i=1;i<=npar;i++) {
3374: for (j=1;j<=npar;j++) {
1.203 brouard 3375: printf("%.6e ",hess[i][j]);
3376: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 3377: }
3378: printf("\n");
3379: fprintf(ficlog,"\n");
3380: }
3381:
1.203 brouard 3382: /* printf("\n#Covariance matrix#\n"); */
3383: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
3384: /* for (i=1;i<=npar;i++) { */
3385: /* for (j=1;j<=npar;j++) { */
3386: /* printf("%.6e ",matcov[i][j]); */
3387: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
3388: /* } */
3389: /* printf("\n"); */
3390: /* fprintf(ficlog,"\n"); */
3391: /* } */
3392:
1.126 brouard 3393: /* Recompute Inverse */
1.203 brouard 3394: /* for (i=1;i<=npar;i++) */
3395: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
3396: /* ludcmp(a,npar,indx,&pd); */
3397:
3398: /* printf("\n#Hessian matrix recomputed#\n"); */
3399:
3400: /* for (j=1;j<=npar;j++) { */
3401: /* for (i=1;i<=npar;i++) x[i]=0; */
3402: /* x[j]=1; */
3403: /* lubksb(a,npar,indx,x); */
3404: /* for (i=1;i<=npar;i++){ */
3405: /* y[i][j]=x[i]; */
3406: /* printf("%.3e ",y[i][j]); */
3407: /* fprintf(ficlog,"%.3e ",y[i][j]); */
3408: /* } */
3409: /* printf("\n"); */
3410: /* fprintf(ficlog,"\n"); */
3411: /* } */
3412:
3413: /* Verifying the inverse matrix */
3414: #ifdef DEBUGHESS
3415: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 3416:
1.203 brouard 3417: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
3418: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 3419:
3420: for (j=1;j<=npar;j++) {
3421: for (i=1;i<=npar;i++){
1.203 brouard 3422: printf("%.2f ",y[i][j]);
3423: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 3424: }
3425: printf("\n");
3426: fprintf(ficlog,"\n");
3427: }
1.203 brouard 3428: #endif
1.126 brouard 3429:
3430: free_matrix(a,1,npar,1,npar);
3431: free_matrix(y,1,npar,1,npar);
3432: free_vector(x,1,npar);
3433: free_ivector(indx,1,npar);
1.203 brouard 3434: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 3435:
3436:
3437: }
3438:
3439: /*************** hessian matrix ****************/
3440: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 3441: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 3442: int i;
3443: int l=1, lmax=20;
1.203 brouard 3444: double k1,k2, res, fx;
1.132 brouard 3445: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 3446: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
3447: int k=0,kmax=10;
3448: double l1;
3449:
3450: fx=func(x);
3451: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 3452: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 3453: l1=pow(10,l);
3454: delts=delt;
3455: for(k=1 ; k <kmax; k=k+1){
3456: delt = delta*(l1*k);
3457: p2[theta]=x[theta] +delt;
1.145 brouard 3458: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 3459: p2[theta]=x[theta]-delt;
3460: k2=func(p2)-fx;
3461: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 3462: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 3463:
1.203 brouard 3464: #ifdef DEBUGHESSII
1.126 brouard 3465: 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);
3466: 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);
3467: #endif
3468: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
3469: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
3470: k=kmax;
3471: }
3472: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 3473: k=kmax; l=lmax*10;
1.126 brouard 3474: }
3475: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
3476: delts=delt;
3477: }
1.203 brouard 3478: } /* End loop k */
1.126 brouard 3479: }
3480: delti[theta]=delts;
3481: return res;
3482:
3483: }
3484:
1.203 brouard 3485: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 3486: {
3487: int i;
1.164 brouard 3488: int l=1, lmax=20;
1.126 brouard 3489: double k1,k2,k3,k4,res,fx;
1.132 brouard 3490: double p2[MAXPARM+1];
1.203 brouard 3491: int k, kmax=1;
3492: double v1, v2, cv12, lc1, lc2;
1.208 brouard 3493:
3494: int firstime=0;
1.203 brouard 3495:
1.126 brouard 3496: fx=func(x);
1.203 brouard 3497: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 3498: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 3499: p2[thetai]=x[thetai]+delti[thetai]*k;
3500: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3501: k1=func(p2)-fx;
3502:
1.203 brouard 3503: p2[thetai]=x[thetai]+delti[thetai]*k;
3504: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3505: k2=func(p2)-fx;
3506:
1.203 brouard 3507: p2[thetai]=x[thetai]-delti[thetai]*k;
3508: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3509: k3=func(p2)-fx;
3510:
1.203 brouard 3511: p2[thetai]=x[thetai]-delti[thetai]*k;
3512: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3513: k4=func(p2)-fx;
1.203 brouard 3514: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
3515: if(k1*k2*k3*k4 <0.){
1.208 brouard 3516: firstime=1;
1.203 brouard 3517: kmax=kmax+10;
1.208 brouard 3518: }
3519: if(kmax >=10 || firstime ==1){
1.218 brouard 3520: 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);
3521: 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 3522: 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);
3523: 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);
3524: }
3525: #ifdef DEBUGHESSIJ
3526: v1=hess[thetai][thetai];
3527: v2=hess[thetaj][thetaj];
3528: cv12=res;
3529: /* Computing eigen value of Hessian matrix */
3530: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3531: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3532: if ((lc2 <0) || (lc1 <0) ){
3533: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3534: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3535: 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);
3536: 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);
3537: }
1.126 brouard 3538: #endif
3539: }
3540: return res;
3541: }
3542:
1.203 brouard 3543: /* Not done yet: Was supposed to fix if not exactly at the maximum */
3544: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
3545: /* { */
3546: /* int i; */
3547: /* int l=1, lmax=20; */
3548: /* double k1,k2,k3,k4,res,fx; */
3549: /* double p2[MAXPARM+1]; */
3550: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
3551: /* int k=0,kmax=10; */
3552: /* double l1; */
3553:
3554: /* fx=func(x); */
3555: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
3556: /* l1=pow(10,l); */
3557: /* delts=delt; */
3558: /* for(k=1 ; k <kmax; k=k+1){ */
3559: /* delt = delti*(l1*k); */
3560: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
3561: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3562: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3563: /* k1=func(p2)-fx; */
3564:
3565: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3566: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3567: /* k2=func(p2)-fx; */
3568:
3569: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3570: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3571: /* k3=func(p2)-fx; */
3572:
3573: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3574: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3575: /* k4=func(p2)-fx; */
3576: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
3577: /* #ifdef DEBUGHESSIJ */
3578: /* 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); */
3579: /* 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); */
3580: /* #endif */
3581: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
3582: /* k=kmax; */
3583: /* } */
3584: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
3585: /* k=kmax; l=lmax*10; */
3586: /* } */
3587: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
3588: /* delts=delt; */
3589: /* } */
3590: /* } /\* End loop k *\/ */
3591: /* } */
3592: /* delti[theta]=delts; */
3593: /* return res; */
3594: /* } */
3595:
3596:
1.126 brouard 3597: /************** Inverse of matrix **************/
3598: void ludcmp(double **a, int n, int *indx, double *d)
3599: {
3600: int i,imax,j,k;
3601: double big,dum,sum,temp;
3602: double *vv;
3603:
3604: vv=vector(1,n);
3605: *d=1.0;
3606: for (i=1;i<=n;i++) {
3607: big=0.0;
3608: for (j=1;j<=n;j++)
3609: if ((temp=fabs(a[i][j])) > big) big=temp;
3610: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
3611: vv[i]=1.0/big;
3612: }
3613: for (j=1;j<=n;j++) {
3614: for (i=1;i<j;i++) {
3615: sum=a[i][j];
3616: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
3617: a[i][j]=sum;
3618: }
3619: big=0.0;
3620: for (i=j;i<=n;i++) {
3621: sum=a[i][j];
3622: for (k=1;k<j;k++)
3623: sum -= a[i][k]*a[k][j];
3624: a[i][j]=sum;
3625: if ( (dum=vv[i]*fabs(sum)) >= big) {
3626: big=dum;
3627: imax=i;
3628: }
3629: }
3630: if (j != imax) {
3631: for (k=1;k<=n;k++) {
3632: dum=a[imax][k];
3633: a[imax][k]=a[j][k];
3634: a[j][k]=dum;
3635: }
3636: *d = -(*d);
3637: vv[imax]=vv[j];
3638: }
3639: indx[j]=imax;
3640: if (a[j][j] == 0.0) a[j][j]=TINY;
3641: if (j != n) {
3642: dum=1.0/(a[j][j]);
3643: for (i=j+1;i<=n;i++) a[i][j] *= dum;
3644: }
3645: }
3646: free_vector(vv,1,n); /* Doesn't work */
3647: ;
3648: }
3649:
3650: void lubksb(double **a, int n, int *indx, double b[])
3651: {
3652: int i,ii=0,ip,j;
3653: double sum;
3654:
3655: for (i=1;i<=n;i++) {
3656: ip=indx[i];
3657: sum=b[ip];
3658: b[ip]=b[i];
3659: if (ii)
3660: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
3661: else if (sum) ii=i;
3662: b[i]=sum;
3663: }
3664: for (i=n;i>=1;i--) {
3665: sum=b[i];
3666: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
3667: b[i]=sum/a[i][i];
3668: }
3669: }
3670:
3671: void pstamp(FILE *fichier)
3672: {
1.196 brouard 3673: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 3674: }
3675:
3676: /************ Frequencies ********************/
1.220 brouard 3677: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
3678: int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
3679: int firstpass, int lastpass, int stepm, int weightopt, char model[])
3680: { /* Some frequencies */
3681:
3682: int i, m, jk, j1, bool, z1,j;
3683: int iind=0, iage=0;
3684: int mi; /* Effective wave */
3685: int first;
3686: double ***freq; /* Frequencies */
3687: double *pp, **prop, *posprop, *pospropt;
3688: double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
3689: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
3690: double agebegin, ageend;
3691:
3692: pp=vector(1,nlstate);
3693: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
3694: posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
3695: pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
3696: /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
3697: strcpy(fileresp,"P_");
3698: strcat(fileresp,fileresu);
3699: /*strcat(fileresphtm,fileresu);*/
3700: if((ficresp=fopen(fileresp,"w"))==NULL) {
3701: printf("Problem with prevalence resultfile: %s\n", fileresp);
3702: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
3703: exit(0);
3704: }
1.214 brouard 3705:
1.220 brouard 3706: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
3707: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
3708: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3709: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3710: fflush(ficlog);
3711: exit(70);
3712: }
3713: else{
3714: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.214 brouard 3715: <hr size=\"2\" color=\"#EC5E5E\"> \n\
3716: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.220 brouard 3717: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
3718: }
3719: 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 3720:
1.220 brouard 3721: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
3722: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
3723: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
3724: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
3725: fflush(ficlog);
3726: exit(70);
3727: }
3728: else{
3729: 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 3730: <hr size=\"2\" color=\"#EC5E5E\"> \n\
3731: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.220 brouard 3732: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
3733: }
3734: 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 3735:
1.220 brouard 3736: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
3737: j1=0;
1.126 brouard 3738:
1.220 brouard 3739: j=cptcoveff;
3740: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3741:
3742: first=1;
3743:
3744: /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
3745: reference=low_education V1=0,V2=0
3746: med_educ V1=1 V2=0,
3747: high_educ V1=0 V2=1
3748: Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
3749: */
1.126 brouard 3750:
1.220 brouard 3751: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ /* Loop on covariates combination */
3752: posproptt=0.;
3753: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
3754: scanf("%d", i);*/
3755: for (i=-5; i<=nlstate+ndeath; i++)
3756: for (jk=-5; jk<=nlstate+ndeath; jk++)
3757: for(m=iagemin; m <= iagemax+3; m++)
3758: freq[i][jk][m]=0;
3759:
3760: for (i=1; i<=nlstate; i++) {
3761: for(m=iagemin; m <= iagemax+3; m++)
3762: prop[i][m]=0;
3763: posprop[i]=0;
3764: pospropt[i]=0;
3765: }
3766:
3767: dateintsum=0;
3768: k2cpt=0;
1.126 brouard 3769:
1.220 brouard 3770: for (iind=1; iind<=imx; iind++) { /* For each individual iind */
3771: bool=1;
3772: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
3773: for (z1=1; z1<=cptcoveff; z1++) {
3774: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
3775: /* Tests if the value of each of the covariates of i is equal to filter j1 */
3776: bool=0;
3777: /* 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",
1.198 brouard 3778: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
3779: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
1.220 brouard 3780: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
3781: }
3782: } /* end z1 */
3783: } /* cptcovn > 0 */
3784:
3785: if (bool==1){
3786: /* for(m=firstpass; m<=lastpass; m++){ */
3787: for(mi=1; mi<wav[iind];mi++){
3788: m=mw[mi][iind];
3789: /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
3790: and mw[mi+1][iind]. dh depends on stepm. */
3791: agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
3792: ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
3793: if(m >=firstpass && m <=lastpass){
3794: k2=anint[m][iind]+(mint[m][iind]/12.);
3795: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
3796: if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
3797: if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
3798: if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
3799: prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
3800: if (m<lastpass) {
3801: /* if(s[m][iind]==4 && s[m+1][iind]==4) */
3802: /* 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]); */
3803: if(s[m][iind]==-1)
3804: 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.));
3805: freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
3806: /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
3807: 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 */
3808: }
3809: }
3810: if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
3811: dateintsum=dateintsum+k2;
3812: k2cpt++;
3813: /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
3814: }
3815: /*}*/
3816: } /* end m */
3817: } /* end bool */
3818: } /* end iind = 1 to imx */
3819: /* prop[s][age] is feeded for any initial and valid live state as well as
3820: freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
3821:
3822:
3823: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
3824: pstamp(ficresp);
3825: if (cptcovn>0) {
3826: fprintf(ficresp, "\n#********** Variable ");
3827: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
3828: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
3829: for (z1=1; z1<=cptcoveff; z1++){
3830: fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
3831: fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
3832: fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
3833: }
3834: fprintf(ficresp, "**********\n#");
3835: fprintf(ficresphtm, "**********</h3>\n");
3836: fprintf(ficresphtmfr, "**********</h3>\n");
3837: fprintf(ficlog, "\n#********** Variable ");
3838: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
3839: fprintf(ficlog, "**********\n");
3840: }
3841: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
3842: for(i=1; i<=nlstate;i++) {
3843: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
3844: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
3845: }
3846: fprintf(ficresp, "\n");
3847: fprintf(ficresphtm, "\n");
3848:
3849: /* Header of frequency table by age */
3850: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
3851: fprintf(ficresphtmfr,"<th>Age</th> ");
3852: for(jk=-1; jk <=nlstate+ndeath; jk++){
3853: for(m=-1; m <=nlstate+ndeath; m++){
3854: if(jk!=0 && m!=0)
3855: fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
3856: }
3857: }
3858: fprintf(ficresphtmfr, "\n");
1.214 brouard 3859:
1.220 brouard 3860: /* For each age */
3861: for(iage=iagemin; iage <= iagemax+3; iage++){
3862: fprintf(ficresphtm,"<tr>");
3863: if(iage==iagemax+1){
3864: fprintf(ficlog,"1");
3865: fprintf(ficresphtmfr,"<tr><th>0</th> ");
3866: }else if(iage==iagemax+2){
3867: fprintf(ficlog,"0");
3868: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
3869: }else if(iage==iagemax+3){
3870: fprintf(ficlog,"Total");
3871: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
3872: }else{
3873: if(first==1){
3874: first=0;
3875: printf("See log file for details...\n");
3876: }
3877: fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
3878: fprintf(ficlog,"Age %d", iage);
3879: }
3880: for(jk=1; jk <=nlstate ; jk++){
3881: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
3882: pp[jk] += freq[jk][m][iage];
3883: }
3884: for(jk=1; jk <=nlstate ; jk++){
3885: for(m=-1, pos=0; m <=0 ; m++)
3886: pos += freq[jk][m][iage];
3887: if(pp[jk]>=1.e-10){
3888: if(first==1){
3889: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3890: }
3891: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3892: }else{
3893: if(first==1)
3894: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3895: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3896: }
3897: }
3898:
3899: for(jk=1; jk <=nlstate ; jk++){
3900: /* posprop[jk]=0; */
3901: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
3902: pp[jk] += freq[jk][m][iage];
3903: } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
3904:
3905: for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
3906: pos += pp[jk]; /* pos is the total number of transitions until this age */
3907: posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
3908: from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
3909: pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
3910: from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
3911: }
3912: for(jk=1; jk <=nlstate ; jk++){
3913: if(pos>=1.e-5){
3914: if(first==1)
3915: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3916: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3917: }else{
3918: if(first==1)
3919: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3920: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3921: }
3922: if( iage <= iagemax){
3923: if(pos>=1.e-5){
3924: fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
3925: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
3926: /*probs[iage][jk][j1]= pp[jk]/pos;*/
3927: /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
3928: }
3929: else{
3930: fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
3931: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
3932: }
3933: }
3934: pospropt[jk] +=posprop[jk];
3935: } /* end loop jk */
3936: /* pospropt=0.; */
3937: for(jk=-1; jk <=nlstate+ndeath; jk++){
3938: for(m=-1; m <=nlstate+ndeath; m++){
3939: if(freq[jk][m][iage] !=0 ) { /* minimizing output */
3940: if(first==1){
3941: printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
3942: }
3943: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
3944: }
3945: if(jk!=0 && m!=0)
3946: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
3947: }
3948: } /* end loop jk */
3949: posproptt=0.;
3950: for(jk=1; jk <=nlstate; jk++){
3951: posproptt += pospropt[jk];
3952: }
3953: fprintf(ficresphtmfr,"</tr>\n ");
3954: if(iage <= iagemax){
3955: fprintf(ficresp,"\n");
3956: fprintf(ficresphtm,"</tr>\n");
3957: }
3958: if(first==1)
3959: printf("Others in log...\n");
3960: fprintf(ficlog,"\n");
3961: } /* end loop age iage */
3962: fprintf(ficresphtm,"<tr><th>Tot</th>");
3963: for(jk=1; jk <=nlstate ; jk++){
3964: if(posproptt < 1.e-5){
1.221 brouard 3965: fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);
3966: }else{
1.220 brouard 3967: fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);
3968: }
3969: }
3970: fprintf(ficresphtm,"</tr>\n");
3971: fprintf(ficresphtm,"</table>\n");
3972: fprintf(ficresphtmfr,"</table>\n");
3973: if(posproptt < 1.e-5){
3974: fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
3975: fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
3976: fprintf(ficres,"\n This combination (%d) is not valid and no result will be produced\n\n",j1);
3977: invalidvarcomb[j1]=1;
3978: }else{
3979: fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
3980: invalidvarcomb[j1]=0;
3981: }
3982: fprintf(ficresphtmfr,"</table>\n");
3983: } /* end selected combination of covariate j1 */
3984: dateintmean=dateintsum/k2cpt;
3985:
3986: fclose(ficresp);
3987: fclose(ficresphtm);
3988: fclose(ficresphtmfr);
3989: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
3990: free_vector(pospropt,1,nlstate);
3991: free_vector(posprop,1,nlstate);
3992: free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
3993: free_vector(pp,1,nlstate);
3994: /* End of Freq */
3995: }
1.126 brouard 3996:
3997: /************ Prevalence ********************/
1.222 ! brouard 3998: 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)
! 3999: {
! 4000: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
! 4001: in each health status at the date of interview (if between dateprev1 and dateprev2).
! 4002: We still use firstpass and lastpass as another selection.
! 4003: */
1.126 brouard 4004:
1.222 ! brouard 4005: int i, m, jk, j1, bool, z1,j;
! 4006: int mi; /* Effective wave */
! 4007: int iage;
! 4008: double agebegin, ageend;
! 4009:
! 4010: double **prop;
! 4011: double posprop;
! 4012: double y2; /* in fractional years */
! 4013: int iagemin, iagemax;
! 4014: int first; /** to stop verbosity which is redirected to log file */
! 4015:
! 4016: iagemin= (int) agemin;
! 4017: iagemax= (int) agemax;
! 4018: /*pp=vector(1,nlstate);*/
! 4019: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
! 4020: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
! 4021: j1=0;
! 4022:
! 4023: /*j=cptcoveff;*/
! 4024: if (cptcovn<1) {j=1;ncodemax[1]=1;}
! 4025:
! 4026: first=1;
! 4027: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
! 4028: for (i=1; i<=nlstate; i++)
! 4029: for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
! 4030: prop[i][iage]=0.0;
! 4031:
! 4032: for (i=1; i<=imx; i++) { /* Each individual */
! 4033: bool=1;
! 4034: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
! 4035: for (z1=1; z1<=cptcoveff; z1++) /* For each covariate, look at the value for individual i and checks if it is equal to the corresponding value of this covariate according to current combination j1*/
! 4036: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
! 4037: bool=0;
! 4038: }
! 4039: if (bool==1) { /* For this combination of covariates values, this individual fits */
! 4040: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
! 4041: for(mi=1; mi<wav[i];mi++){
! 4042: m=mw[mi][i];
! 4043: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
! 4044: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
! 4045: if(m >=firstpass && m <=lastpass){
! 4046: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
! 4047: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
! 4048: if(agev[m][i]==0) agev[m][i]=iagemax+1;
! 4049: if(agev[m][i]==1) agev[m][i]=iagemax+2;
! 4050: if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
! 4051: 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);
! 4052: exit(1);
! 4053: }
! 4054: if (s[m][i]>0 && s[m][i]<=nlstate) {
! 4055: /*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]]);*/
! 4056: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
! 4057: prop[s[m][i]][iagemax+3] += weight[i];
! 4058: } /* end valid statuses */
! 4059: } /* end selection of dates */
! 4060: } /* end selection of waves */
! 4061: } /* end effective waves */
! 4062: } /* end bool */
! 4063: }
! 4064: for(i=iagemin; i <= iagemax+3; i++){
! 4065: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
! 4066: posprop += prop[jk][i];
! 4067: }
! 4068:
! 4069: for(jk=1; jk <=nlstate ; jk++){
! 4070: if( i <= iagemax){
! 4071: if(posprop>=1.e-5){
! 4072: probs[i][jk][j1]= prop[jk][i]/posprop;
! 4073: } else{
! 4074: if(first==1){
! 4075: first=0;
! 4076: printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
! 4077: }
! 4078: }
! 4079: }
! 4080: }/* end jk */
! 4081: }/* end i */
! 4082: /*} *//* end i1 */
! 4083: } /* end j1 */
! 4084:
! 4085: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
! 4086: /*free_vector(pp,1,nlstate);*/
! 4087: free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
! 4088: } /* End of prevalence */
1.126 brouard 4089:
4090: /************* Waves Concatenation ***************/
4091:
4092: 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)
4093: {
4094: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
4095: Death is a valid wave (if date is known).
4096: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
4097: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
4098: and mw[mi+1][i]. dh depends on stepm.
4099: */
4100:
4101: int i, mi, m;
4102: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
4103: double sum=0., jmean=0.;*/
1.218 brouard 4104: int first, firstwo, firsthree, firstfour;
1.126 brouard 4105: int j, k=0,jk, ju, jl;
4106: double sum=0.;
4107: first=0;
1.214 brouard 4108: firstwo=0;
1.217 brouard 4109: firsthree=0;
1.218 brouard 4110: firstfour=0;
1.164 brouard 4111: jmin=100000;
1.126 brouard 4112: jmax=-1;
4113: jmean=0.;
1.214 brouard 4114: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.126 brouard 4115: mi=0;
4116: m=firstpass;
1.214 brouard 4117: while(s[m][i] <= nlstate){ /* a live state */
1.216 brouard 4118: 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 */
1.126 brouard 4119: mw[++mi][i]=m;
1.216 brouard 4120: }
4121: if(m >=lastpass){
4122: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
1.217 brouard 4123: if(firsthree == 0){
4124: printf("Information! Unknown health 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.\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);
4125: firsthree=1;
4126: }
1.218 brouard 4127: 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.\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);
1.216 brouard 4128: mw[++mi][i]=m;
4129: }
4130: if(s[m][i]==-2){ /* Vital status is really unknown */
4131: nbwarn++;
4132: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */
4133: 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);
4134: 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.\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);
4135: }
4136: break;
4137: }
1.126 brouard 4138: break;
1.216 brouard 4139: }
1.126 brouard 4140: else
4141: m++;
4142: }/* end while */
1.216 brouard 4143:
4144: /* After last pass */
1.214 brouard 4145: if (s[m][i] > nlstate){ /* In a death state */
1.126 brouard 4146: mi++; /* Death is another wave */
4147: /* if(mi==0) never been interviewed correctly before death */
4148: /* Only death is a correct wave */
4149: mw[mi][i]=m;
1.216 brouard 4150: }else if ((int) andc[i] != 9999) { /* Status is either death or negative. A death occured after lastpass, we can't take it into account because of potential bias */
4151: /* m++; */
4152: /* mi++; */
4153: /* s[m][i]=nlstate+1; /\* We are setting the status to the last of non live state *\/ */
4154: /* mw[mi][i]=m; */
4155: nberr++;
1.218 brouard 4156: if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
4157: if(firstwo==0){
4158: printf("Error! Death for individual %ld line=%d occurred %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 );
4159: firstwo=1;
4160: }
4161: fprintf(ficlog,"Error! Death for individual %ld line=%d occurred %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 );
4162: }else{ /* end date of interview is known */
4163: /* death is known but not confirmed by death status at any wave */
4164: if(firstfour==0){
4165: 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 );
4166: firstfour=1;
4167: }
4168: 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 4169: }
1.126 brouard 4170: }
4171: wav[i]=mi;
4172: if(mi==0){
4173: nbwarn++;
4174: if(first==0){
4175: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
4176: first=1;
4177: }
4178: if(first==1){
4179: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
4180: }
4181: } /* end mi==0 */
4182: } /* End individuals */
1.214 brouard 4183: /* wav and mw are no more changed */
1.126 brouard 4184:
1.214 brouard 4185:
1.126 brouard 4186: for(i=1; i<=imx; i++){
4187: for(mi=1; mi<wav[i];mi++){
4188: if (stepm <=0)
4189: dh[mi][i]=1;
4190: else{
4191: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
4192: if (agedc[i] < 2*AGESUP) {
4193: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
4194: if(j==0) j=1; /* Survives at least one month after exam */
4195: else if(j<0){
4196: nberr++;
4197: 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]);
4198: j=1; /* Temporary Dangerous patch */
4199: 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);
4200: 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]);
4201: 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);
4202: }
4203: k=k+1;
4204: if (j >= jmax){
4205: jmax=j;
4206: ijmax=i;
4207: }
4208: if (j <= jmin){
4209: jmin=j;
4210: ijmin=i;
4211: }
4212: sum=sum+j;
4213: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
4214: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
4215: }
4216: }
4217: else{
4218: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
4219: /* 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]); */
4220:
4221: k=k+1;
4222: if (j >= jmax) {
4223: jmax=j;
4224: ijmax=i;
4225: }
4226: else if (j <= jmin){
4227: jmin=j;
4228: ijmin=i;
4229: }
4230: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
4231: /*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]);*/
4232: if(j<0){
4233: nberr++;
4234: 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]);
4235: 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]);
4236: }
4237: sum=sum+j;
4238: }
4239: jk= j/stepm;
4240: jl= j -jk*stepm;
4241: ju= j -(jk+1)*stepm;
4242: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
4243: if(jl==0){
4244: dh[mi][i]=jk;
4245: bh[mi][i]=0;
4246: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 4247: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 4248: dh[mi][i]=jk+1;
4249: bh[mi][i]=ju;
4250: }
4251: }else{
4252: if(jl <= -ju){
4253: dh[mi][i]=jk;
4254: bh[mi][i]=jl; /* bias is positive if real duration
4255: * is higher than the multiple of stepm and negative otherwise.
