Annotation of imach/src/imach.c, revision 1.224
1.224 ! brouard 1: /* $Id: imach.c,v 1.223 2016/02/19 09:23:35 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.224 ! brouard 4: Revision 1.223 2016/02/19 09:23:35 brouard
! 5: Summary: temporary
! 6:
1.223 brouard 7: Revision 1.222 2016/02/17 08:14:50 brouard
8: Summary: Probably last 0.98 stable version 0.98r6
9:
1.222 brouard 10: Revision 1.221 2016/02/15 23:35:36 brouard
11: Summary: minor bug
12:
1.220 brouard 13: Revision 1.219 2016/02/15 00:48:12 brouard
14: *** empty log message ***
15:
1.219 brouard 16: Revision 1.218 2016/02/12 11:29:23 brouard
17: Summary: 0.99 Back projections
18:
1.218 brouard 19: Revision 1.217 2015/12/23 17:18:31 brouard
20: Summary: Experimental backcast
21:
1.217 brouard 22: Revision 1.216 2015/12/18 17:32:11 brouard
23: Summary: 0.98r4 Warning and status=-2
24:
25: Version 0.98r4 is now:
26: - displaying an error when status is -1, date of interview unknown and date of death known;
27: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
28: Older changes concerning s=-2, dating from 2005 have been supersed.
29:
1.216 brouard 30: Revision 1.215 2015/12/16 08:52:24 brouard
31: Summary: 0.98r4 working
32:
1.215 brouard 33: Revision 1.214 2015/12/16 06:57:54 brouard
34: Summary: temporary not working
35:
1.214 brouard 36: Revision 1.213 2015/12/11 18:22:17 brouard
37: Summary: 0.98r4
38:
1.213 brouard 39: Revision 1.212 2015/11/21 12:47:24 brouard
40: Summary: minor typo
41:
1.212 brouard 42: Revision 1.211 2015/11/21 12:41:11 brouard
43: Summary: 0.98r3 with some graph of projected cross-sectional
44:
45: Author: Nicolas Brouard
46:
1.211 brouard 47: Revision 1.210 2015/11/18 17:41:20 brouard
48: Summary: Start working on projected prevalences
49:
1.210 brouard 50: Revision 1.209 2015/11/17 22:12:03 brouard
51: Summary: Adding ftolpl parameter
52: Author: N Brouard
53:
54: We had difficulties to get smoothed confidence intervals. It was due
55: to the period prevalence which wasn't computed accurately. The inner
56: parameter ftolpl is now an outer parameter of the .imach parameter
57: file after estepm. If ftolpl is small 1.e-4 and estepm too,
58: computation are long.
59:
1.209 brouard 60: Revision 1.208 2015/11/17 14:31:57 brouard
61: Summary: temporary
62:
1.208 brouard 63: Revision 1.207 2015/10/27 17:36:57 brouard
64: *** empty log message ***
65:
1.207 brouard 66: Revision 1.206 2015/10/24 07:14:11 brouard
67: *** empty log message ***
68:
1.206 brouard 69: Revision 1.205 2015/10/23 15:50:53 brouard
70: Summary: 0.98r3 some clarification for graphs on likelihood contributions
71:
1.205 brouard 72: Revision 1.204 2015/10/01 16:20:26 brouard
73: Summary: Some new graphs of contribution to likelihood
74:
1.204 brouard 75: Revision 1.203 2015/09/30 17:45:14 brouard
76: Summary: looking at better estimation of the hessian
77:
78: Also a better criteria for convergence to the period prevalence And
79: therefore adding the number of years needed to converge. (The
80: prevalence in any alive state shold sum to one
81:
1.203 brouard 82: Revision 1.202 2015/09/22 19:45:16 brouard
83: Summary: Adding some overall graph on contribution to likelihood. Might change
84:
1.202 brouard 85: Revision 1.201 2015/09/15 17:34:58 brouard
86: Summary: 0.98r0
87:
88: - Some new graphs like suvival functions
89: - Some bugs fixed like model=1+age+V2.
90:
1.201 brouard 91: Revision 1.200 2015/09/09 16:53:55 brouard
92: Summary: Big bug thanks to Flavia
93:
94: Even model=1+age+V2. did not work anymore
95:
1.200 brouard 96: Revision 1.199 2015/09/07 14:09:23 brouard
97: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
98:
1.199 brouard 99: Revision 1.198 2015/09/03 07:14:39 brouard
100: Summary: 0.98q5 Flavia
101:
1.198 brouard 102: Revision 1.197 2015/09/01 18:24:39 brouard
103: *** empty log message ***
104:
1.197 brouard 105: Revision 1.196 2015/08/18 23:17:52 brouard
106: Summary: 0.98q5
107:
1.196 brouard 108: Revision 1.195 2015/08/18 16:28:39 brouard
109: Summary: Adding a hack for testing purpose
110:
111: After reading the title, ftol and model lines, if the comment line has
112: a q, starting with #q, the answer at the end of the run is quit. It
113: permits to run test files in batch with ctest. The former workaround was
114: $ echo q | imach foo.imach
115:
1.195 brouard 116: Revision 1.194 2015/08/18 13:32:00 brouard
117: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
118:
1.194 brouard 119: Revision 1.193 2015/08/04 07:17:42 brouard
120: Summary: 0.98q4
121:
1.193 brouard 122: Revision 1.192 2015/07/16 16:49:02 brouard
123: Summary: Fixing some outputs
124:
1.192 brouard 125: Revision 1.191 2015/07/14 10:00:33 brouard
126: Summary: Some fixes
127:
1.191 brouard 128: Revision 1.190 2015/05/05 08:51:13 brouard
129: Summary: Adding digits in output parameters (7 digits instead of 6)
130:
131: Fix 1+age+.