4256: */
4257: }
4258: else{
4259: dh[mi][i]=jk+1;
4260: bh[mi][i]=ju;
4261: }
4262: if(dh[mi][i]==0){
4263: dh[mi][i]=1; /* At least one step */
4264: bh[mi][i]=ju; /* At least one step */
4265: /* 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);*/
4266: }
4267: } /* end if mle */
4268: }
4269: } /* end wave */
4270: }
4271: jmean=sum/k;
4272: 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 4273: 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);
1.126 brouard 4274: }
4275:
4276: /*********** Tricode ****************************/
1.220 brouard 4277: void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 4278: {
1.144 brouard 4279: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
4280: /* 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 4281: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 4282: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.220 brouard 4283: * nbcode[Tvar[5]][1]= nbcode[2][1]=0, nbcode[2][2]=1 (usually);
1.144 brouard 4284: */
1.130 brouard 4285:
1.145 brouard 4286: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 4287: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 4288: int cptcode=0; /* Modality max of covariates j */
4289: int modmincovj=0; /* Modality min of covariates j */
4290:
4291:
1.220 brouard 4292: /* cptcoveff=0; */
4293: *cptcov=0;
1.126 brouard 4294:
1.144 brouard 4295: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 4296:
1.145 brouard 4297: /* Loop on covariates without age and products */
1.186 brouard 4298: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
1.192 brouard 4299: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.186 brouard 4300: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.219 brouard 4301: modality of this covariate Vj*/
1.145 brouard 4302: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
1.219 brouard 4303: * If product of Vn*Vm, still boolean *:
4304: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
4305: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
1.145 brouard 4306: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 4307: modality of the nth covariate of individual i. */
1.145 brouard 4308: if (ij > modmaxcovj)
4309: modmaxcovj=ij;
4310: else if (ij < modmincovj)
1.219 brouard 4311: modmincovj=ij;
1.145 brouard 4312: if ((ij < -1) && (ij > NCOVMAX)){
1.219 brouard 4313: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
4314: exit(1);
1.145 brouard 4315: }else
1.136 brouard 4316: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 4317: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 4318: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 4319: /* getting the maximum value of the modality of the covariate
4320: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
4321: female is 1, then modmaxcovj=1.*/
1.192 brouard 4322: } /* end for loop on individuals i */
1.145 brouard 4323: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.192 brouard 4324: fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.145 brouard 4325: cptcode=modmaxcovj;
1.137 brouard 4326: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 4327: /*for (i=0; i<=cptcode; i++) {*/
1.192 brouard 4328: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
4329: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
4330: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
4331: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
1.219 brouard 4332: if( k != -1){
4333: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
4334: covariate for which somebody answered excluding
4335: undefined. Usually 2: 0 and 1. */
4336: }
4337: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
4338: covariate for which somebody answered including
4339: undefined. Usually 3: -1, 0 and 1. */
1.145 brouard 4340: }
4341: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
1.219 brouard 4342: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 4343: } /* Ndum[-1] number of undefined modalities */
1.219 brouard 4344:
1.136 brouard 4345: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 4346: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
4347: If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
1.145 brouard 4348: modmincovj=3; modmaxcovj = 7;
1.186 brouard 4349: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
4350: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
4351: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 4352: nbcode[Tvar[j]][ij]=k;
4353: nbcode[Tvar[j]][1]=0;
4354: nbcode[Tvar[j]][2]=1;
4355: nbcode[Tvar[j]][3]=2;
1.197 brouard 4356: To be continued (not working yet).
1.145 brouard 4357: */
1.197 brouard 4358: ij=0; /* ij is similar to i but can jump over null modalities */
4359: 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*/
4360: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
1.219 brouard 4361: break;
4362: }
1.192 brouard 4363: ij++;
1.197 brouard 4364: nbcode[Tvar[j]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
1.192 brouard 4365: cptcode = ij; /* New max modality for covar j */
4366: } /* end of loop on modality i=-1 to 1 or more */
4367:
4368: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
4369: /* /\*recode from 0 *\/ */
4370: /* k is a modality. If we have model=V1+V1*sex */
4371: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
4372: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
4373: /* } */
4374: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
4375: /* if (ij > ncodemax[j]) { */
4376: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4377: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4378: /* break; */
4379: /* } */
4380: /* } /\* end of loop on modality k *\/ */
1.137 brouard 4381: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
4382:
1.219 brouard 4383: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 4384:
1.187 brouard 4385: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.219 brouard 4386: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
4387: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
4388: Ndum[ij]++; /* Might be supersed V1 + V1*age */
4389: }
4390:
4391: ij=0;
4392: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
4393: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
4394: if((Ndum[i]!=0) && (i<=ncovcol)){
4395: ij++;
4396: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
4397: Tvaraff[ij]=i; /*For printing (unclear) */
4398: }else{
4399: /* Tvaraff[ij]=0; */
4400: }
4401: }
4402: /* ij--; */
1.220 brouard 4403: /* cptcoveff=ij; /\*Number of total covariates*\/ */
4404: *cptcov=ij; /*Number of total covariates*/
1.219 brouard 4405:
1.126 brouard 4406: }
4407:
1.145 brouard 4408:
1.126 brouard 4409: /*********** Health Expectancies ****************/
4410:
1.127 brouard 4411: 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 4412:
4413: {
4414: /* Health expectancies, no variances */
1.164 brouard 4415: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 4416: int nhstepma, nstepma; /* Decreasing with age */
4417: double age, agelim, hf;
4418: double ***p3mat;
4419: double eip;
4420:
4421: pstamp(ficreseij);
4422: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
4423: fprintf(ficreseij,"# Age");
4424: for(i=1; i<=nlstate;i++){
4425: for(j=1; j<=nlstate;j++){
4426: fprintf(ficreseij," e%1d%1d ",i,j);
4427: }
4428: fprintf(ficreseij," e%1d. ",i);
4429: }
4430: fprintf(ficreseij,"\n");
4431:
4432:
4433: if(estepm < stepm){
4434: printf ("Problem %d lower than %d\n",estepm, stepm);
4435: }
4436: else hstepm=estepm;
4437: /* We compute the life expectancy from trapezoids spaced every estepm months
4438: * This is mainly to measure the difference between two models: for example
4439: * if stepm=24 months pijx are given only every 2 years and by summing them
4440: * we are calculating an estimate of the Life Expectancy assuming a linear
4441: * progression in between and thus overestimating or underestimating according
4442: * to the curvature of the survival function. If, for the same date, we
4443: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4444: * to compare the new estimate of Life expectancy with the same linear
4445: * hypothesis. A more precise result, taking into account a more precise
4446: * curvature will be obtained if estepm is as small as stepm. */
4447:
4448: /* For example we decided to compute the life expectancy with the smallest unit */
4449: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4450: nhstepm is the number of hstepm from age to agelim
4451: nstepm is the number of stepm from age to agelin.
4452: Look at hpijx to understand the reason of that which relies in memory size
4453: and note for a fixed period like estepm months */
4454: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4455: survival function given by stepm (the optimization length). Unfortunately it
4456: means that if the survival funtion is printed only each two years of age and if
4457: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4458: results. So we changed our mind and took the option of the best precision.
4459: */
4460: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4461:
4462: agelim=AGESUP;
4463: /* If stepm=6 months */
4464: /* Computed by stepm unit matrices, product of hstepm matrices, stored
4465: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
4466:
4467: /* nhstepm age range expressed in number of stepm */
4468: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4469: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4470: /* if (stepm >= YEARM) hstepm=1;*/
4471: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4472: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4473:
4474: for (age=bage; age<=fage; age ++){
4475: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4476: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4477: /* if (stepm >= YEARM) hstepm=1;*/
4478: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
4479:
4480: /* If stepm=6 months */
4481: /* Computed by stepm unit matrices, product of hstepma matrices, stored
4482: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
4483:
4484: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
4485:
4486: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4487:
4488: printf("%d|",(int)age);fflush(stdout);
4489: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
4490:
4491: /* Computing expectancies */
4492: for(i=1; i<=nlstate;i++)
4493: for(j=1; j<=nlstate;j++)
4494: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
4495: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
4496:
4497: /* 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]);*/
4498:
4499: }
4500:
4501: fprintf(ficreseij,"%3.0f",age );
4502: for(i=1; i<=nlstate;i++){
4503: eip=0;
4504: for(j=1; j<=nlstate;j++){
4505: eip +=eij[i][j][(int)age];
4506: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
4507: }
4508: fprintf(ficreseij,"%9.4f", eip );
4509: }
4510: fprintf(ficreseij,"\n");
4511:
4512: }
4513: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4514: printf("\n");
4515: fprintf(ficlog,"\n");
4516:
4517: }
4518:
1.127 brouard 4519: 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 4520:
4521: {
4522: /* Covariances of health expectancies eij and of total life expectancies according
1.222 ! brouard 4523: to initial status i, ei. .
1.126 brouard 4524: */
4525: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
4526: int nhstepma, nstepma; /* Decreasing with age */
4527: double age, agelim, hf;
4528: double ***p3matp, ***p3matm, ***varhe;
4529: double **dnewm,**doldm;
4530: double *xp, *xm;
4531: double **gp, **gm;
4532: double ***gradg, ***trgradg;
4533: int theta;
4534:
4535: double eip, vip;
4536:
4537: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
4538: xp=vector(1,npar);
4539: xm=vector(1,npar);
4540: dnewm=matrix(1,nlstate*nlstate,1,npar);
4541: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
4542:
4543: pstamp(ficresstdeij);
4544: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
4545: fprintf(ficresstdeij,"# Age");
4546: for(i=1; i<=nlstate;i++){
4547: for(j=1; j<=nlstate;j++)
4548: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
4549: fprintf(ficresstdeij," e%1d. ",i);
4550: }
4551: fprintf(ficresstdeij,"\n");
4552:
4553: pstamp(ficrescveij);
4554: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
4555: fprintf(ficrescveij,"# Age");
4556: for(i=1; i<=nlstate;i++)
4557: for(j=1; j<=nlstate;j++){
4558: cptj= (j-1)*nlstate+i;
4559: for(i2=1; i2<=nlstate;i2++)
4560: for(j2=1; j2<=nlstate;j2++){
4561: cptj2= (j2-1)*nlstate+i2;
4562: if(cptj2 <= cptj)
4563: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
4564: }
4565: }
4566: fprintf(ficrescveij,"\n");
4567:
4568: if(estepm < stepm){
4569: printf ("Problem %d lower than %d\n",estepm, stepm);
4570: }
4571: else hstepm=estepm;
4572: /* We compute the life expectancy from trapezoids spaced every estepm months
4573: * This is mainly to measure the difference between two models: for example
4574: * if stepm=24 months pijx are given only every 2 years and by summing them
4575: * we are calculating an estimate of the Life Expectancy assuming a linear
4576: * progression in between and thus overestimating or underestimating according
4577: * to the curvature of the survival function. If, for the same date, we
4578: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4579: * to compare the new estimate of Life expectancy with the same linear
4580: * hypothesis. A more precise result, taking into account a more precise
4581: * curvature will be obtained if estepm is as small as stepm. */
4582:
4583: /* For example we decided to compute the life expectancy with the smallest unit */
4584: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4585: nhstepm is the number of hstepm from age to agelim
4586: nstepm is the number of stepm from age to agelin.
4587: Look at hpijx to understand the reason of that which relies in memory size
4588: and note for a fixed period like estepm months */
4589: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4590: survival function given by stepm (the optimization length). Unfortunately it
4591: means that if the survival funtion is printed only each two years of age and if
4592: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4593: results. So we changed our mind and took the option of the best precision.
4594: */
4595: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4596:
4597: /* If stepm=6 months */
4598: /* nhstepm age range expressed in number of stepm */
4599: agelim=AGESUP;
4600: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
4601: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4602: /* if (stepm >= YEARM) hstepm=1;*/
4603: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4604:
4605: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4606: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4607: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
4608: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
4609: gp=matrix(0,nhstepm,1,nlstate*nlstate);
4610: gm=matrix(0,nhstepm,1,nlstate*nlstate);
4611:
4612: for (age=bage; age<=fage; age ++){
4613: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4614: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4615: /* if (stepm >= YEARM) hstepm=1;*/
4616: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218 brouard 4617:
1.126 brouard 4618: /* If stepm=6 months */
4619: /* Computed by stepm unit matrices, product of hstepma matrices, stored
4620: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
4621:
4622: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.218 brouard 4623:
1.126 brouard 4624: /* Computing Variances of health expectancies */
4625: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
4626: decrease memory allocation */
4627: for(theta=1; theta <=npar; theta++){
4628: for(i=1; i<=npar; i++){
1.222 ! brouard 4629: xp[i] = x[i] + (i==theta ?delti[theta]:0);
! 4630: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126 brouard 4631: }
4632: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
4633: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
1.218 brouard 4634:
1.126 brouard 4635: for(j=1; j<= nlstate; j++){
1.222 ! brouard 4636: for(i=1; i<=nlstate; i++){
! 4637: for(h=0; h<=nhstepm-1; h++){
! 4638: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
! 4639: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
! 4640: }
! 4641: }
1.126 brouard 4642: }
1.218 brouard 4643:
1.126 brouard 4644: for(ij=1; ij<= nlstate*nlstate; ij++)
1.222 ! brouard 4645: for(h=0; h<=nhstepm-1; h++){
! 4646: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
! 4647: }
1.126 brouard 4648: }/* End theta */
4649:
4650:
4651: for(h=0; h<=nhstepm-1; h++)
4652: for(j=1; j<=nlstate*nlstate;j++)
1.222 ! brouard 4653: for(theta=1; theta <=npar; theta++)
! 4654: trgradg[h][j][theta]=gradg[h][theta][j];
1.126 brouard 4655:
1.218 brouard 4656:
1.222 ! brouard 4657: for(ij=1;ij<=nlstate*nlstate;ij++)
1.126 brouard 4658: for(ji=1;ji<=nlstate*nlstate;ji++)
1.222 ! brouard 4659: varhe[ij][ji][(int)age] =0.;
1.218 brouard 4660:
1.222 ! brouard 4661: printf("%d|",(int)age);fflush(stdout);
! 4662: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
! 4663: for(h=0;h<=nhstepm-1;h++){
1.126 brouard 4664: for(k=0;k<=nhstepm-1;k++){
1.222 ! brouard 4665: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
! 4666: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
! 4667: for(ij=1;ij<=nlstate*nlstate;ij++)
! 4668: for(ji=1;ji<=nlstate*nlstate;ji++)
! 4669: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126 brouard 4670: }
4671: }
1.218 brouard 4672:
1.126 brouard 4673: /* Computing expectancies */
4674: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
4675: for(i=1; i<=nlstate;i++)
4676: for(j=1; j<=nlstate;j++)
1.222 ! brouard 4677: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
! 4678: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.218 brouard 4679:
1.222 ! brouard 4680: /* 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 4681:
1.222 ! brouard 4682: }
1.218 brouard 4683:
1.126 brouard 4684: fprintf(ficresstdeij,"%3.0f",age );
4685: for(i=1; i<=nlstate;i++){
4686: eip=0.;
4687: vip=0.;
4688: for(j=1; j<=nlstate;j++){
1.222 ! brouard 4689: eip += eij[i][j][(int)age];
! 4690: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
! 4691: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
! 4692: 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 4693: }
4694: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
4695: }
4696: fprintf(ficresstdeij,"\n");
1.218 brouard 4697:
1.126 brouard 4698: fprintf(ficrescveij,"%3.0f",age );
4699: for(i=1; i<=nlstate;i++)
4700: for(j=1; j<=nlstate;j++){
1.222 ! brouard 4701: cptj= (j-1)*nlstate+i;
! 4702: for(i2=1; i2<=nlstate;i2++)
! 4703: for(j2=1; j2<=nlstate;j2++){
! 4704: cptj2= (j2-1)*nlstate+i2;
! 4705: if(cptj2 <= cptj)
! 4706: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
! 4707: }
1.126 brouard 4708: }
4709: fprintf(ficrescveij,"\n");
1.218 brouard 4710:
1.126 brouard 4711: }
4712: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
4713: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
4714: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
4715: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
4716: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4717: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4718: printf("\n");
4719: fprintf(ficlog,"\n");
1.218 brouard 4720:
1.126 brouard 4721: free_vector(xm,1,npar);
4722: free_vector(xp,1,npar);
4723: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
4724: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
4725: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
4726: }
1.218 brouard 4727:
1.126 brouard 4728: /************ Variance ******************/
1.209 brouard 4729: 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 4730: {
4731: /* Variance of health expectancies */
4732: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
4733: /* double **newm;*/
4734: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
4735:
4736: /* int movingaverage(); */
4737: double **dnewm,**doldm;
4738: double **dnewmp,**doldmp;
4739: int i, j, nhstepm, hstepm, h, nstepm ;
4740: int k;
4741: double *xp;
4742: double **gp, **gm; /* for var eij */
4743: double ***gradg, ***trgradg; /*for var eij */
4744: double **gradgp, **trgradgp; /* for var p point j */
4745: double *gpp, *gmp; /* for var p point j */
4746: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
4747: double ***p3mat;
4748: double age,agelim, hf;
4749: /* double ***mobaverage; */
4750: int theta;
4751: char digit[4];
4752: char digitp[25];
4753:
4754: char fileresprobmorprev[FILENAMELENGTH];
4755:
4756: if(popbased==1){
4757: if(mobilav!=0)
4758: strcpy(digitp,"-POPULBASED-MOBILAV_");
4759: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
4760: }
4761: else
4762: strcpy(digitp,"-STABLBASED_");
1.126 brouard 4763:
1.218 brouard 4764: /* if (mobilav!=0) { */
4765: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
4766: /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
4767: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
4768: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
4769: /* } */
4770: /* } */
4771:
4772: strcpy(fileresprobmorprev,"PRMORPREV-");
4773: sprintf(digit,"%-d",ij);
4774: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
4775: strcat(fileresprobmorprev,digit); /* Tvar to be done */
4776: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
4777: strcat(fileresprobmorprev,fileresu);
4778: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
4779: printf("Problem with resultfile: %s\n", fileresprobmorprev);
4780: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
4781: }
4782: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4783: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4784: pstamp(ficresprobmorprev);
4785: 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);
4786: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
4787: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4788: fprintf(ficresprobmorprev," p.%-d SE",j);
4789: for(i=1; i<=nlstate;i++)
4790: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
4791: }
4792: fprintf(ficresprobmorprev,"\n");
4793:
4794: fprintf(ficgp,"\n# Routine varevsij");
4795: fprintf(ficgp,"\nunset title \n");
4796: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
4797: 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");
4798: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
4799: /* } */
4800: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4801: pstamp(ficresvij);
4802: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
4803: if(popbased==1)
4804: 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);
4805: else
4806: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
4807: fprintf(ficresvij,"# Age");
4808: for(i=1; i<=nlstate;i++)
4809: for(j=1; j<=nlstate;j++)
4810: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
4811: fprintf(ficresvij,"\n");
4812:
4813: xp=vector(1,npar);
4814: dnewm=matrix(1,nlstate,1,npar);
4815: doldm=matrix(1,nlstate,1,nlstate);
4816: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
4817: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4818:
4819: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
4820: gpp=vector(nlstate+1,nlstate+ndeath);
4821: gmp=vector(nlstate+1,nlstate+ndeath);
4822: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126 brouard 4823:
1.218 brouard 4824: if(estepm < stepm){
4825: printf ("Problem %d lower than %d\n",estepm, stepm);
4826: }
4827: else hstepm=estepm;
4828: /* For example we decided to compute the life expectancy with the smallest unit */
4829: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4830: nhstepm is the number of hstepm from age to agelim
4831: nstepm is the number of stepm from age to agelim.
4832: Look at function hpijx to understand why because of memory size limitations,
4833: we decided (b) to get a life expectancy respecting the most precise curvature of the
4834: survival function given by stepm (the optimization length). Unfortunately it
4835: means that if the survival funtion is printed every two years of age and if
4836: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4837: results. So we changed our mind and took the option of the best precision.
4838: */
4839: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4840: agelim = AGESUP;
4841: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4842: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4843: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4844: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4845: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
4846: gp=matrix(0,nhstepm,1,nlstate);
4847: gm=matrix(0,nhstepm,1,nlstate);
4848:
4849:
4850: for(theta=1; theta <=npar; theta++){
4851: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
4852: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4853: }
4854:
4855: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
4856:
4857: if (popbased==1) {
4858: if(mobilav ==0){
4859: for(i=1; i<=nlstate;i++)
4860: prlim[i][i]=probs[(int)age][i][ij];
4861: }else{ /* mobilav */
4862: for(i=1; i<=nlstate;i++)
4863: prlim[i][i]=mobaverage[(int)age][i][ij];
4864: }
4865: }
4866:
4867: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); /* Returns p3mat[i][j][h] for h=1 to nhstepm */
4868: for(j=1; j<= nlstate; j++){
4869: for(h=0; h<=nhstepm; h++){
4870: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
4871: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
4872: }
4873: }
4874: /* Next for computing probability of death (h=1 means
4875: computed over hstepm matrices product = hstepm*stepm months)
4876: as a weighted average of prlim.
4877: */
4878: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4879: for(i=1,gpp[j]=0.; i<= nlstate; i++)
4880: gpp[j] += prlim[i][i]*p3mat[i][j][1];
4881: }
4882: /* end probability of death */
4883:
4884: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
4885: xp[i] = x[i] - (i==theta ?delti[theta]:0);
4886:
4887: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
4888:
4889: if (popbased==1) {
4890: if(mobilav ==0){
4891: for(i=1; i<=nlstate;i++)
4892: prlim[i][i]=probs[(int)age][i][ij];
4893: }else{ /* mobilav */
4894: for(i=1; i<=nlstate;i++)
4895: prlim[i][i]=mobaverage[(int)age][i][ij];
4896: }
4897: }
4898:
4899: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
4900:
4901: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
4902: for(h=0; h<=nhstepm; h++){
4903: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
4904: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
4905: }
4906: }
4907: /* This for computing probability of death (h=1 means
4908: computed over hstepm matrices product = hstepm*stepm months)
4909: as a weighted average of prlim.
4910: */
4911: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4912: for(i=1,gmp[j]=0.; i<= nlstate; i++)
4913: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4914: }
4915: /* end probability of death */
4916:
4917: for(j=1; j<= nlstate; j++) /* vareij */
4918: for(h=0; h<=nhstepm; h++){
4919: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
4920: }
4921:
4922: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
4923: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
4924: }
4925:
4926: } /* End theta */
4927:
4928: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
4929:
4930: for(h=0; h<=nhstepm; h++) /* veij */
4931: for(j=1; j<=nlstate;j++)
4932: for(theta=1; theta <=npar; theta++)
4933: trgradg[h][j][theta]=gradg[h][theta][j];
4934:
4935: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
4936: for(theta=1; theta <=npar; theta++)
4937: trgradgp[j][theta]=gradgp[theta][j];
4938:
4939:
4940: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4941: for(i=1;i<=nlstate;i++)
4942: for(j=1;j<=nlstate;j++)
4943: vareij[i][j][(int)age] =0.;
4944:
4945: for(h=0;h<=nhstepm;h++){
4946: for(k=0;k<=nhstepm;k++){
4947: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
4948: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
4949: for(i=1;i<=nlstate;i++)
4950: for(j=1;j<=nlstate;j++)
4951: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
4952: }
4953: }
4954:
4955: /* pptj */
4956: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
4957: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
4958: for(j=nlstate+1;j<=nlstate+ndeath;j++)
4959: for(i=nlstate+1;i<=nlstate+ndeath;i++)
4960: varppt[j][i]=doldmp[j][i];
4961: /* end ppptj */
4962: /* x centered again */
4963:
4964: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
4965:
4966: if (popbased==1) {
4967: if(mobilav ==0){
4968: for(i=1; i<=nlstate;i++)
4969: prlim[i][i]=probs[(int)age][i][ij];
4970: }else{ /* mobilav */
4971: for(i=1; i<=nlstate;i++)
4972: prlim[i][i]=mobaverage[(int)age][i][ij];
4973: }
4974: }
4975:
4976: /* This for computing probability of death (h=1 means
4977: computed over hstepm (estepm) matrices product = hstepm*stepm months)
4978: as a weighted average of prlim.
4979: */
4980: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
4981: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4982: for(i=1,gmp[j]=0.;i<= nlstate; i++)
4983: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4984: }
4985: /* end probability of death */
4986:
4987: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
4988: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4989: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
4990: for(i=1; i<=nlstate;i++){
4991: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
4992: }
4993: }
4994: fprintf(ficresprobmorprev,"\n");
4995:
4996: fprintf(ficresvij,"%.0f ",age );
4997: for(i=1; i<=nlstate;i++)
4998: for(j=1; j<=nlstate;j++){
4999: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
5000: }
5001: fprintf(ficresvij,"\n");
5002: free_matrix(gp,0,nhstepm,1,nlstate);
5003: free_matrix(gm,0,nhstepm,1,nlstate);
5004: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
5005: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
5006: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5007: } /* End age */
5008: free_vector(gpp,nlstate+1,nlstate+ndeath);
5009: free_vector(gmp,nlstate+1,nlstate+ndeath);
5010: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
5011: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
5012: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
5013: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
5014: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
5015: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
5016: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
5017: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
5018: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
5019: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
5020: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
5021: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
5022: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
5023: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
5024: 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);
5025: /* 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 5026: */
1.218 brouard 5027: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
5028: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 5029:
1.218 brouard 5030: free_vector(xp,1,npar);
5031: free_matrix(doldm,1,nlstate,1,nlstate);
5032: free_matrix(dnewm,1,nlstate,1,npar);
5033: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5034: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
5035: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5036: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5037: fclose(ficresprobmorprev);
5038: fflush(ficgp);
5039: fflush(fichtm);
5040: } /* end varevsij */
1.126 brouard 5041:
5042: /************ Variance of prevlim ******************/
1.209 brouard 5043: 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 5044: {
1.205 brouard 5045: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 5046: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 5047:
1.126 brouard 5048: double **dnewm,**doldm;
5049: int i, j, nhstepm, hstepm;
5050: double *xp;
5051: double *gp, *gm;
5052: double **gradg, **trgradg;
1.208 brouard 5053: double **mgm, **mgp;
1.126 brouard 5054: double age,agelim;
5055: int theta;
5056:
5057: pstamp(ficresvpl);
5058: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
5059: fprintf(ficresvpl,"# Age");
5060: for(i=1; i<=nlstate;i++)
5061: fprintf(ficresvpl," %1d-%1d",i,i);
5062: fprintf(ficresvpl,"\n");
5063:
5064: xp=vector(1,npar);
5065: dnewm=matrix(1,nlstate,1,npar);
5066: doldm=matrix(1,nlstate,1,nlstate);
5067:
5068: hstepm=1*YEARM; /* Every year of age */
5069: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
5070: agelim = AGESUP;
5071: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5072: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5073: if (stepm >= YEARM) hstepm=1;
5074: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5075: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 5076: mgp=matrix(1,npar,1,nlstate);
5077: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 5078: gp=vector(1,nlstate);
5079: gm=vector(1,nlstate);
5080:
5081: for(theta=1; theta <=npar; theta++){
5082: for(i=1; i<=npar; i++){ /* Computes gradient */
5083: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5084: }
1.209 brouard 5085: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
5086: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5087: else
5088: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 5089: for(i=1;i<=nlstate;i++){
1.126 brouard 5090: gp[i] = prlim[i][i];
1.208 brouard 5091: mgp[theta][i] = prlim[i][i];
5092: }
1.126 brouard 5093: for(i=1; i<=npar; i++) /* Computes gradient */
5094: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 5095: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
5096: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5097: else
5098: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 5099: for(i=1;i<=nlstate;i++){
1.126 brouard 5100: gm[i] = prlim[i][i];
1.208 brouard 5101: mgm[theta][i] = prlim[i][i];
5102: }
1.126 brouard 5103: for(i=1;i<=nlstate;i++)
5104: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 5105: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 5106: } /* End theta */
5107:
5108: trgradg =matrix(1,nlstate,1,npar);
5109:
5110: for(j=1; j<=nlstate;j++)
5111: for(theta=1; theta <=npar; theta++)
5112: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 5113: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5114: /* printf("\nmgm mgp %d ",(int)age); */
5115: /* for(j=1; j<=nlstate;j++){ */
5116: /* printf(" %d ",j); */
5117: /* for(theta=1; theta <=npar; theta++) */
5118: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
5119: /* printf("\n "); */
5120: /* } */
5121: /* } */
5122: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5123: /* printf("\n gradg %d ",(int)age); */
5124: /* for(j=1; j<=nlstate;j++){ */
5125: /* printf("%d ",j); */
5126: /* for(theta=1; theta <=npar; theta++) */
5127: /* printf("%d %lf ",theta,gradg[theta][j]); */
5128: /* printf("\n "); */
5129: /* } */
5130: /* } */
1.126 brouard 5131:
5132: for(i=1;i<=nlstate;i++)
5133: varpl[i][(int)age] =0.;
1.209 brouard 5134: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.205 brouard 5135: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5136: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
5137: }else{
1.126 brouard 5138: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5139: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 5140: }
1.126 brouard 5141: for(i=1;i<=nlstate;i++)
5142: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
5143:
5144: fprintf(ficresvpl,"%.0f ",age );
5145: for(i=1; i<=nlstate;i++)
5146: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
5147: fprintf(ficresvpl,"\n");
5148: free_vector(gp,1,nlstate);
5149: free_vector(gm,1,nlstate);
1.208 brouard 5150: free_matrix(mgm,1,npar,1,nlstate);
5151: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 5152: free_matrix(gradg,1,npar,1,nlstate);
5153: free_matrix(trgradg,1,nlstate,1,npar);
5154: } /* End age */
5155:
5156: free_vector(xp,1,npar);
5157: free_matrix(doldm,1,nlstate,1,npar);
5158: free_matrix(dnewm,1,nlstate,1,nlstate);
5159:
5160: }
5161:
5162: /************ Variance of one-step probabilities ******************/
5163: 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 5164: {
! 5165: int i, j=0, k1, l1, tj;
! 5166: int k2, l2, j1, z1;
! 5167: int k=0, l;
! 5168: int first=1, first1, first2;
! 5169: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
! 5170: double **dnewm,**doldm;
! 5171: double *xp;
! 5172: double *gp, *gm;
! 5173: double **gradg, **trgradg;
! 5174: double **mu;
! 5175: double age, cov[NCOVMAX+1];
! 5176: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
! 5177: int theta;
! 5178: char fileresprob[FILENAMELENGTH];
! 5179: char fileresprobcov[FILENAMELENGTH];
! 5180: char fileresprobcor[FILENAMELENGTH];
! 5181: double ***varpij;
! 5182:
! 5183: strcpy(fileresprob,"PROB_");
! 5184: strcat(fileresprob,fileres);
! 5185: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
! 5186: printf("Problem with resultfile: %s\n", fileresprob);
! 5187: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
! 5188: }
! 5189: strcpy(fileresprobcov,"PROBCOV_");
! 5190: strcat(fileresprobcov,fileresu);
! 5191: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
! 5192: printf("Problem with resultfile: %s\n", fileresprobcov);
! 5193: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
! 5194: }
! 5195: strcpy(fileresprobcor,"PROBCOR_");
! 5196: strcat(fileresprobcor,fileresu);
! 5197: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
! 5198: printf("Problem with resultfile: %s\n", fileresprobcor);
! 5199: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
! 5200: }
! 5201: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
! 5202: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
! 5203: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
! 5204: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
! 5205: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
! 5206: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
! 5207: pstamp(ficresprob);
! 5208: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
! 5209: fprintf(ficresprob,"# Age");
! 5210: pstamp(ficresprobcov);
! 5211: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
! 5212: fprintf(ficresprobcov,"# Age");
! 5213: pstamp(ficresprobcor);
! 5214: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
! 5215: fprintf(ficresprobcor,"# Age");
1.126 brouard 5216:
5217:
1.222 ! brouard 5218: for(i=1; i<=nlstate;i++)
! 5219: for(j=1; j<=(nlstate+ndeath);j++){
! 5220: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
! 5221: fprintf(ficresprobcov," p%1d-%1d ",i,j);
! 5222: fprintf(ficresprobcor," p%1d-%1d ",i,j);
! 5223: }
! 5224: /* fprintf(ficresprob,"\n");
! 5225: fprintf(ficresprobcov,"\n");
! 5226: fprintf(ficresprobcor,"\n");
! 5227: */
! 5228: xp=vector(1,npar);
! 5229: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
! 5230: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
! 5231: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
! 5232: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
! 5233: first=1;
! 5234: fprintf(ficgp,"\n# Routine varprob");
! 5235: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
! 5236: fprintf(fichtm,"\n");
! 5237:
! 5238: 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);
! 5239: 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);
! 5240: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 5241: and drawn. It helps understanding how is the covariance between two incidences.\
5242: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.222 ! brouard 5243: 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 5244: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
5245: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
5246: standard deviations wide on each axis. <br>\
5247: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
5248: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
5249: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
5250:
1.222 ! brouard 5251: cov[1]=1;
! 5252: /* tj=cptcoveff; */
! 5253: tj = (int) pow(2,cptcoveff);
! 5254: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
! 5255: j1=0;
! 5256: for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates */
! 5257: if (cptcovn>0) {
! 5258: fprintf(ficresprob, "\n#********** Variable ");
! 5259: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
! 5260: fprintf(ficresprob, "**********\n#\n");
! 5261: fprintf(ficresprobcov, "\n#********** Variable ");
! 5262: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
! 5263: fprintf(ficresprobcov, "**********\n#\n");
1.220 brouard 5264:
1.222 ! brouard 5265: fprintf(ficgp, "\n#********** Variable ");
! 5266: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
! 5267: fprintf(ficgp, "**********\n#\n");
1.220 brouard 5268:
5269:
1.222 ! brouard 5270: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
! 5271: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
! 5272: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 5273:
1.222 ! brouard 5274: fprintf(ficresprobcor, "\n#********** Variable ");
! 5275: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
! 5276: fprintf(ficresprobcor, "**********\n#");
! 5277: if(invalidvarcomb[j1]){
! 5278: fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
! 5279: fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
! 5280: continue;
! 5281: }
! 5282: }
! 5283: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
! 5284: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
! 5285: gp=vector(1,(nlstate)*(nlstate+ndeath));
! 5286: gm=vector(1,(nlstate)*(nlstate+ndeath));
! 5287: for (age=bage; age<=fage; age ++){
! 5288: cov[2]=age;
! 5289: if(nagesqr==1)
! 5290: cov[3]= age*age;
! 5291: for (k=1; k<=cptcovn;k++) {
! 5292: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
! 5293: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
! 5294: * 1 1 1 1 1
! 5295: * 2 2 1 1 1
! 5296: * 3 1 2 1 1
! 5297: */
! 5298: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
! 5299: }
! 5300: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
! 5301: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
! 5302: for (k=1; k<=cptcovprod;k++)
! 5303: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.220 brouard 5304:
5305:
1.222 ! brouard 5306: for(theta=1; theta <=npar; theta++){
! 5307: for(i=1; i<=npar; i++)
! 5308: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.220 brouard 5309:
1.222 ! brouard 5310: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1.220 brouard 5311:
1.222 ! brouard 5312: k=0;
! 5313: for(i=1; i<= (nlstate); i++){
! 5314: for(j=1; j<=(nlstate+ndeath);j++){
! 5315: k=k+1;
! 5316: gp[k]=pmmij[i][j];
! 5317: }
! 5318: }
1.220 brouard 5319:
1.222 ! brouard 5320: for(i=1; i<=npar; i++)
! 5321: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.220 brouard 5322:
1.222 ! brouard 5323: pmij(pmmij,cov,ncovmodel,xp,nlstate);
! 5324: k=0;
! 5325: for(i=1; i<=(nlstate); i++){
! 5326: for(j=1; j<=(nlstate+ndeath);j++){
! 5327: k=k+1;
! 5328: gm[k]=pmmij[i][j];
! 5329: }
! 5330: }
1.220 brouard 5331:
1.222 ! brouard 5332: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
! 5333: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
! 5334: }
1.126 brouard 5335:
1.222 ! brouard 5336: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
! 5337: for(theta=1; theta <=npar; theta++)
! 5338: trgradg[j][theta]=gradg[theta][j];
1.220 brouard 5339:
1.222 ! brouard 5340: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
! 5341: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.220 brouard 5342:
1.222 ! brouard 5343: pmij(pmmij,cov,ncovmodel,x,nlstate);
1.220 brouard 5344:
1.222 ! brouard 5345: k=0;
! 5346: for(i=1; i<=(nlstate); i++){
! 5347: for(j=1; j<=(nlstate+ndeath);j++){
! 5348: k=k+1;
! 5349: mu[k][(int) age]=pmmij[i][j];
! 5350: }
! 5351: }
! 5352: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
! 5353: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
! 5354: varpij[i][j][(int)age] = doldm[i][j];
1.220 brouard 5355:
1.222 ! brouard 5356: /*printf("\n%d ",(int)age);
! 5357: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
! 5358: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
! 5359: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
! 5360: }*/
1.220 brouard 5361:
1.222 ! brouard 5362: fprintf(ficresprob,"\n%d ",(int)age);
! 5363: fprintf(ficresprobcov,"\n%d ",(int)age);
! 5364: fprintf(ficresprobcor,"\n%d ",(int)age);
1.220 brouard 5365:
1.222 ! brouard 5366: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
! 5367: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
! 5368: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
! 5369: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
! 5370: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
! 5371: }
! 5372: i=0;
! 5373: for (k=1; k<=(nlstate);k++){
! 5374: for (l=1; l<=(nlstate+ndeath);l++){
! 5375: i++;
! 5376: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
! 5377: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
! 5378: for (j=1; j<=i;j++){
! 5379: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
! 5380: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
! 5381: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
! 5382: }
! 5383: }
! 5384: }/* end of loop for state */
! 5385: } /* end of loop for age */
! 5386: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
! 5387: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
! 5388: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
! 5389: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
! 5390:
! 5391: /* Confidence intervalle of pij */
! 5392: /*
! 5393: fprintf(ficgp,"\nunset parametric;unset label");
! 5394: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
! 5395: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
! 5396: 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);
! 5397: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
! 5398: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
! 5399: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
! 5400: */
! 5401:
! 5402: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
! 5403: first1=1;first2=2;
! 5404: for (k2=1; k2<=(nlstate);k2++){
! 5405: for (l2=1; l2<=(nlstate+ndeath);l2++){
! 5406: if(l2==k2) continue;
! 5407: j=(k2-1)*(nlstate+ndeath)+l2;
! 5408: for (k1=1; k1<=(nlstate);k1++){
! 5409: for (l1=1; l1<=(nlstate+ndeath);l1++){
! 5410: if(l1==k1) continue;
! 5411: i=(k1-1)*(nlstate+ndeath)+l1;
! 5412: if(i<=j) continue;
! 5413: for (age=bage; age<=fage; age ++){
! 5414: if ((int)age %5==0){
! 5415: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
! 5416: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
! 5417: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
! 5418: mu1=mu[i][(int) age]/stepm*YEARM ;
! 5419: mu2=mu[j][(int) age]/stepm*YEARM;
! 5420: c12=cv12/sqrt(v1*v2);
! 5421: /* Computing eigen value of matrix of covariance */
! 5422: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
! 5423: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
! 5424: if ((lc2 <0) || (lc1 <0) ){
! 5425: if(first2==1){
! 5426: first1=0;
! 5427: 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);
! 5428: }
! 5429: 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);
! 5430: /* lc1=fabs(lc1); */ /* If we want to have them positive */
! 5431: /* lc2=fabs(lc2); */
! 5432: }
1.220 brouard 5433:
1.222 ! brouard 5434: /* Eigen vectors */
! 5435: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
! 5436: /*v21=sqrt(1.-v11*v11); *//* error */
! 5437: v21=(lc1-v1)/cv12*v11;
! 5438: v12=-v21;
! 5439: v22=v11;
! 5440: tnalp=v21/v11;
! 5441: if(first1==1){
! 5442: first1=0;
! 5443: 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);
! 5444: }
! 5445: 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);
! 5446: /*printf(fignu*/
! 5447: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
! 5448: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
! 5449: if(first==1){
! 5450: first=0;
! 5451: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
! 5452: fprintf(ficgp,"\nset parametric;unset label");
! 5453: 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);
! 5454: fprintf(ficgp,"\nset ter svg size 640, 480");
! 5455: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.220 brouard 5456: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
1.201 brouard 5457: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.222 ! brouard 5458: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
! 5459: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
! 5460: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
! 5461: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
! 5462: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
! 5463: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
! 5464: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
! 5465: 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", \
! 5466: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
! 5467: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
! 5468: }else{
! 5469: first=0;
! 5470: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
! 5471: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
! 5472: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
! 5473: 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", \
! 5474: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
! 5475: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
! 5476: }/* if first */
! 5477: } /* age mod 5 */
! 5478: } /* end loop age */
! 5479: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
! 5480: first=1;
! 5481: } /*l12 */
! 5482: } /* k12 */
! 5483: } /*l1 */
! 5484: }/* k1 */
! 5485: } /* loop on combination of covariates j1 */
! 5486: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
! 5487: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
! 5488: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
! 5489: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
! 5490: free_vector(xp,1,npar);
! 5491: fclose(ficresprob);
! 5492: fclose(ficresprobcov);
! 5493: fclose(ficresprobcor);
! 5494: fflush(ficgp);
! 5495: fflush(fichtmcov);
! 5496: }
1.126 brouard 5497:
5498:
5499: /******************* Printing html file ***********/
1.201 brouard 5500: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 5501: int lastpass, int stepm, int weightopt, char model[],\
5502: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.217 brouard 5503: int popforecast, int prevfcast, int backcast, int estepm , \
1.213 brouard 5504: double jprev1, double mprev1,double anprev1, double dateprev1, \
5505: double jprev2, double mprev2,double anprev2, double dateprev2){
1.126 brouard 5506: int jj1, k1, i1, cpt;
5507:
5508: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
5509: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
5510: </ul>");
1.214 brouard 5511: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
5512: 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",
5513: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
5514: 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 5515: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
5516: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 5517: fprintf(fichtm,"\
5518: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 5519: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 5520: fprintf(fichtm,"\
1.217 brouard 5521: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
5522: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
5523: fprintf(fichtm,"\
1.126 brouard 5524: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5525: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 5526: fprintf(fichtm,"\
1.217 brouard 5527: - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
5528: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
5529: fprintf(fichtm,"\
1.211 brouard 5530: - (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 5531: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5532: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 5533: if(prevfcast==1){
5534: fprintf(fichtm,"\
5535: - Prevalence projections by age and states: \
1.201 brouard 5536: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 5537: }
1.126 brouard 5538:
1.222 ! brouard 5539: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
1.126 brouard 5540:
1.222 ! brouard 5541: m=pow(2,cptcoveff);
! 5542: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 5543:
1.222 ! brouard 5544: jj1=0;
! 5545: for(k1=1; k1<=m;k1++){
1.220 brouard 5546:
1.222 ! brouard 5547: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
! 5548: jj1++;
! 5549: if (cptcovn > 0) {
! 5550: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
! 5551: for (cpt=1; cpt<=cptcoveff;cpt++){
! 5552: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
! 5553: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
! 5554: }
! 5555: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
! 5556: if(invalidvarcomb[k1]){
! 5557: fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
! 5558: printf("\nCombination (%d) ignored because no cases \n",k1);
! 5559: continue;
! 5560: }
! 5561: }
! 5562: /* aij, bij */
! 5563: 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 5564: <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 ! brouard 5565: /* Pij */
! 5566: 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 5567: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 ! brouard 5568: /* Quasi-incidences */
! 5569: 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 5570: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211 brouard 5571: incidence (rates) are the limit when h tends to zero of the ratio of the probability <sub>h</sub>P<sub>ij</sub> \
5572: 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 5573: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 ! brouard 5574: /* Survival functions (period) in state j */
! 5575: for(cpt=1; cpt<=nlstate;cpt++){
! 5576: 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 5577: <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 5578: }
! 5579: /* State specific survival functions (period) */
! 5580: for(cpt=1; cpt<=nlstate;cpt++){
! 5581: fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
1.220 brouard 5582: Or probability to survive in various states (1 to %d) being in state %d at different ages. \
1.201 brouard 5583: <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 5584: }
! 5585: /* Period (stable) prevalence in each health state */
! 5586: for(cpt=1; cpt<=nlstate;cpt++){
! 5587: 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 5588: <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 5589: }
! 5590: if(backcast==1){
! 5591: /* Period (stable) back prevalence in each health state */
! 5592: for(cpt=1; cpt<=nlstate;cpt++){
! 5593: 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 5594: <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 5595: }
1.217 brouard 5596: }
1.222 ! brouard 5597: if(prevfcast==1){
! 5598: /* Projection of prevalence up to period (stable) prevalence in each health state */
! 5599: for(cpt=1; cpt<=nlstate;cpt++){
! 5600: 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 5601: <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 5602: }
! 5603: }
1.220 brouard 5604:
1.222 ! brouard 5605: for(cpt=1; cpt<=nlstate;cpt++) {
! 5606: 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 5607: <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 5608: }
! 5609: /* } /\* end i1 *\/ */
! 5610: }/* End k1 */
! 5611: fprintf(fichtm,"</ul>");
1.126 brouard 5612:
1.222 ! brouard 5613: fprintf(fichtm,"\
1.126 brouard 5614: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 5615: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 5616: - 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 5617: But because parameters are usually highly correlated (a higher incidence of disability \
5618: and a higher incidence of recovery can give very close observed transition) it might \
5619: be very useful to look not only at linear confidence intervals estimated from the \
5620: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
5621: (parameters) of the logistic regression, it might be more meaningful to visualize the \
5622: covariance matrix of the one-step probabilities. \
5623: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 5624:
1.222 ! brouard 5625: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
! 5626: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
! 5627: fprintf(fichtm,"\
1.126 brouard 5628: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 ! brouard 5629: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 5630:
1.222 ! brouard 5631: fprintf(fichtm,"\
1.126 brouard 5632: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 ! brouard 5633: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
! 5634: fprintf(fichtm,"\
1.126 brouard 5635: - 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): \
5636: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5637: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.222 ! brouard 5638: fprintf(fichtm,"\
1.126 brouard 5639: - (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): \
5640: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5641: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.222 ! brouard 5642: fprintf(fichtm,"\
1.128 brouard 5643: - 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 5644: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
! 5645: fprintf(fichtm,"\
1.128 brouard 5646: - 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 5647: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
! 5648: fprintf(fichtm,"\
1.126 brouard 5649: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.222 ! brouard 5650: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 5651:
5652: /* if(popforecast==1) fprintf(fichtm,"\n */
5653: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
5654: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
5655: /* <br>",fileres,fileres,fileres,fileres); */
5656: /* else */
5657: /* 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 5658: fflush(fichtm);
! 5659: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.126 brouard 5660:
1.222 ! brouard 5661: m=pow(2,cptcoveff);
! 5662: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 5663:
1.222 ! brouard 5664: jj1=0;
! 5665: for(k1=1; k1<=m;k1++){
! 5666: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
! 5667: jj1++;
1.126 brouard 5668: if (cptcovn > 0) {
5669: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
5670: for (cpt=1; cpt<=cptcoveff;cpt++)
1.222 ! brouard 5671: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 5672: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 5673:
1.222 ! brouard 5674: if(invalidvarcomb[k1]){
! 5675: fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
! 5676: continue;
! 5677: }
1.126 brouard 5678: }
5679: for(cpt=1; cpt<=nlstate;cpt++) {
1.218 brouard 5680: fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
5681: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d.svg\"> %s_%d-%d.svg</a>\n <br>\
1.205 brouard 5682: <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 5683: }
5684: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 5685: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
5686: true period expectancies (those weighted with period prevalences are also\
5687: drawn in addition to the population based expectancies computed using\
1.218 brouard 5688: observed and cahotic prevalences: <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\
1.205 brouard 5689: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.222 ! brouard 5690: /* } /\* end i1 *\/ */
! 5691: }/* End k1 */
! 5692: fprintf(fichtm,"</ul>");
! 5693: fflush(fichtm);
1.126 brouard 5694: }
5695:
5696: /******************* Gnuplot file **************/
1.218 brouard 5697: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
1.126 brouard 5698:
5699: char dirfileres[132],optfileres[132];
1.220 brouard 5700: char gplotcondition[132];
1.164 brouard 5701: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.211 brouard 5702: int lv=0, vlv=0, kl=0;
1.130 brouard 5703: int ng=0;
1.201 brouard 5704: int vpopbased;
1.219 brouard 5705: int ioffset; /* variable offset for columns */
5706:
1.126 brouard 5707: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
5708: /* printf("Problem with file %s",optionfilegnuplot); */
5709: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
5710: /* } */
5711:
5712: /*#ifdef windows */
5713: fprintf(ficgp,"cd \"%s\" \n",pathc);
5714: /*#endif */
5715: m=pow(2,cptcoveff);
5716:
1.202 brouard 5717: /* Contribution to likelihood */
5718: /* Plot the probability implied in the likelihood */
5719: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
5720: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
5721: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
1.205 brouard 5722: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 5723: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 5724: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
5725: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
5726: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