132:
1.190 brouard 133: Revision 1.189 2015/04/30 14:45:16 brouard
134: Summary: 0.98q2
135:
1.189 brouard 136: Revision 1.188 2015/04/30 08:27:53 brouard
137: *** empty log message ***
138:
1.188 brouard 139: Revision 1.187 2015/04/29 09:11:15 brouard
140: *** empty log message ***
141:
1.187 brouard 142: Revision 1.186 2015/04/23 12:01:52 brouard
143: Summary: V1*age is working now, version 0.98q1
144:
145: Some codes had been disabled in order to simplify and Vn*age was
146: working in the optimization phase, ie, giving correct MLE parameters,
147: but, as usual, outputs were not correct and program core dumped.
148:
1.186 brouard 149: Revision 1.185 2015/03/11 13:26:42 brouard
150: Summary: Inclusion of compile and links command line for Intel Compiler
151:
1.185 brouard 152: Revision 1.184 2015/03/11 11:52:39 brouard
153: Summary: Back from Windows 8. Intel Compiler
154:
1.184 brouard 155: Revision 1.183 2015/03/10 20:34:32 brouard
156: Summary: 0.98q0, trying with directest, mnbrak fixed
157:
158: We use directest instead of original Powell test; probably no
159: incidence on the results, but better justifications;
160: We fixed Numerical Recipes mnbrak routine which was wrong and gave
161: wrong results.
162:
1.183 brouard 163: Revision 1.182 2015/02/12 08:19:57 brouard
164: Summary: Trying to keep directest which seems simpler and more general
165: Author: Nicolas Brouard
166:
1.182 brouard 167: Revision 1.181 2015/02/11 23:22:24 brouard
168: Summary: Comments on Powell added
169:
170: Author:
171:
1.181 brouard 172: Revision 1.180 2015/02/11 17:33:45 brouard
173: Summary: Finishing move from main to function (hpijx and prevalence_limit)
174:
1.180 brouard 175: Revision 1.179 2015/01/04 09:57:06 brouard
176: Summary: back to OS/X
177:
1.179 brouard 178: Revision 1.178 2015/01/04 09:35:48 brouard
179: *** empty log message ***
180:
1.178 brouard 181: Revision 1.177 2015/01/03 18:40:56 brouard
182: Summary: Still testing ilc32 on OSX
183:
1.177 brouard 184: Revision 1.176 2015/01/03 16:45:04 brouard
185: *** empty log message ***
186:
1.176 brouard 187: Revision 1.175 2015/01/03 16:33:42 brouard
188: *** empty log message ***
189:
1.175 brouard 190: Revision 1.174 2015/01/03 16:15:49 brouard
191: Summary: Still in cross-compilation
192:
1.174 brouard 193: Revision 1.173 2015/01/03 12:06:26 brouard
194: Summary: trying to detect cross-compilation
195:
1.173 brouard 196: Revision 1.172 2014/12/27 12:07:47 brouard
197: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
198:
1.172 brouard 199: Revision 1.171 2014/12/23 13:26:59 brouard
200: Summary: Back from Visual C
201:
202: Still problem with utsname.h on Windows
203:
1.171 brouard 204: Revision 1.170 2014/12/23 11:17:12 brouard
205: Summary: Cleaning some \%% back to %%
206:
207: The escape was mandatory for a specific compiler (which one?), but too many warnings.
208:
1.170 brouard 209: Revision 1.169 2014/12/22 23:08:31 brouard
210: Summary: 0.98p
211:
212: Outputs some informations on compiler used, OS etc. Testing on different platforms.
213:
1.169 brouard 214: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 215: Summary: update
1.169 brouard 216:
1.168 brouard 217: Revision 1.167 2014/12/22 13:50:56 brouard
218: Summary: Testing uname and compiler version and if compiled 32 or 64
219:
220: Testing on Linux 64
221:
1.167 brouard 222: Revision 1.166 2014/12/22 11:40:47 brouard
223: *** empty log message ***
224:
1.166 brouard 225: Revision 1.165 2014/12/16 11:20:36 brouard
226: Summary: After compiling on Visual C
227:
228: * imach.c (Module): Merging 1.61 to 1.162
229:
1.165 brouard 230: Revision 1.164 2014/12/16 10:52:11 brouard
231: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
232:
233: * imach.c (Module): Merging 1.61 to 1.162
234:
1.164 brouard 235: Revision 1.163 2014/12/16 10:30:11 brouard
236: * imach.c (Module): Merging 1.61 to 1.162
237:
1.163 brouard 238: Revision 1.162 2014/09/25 11:43:39 brouard
239: Summary: temporary backup 0.99!