1.204 brouard 5727: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
1.214 brouard 5728: 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));
1.204 brouard 5729: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
1.214 brouard 5730: 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));
1.204 brouard 5731: for (i=1; i<= nlstate ; i ++) {
5732: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
1.205 brouard 5733: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
1.214 brouard 5734: 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);
1.204 brouard 5735: for (j=2; j<= nlstate+ndeath ; j ++) {
1.219 brouard 5736: 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);
1.204 brouard 5737: }
5738: fprintf(ficgp,";\nset out; unset ylabel;\n");
5739: }
5740: /* 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 */
5741: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
5742: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
1.203 brouard 5743: fprintf(ficgp,"\nset out;unset log\n");
1.202 brouard 5744: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
5745:
1.126 brouard 5746: strcpy(dirfileres,optionfilefiname);
5747: strcpy(optfileres,"vpl");
5748: /* 1eme*/
1.211 brouard 5749: for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
1.220 brouard 5750: for (k1=1; k1<= m ; k1 ++) { /* For each valid combination of covariate */
1.211 brouard 5751: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
5752: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
1.219 brouard 5753: for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
5754: lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
5755: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5756: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5757: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5758: vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
5759: /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
1.220 brouard 5760: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 5761: }
5762: fprintf(ficgp,"\n#\n");
1.220 brouard 5763: if(invalidvarcomb[k1]){
5764: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
5765: continue;
5766: }
1.211 brouard 5767:
1.219 brouard 5768: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
5769: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
5770: fprintf(ficgp,"set xlabel \"Age\" \n\
5771: set ylabel \"Probability\" \n \
5772: set ter svg size 640, 480\n \
1.201 brouard 5773: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.219 brouard 5774:
5775: for (i=1; i<= nlstate ; i ++) {
5776: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5777: else fprintf(ficgp," %%*lf (%%*lf)");
5778: }
5779: 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);
5780: for (i=1; i<= nlstate ; i ++) {
5781: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5782: else fprintf(ficgp," %%*lf (%%*lf)");
5783: }
5784: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
5785: for (i=1; i<= nlstate ; i ++) {
5786: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5787: else fprintf(ficgp," %%*lf (%%*lf)");
5788: }
5789: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
5790: if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
5791: /* 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); */
5792: fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
5793: kl=0;
5794: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
5795: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
5796: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5797: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5798: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5799: vlv= nbcode[Tvaraff[k]][lv];
5800: kl++;
5801: /* 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 *\/ */
5802: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
5803: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
5804: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
5805: if(k==cptcoveff){
1.220 brouard 5806: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
5807: 6+(cpt-1), cpt );
1.219 brouard 5808: }else{
1.220 brouard 5809: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
1.219 brouard 5810: kl++;
5811: }
5812: } /* end covariate */
5813: }
5814: fprintf(ficgp,"\nset out \n");
1.201 brouard 5815: } /* k1 */
5816: } /* cpt */
1.126 brouard 5817: /*2 eme*/
5818: for (k1=1; k1<= m ; k1 ++) {
1.220 brouard 5819:
1.211 brouard 5820: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
5821: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.219 brouard 5822: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5823: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5824: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5825: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5826: vlv= nbcode[Tvaraff[k]][lv];
1.220 brouard 5827: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 5828: }
5829: fprintf(ficgp,"\n#\n");
1.220 brouard 5830: if(invalidvarcomb[k1]){
5831: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
5832: continue;
5833: }
1.219 brouard 5834:
5835: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
5836: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
5837: if(vpopbased==0)
5838: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
5839: else
5840: fprintf(ficgp,"\nreplot ");
5841: for (i=1; i<= nlstate+1 ; i ++) {
5842: k=2*i;
5843: 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);
5844: for (j=1; j<= nlstate+1 ; j ++) {
5845: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5846: else fprintf(ficgp," %%*lf (%%*lf)");
5847: }
5848: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
5849: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
5850: 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);
5851: for (j=1; j<= nlstate+1 ; j ++) {
5852: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5853: else fprintf(ficgp," %%*lf (%%*lf)");
5854: }
5855: fprintf(ficgp,"\" t\"\" w l lt 0,");
5856: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
5857: for (j=1; j<= nlstate+1 ; j ++) {
5858: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5859: else fprintf(ficgp," %%*lf (%%*lf)");
5860: }
5861: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
5862: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
5863: } /* state */
5864: } /* vpopbased */
5865: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
1.201 brouard 5866: } /* k1 */
1.219 brouard 5867:
5868:
1.126 brouard 5869: /*3eme*/
5870: for (k1=1; k1<= m ; k1 ++) {
1.220 brouard 5871:
1.126 brouard 5872: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.211 brouard 5873: fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt);
5874: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.219 brouard 5875: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5876: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5877: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5878: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5879: vlv= nbcode[Tvaraff[k]][lv];
1.220 brouard 5880: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 5881: }
5882: fprintf(ficgp,"\n#\n");
1.220 brouard 5883: if(invalidvarcomb[k1]){
5884: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
5885: continue;
5886: }
1.219 brouard 5887:
1.126 brouard 5888: /* k=2+nlstate*(2*cpt-2); */
5889: k=2+(nlstate+1)*(cpt-1);
1.201 brouard 5890: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
1.199 brouard 5891: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 5892: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.126 brouard 5893: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
1.219 brouard 5894: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
5895: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
5896: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
5897: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
5898: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
5899:
1.126 brouard 5900: */
5901: for (i=1; i< nlstate ; i ++) {
1.219 brouard 5902: 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);
5903: /* 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);*/
5904:
1.126 brouard 5905: }
1.201 brouard 5906: 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 5907: }
5908: }
5909:
1.220 brouard 5910: /* 4eme */
1.201 brouard 5911: /* Survival functions (period) from state i in state j by initial state i */
5912: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
1.220 brouard 5913:
1.201 brouard 5914: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.211 brouard 5915: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
5916: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.220 brouard 5917: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5918: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5919: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5920: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5921: vlv= nbcode[Tvaraff[k]][lv];
5922: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 5923: }
5924: fprintf(ficgp,"\n#\n");
1.220 brouard 5925: if(invalidvarcomb[k1]){
5926: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
5927: continue;
5928: }
5929:
1.201 brouard 5930: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
5931: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
1.220 brouard 5932: set ter svg size 640, 480\n \
5933: unset log y\n \
1.201 brouard 5934: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 5935: k=3;
1.201 brouard 5936: for (i=1; i<= nlstate ; i ++){
1.220 brouard 5937: if(i==1){
5938: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5939: }else{
5940: fprintf(ficgp,", '' ");
5941: }
5942: l=(nlstate+ndeath)*(i-1)+1;
5943: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
5944: for (j=2; j<= nlstate+ndeath ; j ++)
5945: fprintf(ficgp,"+$%d",k+l+j-1);
5946: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
1.201 brouard 5947: } /* nlstate */
5948: fprintf(ficgp,"\nset out\n");
5949: } /* end cpt state*/
5950: } /* end covariate */
1.220 brouard 5951:
5952: /* 5eme */
1.201 brouard 5953: /* Survival functions (period) from state i in state j by final state j */
1.202 brouard 5954: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.201 brouard 5955: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
1.220 brouard 5956:
1.201 brouard 5957: 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);
1.211 brouard 5958: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.220 brouard 5959: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5960: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5961: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5962: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5963: vlv= nbcode[Tvaraff[k]][lv];
5964: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 5965: }
5966: fprintf(ficgp,"\n#\n");
1.220 brouard 5967: if(invalidvarcomb[k1]){
5968: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
5969: continue;
5970: }
5971:
1.201 brouard 5972: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
5973: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
1.220 brouard 5974: set ter svg size 640, 480\n \
5975: unset log y\n \
1.201 brouard 5976: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 5977: k=3;
1.201 brouard 5978: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
1.220 brouard 5979: if(j==1)
5980: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5981: else
5982: fprintf(ficgp,", '' ");
5983: l=(nlstate+ndeath)*(cpt-1) +j;
5984: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
5985: /* for (i=2; i<= nlstate+ndeath ; i ++) */
5986: /* fprintf(ficgp,"+$%d",k+l+i-1); */
5987: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
1.201 brouard 5988: } /* nlstate */
5989: fprintf(ficgp,", '' ");
5990: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
5991: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
1.220 brouard 5992: l=(nlstate+ndeath)*(cpt-1) +j;
5993: if(j < nlstate)
5994: fprintf(ficgp,"$%d +",k+l);
5995: else
5996: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
1.201 brouard 5997: }
5998: fprintf(ficgp,"\nset out\n");
5999: } /* end cpt state*/
6000: } /* end covariate */
1.220 brouard 6001:
6002: /* 6eme */
1.202 brouard 6003: /* CV preval stable (period) for each covariate */
1.211 brouard 6004: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.153 brouard 6005: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.220 brouard 6006:
1.211 brouard 6007: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
6008: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.220 brouard 6009: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6010: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6011: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6012: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6013: vlv= nbcode[Tvaraff[k]][lv];
6014: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6015: }
6016: fprintf(ficgp,"\n#\n");
1.220 brouard 6017: if(invalidvarcomb[k1]){
6018: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6019: continue;
6020: }
1.211 brouard 6021:
1.201 brouard 6022: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 6023: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.199 brouard 6024: set ter svg size 640, 480\n\
1.126 brouard 6025: unset log y\n\
1.153 brouard 6026: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6027: k=3; /* Offset */
1.153 brouard 6028: for (i=1; i<= nlstate ; i ++){
1.220 brouard 6029: if(i==1)
6030: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6031: else
6032: fprintf(ficgp,", '' ");
6033: l=(nlstate+ndeath)*(i-1)+1;
6034: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
6035: for (j=2; j<= nlstate ; j ++)
6036: fprintf(ficgp,"+$%d",k+l+j-1);
6037: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153 brouard 6038: } /* nlstate */
1.201 brouard 6039: fprintf(ficgp,"\nset out\n");
1.153 brouard 6040: } /* end cpt state*/
6041: } /* end covariate */
1.220 brouard 6042:
6043:
6044: /* 7eme */
1.218 brouard 6045: if(backcast == 1){
1.217 brouard 6046: /* CV back preval stable (period) for each covariate */
1.218 brouard 6047: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
6048: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.220 brouard 6049: fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
6050: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6051: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6052: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6053: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6054: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6055: vlv= nbcode[Tvaraff[k]][lv];
6056: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6057: }
6058: fprintf(ficgp,"\n#\n");
6059: if(invalidvarcomb[k1]){
6060: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6061: continue;
6062: }
6063:
6064: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
6065: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
6066: set ter svg size 640, 480\n \
6067: unset log y\n \
1.218 brouard 6068: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.220 brouard 6069: k=3; /* Offset */
6070: for (i=1; i<= nlstate ; i ++){
6071: if(i==1)
6072: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
6073: else
6074: fprintf(ficgp,", '' ");
6075: /* l=(nlstate+ndeath)*(i-1)+1; */
6076: l=(nlstate+ndeath)*(cpt-1)+1;
6077: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
6078: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
6079: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
6080: /* for (j=2; j<= nlstate ; j ++) */
6081: /* fprintf(ficgp,"+$%d",k+l+j-1); */
6082: /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
6083: fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
6084: } /* nlstate */
6085: fprintf(ficgp,"\nset out\n");
1.218 brouard 6086: } /* end cpt state*/
6087: } /* end covariate */
6088: } /* End if backcast */
6089:
1.220 brouard 6090: /* 8eme */
1.218 brouard 6091: if(prevfcast==1){
6092: /* Projection from cross-sectional to stable (period) for each covariate */
6093:
6094: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.211 brouard 6095: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.219 brouard 6096: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
6097: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
6098: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
6099: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6100: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6101: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6102: vlv= nbcode[Tvaraff[k]][lv];
1.220 brouard 6103: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.219 brouard 6104: }
6105: fprintf(ficgp,"\n#\n");
1.220 brouard 6106: if(invalidvarcomb[k1]){
6107: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6108: continue;
6109: }
1.219 brouard 6110:
6111: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
6112: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
6113: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
6114: set ter svg size 640, 480\n \
6115: unset log y\n \
6116: plot [%.f:%.f] ", ageminpar, agemaxpar);
6117: for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
6118: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6119: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6120: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6121: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6122: if(i==1){
6123: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
6124: }else{
6125: fprintf(ficgp,",\\\n '' ");
6126: }
6127: if(cptcoveff ==0){ /* No covariate */
6128: ioffset=2; /* Age is in 2 */
6129: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
6130: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
6131: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
6132: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
6133: fprintf(ficgp," u %d:(", ioffset);
6134: if(i==nlstate+1)
6135: fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ", \
6136: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
6137: else
6138: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
6139: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
6140: }else{ /* more than 2 covariates */
6141: if(cptcoveff ==1){
6142: ioffset=4; /* Age is in 4 */
6143: }else{
6144: ioffset=6; /* Age is in 6 */
6145: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6146: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6147: }
1.220 brouard 6148: fprintf(ficgp," u %d:(",ioffset);
1.219 brouard 6149: kl=0;
1.220 brouard 6150: strcpy(gplotcondition,"(");
6151: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
1.219 brouard 6152: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
6153: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6154: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6155: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.220 brouard 6156: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
6157: kl++;
6158: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
1.219 brouard 6159: kl++;
1.220 brouard 6160: if(k <cptcoveff && cptcoveff>1)
6161: sprintf(gplotcondition+strlen(gplotcondition)," && ");
6162: }
6163: strcpy(gplotcondition+strlen(gplotcondition),")");
6164: /* 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 *\/ */
6165: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
6166: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
6167: /* '' 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*/
6168: if(i==nlstate+1){
6169: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
6170: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
6171: }else{
6172: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
6173: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
6174: }
1.219 brouard 6175: } /* end if covariate */
6176: } /* nlstate */
6177: fprintf(ficgp,"\nset out\n");
6178: } /* end cpt state*/
6179: } /* end covariate */
6180: } /* End if prevfcast */
6181:
1.211 brouard 6182:
1.219 brouard 6183: /* proba elementaires */
6184: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 6185: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 6186: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 6187: for(k=1; k <=(nlstate+ndeath); k++){
6188: if (k != i) {
1.187 brouard 6189: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 6190: for(j=1; j <=ncovmodel; j++){
1.187 brouard 6191: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 6192: jk++;
6193: }
1.187 brouard 6194: fprintf(ficgp,"\n");
1.126 brouard 6195: }
6196: }
6197: }
1.187 brouard 6198: fprintf(ficgp,"##############\n#\n");
6199:
1.145 brouard 6200: /*goto avoid;*/
1.200 brouard 6201: fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
1.187 brouard 6202: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
6203: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
6204: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
6205: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
6206: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6207: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
6208: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6209: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
6210: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
6211: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6212: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
6213: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
6214: fprintf(ficgp,"#\n");
1.201 brouard 6215: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.187 brouard 6216: fprintf(ficgp,"# ng=%d\n",ng);
6217: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 6218: for(jk=1; jk <=m; jk++) {
1.187 brouard 6219: fprintf(ficgp,"# jk=%d\n",jk);
1.201 brouard 6220: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
6221: fprintf(ficgp,"\nset ter svg size 640, 480 ");
6222: if (ng==1){
6223: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
6224: fprintf(ficgp,"\nunset log y");
6225: }else if (ng==2){
6226: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
6227: fprintf(ficgp,"\nset log y");
6228: }else if (ng==3){
1.126 brouard 6229: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
1.201 brouard 6230: fprintf(ficgp,"\nset log y");
6231: }else
6232: fprintf(ficgp,"\nunset title ");
6233: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 6234: i=1;
6235: for(k2=1; k2<=nlstate; k2++) {
6236: k3=i;
6237: for(k=1; k<=(nlstate+ndeath); k++) {
6238: if (k != k2){
1.201 brouard 6239: switch( ng) {
6240: case 1:
1.187 brouard 6241: if(nagesqr==0)
1.201 brouard 6242: fprintf(ficgp," p%d+p%d*x",i,i+1);
1.187 brouard 6243: else /* nagesqr =1 */
1.201 brouard 6244: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
6245: break;
6246: case 2: /* ng=2 */
1.187 brouard 6247: if(nagesqr==0)
6248: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
6249: else /* nagesqr =1 */
1.201 brouard 6250: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
6251: break;
6252: case 3:
6253: if(nagesqr==0)
6254: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
6255: else /* nagesqr =1 */
6256: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
6257: break;
6258: }
1.141 brouard 6259: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 brouard 6260: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.197 brouard 6261: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
6262: if(ij <=cptcovage) { /* Bug valgrind */
6263: if((j-2)==Tage[ij]) { /* Bug valgrind */
1.200 brouard 6264: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
6265: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
1.197 brouard 6266: ij++;
6267: }
1.186 brouard 6268: }
6269: else
1.198 brouard 6270: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.126 brouard 6271: }
1.217 brouard 6272: }else{
6273: i=i-ncovmodel;
6274: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
6275: fprintf(ficgp," (1.");
6276: }
6277:
6278: if(ng != 1){
6279: fprintf(ficgp,")/(1");
1.126 brouard 6280:
1.217 brouard 6281: for(k1=1; k1 <=nlstate; k1++){
6282: if(nagesqr==0)
6283: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
6284: else /* nagesqr =1 */
6285: 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);
6286:
6287: ij=1;
6288: for(j=3; j <=ncovmodel-nagesqr; j++){
6289: if(ij <=cptcovage) { /* Bug valgrind */
6290: if((j-2)==Tage[ij]) { /* Bug valgrind */
6291: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
6292: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
6293: ij++;
1.197 brouard 6294: }
1.186 brouard 6295: }
1.217 brouard 6296: else
6297: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.126 brouard 6298: }
6299: fprintf(ficgp,")");
1.217 brouard 6300: }
6301: fprintf(ficgp,")");
6302: if(ng ==2)
6303: fprintf(ficgp," t \"p%d%d\" ", k2,k);
6304: else /* ng= 3 */
6305: fprintf(ficgp," t \"i%d%d\" ", k2,k);
6306: }else{ /* end ng <> 1 */
6307: if( k !=k2) /* logit p11 is hard to draw */
1.201 brouard 6308: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
1.126 brouard 6309: }
1.217 brouard 6310: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
6311: fprintf(ficgp,",");
6312: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
6313: fprintf(ficgp,",");
6314: i=i+ncovmodel;
1.126 brouard 6315: } /* end k */
6316: } /* end k2 */
1.201 brouard 6317: fprintf(ficgp,"\n set out\n");
1.126 brouard 6318: } /* end jk */
6319: } /* end ng */
1.164 brouard 6320: /* avoid: */
1.126 brouard 6321: fflush(ficgp);
6322: } /* end gnuplot */
6323:
6324:
6325: /*************** Moving average **************/
1.219 brouard 6326: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.222 ! brouard 6327: int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
1.218 brouard 6328:
1.222 ! brouard 6329: int i, cpt, cptcod;
! 6330: int modcovmax =1;
! 6331: int mobilavrange, mob;
! 6332: int iage=0;
! 6333:
! 6334: double sum=0.;
! 6335: double age;
! 6336: double *sumnewp, *sumnewm;
! 6337: double *agemingood, *agemaxgood; /* Currently identical for all covariates */
! 6338:
! 6339:
! 6340: /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose */
! 6341: /* a covariate has 2 modalities, should be equal to ncovcombmax *\/ */
! 6342:
! 6343: sumnewp = vector(1,ncovcombmax);
! 6344: sumnewm = vector(1,ncovcombmax);
! 6345: agemingood = vector(1,ncovcombmax);
! 6346: agemaxgood = vector(1,ncovcombmax);
! 6347:
! 6348: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
! 6349: sumnewm[cptcod]=0.;
! 6350: sumnewp[cptcod]=0.;
! 6351: agemingood[cptcod]=0;
! 6352: agemaxgood[cptcod]=0;
! 6353: }
! 6354: if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
! 6355:
! 6356: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
! 6357: if(mobilav==1) mobilavrange=5; /* default */
! 6358: else mobilavrange=mobilav;
! 6359: for (age=bage; age<=fage; age++)
! 6360: for (i=1; i<=nlstate;i++)
! 6361: for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
! 6362: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
! 6363: /* We keep the original values on the extreme ages bage, fage and for
! 6364: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
! 6365: we use a 5 terms etc. until the borders are no more concerned.
! 6366: */
! 6367: for (mob=3;mob <=mobilavrange;mob=mob+2){
! 6368: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
! 6369: for (i=1; i<=nlstate;i++){
! 6370: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
! 6371: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
! 6372: for (cpt=1;cpt<=(mob-1)/2;cpt++){
! 6373: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
! 6374: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
! 6375: }
! 6376: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
! 6377: }
! 6378: }
! 6379: }/* end age */
! 6380: }/* end mob */
! 6381: }else
! 6382: return -1;
! 6383: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
! 6384: /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
! 6385: if(invalidvarcomb[cptcod]){
! 6386: printf("\nCombination (%d) ignored because no cases \n",cptcod);
! 6387: continue;
! 6388: }
1.219 brouard 6389:
1.222 ! brouard 6390: agemingood[cptcod]=fage-(mob-1)/2;
! 6391: for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
! 6392: sumnewm[cptcod]=0.;
! 6393: for (i=1; i<=nlstate;i++){
! 6394: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
! 6395: }
! 6396: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
! 6397: agemingood[cptcod]=age;
! 6398: }else{ /* bad */
! 6399: for (i=1; i<=nlstate;i++){
! 6400: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
! 6401: } /* i */
! 6402: } /* end bad */
! 6403: }/* age */
! 6404: sum=0.;
! 6405: for (i=1; i<=nlstate;i++){
! 6406: sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
! 6407: }
! 6408: if(fabs(sum - 1.) > 1.e-3) { /* bad */
! 6409: 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);
! 6410: /* for (i=1; i<=nlstate;i++){ */
! 6411: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
! 6412: /* } /\* i *\/ */
! 6413: } /* end bad */
! 6414: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
! 6415: /* From youngest, finding the oldest wrong */
! 6416: agemaxgood[cptcod]=bage+(mob-1)/2;
! 6417: for (age=bage+(mob-1)/2; age<=fage; age++){
! 6418: sumnewm[cptcod]=0.;
! 6419: for (i=1; i<=nlstate;i++){
! 6420: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
! 6421: }
! 6422: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
! 6423: agemaxgood[cptcod]=age;
! 6424: }else{ /* bad */
! 6425: for (i=1; i<=nlstate;i++){
! 6426: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
! 6427: } /* i */
! 6428: } /* end bad */
! 6429: }/* age */
! 6430: sum=0.;
! 6431: for (i=1; i<=nlstate;i++){
! 6432: sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
! 6433: }
! 6434: if(fabs(sum - 1.) > 1.e-3) { /* bad */
! 6435: 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);
! 6436: /* for (i=1; i<=nlstate;i++){ */
! 6437: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
! 6438: /* } /\* i *\/ */
! 6439: } /* end bad */
! 6440:
! 6441: for (age=bage; age<=fage; age++){
! 6442: printf("%d %d ", cptcod, (int)age);
! 6443: sumnewp[cptcod]=0.;
! 6444: sumnewm[cptcod]=0.;
! 6445: for (i=1; i<=nlstate;i++){
! 6446: sumnewp[cptcod]+=probs[(int)age][i][cptcod];
! 6447: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
! 6448: /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
! 6449: }
! 6450: /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
! 6451: }
! 6452: /* printf("\n"); */
! 6453: /* } */
! 6454: /* brutal averaging */
! 6455: for (i=1; i<=nlstate;i++){
! 6456: for (age=1; age<=bage; age++){
! 6457: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
! 6458: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
! 6459: }
! 6460: for (age=fage; age<=AGESUP; age++){
! 6461: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
! 6462: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
! 6463: }
! 6464: } /* end i status */
! 6465: for (i=nlstate+1; i<=nlstate+ndeath;i++){
! 6466: for (age=1; age<=AGESUP; age++){
! 6467: /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
! 6468: mobaverage[(int)age][i][cptcod]=0.;
! 6469: }
! 6470: }
! 6471: }/* end cptcod */
! 6472: free_vector(sumnewm,1, ncovcombmax);
! 6473: free_vector(sumnewp,1, ncovcombmax);
! 6474: free_vector(agemaxgood,1, ncovcombmax);
! 6475: free_vector(agemingood,1, ncovcombmax);
! 6476: return 0;
! 6477: }/* End movingaverage */
1.218 brouard 6478:
1.126 brouard 6479:
6480: /************** Forecasting ******************/
1.169 brouard 6481: 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 6482: /* proj1, year, month, day of starting projection
6483: agemin, agemax range of age
6484: dateprev1 dateprev2 range of dates during which prevalence is computed
6485: anproj2 year of en of projection (same day and month as proj1).
6486: */
1.164 brouard 6487: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 6488: double agec; /* generic age */
6489: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
6490: double *popeffectif,*popcount;
6491: double ***p3mat;
1.218 brouard 6492: /* double ***mobaverage; */
1.126 brouard 6493: char fileresf[FILENAMELENGTH];
6494:
6495: agelim=AGESUP;
1.211 brouard 6496: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
6497: in each health status at the date of interview (if between dateprev1 and dateprev2).
6498: We still use firstpass and lastpass as another selection.
6499: */
1.214 brouard 6500: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
6501: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 6502:
1.201 brouard 6503: strcpy(fileresf,"F_");
6504: strcat(fileresf,fileresu);
1.126 brouard 6505: if((ficresf=fopen(fileresf,"w"))==NULL) {
6506: printf("Problem with forecast resultfile: %s\n", fileresf);
6507: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
6508: }
1.215 brouard 6509: printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
6510: fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 6511:
6512: if (cptcoveff==0) ncodemax[cptcoveff]=1;
6513:
6514:
6515: stepsize=(int) (stepm+YEARM-1)/YEARM;
6516: if (stepm<=12) stepsize=1;
6517: if(estepm < stepm){
6518: printf ("Problem %d lower than %d\n",estepm, stepm);
6519: }
6520: else hstepm=estepm;
6521:
6522: hstepm=hstepm/stepm;
6523: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
6524: fractional in yp1 */
6525: anprojmean=yp;
6526: yp2=modf((yp1*12),&yp);
6527: mprojmean=yp;
6528: yp1=modf((yp2*30.5),&yp);
6529: jprojmean=yp;
6530: if(jprojmean==0) jprojmean=1;
6531: if(mprojmean==0) jprojmean=1;
6532:
6533: i1=cptcoveff;
6534: if (cptcovn < 1){i1=1;}
6535:
6536: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
6537:
6538: fprintf(ficresf,"#****** Routine prevforecast **\n");
6539:
6540: /* if (h==(int)(YEARM*yearp)){ */
6541: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
6542: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
6543: k=k+1;
1.211 brouard 6544: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
1.126 brouard 6545: for(j=1;j<=cptcoveff;j++) {
1.219 brouard 6546: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 6547: }
1.211 brouard 6548: fprintf(ficresf," yearproj age");
1.126 brouard 6549: for(j=1; j<=nlstate+ndeath;j++){
1.219 brouard 6550: for(i=1; i<=nlstate;i++)
1.126 brouard 6551: fprintf(ficresf," p%d%d",i,j);
1.219 brouard 6552: fprintf(ficresf," wp.%d",j);
1.126 brouard 6553: }
1.217 brouard 6554: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.219 brouard 6555: fprintf(ficresf,"\n");
6556: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
6557: for (agec=fage; agec>=(ageminpar-1); agec--){
6558: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
6559: nhstepm = nhstepm/hstepm;
6560: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6561: oldm=oldms;savm=savms;
6562: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
6563:
6564: for (h=0; h<=nhstepm; h++){
6565: if (h*hstepm/YEARM*stepm ==yearp) {
1.126 brouard 6566: fprintf(ficresf,"\n");
6567: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6568: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.219 brouard 6569: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
6570: }
6571: for(j=1; j<=nlstate+ndeath;j++) {
6572: ppij=0.;
6573: for(i=1; i<=nlstate;i++) {
6574: if (mobilav==1)
6575: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
6576: else {
6577: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
6578: }
6579: if (h*hstepm/YEARM*stepm== yearp) {
6580: fprintf(ficresf," %.3f", p3mat[i][j][h]);
6581: }
6582: } /* end i */
6583: if (h*hstepm/YEARM*stepm==yearp) {
6584: fprintf(ficresf," %.3f", ppij);
6585: }
6586: }/* end j */
6587: } /* end h */
6588: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6589: } /* end agec */
1.126 brouard 6590: } /* end yearp */
6591: } /* end cptcod */
6592: } /* end cptcov */
1.219 brouard 6593:
1.126 brouard 6594: fclose(ficresf);
1.215 brouard 6595: printf("End of Computing forecasting \n");
6596: fprintf(ficlog,"End of Computing forecasting\n");
6597:
1.126 brouard 6598: }
6599:
1.218 brouard 6600: /* /\************** Back Forecasting ******************\/ */
6601: /* 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){ */
6602: /* /\* back1, year, month, day of starting backection */
6603: /* agemin, agemax range of age */
6604: /* dateprev1 dateprev2 range of dates during which prevalence is computed */
6605: /* anback2 year of en of backection (same day and month as back1). */
6606: /* *\/ */
6607: /* int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */
6608: /* double agec; /\* generic age *\/ */
6609: /* double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */
6610: /* double *popeffectif,*popcount; */
6611: /* double ***p3mat; */
6612: /* /\* double ***mobaverage; *\/ */
6613: /* char fileresfb[FILENAMELENGTH]; */
6614:
6615: /* agelim=AGESUP; */
6616: /* /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */
6617: /* in each health status at the date of interview (if between dateprev1 and dateprev2). */
6618: /* We still use firstpass and lastpass as another selection. */
6619: /* *\/ */
6620: /* /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */
6621: /* /\* firstpass, lastpass, stepm, weightopt, model); *\/ */
6622: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
6623:
6624: /* strcpy(fileresfb,"FB_"); */
6625: /* strcat(fileresfb,fileresu); */
6626: /* if((ficresfb=fopen(fileresfb,"w"))==NULL) { */
6627: /* printf("Problem with back forecast resultfile: %s\n", fileresfb); */
6628: /* fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */
6629: /* } */
6630: /* printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
6631: /* fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
6632:
6633: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
6634:
6635: /* /\* if (mobilav!=0) { *\/ */
6636: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
6637: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
6638: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
6639: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
6640: /* /\* } *\/ */
6641: /* /\* } *\/ */
6642:
6643: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
6644: /* if (stepm<=12) stepsize=1; */
6645: /* if(estepm < stepm){ */
6646: /* printf ("Problem %d lower than %d\n",estepm, stepm); */
6647: /* } */
6648: /* else hstepm=estepm; */
6649:
6650: /* hstepm=hstepm/stepm; */
6651: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
6652: /* fractional in yp1 *\/ */
6653: /* anprojmean=yp; */
6654: /* yp2=modf((yp1*12),&yp); */
6655: /* mprojmean=yp; */
6656: /* yp1=modf((yp2*30.5),&yp); */
6657: /* jprojmean=yp; */
6658: /* if(jprojmean==0) jprojmean=1; */
6659: /* if(mprojmean==0) jprojmean=1; */
6660:
6661: /* i1=cptcoveff; */
6662: /* if (cptcovn < 1){i1=1;} */
1.217 brouard 6663:
1.218 brouard 6664: /* fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); */
1.217 brouard 6665:
1.218 brouard 6666: /* fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */
6667:
6668: /* /\* if (h==(int)(YEARM*yearp)){ *\/ */
6669: /* for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
6670: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
6671: /* k=k+1; */
6672: /* fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
6673: /* for(j=1;j<=cptcoveff;j++) { */
6674: /* fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
6675: /* } */
6676: /* fprintf(ficresfb," yearbproj age"); */
6677: /* for(j=1; j<=nlstate+ndeath;j++){ */
6678: /* for(i=1; i<=nlstate;i++) */
6679: /* fprintf(ficresfb," p%d%d",i,j); */
6680: /* fprintf(ficresfb," p.%d",j); */
6681: /* } */
6682: /* for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) { */
6683: /* /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { *\/ */
6684: /* fprintf(ficresfb,"\n"); */
6685: /* fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
6686: /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
6687: /* nhstepm=(int) rint((agelim-agec)*YEARM/stepm); */
6688: /* nhstepm = nhstepm/hstepm; */
6689: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
6690: /* oldm=oldms;savm=savms; */
6691: /* hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k); */
6692: /* for (h=0; h<=nhstepm; h++){ */
6693: /* if (h*hstepm/YEARM*stepm ==yearp) { */
6694: /* fprintf(ficresfb,"\n"); */
6695: /* for(j=1;j<=cptcoveff;j++) */
6696: /* fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
6697: /* fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */
6698: /* } */
6699: /* for(j=1; j<=nlstate+ndeath;j++) { */
6700: /* ppij=0.; */
6701: /* for(i=1; i<=nlstate;i++) { */
6702: /* if (mobilav==1) */
6703: /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */
6704: /* else { */
6705: /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */
6706: /* } */
6707: /* if (h*hstepm/YEARM*stepm== yearp) { */
6708: /* fprintf(ficresfb," %.3f", p3mat[i][j][h]); */
6709: /* } */
6710: /* } /\* end i *\/ */
6711: /* if (h*hstepm/YEARM*stepm==yearp) { */
6712: /* fprintf(ficresfb," %.3f", ppij); */
6713: /* } */
6714: /* }/\* end j *\/ */
6715: /* } /\* end h *\/ */
6716: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
6717: /* } /\* end agec *\/ */
6718: /* } /\* end yearp *\/ */
6719: /* } /\* end cptcod *\/ */
6720: /* } /\* end cptcov *\/ */
6721:
6722: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
6723:
6724: /* fclose(ficresfb); */
6725: /* printf("End of Computing Back forecasting \n"); */
6726: /* fprintf(ficlog,"End of Computing Back forecasting\n"); */
1.217 brouard 6727:
1.218 brouard 6728: /* } */
1.217 brouard 6729:
1.126 brouard 6730: /************** Forecasting *****not tested NB*************/
1.169 brouard 6731: void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
1.126 brouard 6732:
6733: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
6734: int *popage;
6735: double calagedatem, agelim, kk1, kk2;
6736: double *popeffectif,*popcount;
6737: double ***p3mat,***tabpop,***tabpopprev;
1.218 brouard 6738: /* double ***mobaverage; */
1.126 brouard 6739: char filerespop[FILENAMELENGTH];
6740:
6741: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6742: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6743: agelim=AGESUP;
6744: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
6745:
6746: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6747:
6748:
1.201 brouard 6749: strcpy(filerespop,"POP_");
6750: strcat(filerespop,fileresu);
1.126 brouard 6751: if((ficrespop=fopen(filerespop,"w"))==NULL) {
6752: printf("Problem with forecast resultfile: %s\n", filerespop);
6753: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
6754: }
6755: printf("Computing forecasting: result on file '%s' \n", filerespop);
6756: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
6757:
6758: if (cptcoveff==0) ncodemax[cptcoveff]=1;
6759:
1.218 brouard 6760: /* if (mobilav!=0) { */
6761: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
6762: /* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ */
6763: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
6764: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
6765: /* } */
6766: /* } */
1.126 brouard 6767:
6768: stepsize=(int) (stepm+YEARM-1)/YEARM;
6769: if (stepm<=12) stepsize=1;
6770:
6771: agelim=AGESUP;
6772:
6773: hstepm=1;
6774: hstepm=hstepm/stepm;
1.218 brouard 6775:
1.126 brouard 6776: if (popforecast==1) {
6777: if((ficpop=fopen(popfile,"r"))==NULL) {
6778: printf("Problem with population file : %s\n",popfile);exit(0);
6779: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
6780: }
6781: popage=ivector(0,AGESUP);
6782: popeffectif=vector(0,AGESUP);
6783: popcount=vector(0,AGESUP);
6784:
6785: i=1;
6786: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
1.218 brouard 6787:
1.126 brouard 6788: imx=i;
6789: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
6790: }
1.218 brouard 6791:
1.126 brouard 6792: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.218 brouard 6793: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
1.126 brouard 6794: k=k+1;
6795: fprintf(ficrespop,"\n#******");
6796: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 6797: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 6798: }
6799: fprintf(ficrespop,"******\n");
6800: fprintf(ficrespop,"# Age");
6801: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
6802: if (popforecast==1) fprintf(ficrespop," [Population]");
6803:
6804: for (cpt=0; cpt<=0;cpt++) {
6805: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
6806:
1.218 brouard 6807: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.126 brouard 6808: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
6809: nhstepm = nhstepm/hstepm;
6810:
6811: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6812: oldm=oldms;savm=savms;
6813: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.218 brouard 6814:
1.126 brouard 6815: for (h=0; h<=nhstepm; h++){
6816: if (h==(int) (calagedatem+YEARM*cpt)) {
6817: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
6818: }
6819: for(j=1; j<=nlstate+ndeath;j++) {
6820: kk1=0.;kk2=0;
6821: for(i=1; i<=nlstate;i++) {
6822: if (mobilav==1)
6823: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
6824: else {
6825: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
6826: }
6827: }
6828: if (h==(int)(calagedatem+12*cpt)){
6829: tabpop[(int)(agedeb)][j][cptcod]=kk1;
1.218 brouard 6830: /*fprintf(ficrespop," %.3f", kk1);
6831: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
1.126 brouard 6832: }
6833: }
6834: for(i=1; i<=nlstate;i++){
6835: kk1=0.;
1.218 brouard 6836: for(j=1; j<=nlstate;j++){
6837: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
6838: }
6839: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.126 brouard 6840: }
1.218 brouard 6841:
6842: if (h==(int)(calagedatem+12*cpt))
6843: for(j=1; j<=nlstate;j++)
6844: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
1.126 brouard 6845: }
6846: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6847: }
6848: }
1.218 brouard 6849:
6850: /******/
6851:
1.126 brouard 6852: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
6853: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
6854: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
6855: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
6856: nhstepm = nhstepm/hstepm;
6857:
6858: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6859: oldm=oldms;savm=savms;
6860: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6861: for (h=0; h<=nhstepm; h++){
6862: if (h==(int) (calagedatem+YEARM*cpt)) {
6863: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
6864: }
6865: for(j=1; j<=nlstate+ndeath;j++) {
6866: kk1=0.;kk2=0;
6867: for(i=1; i<=nlstate;i++) {
6868: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
6869: }
6870: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
6871: }
6872: }
6873: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6874: }
6875: }
1.218 brouard 6876: }
1.126 brouard 6877: }
1.218 brouard 6878:
6879: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
6880:
1.126 brouard 6881: if (popforecast==1) {
6882: free_ivector(popage,0,AGESUP);
6883: free_vector(popeffectif,0,AGESUP);
6884: free_vector(popcount,0,AGESUP);
6885: }
6886: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6887: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6888: fclose(ficrespop);
6889: } /* End of popforecast */
1.218 brouard 6890:
1.126 brouard 6891: int fileappend(FILE *fichier, char *optionfich)
6892: {
6893: if((fichier=fopen(optionfich,"a"))==NULL) {
6894: printf("Problem with file: %s\n", optionfich);
6895: fprintf(ficlog,"Problem with file: %s\n", optionfich);
6896: return (0);
6897: }
6898: fflush(fichier);
6899: return (1);
6900: }
6901:
6902:
6903: /**************** function prwizard **********************/
6904: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
6905: {
6906:
6907: /* Wizard to print covariance matrix template */
6908:
1.164 brouard 6909: char ca[32], cb[32];
6910: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 6911: int numlinepar;
6912:
6913: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6914: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6915: for(i=1; i <=nlstate; i++){
6916: jj=0;
6917: for(j=1; j <=nlstate+ndeath; j++){
6918: if(j==i) continue;
6919: jj++;
6920: /*ca[0]= k+'a'-1;ca[1]='\0';*/
6921: printf("%1d%1d",i,j);
6922: fprintf(ficparo,"%1d%1d",i,j);
6923: for(k=1; k<=ncovmodel;k++){
6924: /* printf(" %lf",param[i][j][k]); */
6925: /* fprintf(ficparo," %lf",param[i][j][k]); */
6926: printf(" 0.");
6927: fprintf(ficparo," 0.");
6928: }
6929: printf("\n");
6930: fprintf(ficparo,"\n");
6931: }
6932: }
6933: printf("# Scales (for hessian or gradient estimation)\n");
6934: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
6935: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
6936: for(i=1; i <=nlstate; i++){
6937: jj=0;
6938: for(j=1; j <=nlstate+ndeath; j++){
6939: if(j==i) continue;
6940: jj++;
6941: fprintf(ficparo,"%1d%1d",i,j);
6942: printf("%1d%1d",i,j);
6943: fflush(stdout);
6944: for(k=1; k<=ncovmodel;k++){
6945: /* printf(" %le",delti3[i][j][k]); */
6946: /* fprintf(ficparo," %le",delti3[i][j][k]); */
6947: printf(" 0.");
6948: fprintf(ficparo," 0.");
6949: }
6950: numlinepar++;
6951: printf("\n");
6952: fprintf(ficparo,"\n");
6953: }
6954: }
6955: printf("# Covariance matrix\n");
6956: /* # 121 Var(a12)\n\ */
6957: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6958: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6959: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6960: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6961: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6962: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6963: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6964: fflush(stdout);
6965: fprintf(ficparo,"# Covariance matrix\n");
6966: /* # 121 Var(a12)\n\ */
6967: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6968: /* # ...\n\ */
6969: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6970:
6971: for(itimes=1;itimes<=2;itimes++){
6972: jj=0;
6973: for(i=1; i <=nlstate; i++){
6974: for(j=1; j <=nlstate+ndeath; j++){
6975: if(j==i) continue;
6976: for(k=1; k<=ncovmodel;k++){
6977: jj++;
6978: ca[0]= k+'a'-1;ca[1]='\0';
6979: if(itimes==1){
6980: printf("#%1d%1d%d",i,j,k);
6981: fprintf(ficparo,"#%1d%1d%d",i,j,k);
6982: }else{
6983: printf("%1d%1d%d",i,j,k);
6984: fprintf(ficparo,"%1d%1d%d",i,j,k);
6985: /* printf(" %.5le",matcov[i][j]); */
6986: }
6987: ll=0;
6988: for(li=1;li <=nlstate; li++){
6989: for(lj=1;lj <=nlstate+ndeath; lj++){
6990: if(lj==li) continue;
6991: for(lk=1;lk<=ncovmodel;lk++){
6992: ll++;
6993: if(ll<=jj){
6994: cb[0]= lk +'a'-1;cb[1]='\0';
6995: if(ll<jj){
6996: if(itimes==1){
6997: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6998: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6999: }else{
7000: printf(" 0.");
7001: fprintf(ficparo," 0.");
7002: }
7003: }else{
7004: if(itimes==1){
7005: printf(" Var(%s%1d%1d)",ca,i,j);
7006: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
7007: }else{
7008: printf(" 0.");
7009: fprintf(ficparo," 0.");
7010: }
7011: }
7012: }
7013: } /* end lk */
7014: } /* end lj */
7015: } /* end li */
7016: printf("\n");
7017: fprintf(ficparo,"\n");
7018: numlinepar++;
7019: } /* end k*/
7020: } /*end j */
7021: } /* end i */
7022: } /* end itimes */
7023:
7024: } /* end of prwizard */
7025: /******************* Gompertz Likelihood ******************************/
7026: double gompertz(double x[])
7027: {
7028: double A,B,L=0.0,sump=0.,num=0.;
7029: int i,n=0; /* n is the size of the sample */
7030:
1.220 brouard 7031: for (i=1;i<=imx ; i++) {
1.126 brouard 7032: sump=sump+weight[i];
7033: /* sump=sump+1;*/
7034: num=num+1;
7035: }
7036:
7037:
7038: /* for (i=0; i<=imx; i++)
7039: 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]);*/
7040:
7041: for (i=1;i<=imx ; i++)
7042: {
7043: if (cens[i] == 1 && wav[i]>1)
7044: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
7045:
7046: if (cens[i] == 0 && wav[i]>1)
7047: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
7048: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
7049:
7050: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
7051: if (wav[i] > 1 ) { /* ??? */
7052: L=L+A*weight[i];
7053: /* 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]);*/
7054: }
7055: }
7056:
7057: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
7058:
7059: return -2*L*num/sump;
7060: }
7061:
1.136 brouard 7062: #ifdef GSL
7063: /******************* Gompertz_f Likelihood ******************************/
7064: double gompertz_f(const gsl_vector *v, void *params)
7065: {
7066: double A,B,LL=0.0,sump=0.,num=0.;
7067: double *x= (double *) v->data;
7068: int i,n=0; /* n is the size of the sample */
7069:
7070: for (i=0;i<=imx-1 ; i++) {
7071: sump=sump+weight[i];
7072: /* sump=sump+1;*/
7073: num=num+1;
7074: }
7075:
7076:
7077: /* for (i=0; i<=imx; i++)
7078: 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]);*/
7079: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
7080: for (i=1;i<=imx ; i++)
7081: {
7082: if (cens[i] == 1 && wav[i]>1)
7083: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
7084:
7085: if (cens[i] == 0 && wav[i]>1)
7086: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
7087: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
7088:
7089: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
7090: if (wav[i] > 1 ) { /* ??? */
7091: LL=LL+A*weight[i];
7092: /* 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]);*/
7093: }
7094: }
7095:
7096: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
7097: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
7098:
7099: return -2*LL*num/sump;
7100: }
7101: #endif
7102:
1.126 brouard 7103: /******************* Printing html file ***********/
1.201 brouard 7104: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 7105: int lastpass, int stepm, int weightopt, char model[],\
7106: int imx, double p[],double **matcov,double agemortsup){
7107: int i,k;
7108:
7109: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
7110: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
7111: for (i=1;i<=2;i++)
7112: 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 7113: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 7114: fprintf(fichtm,"</ul>");
7115:
7116: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
7117:
7118: 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>");
7119:
7120: for (k=agegomp;k<(agemortsup-2);k++)
7121: 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]);
7122:
7123:
7124: fflush(fichtm);
7125: }
7126:
7127: /******************* Gnuplot file **************/
1.201 brouard 7128: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 7129:
7130: char dirfileres[132],optfileres[132];
1.164 brouard 7131:
1.126 brouard 7132: int ng;
7133:
7134:
7135: /*#ifdef windows */
7136: fprintf(ficgp,"cd \"%s\" \n",pathc);
7137: /*#endif */
7138:
7139:
7140: strcpy(dirfileres,optionfilefiname);
7141: strcpy(optfileres,"vpl");
1.199 brouard 7142: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 7143: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 7144: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 7145: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 7146: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
7147:
7148: }
7149:
1.136 brouard 7150: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
7151: {
1.126 brouard 7152:
1.136 brouard 7153: /*-------- data file ----------*/
7154: FILE *fic;
7155: char dummy[]=" ";
1.164 brouard 7156: int i=0, j=0, n=0;
1.136 brouard 7157: int linei, month, year,iout;
7158: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 7159: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 7160: char *stratrunc;
7161: int lstra;
1.126 brouard 7162:
7163:
1.136 brouard 7164: if((fic=fopen(datafile,"r"))==NULL) {
1.218 brouard 7165: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
7166: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136 brouard 7167: }
1.126 brouard 7168:
1.136 brouard 7169: i=1;
7170: linei=0;
7171: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
7172: linei=linei+1;
7173: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
7174: if(line[j] == '\t')
7175: line[j] = ' ';
7176: }
7177: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
7178: ;
7179: };
7180: line[j+1]=0; /* Trims blanks at end of line */
7181: if(line[0]=='#'){
7182: fprintf(ficlog,"Comment line\n%s\n",line);
7183: printf("Comment line\n%s\n",line);
7184: continue;
7185: }
7186: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 7187: strcpy(line, linetmp);
1.136 brouard 7188:
1.126 brouard 7189:
1.136 brouard 7190: for (j=maxwav;j>=1;j--){
1.137 brouard 7191: cutv(stra, strb, line, ' ');
1.136 brouard 7192: if(strb[0]=='.') { /* Missing status */
7193: lval=-1;
7194: }else{
7195: errno=0;
7196: lval=strtol(strb,&endptr,10);
7197: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
7198: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 7199: 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);
7200: 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);
1.136 brouard 7201: return 1;
7202: }
7203: }
7204: s[j][i]=lval;
7205:
7206: strcpy(line,stra);
7207: cutv(stra, strb,line,' ');
1.169 brouard 7208: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7209: }
1.169 brouard 7210: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 7211: month=99;
7212: year=9999;
7213: }else{
1.141 brouard 7214: 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);
7215: 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);
1.136 brouard 7216: return 1;
7217: }
7218: anint[j][i]= (double) year;
7219: mint[j][i]= (double)month;
7220: strcpy(line,stra);
7221: } /* ENd Waves */
7222:
7223: cutv(stra, strb,line,' ');
1.169 brouard 7224: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7225: }
1.169 brouard 7226: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 7227: month=99;
7228: year=9999;
7229: }else{
1.141 brouard 7230: 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);
7231: 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);
1.136 brouard 7232: return 1;
7233: }
7234: andc[i]=(double) year;
7235: moisdc[i]=(double) month;
7236: strcpy(line,stra);
7237:
7238: cutv(stra, strb,line,' ');
1.169 brouard 7239: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7240: }
1.169 brouard 7241: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 7242: month=99;
7243: year=9999;
7244: }else{
1.141 brouard 7245: 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);
7246: 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);
1.136 brouard 7247: return 1;
7248: }
7249: if (year==9999) {
1.141 brouard 7250: 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);
7251: 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);
1.136 brouard 7252: return 1;
1.126 brouard 7253:
1.136 brouard 7254: }
7255: annais[i]=(double)(year);
7256: moisnais[i]=(double)(month);
7257: strcpy(line,stra);
7258:
7259: cutv(stra, strb,line,' ');
7260: errno=0;
7261: dval=strtod(strb,&endptr);
7262: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 7263: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
7264: 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 7265: fflush(ficlog);
7266: return 1;
7267: }
7268: weight[i]=dval;
7269: strcpy(line,stra);
7270:
7271: for (j=ncovcol;j>=1;j--){
7272: cutv(stra, strb,line,' ');
7273: if(strb[0]=='.') { /* Missing status */
7274: lval=-1;
7275: }else{
7276: errno=0;
7277: lval=strtol(strb,&endptr,10);
7278: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 7279: 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);
7280: 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);
1.136 brouard 7281: return 1;
7282: }
7283: }
7284: if(lval <-1 || lval >1){
1.141 brouard 7285: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 7286: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7287: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
7288: For example, for multinomial values like 1, 2 and 3,\n \
7289: build V1=0 V2=0 for the reference value (1),\n \
7290: V1=1 V2=0 for (2) \n \
7291: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
7292: output of IMaCh is often meaningless.\n \
7293: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 7294: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 7295: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7296: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
7297: For example, for multinomial values like 1, 2 and 3,\n \
7298: build V1=0 V2=0 for the reference value (1),\n \
7299: V1=1 V2=0 for (2) \n \
7300: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
7301: output of IMaCh is often meaningless.\n \
7302: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
7303: return 1;
7304: }
7305: covar[j][i]=(double)(lval);
7306: strcpy(line,stra);
7307: }
7308: lstra=strlen(stra);
7309:
7310: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
7311: stratrunc = &(stra[lstra-9]);
7312: num[i]=atol(stratrunc);
7313: }
7314: else
7315: num[i]=atol(stra);
7316: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
7317: 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;}*/
7318:
7319: i=i+1;
7320: } /* End loop reading data */
1.126 brouard 7321:
1.136 brouard 7322: *imax=i-1; /* Number of individuals */
7323: fclose(fic);
7324:
7325: return (0);
1.164 brouard 7326: /* endread: */
1.136 brouard 7327: printf("Exiting readdata: ");
7328: fclose(fic);
7329: return (1);
1.126 brouard 7330:
7331:
7332:
1.136 brouard 7333: }
1.145 brouard 7334: void removespace(char *str) {
7335: char *p1 = str, *p2 = str;
7336: do
7337: while (*p2 == ' ')
7338: p2++;
1.169 brouard 7339: while (*p1++ == *p2++);
1.145 brouard 7340: }
7341:
7342: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 7343: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
7344: * - nagesqr = 1 if age*age in the model, otherwise 0.
7345: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
7346: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 7347: * - cptcovage number of covariates with age*products =2
7348: * - cptcovs number of simple covariates
7349: * - 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
7350: * which is a new column after the 9 (ncovcol) variables.
7351: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
7352: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
7353: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
7354: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
7355: */
1.136 brouard 7356: {
1.145 brouard 7357: int i, j, k, ks;
1.164 brouard 7358: int j1, k1, k2;
1.136 brouard 7359: char modelsav[80];
1.145 brouard 7360: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 7361: char *strpt;
1.136 brouard 7362:
1.145 brouard 7363: /*removespace(model);*/
1.136 brouard 7364: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 7365: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 7366: if (strstr(model,"AGE") !=0){
1.192 brouard 7367: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
7368: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 7369: return 1;
7370: }
1.141 brouard 7371: if (strstr(model,"v") !=0){
7372: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
7373: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
7374: return 1;
7375: }
1.187 brouard 7376: strcpy(modelsav,model);
7377: if ((strpt=strstr(model,"age*age")) !=0){
7378: printf(" strpt=%s, model=%s\n",strpt, model);
7379: if(strpt != model){
7380: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 7381: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 7382: corresponding column of parameters.\n",model);
7383: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 7384: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 7385: corresponding column of parameters.\n",model); fflush(ficlog);
7386: return 1;
7387: }
7388:
7389: nagesqr=1;
7390: if (strstr(model,"+age*age") !=0)
7391: substrchaine(modelsav, model, "+age*age");
7392: else if (strstr(model,"age*age+") !=0)
7393: substrchaine(modelsav, model, "age*age+");
7394: else
7395: substrchaine(modelsav, model, "age*age");
7396: }else
7397: nagesqr=0;
7398: if (strlen(modelsav) >1){
7399: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
7400: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
7401: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
7402: cptcovt= j+1; /* Number of total covariates in the model, not including
7403: * cst, age and age*age
7404: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
7405: /* including age products which are counted in cptcovage.
7406: * but the covariates which are products must be treated
7407: * separately: ncovn=4- 2=2 (V1+V3). */
7408: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
7409: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
7410:
7411:
7412: /* Design
7413: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
7414: * < ncovcol=8 >
7415: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
7416: * k= 1 2 3 4 5 6 7 8
7417: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
7418: * covar[k,i], value of kth covariate if not including age for individual i:
7419: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
7420: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
7421: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
7422: * Tage[++cptcovage]=k
7423: * if products, new covar are created after ncovcol with k1
7424: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
7425: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
7426: * 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
7427: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
7428: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
7429: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
7430: * < ncovcol=8 >
7431: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
7432: * k= 1 2 3 4 5 6 7 8 9 10 11 12
7433: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
7434: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
7435: * p Tprod[1]@2={ 6, 5}
7436: *p Tvard[1][1]@4= {7, 8, 5, 6}
7437: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
7438: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
7439: *How to reorganize?