240:
1.162 brouard 241: Revision 1.1 2014/09/16 11:06:58 brouard
242: Summary: With some code (wrong) for nlopt
243:
244: Author:
245:
246: Revision 1.161 2014/09/15 20:41:41 brouard
247: Summary: Problem with macro SQR on Intel compiler
248:
1.161 brouard 249: Revision 1.160 2014/09/02 09:24:05 brouard
250: *** empty log message ***
251:
1.160 brouard 252: Revision 1.159 2014/09/01 10:34:10 brouard
253: Summary: WIN32
254: Author: Brouard
255:
1.159 brouard 256: Revision 1.158 2014/08/27 17:11:51 brouard
257: *** empty log message ***
258:
1.158 brouard 259: Revision 1.157 2014/08/27 16:26:55 brouard
260: Summary: Preparing windows Visual studio version
261: Author: Brouard
262:
263: In order to compile on Visual studio, time.h is now correct and time_t
264: and tm struct should be used. difftime should be used but sometimes I
265: just make the differences in raw time format (time(&now).
266: Trying to suppress #ifdef LINUX
267: Add xdg-open for __linux in order to open default browser.
268:
1.157 brouard 269: Revision 1.156 2014/08/25 20:10:10 brouard
270: *** empty log message ***
271:
1.156 brouard 272: Revision 1.155 2014/08/25 18:32:34 brouard
273: Summary: New compile, minor changes
274: Author: Brouard
275:
1.155 brouard 276: Revision 1.154 2014/06/20 17:32:08 brouard
277: Summary: Outputs now all graphs of convergence to period prevalence
278:
1.154 brouard 279: Revision 1.153 2014/06/20 16:45:46 brouard
280: Summary: If 3 live state, convergence to period prevalence on same graph
281: Author: Brouard
282:
1.153 brouard 283: Revision 1.152 2014/06/18 17:54:09 brouard
284: Summary: open browser, use gnuplot on same dir than imach if not found in the path
285:
1.152 brouard 286: Revision 1.151 2014/06/18 16:43:30 brouard
287: *** empty log message ***
288:
1.151 brouard 289: Revision 1.150 2014/06/18 16:42:35 brouard
290: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
291: Author: brouard
292:
1.150 brouard 293: Revision 1.149 2014/06/18 15:51:14 brouard
294: Summary: Some fixes in parameter files errors
295: Author: Nicolas Brouard
296:
1.149 brouard 297: Revision 1.148 2014/06/17 17:38:48 brouard
298: Summary: Nothing new
299: Author: Brouard
300:
301: Just a new packaging for OS/X version 0.98nS
302:
1.148 brouard 303: Revision 1.147 2014/06/16 10:33:11 brouard
304: *** empty log message ***
305:
1.147 brouard 306: Revision 1.146 2014/06/16 10:20:28 brouard
307: Summary: Merge
308: Author: Brouard
309:
310: Merge, before building revised version.
311:
1.146 brouard 312: Revision 1.145 2014/06/10 21:23:15 brouard
313: Summary: Debugging with valgrind
314: Author: Nicolas Brouard
315:
316: Lot of changes in order to output the results with some covariates
317: After the Edimburgh REVES conference 2014, it seems mandatory to
318: improve the code.
319: No more memory valgrind error but a lot has to be done in order to
320: continue the work of splitting the code into subroutines.
321: Also, decodemodel has been improved. Tricode is still not
322: optimal. nbcode should be improved. Documentation has been added in
323: the source code.
324:
1.144 brouard 325: Revision 1.143 2014/01/26 09:45:38 brouard
326: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
327:
328: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
329: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
330:
1.143 brouard 331: Revision 1.142 2014/01/26 03:57:36 brouard
332: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
333:
334: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
335:
1.142 brouard 336: Revision 1.141 2014/01/26 02:42:01 brouard
337: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
338:
1.141 brouard 339: Revision 1.140 2011/09/02 10:37:54 brouard
340: Summary: times.h is ok with mingw32 now.
341:
1.140 brouard 342: Revision 1.139 2010/06/14 07:50:17 brouard
343: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
344: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
345:
1.139 brouard 346: Revision 1.138 2010/04/30 18:19:40 brouard
347: *** empty log message ***
348:
1.138 brouard 349: Revision 1.137 2010/04/29 18:11:38 brouard
350: (Module): Checking covariates for more complex models
351: than V1+V2. A lot of change to be done. Unstable.
352:
1.137 brouard 353: Revision 1.136 2010/04/26 20:30:53 brouard
354: (Module): merging some libgsl code. Fixing computation
355: of likelione (using inter/intrapolation if mle = 0) in order to
356: get same likelihood as if mle=1.
357: Some cleaning of code and comments added.
358:
1.136 brouard 359: Revision 1.135 2009/10/29 15:33:14 brouard
360: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
361:
1.135 brouard 362: Revision 1.134 2009/10/29 13:18:53 brouard
363: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
364:
1.134 brouard 365: Revision 1.133 2009/07/06 10:21:25 brouard
366: just nforces
367:
1.133 brouard 368: Revision 1.132 2009/07/06 08:22:05 brouard
369: Many tings
370:
1.132 brouard 371: Revision 1.131 2009/06/20 16:22:47 brouard
372: Some dimensions resccaled
373:
1.131 brouard 374: Revision 1.130 2009/05/26 06:44:34 brouard
375: (Module): Max Covariate is now set to 20 instead of 8. A
376: lot of cleaning with variables initialized to 0. Trying to make
377: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
378:
1.130 brouard 379: Revision 1.129 2007/08/31 13:49:27 lievre
380: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
381:
1.129 lievre 382: Revision 1.128 2006/06/30 13:02:05 brouard
383: (Module): Clarifications on computing e.j
384:
1.128 brouard 385: Revision 1.127 2006/04/28 18:11:50 brouard
386: (Module): Yes the sum of survivors was wrong since
387: imach-114 because nhstepm was no more computed in the age
388: loop. Now we define nhstepma in the age loop.
389: (Module): In order to speed up (in case of numerous covariates) we
390: compute health expectancies (without variances) in a first step
391: and then all the health expectancies with variances or standard
392: deviation (needs data from the Hessian matrices) which slows the
393: computation.
394: In the future we should be able to stop the program is only health
395: expectancies and graph are needed without standard deviations.
396:
1.127 brouard 397: Revision 1.126 2006/04/28 17:23:28 brouard
398: (Module): Yes the sum of survivors was wrong since
399: imach-114 because nhstepm was no more computed in the age
400: loop. Now we define nhstepma in the age loop.
401: Version 0.98h
402:
1.126 brouard 403: Revision 1.125 2006/04/04 15:20:31 lievre
404: Errors in calculation of health expectancies. Age was not initialized.
405: Forecasting file added.
406:
407: Revision 1.124 2006/03/22 17:13:53 lievre
408: Parameters are printed with %lf instead of %f (more numbers after the comma).
409: The log-likelihood is printed in the log file
410:
411: Revision 1.123 2006/03/20 10:52:43 brouard
412: * imach.c (Module): <title> changed, corresponds to .htm file
413: name. <head> headers where missing.
414:
415: * imach.c (Module): Weights can have a decimal point as for
416: English (a comma might work with a correct LC_NUMERIC environment,
417: otherwise the weight is truncated).
418: Modification of warning when the covariates values are not 0 or
419: 1.
420: Version 0.98g
421:
422: Revision 1.122 2006/03/20 09:45:41 brouard
423: (Module): Weights can have a decimal point as for
424: English (a comma might work with a correct LC_NUMERIC environment,
425: otherwise the weight is truncated).
426: Modification of warning when the covariates values are not 0 or
427: 1.
428: Version 0.98g
429:
430: Revision 1.121 2006/03/16 17:45:01 lievre
431: * imach.c (Module): Comments concerning covariates added
432:
433: * imach.c (Module): refinements in the computation of lli if
434: status=-2 in order to have more reliable computation if stepm is
435: not 1 month. Version 0.98f
436:
437: Revision 1.120 2006/03/16 15:10:38 lievre
438: (Module): refinements in the computation of lli if
439: status=-2 in order to have more reliable computation if stepm is
440: not 1 month. Version 0.98f
441:
442: Revision 1.119 2006/03/15 17:42:26 brouard
443: (Module): Bug if status = -2, the loglikelihood was
444: computed as likelihood omitting the logarithm. Version O.98e
445:
446: Revision 1.118 2006/03/14 18:20:07 brouard
447: (Module): varevsij Comments added explaining the second
448: table of variances if popbased=1 .
449: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
450: (Module): Function pstamp added
451: (Module): Version 0.98d
452:
453: Revision 1.117 2006/03/14 17:16:22 brouard
454: (Module): varevsij Comments added explaining the second
455: table of variances if popbased=1 .
456: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
457: (Module): Function pstamp added
458: (Module): Version 0.98d
459:
460: Revision 1.116 2006/03/06 10:29:27 brouard
461: (Module): Variance-covariance wrong links and
462: varian-covariance of ej. is needed (Saito).
463:
464: Revision 1.115 2006/02/27 12:17:45 brouard
465: (Module): One freematrix added in mlikeli! 0.98c
466:
467: Revision 1.114 2006/02/26 12:57:58 brouard
468: (Module): Some improvements in processing parameter
469: filename with strsep.
470:
471: Revision 1.113 2006/02/24 14:20:24 brouard
472: (Module): Memory leaks checks with valgrind and:
473: datafile was not closed, some imatrix were not freed and on matrix
474: allocation too.