7440: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
7441: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
7442: * {2, 1, 4, 8, 5, 6, 3, 7}
7443: * Struct []
7444: */
1.145 brouard 7445:
1.187 brouard 7446: /* This loop fills the array Tvar from the string 'model'.*/
7447: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
7448: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
7449: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
7450: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
7451: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
7452: /* k=1 Tvar[1]=2 (from V2) */
7453: /* k=5 Tvar[5] */
7454: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 7455: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 7456: /* } */
1.198 brouard 7457: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 7458: /*
7459: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
7460: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 7461: Tvar[k]=0;
1.187 brouard 7462: cptcovage=0;
7463: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
7464: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
7465: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
7466: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
7467: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
7468: /*scanf("%d",i);*/
7469: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
7470: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
7471: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
7472: /* covar is not filled and then is empty */
7473: cptcovprod--;
7474: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
7475: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
7476: cptcovage++; /* Sums the number of covariates which include age as a product */
7477: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
7478: /*printf("stre=%s ", stre);*/
7479: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
7480: cptcovprod--;
7481: cutl(stre,strb,strc,'V');
7482: Tvar[k]=atoi(stre);
7483: cptcovage++;
7484: Tage[cptcovage]=k;
7485: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
7486: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
7487: cptcovn++;
7488: cptcovprodnoage++;k1++;
7489: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
7490: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
7491: because this model-covariate is a construction we invent a new column
7492: ncovcol + k1
7493: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
7494: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
7495: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
7496: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
7497: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
7498: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
7499: k2=k2+2;
7500: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
7501: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
7502: for (i=1; i<=lastobs;i++){
7503: /* Computes the new covariate which is a product of
7504: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
7505: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
7506: }
7507: } /* End age is not in the model */
7508: } /* End if model includes a product */
7509: else { /* no more sum */
7510: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
7511: /* scanf("%d",i);*/
7512: cutl(strd,strc,strb,'V');
7513: ks++; /**< Number of simple covariates */
1.145 brouard 7514: cptcovn++;
1.187 brouard 7515: Tvar[k]=atoi(strd);
7516: }
7517: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
7518: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
7519: scanf("%d",i);*/
7520: } /* end of loop + on total covariates */
7521: } /* end if strlen(modelsave == 0) age*age might exist */
7522: } /* end if strlen(model == 0) */
1.136 brouard 7523:
7524: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
7525: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
7526:
7527: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
7528: printf("cptcovprod=%d ", cptcovprod);
7529: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
7530:
7531: scanf("%d ",i);*/
7532:
7533:
1.137 brouard 7534: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 7535: /*endread:*/
1.136 brouard 7536: printf("Exiting decodemodel: ");
7537: return (1);
7538: }
7539:
1.169 brouard 7540: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 7541: {
7542: int i, m;
1.218 brouard 7543: int firstone=0;
7544:
1.136 brouard 7545: for (i=1; i<=imx; i++) {
7546: for(m=2; (m<= maxwav); m++) {
7547: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
7548: anint[m][i]=9999;
1.216 brouard 7549: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
7550: s[m][i]=-1;
1.136 brouard 7551: }
7552: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 7553: *nberr = *nberr + 1;
1.218 brouard 7554: if(firstone == 0){
7555: firstone=1;
7556: 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);
7557: }
7558: 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 7559: s[m][i]=-1;
7560: }
7561: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 7562: (*nberr)++;
1.136 brouard 7563: 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]);
7564: 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]);
7565: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
7566: }
7567: }
7568: }
7569:
7570: for (i=1; i<=imx; i++) {
7571: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
7572: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 7573: 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 7574: if (s[m][i] >= nlstate+1) {
1.169 brouard 7575: if(agedc[i]>0){
7576: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 7577: agev[m][i]=agedc[i];
1.214 brouard 7578: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 7579: }else {
1.136 brouard 7580: if ((int)andc[i]!=9999){
7581: nbwarn++;
7582: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
7583: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
7584: agev[m][i]=-1;
7585: }
7586: }
1.169 brouard 7587: } /* agedc > 0 */
1.214 brouard 7588: } /* end if */
1.136 brouard 7589: else if(s[m][i] !=9){ /* Standard case, age in fractional
7590: years but with the precision of a month */
7591: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
7592: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
7593: agev[m][i]=1;
7594: else if(agev[m][i] < *agemin){
7595: *agemin=agev[m][i];
7596: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
7597: }
7598: else if(agev[m][i] >*agemax){
7599: *agemax=agev[m][i];
1.156 brouard 7600: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 7601: }
7602: /*agev[m][i]=anint[m][i]-annais[i];*/
7603: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 7604: } /* en if 9*/
1.136 brouard 7605: else { /* =9 */
1.214 brouard 7606: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 7607: agev[m][i]=1;
7608: s[m][i]=-1;
7609: }
7610: }
1.214 brouard 7611: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 7612: agev[m][i]=1;
1.214 brouard 7613: else{
7614: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
7615: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
7616: agev[m][i]=0;
7617: }
7618: } /* End for lastpass */
7619: }
1.136 brouard 7620:
7621: for (i=1; i<=imx; i++) {
7622: for(m=firstpass; (m<=lastpass); m++){
7623: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 7624: (*nberr)++;
1.136 brouard 7625: 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);
7626: 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);
7627: return 1;
7628: }
7629: }
7630: }
7631:
7632: /*for (i=1; i<=imx; i++){
7633: for (m=firstpass; (m<lastpass); m++){
7634: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
7635: }
7636:
7637: }*/
7638:
7639:
1.139 brouard 7640: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
7641: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 7642:
7643: return (0);
1.164 brouard 7644: /* endread:*/
1.136 brouard 7645: printf("Exiting calandcheckages: ");
7646: return (1);
7647: }
7648:
1.172 brouard 7649: #if defined(_MSC_VER)
7650: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
7651: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
7652: //#include "stdafx.h"
7653: //#include <stdio.h>
7654: //#include <tchar.h>
7655: //#include <windows.h>
7656: //#include <iostream>
7657: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
7658:
7659: LPFN_ISWOW64PROCESS fnIsWow64Process;
7660:
7661: BOOL IsWow64()
7662: {
7663: BOOL bIsWow64 = FALSE;
7664:
7665: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
7666: // (HANDLE, PBOOL);
7667:
7668: //LPFN_ISWOW64PROCESS fnIsWow64Process;
7669:
7670: HMODULE module = GetModuleHandle(_T("kernel32"));
7671: const char funcName[] = "IsWow64Process";
7672: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
7673: GetProcAddress(module, funcName);
7674:
7675: if (NULL != fnIsWow64Process)
7676: {
7677: if (!fnIsWow64Process(GetCurrentProcess(),
7678: &bIsWow64))
7679: //throw std::exception("Unknown error");
7680: printf("Unknown error\n");
7681: }
7682: return bIsWow64 != FALSE;
7683: }
7684: #endif
1.177 brouard 7685:
1.191 brouard 7686: void syscompilerinfo(int logged)
1.167 brouard 7687: {
7688: /* #include "syscompilerinfo.h"*/
1.185 brouard 7689: /* command line Intel compiler 32bit windows, XP compatible:*/
7690: /* /GS /W3 /Gy
7691: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
7692: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
7693: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 7694: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
7695: */
7696: /* 64 bits */
1.185 brouard 7697: /*
7698: /GS /W3 /Gy
7699: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
7700: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
7701: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
7702: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
7703: /* Optimization are useless and O3 is slower than O2 */
7704: /*
7705: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
7706: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
7707: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
7708: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
7709: */
1.186 brouard 7710: /* Link is */ /* /OUT:"visual studio
1.185 brouard 7711: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
7712: /PDB:"visual studio
7713: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
7714: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
7715: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
7716: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
7717: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
7718: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
7719: uiAccess='false'"
7720: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
7721: /NOLOGO /TLBID:1
7722: */
1.177 brouard 7723: #if defined __INTEL_COMPILER
1.178 brouard 7724: #if defined(__GNUC__)
7725: struct utsname sysInfo; /* For Intel on Linux and OS/X */
7726: #endif
1.177 brouard 7727: #elif defined(__GNUC__)
1.179 brouard 7728: #ifndef __APPLE__
1.174 brouard 7729: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 7730: #endif
1.177 brouard 7731: struct utsname sysInfo;
1.178 brouard 7732: int cross = CROSS;
7733: if (cross){
7734: printf("Cross-");
1.191 brouard 7735: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 7736: }
1.174 brouard 7737: #endif
7738:
1.171 brouard 7739: #include <stdint.h>
1.178 brouard 7740:
1.191 brouard 7741: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 7742: #if defined(__clang__)
1.191 brouard 7743: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 7744: #endif
7745: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 7746: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 7747: #endif
7748: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 7749: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 7750: #endif
7751: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 7752: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 7753: #endif
7754: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 7755: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 7756: #endif
7757: #if defined(_MSC_VER)
1.191 brouard 7758: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 7759: #endif
7760: #if defined(__PGI)
1.191 brouard 7761: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 7762: #endif
7763: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 7764: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 7765: #endif
1.191 brouard 7766: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 7767:
1.167 brouard 7768: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
7769: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
7770: // Windows (x64 and x86)
1.191 brouard 7771: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 7772: #elif __unix__ // all unices, not all compilers
7773: // Unix
1.191 brouard 7774: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 7775: #elif __linux__
7776: // linux
1.191 brouard 7777: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 7778: #elif __APPLE__
1.174 brouard 7779: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 7780: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 7781: #endif
7782:
7783: /* __MINGW32__ */
7784: /* __CYGWIN__ */
7785: /* __MINGW64__ */
7786: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
7787: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
7788: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
7789: /* _WIN64 // Defined for applications for Win64. */
7790: /* _M_X64 // Defined for compilations that target x64 processors. */
7791: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 7792:
1.167 brouard 7793: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 7794: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 7795: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 7796: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 7797: #else
1.191 brouard 7798: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 7799: #endif
7800:
1.169 brouard 7801: #if defined(__GNUC__)
7802: # if defined(__GNUC_PATCHLEVEL__)
7803: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
7804: + __GNUC_MINOR__ * 100 \
7805: + __GNUC_PATCHLEVEL__)
7806: # else
7807: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
7808: + __GNUC_MINOR__ * 100)
7809: # endif
1.174 brouard 7810: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 7811: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 7812:
7813: if (uname(&sysInfo) != -1) {
7814: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 7815: 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 7816: }
7817: else
7818: perror("uname() error");
1.179 brouard 7819: //#ifndef __INTEL_COMPILER
7820: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 7821: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 7822: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 7823: #endif
1.169 brouard 7824: #endif
1.172 brouard 7825:
7826: // void main()
7827: // {
1.169 brouard 7828: #if defined(_MSC_VER)
1.174 brouard 7829: if (IsWow64()){
1.191 brouard 7830: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
7831: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 7832: }
7833: else{
1.191 brouard 7834: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
7835: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 7836: }
1.172 brouard 7837: // printf("\nPress Enter to continue...");
7838: // getchar();
7839: // }
7840:
1.169 brouard 7841: #endif
7842:
1.167 brouard 7843:
1.219 brouard 7844: }
1.136 brouard 7845:
1.219 brouard 7846: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.180 brouard 7847: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
7848: int i, j, k, i1 ;
1.202 brouard 7849: /* double ftolpl = 1.e-10; */
1.180 brouard 7850: double age, agebase, agelim;
1.203 brouard 7851: double tot;
1.180 brouard 7852:
1.202 brouard 7853: strcpy(filerespl,"PL_");
7854: strcat(filerespl,fileresu);
7855: if((ficrespl=fopen(filerespl,"w"))==NULL) {
7856: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
7857: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
7858: }
7859: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
7860: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
7861: pstamp(ficrespl);
1.203 brouard 7862: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 7863: fprintf(ficrespl,"#Age ");
7864: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
7865: fprintf(ficrespl,"\n");
1.180 brouard 7866:
1.219 brouard 7867: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180 brouard 7868:
1.219 brouard 7869: agebase=ageminpar;
7870: agelim=agemaxpar;
1.180 brouard 7871:
1.219 brouard 7872: i1=pow(2,cptcoveff);
7873: if (cptcovn < 1){i1=1;}
1.180 brouard 7874:
1.220 brouard 7875: for(k=1; k<=i1;k++){
7876: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
1.180 brouard 7877: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
1.219 brouard 7878: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.220 brouard 7879: /* k=k+1; */
1.219 brouard 7880: /* to clean */
7881: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
7882: fprintf(ficrespl,"#******");
7883: printf("#******");
7884: fprintf(ficlog,"#******");
7885: for(j=1;j<=cptcoveff;j++) {
7886: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7887: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7888: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7889: }
7890: fprintf(ficrespl,"******\n");
7891: printf("******\n");
7892: fprintf(ficlog,"******\n");
1.220 brouard 7893: if(invalidvarcomb[k]){
7894: printf("\nCombination (%d) ignored because no cases \n",k);
7895: fprintf(ficrespl,"#Combination (%d) ignored because no cases \n",k);
7896: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
7897: continue;
7898: }
1.219 brouard 7899:
7900: fprintf(ficrespl,"#Age ");
7901: for(j=1;j<=cptcoveff;j++) {
7902: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7903: }
7904: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
7905: fprintf(ficrespl,"Total Years_to_converge\n");
7906:
7907: for (age=agebase; age<=agelim; age++){
7908: /* for (age=agebase; age<=agebase; age++){ */
7909: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
7910: fprintf(ficrespl,"%.0f ",age );
7911: for(j=1;j<=cptcoveff;j++)
1.220 brouard 7912: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.219 brouard 7913: tot=0.;
7914: for(i=1; i<=nlstate;i++){
1.220 brouard 7915: tot += prlim[i][i];
7916: fprintf(ficrespl," %.5f", prlim[i][i]);
1.219 brouard 7917: }
7918: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
7919: } /* Age */
7920: /* was end of cptcod */
7921: } /* cptcov */
7922: return 0;
1.180 brouard 7923: }
7924:
1.218 brouard 7925: 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){
7926: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
7927:
7928: /* Computes the back prevalence limit for any combination of covariate values
7929: * at any age between ageminpar and agemaxpar
7930: */
1.217 brouard 7931: int i, j, k, i1 ;
7932: /* double ftolpl = 1.e-10; */
7933: double age, agebase, agelim;
7934: double tot;
1.218 brouard 7935: /* double ***mobaverage; */
7936: /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
1.217 brouard 7937:
7938: strcpy(fileresplb,"PLB_");
7939: strcat(fileresplb,fileresu);
7940: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
7941: printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
7942: fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
7943: }
7944: printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
7945: fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
7946: pstamp(ficresplb);
7947: fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
7948: fprintf(ficresplb,"#Age ");
7949: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
7950: fprintf(ficresplb,"\n");
7951:
1.218 brouard 7952:
7953: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
7954:
7955: agebase=ageminpar;
7956: agelim=agemaxpar;
7957:
7958:
7959: i1=pow(2,cptcoveff);
7960: if (cptcovn < 1){i1=1;}
1.220 brouard 7961:
7962: for(k=1; k<=i1;k++){
7963: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
1.217 brouard 7964: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
1.218 brouard 7965: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.220 brouard 7966: /* k=k+1; */
1.218 brouard 7967: /* to clean */
7968: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
7969: fprintf(ficresplb,"#******");
7970: printf("#******");
7971: fprintf(ficlog,"#******");
7972: for(j=1;j<=cptcoveff;j++) {
7973: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7974: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7975: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7976: }
7977: fprintf(ficresplb,"******\n");
7978: printf("******\n");
7979: fprintf(ficlog,"******\n");
1.220 brouard 7980: if(invalidvarcomb[k]){
7981: printf("\nCombination (%d) ignored because no cases \n",k);
7982: fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
7983: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
7984: continue;
7985: }
1.218 brouard 7986:
7987: fprintf(ficresplb,"#Age ");
7988: for(j=1;j<=cptcoveff;j++) {
7989: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7990: }
7991: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
7992: fprintf(ficresplb,"Total Years_to_converge\n");
7993:
7994:
7995: for (age=agebase; age<=agelim; age++){
7996: /* for (age=agebase; age<=agebase; age++){ */
7997: if(mobilavproj > 0){
7998: /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
7999: /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.219 brouard 8000: bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);
1.218 brouard 8001: }else if (mobilavproj == 0){
1.219 brouard 8002: 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);
8003: 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);
8004: exit(1);
1.218 brouard 8005: }else{
1.219 brouard 8006: /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
8007: bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);
1.218 brouard 8008: }
8009: fprintf(ficresplb,"%.0f ",age );
8010: for(j=1;j<=cptcoveff;j++)
1.219 brouard 8011: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.218 brouard 8012: tot=0.;
8013: for(i=1; i<=nlstate;i++){
1.219 brouard 8014: tot += bprlim[i][i];
8015: fprintf(ficresplb," %.5f", bprlim[i][i]);
1.218 brouard 8016: }
8017: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
8018: } /* Age */
8019: /* was end of cptcod */
8020: } /* cptcov */
8021:
8022: /* hBijx(p, bage, fage); */
8023: /* fclose(ficrespijb); */
8024:
8025: return 0;
1.217 brouard 8026: }
1.218 brouard 8027:
1.180 brouard 8028: int hPijx(double *p, int bage, int fage){
8029: /*------------- h Pij x at various ages ------------*/
8030:
8031: int stepsize;
8032: int agelim;
8033: int hstepm;
8034: int nhstepm;
8035: int h, i, i1, j, k;
8036:
8037: double agedeb;
8038: double ***p3mat;
8039:
1.201 brouard 8040: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 8041: if((ficrespij=fopen(filerespij,"w"))==NULL) {
8042: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
8043: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
8044: }
8045: printf("Computing pij: result on file '%s' \n", filerespij);
8046: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
8047:
8048: stepsize=(int) (stepm+YEARM-1)/YEARM;
8049: /*if (stepm<=24) stepsize=2;*/
8050:
8051: agelim=AGESUP;
8052: hstepm=stepsize*YEARM; /* Every year of age */
8053: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.218 brouard 8054:
1.180 brouard 8055: /* hstepm=1; aff par mois*/
8056: pstamp(ficrespij);
8057: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
8058: i1= pow(2,cptcoveff);
1.218 brouard 8059: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
8060: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
8061: /* k=k+1; */
1.183 brouard 8062: for (k=1; k <= (int) pow(2,cptcoveff); k++){
8063: fprintf(ficrespij,"\n#****** ");
8064: for(j=1;j<=cptcoveff;j++)
1.198 brouard 8065: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.183 brouard 8066: fprintf(ficrespij,"******\n");
8067:
8068: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
8069: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
8070: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
8071:
8072: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 8073:
1.183 brouard 8074: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8075: oldm=oldms;savm=savms;
8076: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
8077: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
8078: for(i=1; i<=nlstate;i++)
8079: for(j=1; j<=nlstate+ndeath;j++)
8080: fprintf(ficrespij," %1d-%1d",i,j);
8081: fprintf(ficrespij,"\n");
8082: for (h=0; h<=nhstepm; h++){
8083: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
8084: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 8085: for(i=1; i<=nlstate;i++)
8086: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 8087: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 8088: fprintf(ficrespij,"\n");
8089: }
1.183 brouard 8090: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8091: fprintf(ficrespij,"\n");
8092: }
1.180 brouard 8093: /*}*/
8094: }
1.218 brouard 8095: return 0;
1.180 brouard 8096: }
1.218 brouard 8097:
8098: int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217 brouard 8099: /*------------- h Bij x at various ages ------------*/
8100:
8101: int stepsize;
1.218 brouard 8102: /* int agelim; */
8103: int ageminl;
1.217 brouard 8104: int hstepm;
8105: int nhstepm;
8106: int h, i, i1, j, k;
1.218 brouard 8107:
1.217 brouard 8108: double agedeb;
8109: double ***p3mat;
1.218 brouard 8110:
8111: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
8112: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
8113: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
8114: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
8115: }
8116: printf("Computing pij back: result on file '%s' \n", filerespijb);
8117: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
8118:
8119: stepsize=(int) (stepm+YEARM-1)/YEARM;
8120: /*if (stepm<=24) stepsize=2;*/
1.217 brouard 8121:
1.218 brouard 8122: /* agelim=AGESUP; */
8123: ageminl=30;
8124: hstepm=stepsize*YEARM; /* Every year of age */
8125: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
8126:
8127: /* hstepm=1; aff par mois*/
8128: pstamp(ficrespijb);
8129: fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");
8130: i1= pow(2,cptcoveff);
8131: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
8132: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
8133: /* k=k+1; */
8134: for (k=1; k <= (int) pow(2,cptcoveff); k++){
8135: fprintf(ficrespijb,"\n#****** ");
8136: for(j=1;j<=cptcoveff;j++)
8137: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8138: fprintf(ficrespijb,"******\n");
1.222 ! brouard 8139: if(invalidvarcomb[k]){
! 8140: fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
! 8141: continue;
! 8142: }
1.218 brouard 8143:
8144: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
8145: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
8146: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
8147: nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
8148: nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
8149:
8150: /* nhstepm=nhstepm*YEARM; aff par mois*/
8151:
8152: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8153: /* oldm=oldms;savm=savms; */
8154: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
8155: hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
8156: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
8157: fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
8158: for(i=1; i<=nlstate;i++)
8159: for(j=1; j<=nlstate+ndeath;j++)
8160: fprintf(ficrespijb," %1d-%1d",i,j);
8161: fprintf(ficrespijb,"\n");
8162: for (h=0; h<=nhstepm; h++){
8163: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
8164: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
8165: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
1.217 brouard 8166: for(i=1; i<=nlstate;i++)
8167: for(j=1; j<=nlstate+ndeath;j++)
1.218 brouard 8168: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
1.217 brouard 8169: fprintf(ficrespijb,"\n");
8170: }
1.218 brouard 8171: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8172: fprintf(ficrespijb,"\n");
1.217 brouard 8173: }
1.218 brouard 8174: /*}*/
8175: }
8176: return 0;
8177: } /* hBijx */
1.217 brouard 8178:
1.180 brouard 8179:
1.136 brouard 8180: /***********************************************/
8181: /**************** Main Program *****************/
8182: /***********************************************/
8183:
8184: int main(int argc, char *argv[])
8185: {
8186: #ifdef GSL
8187: const gsl_multimin_fminimizer_type *T;
8188: size_t iteri = 0, it;
8189: int rval = GSL_CONTINUE;
8190: int status = GSL_SUCCESS;
8191: double ssval;
8192: #endif
8193: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 8194: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.209 brouard 8195: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 8196: int jj, ll, li, lj, lk;
1.136 brouard 8197: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 8198: int num_filled;
1.136 brouard 8199: int itimes;
8200: int NDIM=2;
8201: int vpopbased=0;
8202:
1.164 brouard 8203: char ca[32], cb[32];
1.136 brouard 8204: /* FILE *fichtm; *//* Html File */
8205: /* FILE *ficgp;*/ /*Gnuplot File */
8206: struct stat info;
1.191 brouard 8207: double agedeb=0.;
1.194 brouard 8208:
8209: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219 brouard 8210: double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136 brouard 8211:
1.165 brouard 8212: double fret;
1.191 brouard 8213: double dum=0.; /* Dummy variable */
1.136 brouard 8214: double ***p3mat;
1.218 brouard 8215: /* double ***mobaverage; */
1.164 brouard 8216:
8217: char line[MAXLINE];
1.197 brouard 8218: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
8219:
8220: char model[MAXLINE], modeltemp[MAXLINE];
1.136 brouard 8221: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 8222: char *tok, *val; /* pathtot */
1.136 brouard 8223: int firstobs=1, lastobs=10;
1.195 brouard 8224: int c, h , cpt, c2;
1.191 brouard 8225: int jl=0;
8226: int i1, j1, jk, stepsize=0;
1.194 brouard 8227: int count=0;
8228:
1.164 brouard 8229: int *tab;
1.136 brouard 8230: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.217 brouard 8231: int backcast=0;
1.136 brouard 8232: int mobilav=0,popforecast=0;
1.191 brouard 8233: int hstepm=0, nhstepm=0;
1.136 brouard 8234: int agemortsup;
8235: float sumlpop=0.;
8236: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
8237: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
8238:
1.191 brouard 8239: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 8240: double ftolpl=FTOL;
8241: double **prlim;
1.217 brouard 8242: double **bprlim;
1.136 brouard 8243: double ***param; /* Matrix of parameters */
8244: double *p;
8245: double **matcov; /* Matrix of covariance */
1.203 brouard 8246: double **hess; /* Hessian matrix */
1.136 brouard 8247: double ***delti3; /* Scale */
8248: double *delti; /* Scale */
8249: double ***eij, ***vareij;
8250: double **varpl; /* Variances of prevalence limits by age */
8251: double *epj, vepp;
1.164 brouard 8252:
1.136 brouard 8253: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.217 brouard 8254: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;
8255:
1.136 brouard 8256: double **ximort;
1.145 brouard 8257: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 8258: int *dcwave;
8259:
1.164 brouard 8260: char z[1]="c";
1.136 brouard 8261:
8262: /*char *strt;*/
8263: char strtend[80];
1.126 brouard 8264:
1.164 brouard 8265:
1.126 brouard 8266: /* setlocale (LC_ALL, ""); */
8267: /* bindtextdomain (PACKAGE, LOCALEDIR); */
8268: /* textdomain (PACKAGE); */
8269: /* setlocale (LC_CTYPE, ""); */
8270: /* setlocale (LC_MESSAGES, ""); */
8271:
8272: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 8273: rstart_time = time(NULL);
8274: /* (void) gettimeofday(&start_time,&tzp);*/
8275: start_time = *localtime(&rstart_time);
1.126 brouard 8276: curr_time=start_time;
1.157 brouard 8277: /*tml = *localtime(&start_time.tm_sec);*/
8278: /* strcpy(strstart,asctime(&tml)); */
8279: strcpy(strstart,asctime(&start_time));
1.126 brouard 8280:
8281: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 8282: /* tp.tm_sec = tp.tm_sec +86400; */
8283: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 8284: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
8285: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
8286: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 8287: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 8288: /* strt=asctime(&tmg); */