475:
476: Revision 1.112 2006/01/30 09:55:26 brouard
477: (Module): Back to gnuplot.exe instead of wgnuplot.exe
478:
479: Revision 1.111 2006/01/25 20:38:18 brouard
480: (Module): Lots of cleaning and bugs added (Gompertz)
481: (Module): Comments can be added in data file. Missing date values
482: can be a simple dot '.'.
483:
484: Revision 1.110 2006/01/25 00:51:50 brouard
485: (Module): Lots of cleaning and bugs added (Gompertz)
486:
487: Revision 1.109 2006/01/24 19:37:15 brouard
488: (Module): Comments (lines starting with a #) are allowed in data.
489:
490: Revision 1.108 2006/01/19 18:05:42 lievre
491: Gnuplot problem appeared...
492: To be fixed
493:
494: Revision 1.107 2006/01/19 16:20:37 brouard
495: Test existence of gnuplot in imach path
496:
497: Revision 1.106 2006/01/19 13:24:36 brouard
498: Some cleaning and links added in html output
499:
500: Revision 1.105 2006/01/05 20:23:19 lievre
501: *** empty log message ***
502:
503: Revision 1.104 2005/09/30 16:11:43 lievre
504: (Module): sump fixed, loop imx fixed, and simplifications.
505: (Module): If the status is missing at the last wave but we know
506: that the person is alive, then we can code his/her status as -2
507: (instead of missing=-1 in earlier versions) and his/her
508: contributions to the likelihood is 1 - Prob of dying from last
509: health status (= 1-p13= p11+p12 in the easiest case of somebody in
510: the healthy state at last known wave). Version is 0.98
511:
512: Revision 1.103 2005/09/30 15:54:49 lievre
513: (Module): sump fixed, loop imx fixed, and simplifications.
514:
515: Revision 1.102 2004/09/15 17:31:30 brouard
516: Add the possibility to read data file including tab characters.
517:
518: Revision 1.101 2004/09/15 10:38:38 brouard
519: Fix on curr_time
520:
521: Revision 1.100 2004/07/12 18:29:06 brouard
522: Add version for Mac OS X. Just define UNIX in Makefile
523:
524: Revision 1.99 2004/06/05 08:57:40 brouard
525: *** empty log message ***
526:
527: Revision 1.98 2004/05/16 15:05:56 brouard
528: New version 0.97 . First attempt to estimate force of mortality
529: directly from the data i.e. without the need of knowing the health
530: state at each age, but using a Gompertz model: log u =a + b*age .
531: This is the basic analysis of mortality and should be done before any
532: other analysis, in order to test if the mortality estimated from the
533: cross-longitudinal survey is different from the mortality estimated
534: from other sources like vital statistic data.
535:
536: The same imach parameter file can be used but the option for mle should be -3.
537:
1.133 brouard 538: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 539: former routines in order to include the new code within the former code.
540:
541: The output is very simple: only an estimate of the intercept and of
542: the slope with 95% confident intervals.
543:
544: Current limitations:
545: A) Even if you enter covariates, i.e. with the
546: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
547: B) There is no computation of Life Expectancy nor Life Table.
548:
549: Revision 1.97 2004/02/20 13:25:42 lievre
550: Version 0.96d. Population forecasting command line is (temporarily)
551: suppressed.
552:
553: Revision 1.96 2003/07/15 15:38:55 brouard
554: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
555: rewritten within the same printf. Workaround: many printfs.
556:
557: Revision 1.95 2003/07/08 07:54:34 brouard
558: * imach.c (Repository):
559: (Repository): Using imachwizard code to output a more meaningful covariance
560: matrix (cov(a12,c31) instead of numbers.
561:
562: Revision 1.94 2003/06/27 13:00:02 brouard
563: Just cleaning
564:
565: Revision 1.93 2003/06/25 16:33:55 brouard
566: (Module): On windows (cygwin) function asctime_r doesn't
567: exist so I changed back to asctime which exists.
568: (Module): Version 0.96b
569:
570: Revision 1.92 2003/06/25 16:30:45 brouard
571: (Module): On windows (cygwin) function asctime_r doesn't
572: exist so I changed back to asctime which exists.
573:
574: Revision 1.91 2003/06/25 15:30:29 brouard
575: * imach.c (Repository): Duplicated warning errors corrected.
576: (Repository): Elapsed time after each iteration is now output. It
577: helps to forecast when convergence will be reached. Elapsed time
578: is stamped in powell. We created a new html file for the graphs
579: concerning matrix of covariance. It has extension -cov.htm.
580:
581: Revision 1.90 2003/06/24 12:34:15 brouard
582: (Module): Some bugs corrected for windows. Also, when
583: mle=-1 a template is output in file "or"mypar.txt with the design
584: of the covariance matrix to be input.
585:
586: Revision 1.89 2003/06/24 12:30:52 brouard
587: (Module): Some bugs corrected for windows. Also, when
588: mle=-1 a template is output in file "or"mypar.txt with the design
589: of the covariance matrix to be input.
590:
591: Revision 1.88 2003/06/23 17:54:56 brouard
592: * 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.