8289: /* printf("Time(after) =%s",strstart); */
8290: /* (void) time (&time_value);
8291: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
8292: * tm = *localtime(&time_value);
8293: * strstart=asctime(&tm);
8294: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
8295: */
8296:
8297: nberr=0; /* Number of errors and warnings */
8298: nbwarn=0;
1.184 brouard 8299: #ifdef WIN32
8300: _getcwd(pathcd, size);
8301: #else
1.126 brouard 8302: getcwd(pathcd, size);
1.184 brouard 8303: #endif
1.191 brouard 8304: syscompilerinfo(0);
1.196 brouard 8305: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 8306: if(argc <=1){
8307: printf("\nEnter the parameter file name: ");
1.205 brouard 8308: if(!fgets(pathr,FILENAMELENGTH,stdin)){
8309: printf("ERROR Empty parameter file name\n");
8310: goto end;
8311: }
1.126 brouard 8312: i=strlen(pathr);
8313: if(pathr[i-1]=='\n')
8314: pathr[i-1]='\0';
1.156 brouard 8315: i=strlen(pathr);
1.205 brouard 8316: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 8317: pathr[i-1]='\0';
1.205 brouard 8318: }
8319: i=strlen(pathr);
8320: if( i==0 ){
8321: printf("ERROR Empty parameter file name\n");
8322: goto end;
8323: }
8324: for (tok = pathr; tok != NULL; ){
1.126 brouard 8325: printf("Pathr |%s|\n",pathr);
8326: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
8327: printf("val= |%s| pathr=%s\n",val,pathr);
8328: strcpy (pathtot, val);
8329: if(pathr[0] == '\0') break; /* Dirty */
8330: }
8331: }
8332: else{
8333: strcpy(pathtot,argv[1]);
8334: }
8335: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
8336: /*cygwin_split_path(pathtot,path,optionfile);
8337: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
8338: /* cutv(path,optionfile,pathtot,'\\');*/
8339:
8340: /* Split argv[0], imach program to get pathimach */
8341: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
8342: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
8343: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
8344: /* strcpy(pathimach,argv[0]); */
8345: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
8346: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
8347: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 8348: #ifdef WIN32
8349: _chdir(path); /* Can be a relative path */
8350: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
8351: #else
1.126 brouard 8352: chdir(path); /* Can be a relative path */
1.184 brouard 8353: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
8354: #endif
8355: printf("Current directory %s!\n",pathcd);
1.126 brouard 8356: strcpy(command,"mkdir ");
8357: strcat(command,optionfilefiname);
8358: if((outcmd=system(command)) != 0){
1.169 brouard 8359: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 8360: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
8361: /* fclose(ficlog); */
8362: /* exit(1); */
8363: }
8364: /* if((imk=mkdir(optionfilefiname))<0){ */
8365: /* perror("mkdir"); */
8366: /* } */
8367:
8368: /*-------- arguments in the command line --------*/
8369:
1.186 brouard 8370: /* Main Log file */
1.126 brouard 8371: strcat(filelog, optionfilefiname);
8372: strcat(filelog,".log"); /* */
8373: if((ficlog=fopen(filelog,"w"))==NULL) {
8374: printf("Problem with logfile %s\n",filelog);
8375: goto end;
8376: }
8377: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 8378: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 8379: fprintf(ficlog,"\nEnter the parameter file name: \n");
8380: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
8381: path=%s \n\
8382: optionfile=%s\n\
8383: optionfilext=%s\n\
1.156 brouard 8384: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 8385:
1.197 brouard 8386: syscompilerinfo(1);
1.167 brouard 8387:
1.126 brouard 8388: printf("Local time (at start):%s",strstart);
8389: fprintf(ficlog,"Local time (at start): %s",strstart);
8390: fflush(ficlog);
8391: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 8392: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 8393:
8394: /* */
8395: strcpy(fileres,"r");
8396: strcat(fileres, optionfilefiname);
1.201 brouard 8397: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 8398: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 8399: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 8400:
1.186 brouard 8401: /* Main ---------arguments file --------*/
1.126 brouard 8402:
8403: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 8404: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
8405: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 8406: fflush(ficlog);
1.149 brouard 8407: /* goto end; */
8408: exit(70);
1.126 brouard 8409: }
8410:
8411:
8412:
8413: strcpy(filereso,"o");
1.201 brouard 8414: strcat(filereso,fileresu);
1.126 brouard 8415: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
8416: printf("Problem with Output resultfile: %s\n", filereso);
8417: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
8418: fflush(ficlog);
8419: goto end;
8420: }
8421:
8422: /* Reads comments: lines beginning with '#' */
8423: numlinepar=0;
1.197 brouard 8424:
8425: /* First parameter line */
8426: while(fgets(line, MAXLINE, ficpar)) {
8427: /* If line starts with a # it is a comment */
8428: if (line[0] == '#') {
8429: numlinepar++;
8430: fputs(line,stdout);
8431: fputs(line,ficparo);
8432: fputs(line,ficlog);
8433: continue;
8434: }else
8435: break;
8436: }
8437: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
8438: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
8439: if (num_filled != 5) {
8440: printf("Should be 5 parameters\n");
8441: }
1.126 brouard 8442: numlinepar++;
1.197 brouard 8443: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
8444: }
8445: /* Second parameter line */
8446: while(fgets(line, MAXLINE, ficpar)) {
8447: /* If line starts with a # it is a comment */
8448: if (line[0] == '#') {
8449: numlinepar++;
8450: fputs(line,stdout);
8451: fputs(line,ficparo);
8452: fputs(line,ficlog);
8453: continue;
8454: }else
8455: break;
8456: }
8457: if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
8458: &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
8459: if (num_filled != 8) {
1.209 brouard 8460: printf("Not 8 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
8461: printf("but line=%s\n",line);
1.197 brouard 8462: }
8463: printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);
1.126 brouard 8464: }
1.203 brouard 8465: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 8466: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 8467: /* Third parameter line */
8468: while(fgets(line, MAXLINE, ficpar)) {
8469: /* If line starts with a # it is a comment */
8470: if (line[0] == '#') {
8471: numlinepar++;
8472: fputs(line,stdout);
8473: fputs(line,ficparo);
8474: fputs(line,ficlog);
8475: continue;
8476: }else
8477: break;
8478: }
1.201 brouard 8479: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
8480: if (num_filled == 0)
8481: model[0]='\0';
8482: else if (num_filled != 1){
1.197 brouard 8483: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
8484: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
8485: model[0]='\0';
8486: goto end;
8487: }
8488: else{
8489: if (model[0]=='+'){
8490: for(i=1; i<=strlen(model);i++)
8491: modeltemp[i-1]=model[i];
1.201 brouard 8492: strcpy(model,modeltemp);
1.197 brouard 8493: }
8494: }
1.199 brouard 8495: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 8496: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 8497: }
8498: /* 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); */
8499: /* numlinepar=numlinepar+3; /\* In general *\/ */
8500: /* 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); */
1.203 brouard 8501: fprintf(ficparo,"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);
8502: fprintf(ficlog,"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);
1.126 brouard 8503: fflush(ficlog);
1.190 brouard 8504: /* if(model[0]=='#'|| model[0]== '\0'){ */
8505: if(model[0]=='#'){
1.187 brouard 8506: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
8507: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
8508: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
8509: if(mle != -1){
8510: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
8511: exit(1);
8512: }
8513: }
1.126 brouard 8514: while((c=getc(ficpar))=='#' && c!= EOF){
8515: ungetc(c,ficpar);
8516: fgets(line, MAXLINE, ficpar);
8517: numlinepar++;
1.195 brouard 8518: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
8519: z[0]=line[1];
8520: }
8521: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 8522: fputs(line, stdout);
8523: //puts(line);
1.126 brouard 8524: fputs(line,ficparo);
8525: fputs(line,ficlog);
8526: }
8527: ungetc(c,ficpar);
8528:
8529:
1.145 brouard 8530: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 8531: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
8532: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
8533: v1+v2*age+v2*v3 makes cptcovn = 3
8534: */
8535: if (strlen(model)>1)
1.187 brouard 8536: 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 8537: else
1.187 brouard 8538: ncovmodel=2; /* Constant and age */
1.133 brouard 8539: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
8540: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 8541: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
8542: 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);
8543: 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);
8544: fflush(stdout);
8545: fclose (ficlog);
8546: goto end;
8547: }
1.126 brouard 8548: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
8549: delti=delti3[1][1];
8550: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
8551: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
8552: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 8553: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
8554: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 8555: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8556: fclose (ficparo);
8557: fclose (ficlog);
8558: goto end;
8559: exit(0);
1.220 brouard 8560: } else if(mle==-5) { /* Main Wizard */
1.126 brouard 8561: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 8562: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
8563: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 8564: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
8565: matcov=matrix(1,npar,1,npar);
1.203 brouard 8566: hess=matrix(1,npar,1,npar);
1.220 brouard 8567: } else{ /* Begin of mle != -1 or -5 */
1.145 brouard 8568: /* Read guessed parameters */
1.126 brouard 8569: /* Reads comments: lines beginning with '#' */
8570: while((c=getc(ficpar))=='#' && c!= EOF){
8571: ungetc(c,ficpar);
8572: fgets(line, MAXLINE, ficpar);
8573: numlinepar++;
1.141 brouard 8574: fputs(line,stdout);
1.126 brouard 8575: fputs(line,ficparo);
8576: fputs(line,ficlog);
8577: }
8578: ungetc(c,ficpar);
8579:
8580: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
8581: for(i=1; i <=nlstate; i++){
1.220 brouard 8582: j=0;
1.126 brouard 8583: for(jj=1; jj <=nlstate+ndeath; jj++){
1.220 brouard 8584: if(jj==i) continue;
8585: j++;
8586: fscanf(ficpar,"%1d%1d",&i1,&j1);
8587: if ((i1 != i) || (j1 != jj)){
8588: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126 brouard 8589: It might be a problem of design; if ncovcol and the model are correct\n \
8590: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.220 brouard 8591: exit(1);
8592: }
8593: fprintf(ficparo,"%1d%1d",i1,j1);
8594: if(mle==1)
8595: printf("%1d%1d",i,jj);
8596: fprintf(ficlog,"%1d%1d",i,jj);
8597: for(k=1; k<=ncovmodel;k++){
8598: fscanf(ficpar," %lf",¶m[i][j][k]);
8599: if(mle==1){
8600: printf(" %lf",param[i][j][k]);
8601: fprintf(ficlog," %lf",param[i][j][k]);
8602: }
8603: else
8604: fprintf(ficlog," %lf",param[i][j][k]);
8605: fprintf(ficparo," %lf",param[i][j][k]);
8606: }
8607: fscanf(ficpar,"\n");
8608: numlinepar++;
8609: if(mle==1)
8610: printf("\n");
8611: fprintf(ficlog,"\n");
8612: fprintf(ficparo,"\n");
1.126 brouard 8613: }
8614: }
8615: fflush(ficlog);
8616:
1.145 brouard 8617: /* Reads scales values */
1.126 brouard 8618: p=param[1][1];
8619:
8620: /* Reads comments: lines beginning with '#' */
8621: while((c=getc(ficpar))=='#' && c!= EOF){
8622: ungetc(c,ficpar);
8623: fgets(line, MAXLINE, ficpar);
8624: numlinepar++;
1.141 brouard 8625: fputs(line,stdout);
1.126 brouard 8626: fputs(line,ficparo);
8627: fputs(line,ficlog);
8628: }
8629: ungetc(c,ficpar);
8630:
8631: for(i=1; i <=nlstate; i++){
8632: for(j=1; j <=nlstate+ndeath-1; j++){
1.220 brouard 8633: fscanf(ficpar,"%1d%1d",&i1,&j1);
8634: if ( (i1-i) * (j1-j) != 0){
8635: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
8636: exit(1);
8637: }
8638: printf("%1d%1d",i,j);
8639: fprintf(ficparo,"%1d%1d",i1,j1);
8640: fprintf(ficlog,"%1d%1d",i1,j1);
8641: for(k=1; k<=ncovmodel;k++){
8642: fscanf(ficpar,"%le",&delti3[i][j][k]);
8643: printf(" %le",delti3[i][j][k]);
8644: fprintf(ficparo," %le",delti3[i][j][k]);
8645: fprintf(ficlog," %le",delti3[i][j][k]);
8646: }
8647: fscanf(ficpar,"\n");
8648: numlinepar++;
8649: printf("\n");
8650: fprintf(ficparo,"\n");
8651: fprintf(ficlog,"\n");
1.126 brouard 8652: }
8653: }
8654: fflush(ficlog);
1.220 brouard 8655:
1.145 brouard 8656: /* Reads covariance matrix */
1.126 brouard 8657: delti=delti3[1][1];
1.220 brouard 8658:
8659:
1.126 brouard 8660: /* 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 8661:
1.126 brouard 8662: /* Reads comments: lines beginning with '#' */
8663: while((c=getc(ficpar))=='#' && c!= EOF){
8664: ungetc(c,ficpar);
8665: fgets(line, MAXLINE, ficpar);
8666: numlinepar++;
1.141 brouard 8667: fputs(line,stdout);
1.126 brouard 8668: fputs(line,ficparo);
8669: fputs(line,ficlog);
8670: }
8671: ungetc(c,ficpar);
1.220 brouard 8672:
1.126 brouard 8673: matcov=matrix(1,npar,1,npar);
1.203 brouard 8674: hess=matrix(1,npar,1,npar);
1.131 brouard 8675: for(i=1; i <=npar; i++)
8676: for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220 brouard 8677:
1.194 brouard 8678: /* Scans npar lines */
1.126 brouard 8679: for(i=1; i <=npar; i++){
1.194 brouard 8680: count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
8681: if(count != 3){
1.220 brouard 8682: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 8683: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
8684: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.220 brouard 8685: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 8686: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
8687: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.220 brouard 8688: exit(1);
8689: }else{
8690: if(mle==1)
8691: printf("%1d%1d%1d",i1,j1,jk);
8692: }
1.194 brouard 8693: fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
8694: fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
1.126 brouard 8695: for(j=1; j <=i; j++){
1.220 brouard 8696: fscanf(ficpar," %le",&matcov[i][j]);
8697: if(mle==1){
8698: printf(" %.5le",matcov[i][j]);
8699: }
8700: fprintf(ficlog," %.5le",matcov[i][j]);
8701: fprintf(ficparo," %.5le",matcov[i][j]);
1.126 brouard 8702: }
8703: fscanf(ficpar,"\n");
8704: numlinepar++;
8705: if(mle==1)
1.220 brouard 8706: printf("\n");
1.126 brouard 8707: fprintf(ficlog,"\n");
8708: fprintf(ficparo,"\n");
8709: }
1.194 brouard 8710: /* End of read covariance matrix npar lines */
1.126 brouard 8711: for(i=1; i <=npar; i++)
8712: for(j=i+1;j<=npar;j++)
1.220 brouard 8713: matcov[i][j]=matcov[j][i];
1.126 brouard 8714:
8715: if(mle==1)
8716: printf("\n");
8717: fprintf(ficlog,"\n");
8718:
8719: fflush(ficlog);
8720:
8721: /*-------- Rewriting parameter file ----------*/
8722: strcpy(rfileres,"r"); /* "Rparameterfile */
8723: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
8724: strcat(rfileres,"."); /* */
8725: strcat(rfileres,optionfilext); /* Other files have txt extension */
8726: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 8727: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
8728: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 8729: }
8730: fprintf(ficres,"#%s\n",version);
8731: } /* End of mle != -3 */
1.218 brouard 8732:
1.186 brouard 8733: /* Main data
8734: */
1.126 brouard 8735: n= lastobs;
8736: num=lvector(1,n);
8737: moisnais=vector(1,n);
8738: annais=vector(1,n);
8739: moisdc=vector(1,n);
8740: andc=vector(1,n);
1.220 brouard 8741: weight=vector(1,n);
1.126 brouard 8742: agedc=vector(1,n);
8743: cod=ivector(1,n);
1.220 brouard 8744: for(i=1;i<=n;i++){
8745: num[i]=0;
8746: moisnais[i]=0;
8747: annais[i]=0;
8748: moisdc[i]=0;
8749: andc[i]=0;
8750: agedc[i]=0;
8751: cod[i]=0;
8752: weight[i]=1.0; /* Equal weights, 1 by default */
8753: }
1.126 brouard 8754: mint=matrix(1,maxwav,1,n);
8755: anint=matrix(1,maxwav,1,n);
1.131 brouard 8756: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 8757: tab=ivector(1,NCOVMAX);
1.144 brouard 8758: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 8759: 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 8760:
1.136 brouard 8761: /* Reads data from file datafile */
8762: if (readdata(datafile, firstobs, lastobs, &imx)==1)
8763: goto end;
8764:
8765: /* Calculation of the number of parameters from char model */
1.137 brouard 8766: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
8767: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
8768: k=3 V4 Tvar[k=3]= 4 (from V4)
8769: k=2 V1 Tvar[k=2]= 1 (from V1)
8770: k=1 Tvar[1]=2 (from V2)
8771: */
8772: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
8773: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
8774: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
8775: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
8776: */
8777: /* For model-covariate k tells which data-covariate to use but
8778: because this model-covariate is a construction we invent a new column
8779: ncovcol + k1
8780: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
8781: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 8782: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 8783: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
8784: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
8785: */
1.145 brouard 8786: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
8787: 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 8788: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
8789: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 8790: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 8791: 4 covariates (3 plus signs)
8792: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
8793: */
1.136 brouard 8794:
1.186 brouard 8795: /* Main decodemodel */
8796:
1.187 brouard 8797:
1.136 brouard 8798: if(decodemodel(model, lastobs) == 1)
8799: goto end;
8800:
1.137 brouard 8801: if((double)(lastobs-imx)/(double)imx > 1.10){
8802: nbwarn++;
8803: 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);
8804: 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);
8805: }
1.136 brouard 8806: /* if(mle==1){*/
1.137 brouard 8807: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
8808: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 8809: }
8810:
8811: /*-calculation of age at interview from date of interview and age at death -*/
8812: agev=matrix(1,maxwav,1,imx);
8813:
8814: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
8815: goto end;
8816:
1.126 brouard 8817:
1.136 brouard 8818: agegomp=(int)agemin;
8819: free_vector(moisnais,1,n);
8820: free_vector(annais,1,n);
1.126 brouard 8821: /* free_matrix(mint,1,maxwav,1,n);
8822: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 8823: /* free_vector(moisdc,1,n); */
8824: /* free_vector(andc,1,n); */
1.145 brouard 8825: /* */
8826:
1.126 brouard 8827: wav=ivector(1,imx);
1.214 brouard 8828: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
8829: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
8830: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
8831: 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.*/
8832: bh=imatrix(1,lastpass-firstpass+2,1,imx);
8833: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 8834:
8835: /* Concatenates waves */
1.214 brouard 8836: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
8837: Death is a valid wave (if date is known).
8838: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
8839: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
8840: and mw[mi+1][i]. dh depends on stepm.
8841: */
8842:
1.126 brouard 8843: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 8844: /* */
8845:
1.215 brouard 8846: free_vector(moisdc,1,n);
8847: free_vector(andc,1,n);
8848:
1.126 brouard 8849: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
8850: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
8851: ncodemax[1]=1;
1.145 brouard 8852: Ndum =ivector(-1,NCOVMAX);
1.220 brouard 8853: cptcoveff=0;
8854: if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
8855: tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
8856: }
8857:
8858: ncovcombmax=pow(2,cptcoveff);
8859: invalidvarcomb=ivector(1, ncovcombmax);
8860: for(i=1;i<ncovcombmax;i++)
8861: invalidvarcomb[i]=0;
8862:
1.211 brouard 8863: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 8864: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 8865: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.145 brouard 8866:
1.200 brouard 8867: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 8868: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 8869: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 8870: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
8871: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
8872: * (currently 0 or 1) in the data.
8873: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
8874: * corresponding modality (h,j).
8875: */
8876:
1.145 brouard 8877: h=0;
8878: /*if (cptcovn > 0) */
1.126 brouard 8879: m=pow(2,cptcoveff);
8880:
1.144 brouard 8881: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 8882: * For k=4 covariates, h goes from 1 to m=2**k
8883: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
8884: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 8885: * h\k 1 2 3 4
1.143 brouard 8886: *______________________________
8887: * 1 i=1 1 i=1 1 i=1 1 i=1 1
8888: * 2 2 1 1 1
8889: * 3 i=2 1 2 1 1
8890: * 4 2 2 1 1
8891: * 5 i=3 1 i=2 1 2 1
8892: * 6 2 1 2 1
8893: * 7 i=4 1 2 2 1
8894: * 8 2 2 2 1
1.197 brouard 8895: * 9 i=5 1 i=3 1 i=2 1 2
8896: * 10 2 1 1 2
8897: * 11 i=6 1 2 1 2
8898: * 12 2 2 1 2
8899: * 13 i=7 1 i=4 1 2 2
8900: * 14 2 1 2 2
8901: * 15 i=8 1 2 2 2
8902: * 16 2 2 2 2
1.143 brouard 8903: */
1.212 brouard 8904: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 8905: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
8906: * and the value of each covariate?
8907: * V1=1, V2=1, V3=2, V4=1 ?
8908: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
8909: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
8910: * In order to get the real value in the data, we use nbcode
8911: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
8912: * We are keeping this crazy system in order to be able (in the future?)
8913: * to have more than 2 values (0 or 1) for a covariate.
8914: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
8915: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
8916: * bbbbbbbb
8917: * 76543210
8918: * h-1 00000101 (6-1=5)
1.219 brouard 8919: *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211 brouard 8920: * &
8921: * 1 00000001 (1)
1.219 brouard 8922: * 00000000 = 1 & ((h-1) >> (k-1))
8923: * +1= 00000001 =1
1.211 brouard 8924: *
8925: * h=14, k=3 => h'=h-1=13, k'=k-1=2
8926: * h' 1101 =2^3+2^2+0x2^1+2^0
8927: * >>k' 11
8928: * & 00000001
8929: * = 00000001
8930: * +1 = 00000010=2 = codtabm(14,3)
8931: * Reverse h=6 and m=16?
8932: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
8933: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
8934: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
8935: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
8936: * V3=decodtabm(14,3,2**4)=2
8937: * h'=13 1101 =2^3+2^2+0x2^1+2^0
8938: *(h-1) >> (j-1) 0011 =13 >> 2
8939: * &1 000000001
8940: * = 000000001
8941: * +1= 000000010 =2
8942: * 2211
8943: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
8944: * V3=2
1.220 brouard 8945: * codtabm and decodtabm are identical
1.211 brouard 8946: */
8947:
1.145 brouard 8948:
8949: free_ivector(Ndum,-1,NCOVMAX);
8950:
8951:
1.126 brouard 8952:
1.186 brouard 8953: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 8954: strcpy(optionfilegnuplot,optionfilefiname);
8955: if(mle==-3)
1.201 brouard 8956: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 8957: strcat(optionfilegnuplot,".gp");
8958:
8959: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
8960: printf("Problem with file %s",optionfilegnuplot);
8961: }
8962: else{
1.204 brouard 8963: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 8964: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 8965: //fprintf(ficgp,"set missing 'NaNq'\n");
8966: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 8967: }
8968: /* fclose(ficgp);*/
1.186 brouard 8969:
8970:
8971: /* Initialisation of --------- index.htm --------*/
1.126 brouard 8972:
8973: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
8974: if(mle==-3)
1.201 brouard 8975: strcat(optionfilehtm,"-MORT_");
1.126 brouard 8976: strcat(optionfilehtm,".htm");
8977: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 8978: printf("Problem with %s \n",optionfilehtm);
8979: exit(0);
1.126 brouard 8980: }
8981:
8982: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
8983: strcat(optionfilehtmcov,"-cov.htm");
8984: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
8985: printf("Problem with %s \n",optionfilehtmcov), exit(0);
8986: }
8987: else{
8988: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
8989: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 8990: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 8991: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
8992: }
8993:
1.213 brouard 8994: 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 8995: <hr size=\"2\" color=\"#EC5E5E\"> \n\
8996: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 8997: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 8998: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 8999: \n\
9000: <hr size=\"2\" color=\"#EC5E5E\">\
9001: <ul><li><h4>Parameter files</h4>\n\
9002: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
9003: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
9004: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
9005: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
9006: - Date and time at start: %s</ul>\n",\
9007: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
9008: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
9009: fileres,fileres,\
9010: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
9011: fflush(fichtm);
9012:
9013: strcpy(pathr,path);
9014: strcat(pathr,optionfilefiname);
1.184 brouard 9015: #ifdef WIN32
9016: _chdir(optionfilefiname); /* Move to directory named optionfile */
9017: #else
1.126 brouard 9018: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 9019: #endif
9020:
1.126 brouard 9021:
1.220 brouard 9022: /* Calculates basic frequencies. Computes observed prevalence at single age
9023: and for any valid combination of covariates
1.126 brouard 9024: and prints on file fileres'p'. */
1.220 brouard 9025: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
1.214 brouard 9026: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 9027:
9028: fprintf(fichtm,"\n");
9029: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
9030: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
9031: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
9032: imx,agemin,agemax,jmin,jmax,jmean);
9033: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.220 brouard 9034: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9035: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9036: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9037: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218 brouard 9038:
1.126 brouard 9039: /* For Powell, parameters are in a vector p[] starting at p[1]
9040: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
9041: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
9042:
9043: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 9044: /* For mortality only */
1.126 brouard 9045: if (mle==-3){
1.136 brouard 9046: ximort=matrix(1,NDIM,1,NDIM);
1.220 brouard 9047: for(i=1;i<=NDIM;i++)
9048: for(j=1;j<=NDIM;j++)
9049: ximort[i][j]=0.;
1.186 brouard 9050: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 9051: cens=ivector(1,n);
9052: ageexmed=vector(1,n);
9053: agecens=vector(1,n);
9054: dcwave=ivector(1,n);
9055:
9056: for (i=1; i<=imx; i++){
9057: dcwave[i]=-1;
9058: for (m=firstpass; m<=lastpass; m++)
1.218 brouard 9059: if (s[m][i]>nlstate) {
9060: dcwave[i]=m;
9061: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
9062: break;
9063: }
1.126 brouard 9064: }
1.218 brouard 9065:
1.126 brouard 9066: for (i=1; i<=imx; i++) {
9067: if (wav[i]>0){
1.218 brouard 9068: ageexmed[i]=agev[mw[1][i]][i];
9069: j=wav[i];
9070: agecens[i]=1.;
9071:
9072: if (ageexmed[i]> 1 && wav[i] > 0){
9073: agecens[i]=agev[mw[j][i]][i];
9074: cens[i]= 1;
9075: }else if (ageexmed[i]< 1)
9076: cens[i]= -1;
9077: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
9078: cens[i]=0 ;
1.126 brouard 9079: }
9080: else cens[i]=-1;
9081: }
9082:
9083: for (i=1;i<=NDIM;i++) {
9084: for (j=1;j<=NDIM;j++)
1.218 brouard 9085: ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126 brouard 9086: }
9087:
1.145 brouard 9088: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 9089: /*printf("%lf %lf", p[1], p[2]);*/
9090:
9091:
1.136 brouard 9092: #ifdef GSL
9093: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 9094: #else
1.126 brouard 9095: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 9096: #endif
1.201 brouard 9097: strcpy(filerespow,"POW-MORT_");
9098: strcat(filerespow,fileresu);
1.126 brouard 9099: if((ficrespow=fopen(filerespow,"w"))==NULL) {
9100: printf("Problem with resultfile: %s\n", filerespow);
9101: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
9102: }
1.136 brouard 9103: #ifdef GSL
9104: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 9105: #else
1.126 brouard 9106: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 9107: #endif
1.126 brouard 9108: /* for (i=1;i<=nlstate;i++)
9109: for(j=1;j<=nlstate+ndeath;j++)
9110: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
9111: */
9112: fprintf(ficrespow,"\n");
1.136 brouard 9113: #ifdef GSL
9114: /* gsl starts here */
9115: T = gsl_multimin_fminimizer_nmsimplex;
9116: gsl_multimin_fminimizer *sfm = NULL;
9117: gsl_vector *ss, *x;
9118: gsl_multimin_function minex_func;
9119:
9120: /* Initial vertex size vector */
9121: ss = gsl_vector_alloc (NDIM);
9122:
9123: if (ss == NULL){
9124: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
9125: }
9126: /* Set all step sizes to 1 */
9127: gsl_vector_set_all (ss, 0.001);
9128:
9129: /* Starting point */
1.126 brouard 9130:
1.136 brouard 9131: x = gsl_vector_alloc (NDIM);
9132:
9133: if (x == NULL){
9134: gsl_vector_free(ss);
9135: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
9136: }
9137:
9138: /* Initialize method and iterate */
9139: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 9140: /* gsl_vector_set(x, 0, 0.0268); */
9141: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 9142: gsl_vector_set(x, 0, p[1]);
9143: gsl_vector_set(x, 1, p[2]);
9144:
9145: minex_func.f = &gompertz_f;
9146: minex_func.n = NDIM;
9147: minex_func.params = (void *)&p; /* ??? */
9148:
9149: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
9150: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
9151:
9152: printf("Iterations beginning .....\n\n");
9153: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
9154:
9155: iteri=0;
9156: while (rval == GSL_CONTINUE){
9157: iteri++;
9158: status = gsl_multimin_fminimizer_iterate(sfm);
9159:
9160: if (status) printf("error: %s\n", gsl_strerror (status));
9161: fflush(0);
9162:
9163: if (status)
9164: break;
9165:
9166: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
9167: ssval = gsl_multimin_fminimizer_size (sfm);
9168:
9169: if (rval == GSL_SUCCESS)
9170: printf ("converged to a local maximum at\n");
9171:
9172: printf("%5d ", iteri);
9173: for (it = 0; it < NDIM; it++){
9174: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
9175: }
9176: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
9177: }
9178:
9179: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
9180:
9181: gsl_vector_free(x); /* initial values */
9182: gsl_vector_free(ss); /* inital step size */
9183: for (it=0; it<NDIM; it++){
9184: p[it+1]=gsl_vector_get(sfm->x,it);