593:
594: Revision 1.87 2003/06/18 12:26:01 brouard
595: Version 0.96
596:
597: Revision 1.86 2003/06/17 20:04:08 brouard
598: (Module): Change position of html and gnuplot routines and added
599: routine fileappend.
600:
601: Revision 1.85 2003/06/17 13:12:43 brouard
602: * imach.c (Repository): Check when date of death was earlier that
603: current date of interview. It may happen when the death was just
604: prior to the death. In this case, dh was negative and likelihood
605: was wrong (infinity). We still send an "Error" but patch by
606: assuming that the date of death was just one stepm after the
607: interview.
608: (Repository): Because some people have very long ID (first column)
609: we changed int to long in num[] and we added a new lvector for
610: memory allocation. But we also truncated to 8 characters (left
611: truncation)
612: (Repository): No more line truncation errors.
613:
614: Revision 1.84 2003/06/13 21:44:43 brouard
615: * imach.c (Repository): Replace "freqsummary" at a correct
616: place. It differs from routine "prevalence" which may be called
617: many times. Probs is memory consuming and must be used with
618: parcimony.
619: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
620:
621: Revision 1.83 2003/06/10 13:39:11 lievre
622: *** empty log message ***
623:
624: Revision 1.82 2003/06/05 15:57:20 brouard
625: Add log in imach.c and fullversion number is now printed.
626:
627: */
628: /*
629: Interpolated Markov Chain
630:
631: Short summary of the programme:
632:
633: This program computes Healthy Life Expectancies from
634: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
635: first survey ("cross") where individuals from different ages are
636: interviewed on their health status or degree of disability (in the
637: case of a health survey which is our main interest) -2- at least a
638: second wave of interviews ("longitudinal") which measure each change
639: (if any) in individual health status. Health expectancies are
640: computed from the time spent in each health state according to a
641: model. More health states you consider, more time is necessary to reach the
642: Maximum Likelihood of the parameters involved in the model. The
643: simplest model is the multinomial logistic model where pij is the
644: probability to be observed in state j at the second wave
645: conditional to be observed in state i at the first wave. Therefore
646: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
647: 'age' is age and 'sex' is a covariate. If you want to have a more
648: complex model than "constant and age", you should modify the program
649: where the markup *Covariates have to be included here again* invites
650: you to do it. More covariates you add, slower the
651: convergence.
652:
653: The advantage of this computer programme, compared to a simple
654: multinomial logistic model, is clear when the delay between waves is not
655: identical for each individual. Also, if a individual missed an
656: intermediate interview, the information is lost, but taken into
657: account using an interpolation or extrapolation.
658:
659: hPijx is the probability to be observed in state i at age x+h
660: conditional to the observed state i at age x. The delay 'h' can be
661: split into an exact number (nh*stepm) of unobserved intermediate
662: states. This elementary transition (by month, quarter,
663: semester or year) is modelled as a multinomial logistic. The hPx
664: matrix is simply the matrix product of nh*stepm elementary matrices
665: and the contribution of each individual to the likelihood is simply
666: hPijx.
667:
668: Also this programme outputs the covariance matrix of the parameters but also
1.218 brouard 669: of the life expectancies. It also computes the period (stable) prevalence.
670:
671: Back prevalence and projections:
672: - 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)
673: Computes the back prevalence limit for any combination of covariate values k
674: at any age between ageminpar and agemaxpar and returns it in **bprlim. In the loops,
675: - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm, **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
676: - hBijx Back Probability to be in state i at age x-h being in j at x
677: Computes for any combination of covariates k and any age between bage and fage
678: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
679: oldm=oldms;savm=savms;
680: - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
681: Computes the transition matrix starting at age 'age' over
682: 'nhstepm*hstepm*stepm' months (i.e. until
683: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
684: nhstepm*hstepm matrices. Returns p3mat[i][j][h] after calling
685: p3mat[i][j][h]=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\
686: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
687:
1.133 brouard 688: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
689: Institut national d'études démographiques, Paris.
1.126 brouard 690: This software have been partly granted by Euro-REVES, a concerted action
691: from the European Union.
692: It is copyrighted identically to a GNU software product, ie programme and
693: software can be distributed freely for non commercial use. Latest version
694: can be accessed at http://euroreves.ined.fr/imach .
695:
696: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
697: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
698:
699: **********************************************************************/
700: /*
701: main
702: read parameterfile
703: read datafile
704: concatwav
705: freqsummary
706: if (mle >= 1)
707: mlikeli
708: print results files
709: if mle==1
710: computes hessian
711: read end of parameter file: agemin, agemax, bage, fage, estepm
712: begin-prev-date,...
713: open gnuplot file
714: open html file
1.145 brouard 715: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
716: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
717: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
718: freexexit2 possible for memory heap.