9185: fprintf(ficrespow," %.12lf", p[it]);
9186: }
9187: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
9188: #endif
9189: #ifdef POWELL
9190: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
9191: #endif
1.126 brouard 9192: fclose(ficrespow);
9193:
1.203 brouard 9194: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 9195:
9196: for(i=1; i <=NDIM; i++)
9197: for(j=i+1;j<=NDIM;j++)
1.220 brouard 9198: matcov[i][j]=matcov[j][i];
1.126 brouard 9199:
9200: printf("\nCovariance matrix\n ");
1.203 brouard 9201: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 9202: for(i=1; i <=NDIM; i++) {
9203: for(j=1;j<=NDIM;j++){
1.220 brouard 9204: printf("%f ",matcov[i][j]);
9205: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 9206: }
1.203 brouard 9207: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 9208: }
9209:
9210: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 9211: for (i=1;i<=NDIM;i++) {
1.126 brouard 9212: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 9213: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
9214: }
1.126 brouard 9215: lsurv=vector(1,AGESUP);
9216: lpop=vector(1,AGESUP);
9217: tpop=vector(1,AGESUP);
9218: lsurv[agegomp]=100000;
9219:
9220: for (k=agegomp;k<=AGESUP;k++) {
9221: agemortsup=k;
9222: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
9223: }
9224:
9225: for (k=agegomp;k<agemortsup;k++)
9226: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
9227:
9228: for (k=agegomp;k<agemortsup;k++){
9229: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
9230: sumlpop=sumlpop+lpop[k];
9231: }
9232:
9233: tpop[agegomp]=sumlpop;
9234: for (k=agegomp;k<(agemortsup-3);k++){
9235: /* tpop[k+1]=2;*/
9236: tpop[k+1]=tpop[k]-lpop[k];
9237: }
9238:
9239:
9240: printf("\nAge lx qx dx Lx Tx e(x)\n");
9241: for (k=agegomp;k<(agemortsup-2);k++)
9242: 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]);
9243:
9244:
9245: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220 brouard 9246: ageminpar=50;
9247: agemaxpar=100;
1.194 brouard 9248: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
9249: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
9250: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9251: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
9252: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
9253: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9254: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 9255: }else{
9256: printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
9257: 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 9258: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220 brouard 9259: }
1.201 brouard 9260: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 9261: stepm, weightopt,\
9262: model,imx,p,matcov,agemortsup);
9263:
9264: free_vector(lsurv,1,AGESUP);
9265: free_vector(lpop,1,AGESUP);
9266: free_vector(tpop,1,AGESUP);
1.220 brouard 9267: free_matrix(ximort,1,NDIM,1,NDIM);
1.136 brouard 9268: free_ivector(cens,1,n);
9269: free_vector(agecens,1,n);
9270: free_ivector(dcwave,1,n);
1.220 brouard 9271: #ifdef GSL
1.136 brouard 9272: #endif
1.186 brouard 9273: } /* Endof if mle==-3 mortality only */
1.205 brouard 9274: /* Standard */
9275: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
9276: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
9277: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 9278: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 9279: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
9280: for (k=1; k<=npar;k++)
9281: printf(" %d %8.5f",k,p[k]);
9282: printf("\n");
1.205 brouard 9283: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
9284: /* mlikeli uses func not funcone */
9285: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
9286: }
9287: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
9288: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
9289: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
9290: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
9291: }
9292: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 9293: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
9294: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
9295: for (k=1; k<=npar;k++)
9296: printf(" %d %8.5f",k,p[k]);
9297: printf("\n");
9298:
9299: /*--------- results files --------------*/
1.192 brouard 9300: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
1.126 brouard 9301:
9302:
9303: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9304: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9305: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9306: for(i=1,jk=1; i <=nlstate; i++){
9307: for(k=1; k <=(nlstate+ndeath); k++){
1.220 brouard 9308: if (k != i) {
9309: printf("%d%d ",i,k);
9310: fprintf(ficlog,"%d%d ",i,k);
9311: fprintf(ficres,"%1d%1d ",i,k);
9312: for(j=1; j <=ncovmodel; j++){
9313: printf("%12.7f ",p[jk]);
9314: fprintf(ficlog,"%12.7f ",p[jk]);
9315: fprintf(ficres,"%12.7f ",p[jk]);
9316: jk++;
9317: }
9318: printf("\n");
9319: fprintf(ficlog,"\n");
9320: fprintf(ficres,"\n");
9321: }
1.126 brouard 9322: }
9323: }
1.203 brouard 9324: if(mle != 0){
9325: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 9326: ftolhess=ftol; /* Usually correct */
1.203 brouard 9327: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
9328: 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");
9329: 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");
9330: for(i=1,jk=1; i <=nlstate; i++){
1.220 brouard 9331: for(k=1; k <=(nlstate+ndeath); k++){
9332: if (k != i) {
9333: printf("%d%d ",i,k);
9334: fprintf(ficlog,"%d%d ",i,k);
9335: for(j=1; j <=ncovmodel; j++){
9336: 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]));
9337: 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]));
9338: jk++;
9339: }
9340: printf("\n");
9341: fprintf(ficlog,"\n");
9342: }
9343: }
1.193 brouard 9344: }
1.203 brouard 9345: } /* end of hesscov and Wald tests */
1.220 brouard 9346:
1.203 brouard 9347: /* */
1.126 brouard 9348: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
9349: printf("# Scales (for hessian or gradient estimation)\n");
9350: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
9351: for(i=1,jk=1; i <=nlstate; i++){
9352: for(j=1; j <=nlstate+ndeath; j++){
1.220 brouard 9353: if (j!=i) {
9354: fprintf(ficres,"%1d%1d",i,j);
9355: printf("%1d%1d",i,j);
9356: fprintf(ficlog,"%1d%1d",i,j);
9357: for(k=1; k<=ncovmodel;k++){
9358: printf(" %.5e",delti[jk]);
9359: fprintf(ficlog," %.5e",delti[jk]);
9360: fprintf(ficres," %.5e",delti[jk]);
9361: jk++;
9362: }
9363: printf("\n");
9364: fprintf(ficlog,"\n");
9365: fprintf(ficres,"\n");
9366: }
1.126 brouard 9367: }
9368: }
9369:
9370: 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 9371: if(mle >= 1) /* To big for the screen */
1.126 brouard 9372: 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");
9373: 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");
9374: /* # 121 Var(a12)\n\ */
9375: /* # 122 Cov(b12,a12) Var(b12)\n\ */
9376: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
9377: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
9378: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
9379: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
9380: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
9381: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
9382:
9383:
9384: /* Just to have a covariance matrix which will be more understandable
9385: even is we still don't want to manage dictionary of variables
9386: */
9387: for(itimes=1;itimes<=2;itimes++){
9388: jj=0;
9389: for(i=1; i <=nlstate; i++){
1.220 brouard 9390: for(j=1; j <=nlstate+ndeath; j++){
9391: if(j==i) continue;
9392: for(k=1; k<=ncovmodel;k++){
9393: jj++;
9394: ca[0]= k+'a'-1;ca[1]='\0';
9395: if(itimes==1){
9396: if(mle>=1)
9397: printf("#%1d%1d%d",i,j,k);
9398: fprintf(ficlog,"#%1d%1d%d",i,j,k);
9399: fprintf(ficres,"#%1d%1d%d",i,j,k);
9400: }else{
9401: if(mle>=1)
9402: printf("%1d%1d%d",i,j,k);
9403: fprintf(ficlog,"%1d%1d%d",i,j,k);
9404: fprintf(ficres,"%1d%1d%d",i,j,k);
9405: }
9406: ll=0;
9407: for(li=1;li <=nlstate; li++){
9408: for(lj=1;lj <=nlstate+ndeath; lj++){
9409: if(lj==li) continue;
9410: for(lk=1;lk<=ncovmodel;lk++){
9411: ll++;
9412: if(ll<=jj){
9413: cb[0]= lk +'a'-1;cb[1]='\0';
9414: if(ll<jj){
9415: if(itimes==1){
9416: if(mle>=1)
9417: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9418: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9419: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9420: }else{
9421: if(mle>=1)
9422: printf(" %.5e",matcov[jj][ll]);
9423: fprintf(ficlog," %.5e",matcov[jj][ll]);
9424: fprintf(ficres," %.5e",matcov[jj][ll]);
9425: }
9426: }else{
9427: if(itimes==1){
9428: if(mle>=1)
9429: printf(" Var(%s%1d%1d)",ca,i,j);
9430: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
9431: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
9432: }else{
9433: if(mle>=1)
9434: printf(" %.7e",matcov[jj][ll]);
9435: fprintf(ficlog," %.7e",matcov[jj][ll]);
9436: fprintf(ficres," %.7e",matcov[jj][ll]);
9437: }
9438: }
9439: }
9440: } /* end lk */
9441: } /* end lj */
9442: } /* end li */
9443: if(mle>=1)
9444: printf("\n");
9445: fprintf(ficlog,"\n");
9446: fprintf(ficres,"\n");
9447: numlinepar++;
9448: } /* end k*/
9449: } /*end j */
1.126 brouard 9450: } /* end i */
9451: } /* end itimes */
9452:
9453: fflush(ficlog);
9454: fflush(ficres);
1.220 brouard 9455: while(fgets(line, MAXLINE, ficpar)) {
9456: /* If line starts with a # it is a comment */
9457: if (line[0] == '#') {
9458: numlinepar++;
9459: fputs(line,stdout);
9460: fputs(line,ficparo);
9461: fputs(line,ficlog);
9462: continue;
9463: }else
9464: break;
9465: }
9466:
1.209 brouard 9467: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
9468: /* ungetc(c,ficpar); */
9469: /* fgets(line, MAXLINE, ficpar); */
9470: /* fputs(line,stdout); */
9471: /* fputs(line,ficparo); */
9472: /* } */
9473: /* ungetc(c,ficpar); */
1.126 brouard 9474:
9475: estepm=0;
1.209 brouard 9476: 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){
1.220 brouard 9477:
9478: if (num_filled != 6) {
9479: 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);
9480: 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);
9481: goto end;
9482: }
9483: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
9484: }
9485: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
9486: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
9487:
1.209 brouard 9488: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 9489: if (estepm==0 || estepm < stepm) estepm=stepm;
9490: if (fage <= 2) {
9491: bage = ageminpar;
9492: fage = agemaxpar;
9493: }
9494:
9495: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 9496: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
9497: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220 brouard 9498:
1.186 brouard 9499: /* Other stuffs, more or less useful */
1.126 brouard 9500: while((c=getc(ficpar))=='#' && c!= EOF){
9501: ungetc(c,ficpar);
9502: fgets(line, MAXLINE, ficpar);
1.141 brouard 9503: fputs(line,stdout);
1.126 brouard 9504: fputs(line,ficparo);
9505: }
9506: ungetc(c,ficpar);
9507:
9508: 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);
9509: 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);
9510: 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);
9511: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
9512: 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);
9513:
9514: while((c=getc(ficpar))=='#' && c!= EOF){
9515: ungetc(c,ficpar);
9516: fgets(line, MAXLINE, ficpar);
1.141 brouard 9517: fputs(line,stdout);
1.126 brouard 9518: fputs(line,ficparo);
9519: }
9520: ungetc(c,ficpar);
9521:
9522:
9523: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
9524: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
9525:
9526: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 9527: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 9528: fprintf(ficparo,"pop_based=%d\n",popbased);
9529: fprintf(ficres,"pop_based=%d\n",popbased);
9530:
9531: while((c=getc(ficpar))=='#' && c!= EOF){
9532: ungetc(c,ficpar);
9533: fgets(line, MAXLINE, ficpar);
1.141 brouard 9534: fputs(line,stdout);
1.126 brouard 9535: fputs(line,ficparo);
9536: }
9537: ungetc(c,ficpar);
9538:
9539: 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);
9540: 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);
9541: 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);
9542: 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);
9543: 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);
9544: /* day and month of proj2 are not used but only year anproj2.*/
9545:
1.217 brouard 9546: while((c=getc(ficpar))=='#' && c!= EOF){
9547: ungetc(c,ficpar);
9548: fgets(line, MAXLINE, ficpar);
9549: fputs(line,stdout);
9550: fputs(line,ficparo);
9551: }
9552: ungetc(c,ficpar);
9553:
9554: 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);
1.219 brouard 9555: 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);
9556: 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);
9557: 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 9558: /* day and month of proj2 are not used but only year anproj2.*/
1.126 brouard 9559:
9560:
1.220 brouard 9561: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145 brouard 9562: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 9563:
9564: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 9565: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.220 brouard 9566: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 9567: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9568: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 9569: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 9570: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9571: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 9572: }else{
1.218 brouard 9573: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
1.220 brouard 9574: }
9575: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
9576: model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
9577: jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
9578:
9579: /*------------ free_vector -------------*/
9580: /* chdir(path); */
9581:
1.215 brouard 9582: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
9583: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
9584: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
9585: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.126 brouard 9586: free_lvector(num,1,n);
9587: free_vector(agedc,1,n);
9588: /*free_matrix(covar,0,NCOVMAX,1,n);*/
9589: /*free_matrix(covar,1,NCOVMAX,1,n);*/
9590: fclose(ficparo);
9591: fclose(ficres);
1.220 brouard 9592:
9593:
1.186 brouard 9594: /* Other results (useful)*/
1.220 brouard 9595:
9596:
1.126 brouard 9597: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 9598: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
9599: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 9600: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 9601: fclose(ficrespl);
9602:
9603: /*------------- h Pij x at various ages ------------*/
1.180 brouard 9604: /*#include "hpijx.h"*/
9605: hPijx(p, bage, fage);
1.145 brouard 9606: fclose(ficrespij);
1.126 brouard 9607:
1.220 brouard 9608: /* ncovcombmax= pow(2,cptcoveff); */
1.219 brouard 9609: /*-------------- Variance of one-step probabilities---*/
1.145 brouard 9610: k=1;
1.126 brouard 9611: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
9612:
1.219 brouard 9613: /* Prevalence for each covariates in probs[age][status][cov] */
1.218 brouard 9614: probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.126 brouard 9615: for(i=1;i<=AGESUP;i++)
1.219 brouard 9616: for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.218 brouard 9617: for(k=1;k<=ncovcombmax;k++)
9618: probs[i][j][k]=0.;
1.219 brouard 9619: prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
9620: if (mobilav!=0 ||mobilavproj !=0 ) {
9621: mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
9622: for(i=1;i<=AGESUP;i++)
9623: for(j=1;j<=nlstate;j++)
9624: for(k=1;k<=ncovcombmax;k++)
9625: mobaverages[i][j][k]=0.;
9626: mobaverage=mobaverages;
9627: if (mobilav!=0) {
1.218 brouard 9628: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
9629: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
9630: printf(" Error in movingaverage mobilav=%d\n",mobilav);
9631: }
1.219 brouard 9632: }
9633: /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
9634: /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
9635: else if (mobilavproj !=0) {
1.218 brouard 9636: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
9637: fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
9638: printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
9639: }
1.219 brouard 9640: }
9641: }/* end if moving average */
9642:
1.126 brouard 9643: /*---------- Forecasting ------------------*/
9644: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
9645: if(prevfcast==1){
9646: /* if(stepm ==1){*/
1.201 brouard 9647: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 9648: }
1.217 brouard 9649: if(backcast==1){
1.219 brouard 9650: ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
9651: ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
9652: ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
9653:
9654: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
9655:
9656: bprlim=matrix(1,nlstate,1,nlstate);
9657: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
9658: fclose(ficresplb);
9659:
1.222 ! brouard 9660: hBijx(p, bage, fage, mobaverage);
! 9661: fclose(ficrespijb);
1.219 brouard 9662: free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
9663:
9664: /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
9665: bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
9666: free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
9667: free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
9668: free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
9669: }
1.217 brouard 9670:
1.186 brouard 9671:
9672: /* ------ Other prevalence ratios------------ */
1.126 brouard 9673:
1.215 brouard 9674: free_ivector(wav,1,imx);
9675: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
9676: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
9677: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.218 brouard 9678:
9679:
1.127 brouard 9680: /*---------- Health expectancies, no variances ------------*/
1.218 brouard 9681:
1.201 brouard 9682: strcpy(filerese,"E_");
9683: strcat(filerese,fileresu);
1.126 brouard 9684: if((ficreseij=fopen(filerese,"w"))==NULL) {
9685: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
9686: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
9687: }
1.208 brouard 9688: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
9689: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.219 brouard 9690:
1.145 brouard 9691: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.219 brouard 9692: fprintf(ficreseij,"\n#****** ");
9693: for(j=1;j<=cptcoveff;j++) {
1.220 brouard 9694: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.219 brouard 9695: }
9696: fprintf(ficreseij,"******\n");
9697:
9698: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
9699: oldm=oldms;savm=savms;
9700: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
1.127 brouard 9701:
1.219 brouard 9702: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127 brouard 9703: }
9704: fclose(ficreseij);
1.208 brouard 9705: printf("done evsij\n");fflush(stdout);
9706: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.218 brouard 9707:
1.127 brouard 9708: /*---------- Health expectancies and variances ------------*/
1.218 brouard 9709:
9710:
1.201 brouard 9711: strcpy(filerest,"T_");
9712: strcat(filerest,fileresu);
1.127 brouard 9713: if((ficrest=fopen(filerest,"w"))==NULL) {
9714: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
9715: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
9716: }
1.208 brouard 9717: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
9718: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.218 brouard 9719:
1.126 brouard 9720:
1.201 brouard 9721: strcpy(fileresstde,"STDE_");
9722: strcat(fileresstde,fileresu);
1.126 brouard 9723: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
9724: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
9725: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
9726: }
1.208 brouard 9727: printf(" Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
9728: fprintf(ficlog," Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 9729:
1.201 brouard 9730: strcpy(filerescve,"CVE_");
9731: strcat(filerescve,fileresu);
1.126 brouard 9732: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
9733: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
9734: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
9735: }
1.208 brouard 9736: printf(" Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
9737: fprintf(ficlog," Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 9738:
1.201 brouard 9739: strcpy(fileresv,"V_");
9740: strcat(fileresv,fileresu);
1.126 brouard 9741: if((ficresvij=fopen(fileresv,"w"))==NULL) {
9742: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
9743: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
9744: }
1.208 brouard 9745: printf(" Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(stdout);
9746: fprintf(ficlog," Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 9747:
1.145 brouard 9748: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
9749: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
9750:
9751: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.208 brouard 9752: fprintf(ficrest,"\n#****** ");
9753: for(j=1;j<=cptcoveff;j++)
1.218 brouard 9754: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 9755: fprintf(ficrest,"******\n");
9756:
9757: fprintf(ficresstdeij,"\n#****** ");
9758: fprintf(ficrescveij,"\n#****** ");
9759: for(j=1;j<=cptcoveff;j++) {
1.218 brouard 9760: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9761: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 9762: }
9763: fprintf(ficresstdeij,"******\n");
9764: fprintf(ficrescveij,"******\n");
9765:
9766: fprintf(ficresvij,"\n#****** ");
9767: for(j=1;j<=cptcoveff;j++)
1.218 brouard 9768: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 9769: fprintf(ficresvij,"******\n");
9770:
9771: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
9772: oldm=oldms;savm=savms;
9773: printf(" cvevsij %d, ",k);
9774: fprintf(ficlog, " cvevsij %d, ",k);
9775: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
9776: printf(" end cvevsij \n ");
9777: fprintf(ficlog, " end cvevsij \n ");
9778:
9779: /*
9780: */
9781: /* goto endfree; */
9782:
9783: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
9784: pstamp(ficrest);
9785:
9786:
9787: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.220 brouard 9788: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
9789: cptcod= 0; /* To be deleted */
9790: printf("varevsij %d \n",vpopbased);
9791: fprintf(ficlog, "varevsij %d \n",vpopbased);
9792: 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 */
9793: 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 ");
9794: if(vpopbased==1)
9795: 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);
9796: else
9797: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
9798: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
9799: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
9800: fprintf(ficrest,"\n");
9801: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
9802: epj=vector(1,nlstate+1);
9803: printf("Computing age specific period (stable) prevalences in each health state \n");
9804: fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
9805: for(age=bage; age <=fage ;age++){
9806: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
9807: if (vpopbased==1) {
9808: if(mobilav ==0){
9809: for(i=1; i<=nlstate;i++)
9810: prlim[i][i]=probs[(int)age][i][k];
9811: }else{ /* mobilav */
9812: for(i=1; i<=nlstate;i++)
9813: prlim[i][i]=mobaverage[(int)age][i][k];
9814: }
9815: }
1.219 brouard 9816:
1.220 brouard 9817: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
9818: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
9819: /* printf(" age %4.0f ",age); */
9820: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
9821: for(i=1, epj[j]=0.;i <=nlstate;i++) {
9822: epj[j] += prlim[i][i]*eij[i][j][(int)age];
9823: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
9824: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
9825: }
9826: epj[nlstate+1] +=epj[j];
9827: }
9828: /* printf(" age %4.0f \n",age); */
1.219 brouard 9829:
1.220 brouard 9830: for(i=1, vepp=0.;i <=nlstate;i++)
9831: for(j=1;j <=nlstate;j++)
9832: vepp += vareij[i][j][(int)age];
9833: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
9834: for(j=1;j <=nlstate;j++){
9835: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
9836: }
9837: fprintf(ficrest,"\n");
9838: }
1.208 brouard 9839: } /* End vpopbased */
9840: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
9841: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
9842: free_vector(epj,1,nlstate+1);
9843: printf("done \n");fflush(stdout);
9844: fprintf(ficlog,"done\n");fflush(ficlog);
9845:
1.145 brouard 9846: /*}*/
1.208 brouard 9847: } /* End k */
1.126 brouard 9848: free_vector(weight,1,n);
1.145 brouard 9849: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 9850: free_imatrix(s,1,maxwav+1,1,n);
9851: free_matrix(anint,1,maxwav,1,n);
9852: free_matrix(mint,1,maxwav,1,n);
9853: free_ivector(cod,1,n);
9854: free_ivector(tab,1,NCOVMAX);
9855: fclose(ficresstdeij);
9856: fclose(ficrescveij);
9857: fclose(ficresvij);
9858: fclose(ficrest);
1.208 brouard 9859: printf("done Health expectancies\n");fflush(stdout);
9860: fprintf(ficlog,"done Health expectancies\n");fflush(ficlog);
1.126 brouard 9861: fclose(ficpar);
9862:
9863: /*------- Variance of period (stable) prevalence------*/
9864:
1.201 brouard 9865: strcpy(fileresvpl,"VPL_");
9866: strcat(fileresvpl,fileresu);
1.126 brouard 9867: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
9868: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
9869: exit(0);
9870: }
1.208 brouard 9871: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
9872: fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.126 brouard 9873:
1.145 brouard 9874: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
9875: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
9876:
9877: for (k=1; k <= (int) pow(2,cptcoveff); k++){
9878: fprintf(ficresvpl,"\n#****** ");
1.218 brouard 9879: for(j=1;j<=cptcoveff;j++)
9880: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9881: fprintf(ficresvpl,"******\n");
9882:
9883: varpl=matrix(1,nlstate,(int) bage, (int) fage);
9884: oldm=oldms;savm=savms;
9885: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
9886: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 9887: /*}*/
1.126 brouard 9888: }
1.218 brouard 9889:
1.126 brouard 9890: fclose(ficresvpl);
1.208 brouard 9891: printf("done variance-covariance of period prevalence\n");fflush(stdout);
9892: fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
1.126 brouard 9893:
9894: /*---------- End : free ----------------*/
1.219 brouard 9895: if (mobilav!=0 ||mobilavproj !=0)
9896: 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 9897: free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220 brouard 9898: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
9899: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126 brouard 9900: } /* mle==-3 arrives here for freeing */
1.164 brouard 9901: /* endfree:*/
1.126 brouard 9902: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
9903: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
9904: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
9905: free_matrix(covar,0,NCOVMAX,1,n);
9906: free_matrix(matcov,1,npar,1,npar);
1.203 brouard 9907: free_matrix(hess,1,npar,1,npar);
1.126 brouard 9908: /*free_vector(delti,1,npar);*/
9909: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
9910: free_matrix(agev,1,maxwav,1,imx);
9911: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
9912:
1.145 brouard 9913: free_ivector(ncodemax,1,NCOVMAX);
1.192 brouard 9914: free_ivector(ncodemaxwundef,1,NCOVMAX);
1.145 brouard 9915: free_ivector(Tvar,1,NCOVMAX);
9916: free_ivector(Tprod,1,NCOVMAX);
9917: free_ivector(Tvaraff,1,NCOVMAX);
1.220 brouard 9918: free_ivector(invalidvarcomb,1,ncovcombmax);
1.145 brouard 9919: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 9920:
9921: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
1.200 brouard 9922: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 9923: fflush(fichtm);
9924: fflush(ficgp);
9925:
9926:
9927: if((nberr >0) || (nbwarn>0)){
1.216 brouard 9928: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
9929: 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 9930: }else{
9931: printf("End of Imach\n");
9932: fprintf(ficlog,"End of Imach\n");
9933: }
9934: printf("See log file on %s\n",filelog);
9935: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 9936: /*(void) gettimeofday(&end_time,&tzp);*/
9937: rend_time = time(NULL);
9938: end_time = *localtime(&rend_time);
9939: /* tml = *localtime(&end_time.tm_sec); */
9940: strcpy(strtend,asctime(&end_time));
1.126 brouard 9941: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
9942: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 9943: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 9944:
1.157 brouard 9945: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
9946: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
9947: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 9948: /* printf("Total time was %d uSec.\n", total_usecs);*/
9949: /* if(fileappend(fichtm,optionfilehtm)){ */
9950: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
9951: fclose(fichtm);
9952: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
9953: fclose(fichtmcov);
9954: fclose(ficgp);
9955: fclose(ficlog);
9956: /*------ End -----------*/
9957:
9958:
9959: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 9960: #ifdef WIN32
9961: if (_chdir(pathcd) != 0)
9962: printf("Can't move to directory %s!\n",path);
9963: if(_getcwd(pathcd,MAXLINE) > 0)
9964: #else
1.126 brouard 9965: if(chdir(pathcd) != 0)
1.184 brouard 9966: printf("Can't move to directory %s!\n", path);
9967: if (getcwd(pathcd, MAXLINE) > 0)
9968: #endif
1.126 brouard 9969: printf("Current directory %s!\n",pathcd);
9970: /*strcat(plotcmd,CHARSEPARATOR);*/
9971: sprintf(plotcmd,"gnuplot");
1.157 brouard 9972: #ifdef _WIN32
1.126 brouard 9973: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
9974: #endif
9975: if(!stat(plotcmd,&info)){
1.158 brouard 9976: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 9977: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 9978: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 9979: }else
9980: strcpy(pplotcmd,plotcmd);
1.157 brouard 9981: #ifdef __unix
1.126 brouard 9982: strcpy(plotcmd,GNUPLOTPROGRAM);
9983: if(!stat(plotcmd,&info)){
1.158 brouard 9984: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 9985: }else
9986: strcpy(pplotcmd,plotcmd);
9987: #endif
9988: }else
9989: strcpy(pplotcmd,plotcmd);
9990:
9991: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 9992: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 9993:
9994: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 9995: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 9996: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 9997: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 9998: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 9999: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 10000: }
1.158 brouard 10001: printf(" Successful, please wait...");
1.126 brouard 10002: while (z[0] != 'q') {
10003: /* chdir(path); */
1.154 brouard 10004: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 10005: scanf("%s",z);
10006: /* if (z[0] == 'c') system("./imach"); */
10007: if (z[0] == 'e') {
1.158 brouard 10008: #ifdef __APPLE__
1.152 brouard 10009: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 10010: #elif __linux
10011: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 10012: #else
1.152 brouard 10013: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 10014: #endif
10015: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
10016: system(pplotcmd);
1.126 brouard 10017: }
10018: else if (z[0] == 'g') system(plotcmd);
10019: else if (z[0] == 'q') exit(0);
10020: }
10021: end:
10022: while (z[0] != 'q') {
1.195 brouard 10023: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 10024: scanf("%s",z);
10025: }
10026: }
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