719:
720: h Pij x | pij_nom ficrestpij
721: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
722: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
723: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
724:
725: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
726: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
727: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
728: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
729: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
730:
1.126 brouard 731: forecasting if prevfcast==1 prevforecast call prevalence()
732: health expectancies
733: Variance-covariance of DFLE
734: prevalence()
735: movingaverage()
736: varevsij()
737: if popbased==1 varevsij(,popbased)
738: total life expectancies
739: Variance of period (stable) prevalence
740: end
741: */
742:
1.187 brouard 743: /* #define DEBUG */
744: /* #define DEBUGBRENT */
1.203 brouard 745: /* #define DEBUGLINMIN */
746: /* #define DEBUGHESS */
747: #define DEBUGHESSIJ
1.224 ! brouard 748: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan) *\/ */
1.165 brouard 749: #define POWELL /* Instead of NLOPT */
1.224 ! brouard 750: #define POWELLNOF3INFF1TEST /* Skip test */
1.186 brouard 751: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
752: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 753:
754: #include <math.h>
755: #include <stdio.h>
756: #include <stdlib.h>
757: #include <string.h>
1.159 brouard 758:
759: #ifdef _WIN32
760: #include <io.h>
1.172 brouard 761: #include <windows.h>
762: #include <tchar.h>
1.159 brouard 763: #else
1.126 brouard 764: #include <unistd.h>
1.159 brouard 765: #endif
1.126 brouard 766:
767: #include <limits.h>
768: #include <sys/types.h>
1.171 brouard 769:
770: #if defined(__GNUC__)
771: #include <sys/utsname.h> /* Doesn't work on Windows */
772: #endif
773:
1.126 brouard 774: #include <sys/stat.h>
775: #include <errno.h>
1.159 brouard 776: /* extern int errno; */
1.126 brouard 777:
1.157 brouard 778: /* #ifdef LINUX */
779: /* #include <time.h> */
780: /* #include "timeval.h" */
781: /* #else */
782: /* #include <sys/time.h> */
783: /* #endif */
784:
1.126 brouard 785: #include <time.h>
786:
1.136 brouard 787: #ifdef GSL
788: #include <gsl/gsl_errno.h>
789: #include <gsl/gsl_multimin.h>
790: #endif
791:
1.167 brouard 792:
1.162 brouard 793: #ifdef NLOPT
794: #include <nlopt.h>
795: typedef struct {
796: double (* function)(double [] );
797: } myfunc_data ;
798: #endif
799:
1.126 brouard 800: /* #include <libintl.h> */
801: /* #define _(String) gettext (String) */
802:
1.141 brouard 803: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 804:
805: #define GNUPLOTPROGRAM "gnuplot"
806: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
807: #define FILENAMELENGTH 132
808:
809: #define GLOCK_ERROR_NOPATH -1 /* empty path */
810: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
811:
1.144 brouard 812: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
813: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 814:
815: #define NINTERVMAX 8
1.144 brouard 816: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
817: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
818: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 819: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 820: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
821: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.126 brouard 822: #define MAXN 20000
1.144 brouard 823: #define YEARM 12. /**< Number of months per year */
1.218 brouard 824: /* #define AGESUP 130 */
825: #define AGESUP 150
826: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126 brouard 827: #define AGEBASE 40
1.194 brouard 828: #define AGEOVERFLOW 1.e20
1.164 brouard 829: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 830: #ifdef _WIN32
831: #define DIRSEPARATOR '\\'
832: #define CHARSEPARATOR "\\"
833: #define ODIRSEPARATOR '/'
834: #else
1.126 brouard 835: #define DIRSEPARATOR '/'
836: #define CHARSEPARATOR "/"
837: #define ODIRSEPARATOR '\\'
838: #endif
839:
1.224 ! brouard 840: /* $Id: imach.c,v 1.223 2016/02/19 09:23:35 brouard Exp $ */
1.126 brouard 841: /* $State: Exp $ */
1.196 brouard 842: #include "version.h"
843: char version[]=__IMACH_VERSION__;
1.224 ! brouard 844: char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";
! 845: char fullversion[]="$Revision: 1.223 $ $Date: 2016/02/19 09:23:35 $";
1.126 brouard 846: char strstart[80];
847: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 848: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 849: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 850: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
851: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
852: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
853: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
854: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
855: int cptcovprodnoage=0; /**< Number of covariate products without age */
856: int cptcoveff=0; /* Total number of covariates to vary for printing results */
1.224 ! brouard 857: int ncoveff=0; /* Total number of effective covariates in the model */
! 858: int nqveff=0; /**< nqveff number of effective quantitative variables */
! 859: int ntveff=0; /**< ntveff number of effective time varying variables */
! 860: int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
1.145 brouard 861: int cptcov=0; /* Working variable */
1.218 brouard 862: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.126 brouard 863: int npar=NPARMAX;
864: int nlstate=2; /* Number of live states */
865: int ndeath=1; /* Number of dead states */
1.130 brouard 866: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.223 brouard 867: int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
1.126 brouard 868: int popbased=0;
869:
870: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 871: int maxwav=0; /* Maxim number of waves */
872: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
873: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
874: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 875: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 876: int mle=1, weightopt=0;
1.126 brouard 877: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
878: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
879: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
880: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 881: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 882: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 883: double **matprod2(); /* test */
1.126 brouard 884: double **oldm, **newm, **savm; /* Working pointers to matrices */
885: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218 brouard 886: double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
887:
1.136 brouard 888: /*FILE *fic ; */ /* Used in readdata only */
1.217 brouard 889: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 890: FILE *ficlog, *ficrespow;
1.130 brouard 891: int globpr=0; /* Global variable for printing or not */
1.126 brouard 892: double fretone; /* Only one call to likelihood */
1.130 brouard 893: long ipmx=0; /* Number of contributions */
1.126 brouard 894: double sw; /* Sum of weights */
895: char filerespow[FILENAMELENGTH];
896: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
897: FILE *ficresilk;
898: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
899: FILE *ficresprobmorprev;
900: FILE *fichtm, *fichtmcov; /* Html File */
901: FILE *ficreseij;
902: char filerese[FILENAMELENGTH];
903: FILE *ficresstdeij;
904: char fileresstde[FILENAMELENGTH];
905: FILE *ficrescveij;
906: char filerescve[FILENAMELENGTH];
907: FILE *ficresvij;
908: char fileresv[FILENAMELENGTH];
909: FILE *ficresvpl;
910: char fileresvpl[FILENAMELENGTH];
911: char title[MAXLINE];
1.217 brouard 912: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 913: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
914: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
915: char command[FILENAMELENGTH];
916: int outcmd=0;
917:
1.217 brouard 918: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 919: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 920: char filelog[FILENAMELENGTH]; /* Log file */
921: char filerest[FILENAMELENGTH];
922: char fileregp[FILENAMELENGTH];
923: char popfile[FILENAMELENGTH];
924:
925: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
926:
1.157 brouard 927: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
928: /* struct timezone tzp; */
929: /* extern int gettimeofday(); */
930: struct tm tml, *gmtime(), *localtime();
931:
932: extern time_t time();
933:
934: struct tm start_time, end_time, curr_time, last_time, forecast_time;
935: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
936: struct tm tm;
937:
1.126 brouard 938: char strcurr[80], strfor[80];
939:
940: char *endptr;
941: long lval;
942: double dval;
943:
944: #define NR_END 1
945: #define FREE_ARG char*
946: #define FTOL 1.0e-10
947:
948: #define NRANSI
949: #define ITMAX 200
950:
951: #define TOL 2.0e-4
952:
953: #define CGOLD 0.3819660
954: #define ZEPS 1.0e-10
955: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
956:
957: #define GOLD 1.618034
958: #define GLIMIT 100.0
959: #define TINY 1.0e-20
960:
961: static double maxarg1,maxarg2;
962: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
963: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
964:
965: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
966: #define rint(a) floor(a+0.5)
1.166 brouard 967: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 968: #define mytinydouble 1.0e-16
1.166 brouard 969: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
970: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
971: /* static double dsqrarg; */
972: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 973: static double sqrarg;
974: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
975: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
976: int agegomp= AGEGOMP;
977:
978: int imx;
979: int stepm=1;
980: /* Stepm, step in month: minimum step interpolation*/
981:
982: int estepm;
983: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
984:
985: int m,nb;
986: long *num;
1.197 brouard 987: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 988: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
989: covariate for which somebody answered excluding
990: undefined. Usually 2: 0 and 1. */
991: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
992: covariate for which somebody answered including
993: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 994: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218 brouard 995: double **pmmij, ***probs; /* Global pointer */
1.219 brouard 996: double ***mobaverage, ***mobaverages; /* New global variable */
1.126 brouard 997: double *ageexmed,*agecens;
998: double dateintmean=0;
999:
1000: double *weight;
1001: int **s; /* Status */
1.141 brouard 1002: double *agedc;
1.145 brouard 1003: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 1004: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 1005: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.224 ! brouard 1006: double **coqvar; /* Fixed quantitative covariate */
1.223 brouard 1007: double ***cotvar; /* Time varying covariate */
1008: double ***cotqvar; /* Time varying quantitative covariate */
1.141 brouard 1009: double idx;
1010: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.197 brouard 1011: int *Tage;
1.145 brouard 1012: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 1013: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.220 brouard 1014: int **Tvard, *Tprod, cptcovprod, *Tvaraff, *invalidvarcomb;
1.126 brouard 1015: double *lsurv, *lpop, *tpop;
1016:
1.143 brouard 1017: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
1018: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 1019:
1020: /**************** split *************************/
1021: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1022: {
1023: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1024: the name of the file (name), its extension only (ext) and its first part of the name (finame)
1025: */
1026: char *ss; /* pointer */
1.186 brouard 1027: int l1=0, l2=0; /* length counters */
1.126 brouard 1028:
1029: l1 = strlen(path ); /* length of path */
1030: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1031: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1032: if ( ss == NULL ) { /* no directory, so determine current directory */
1033: strcpy( name, path ); /* we got the fullname name because no directory */
1034: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
1035: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1036: /* get current working directory */
1037: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 1038: #ifdef WIN32
1039: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
1040: #else
1041: if (getcwd(dirc, FILENAME_MAX) == NULL) {
1042: #endif
1.126 brouard 1043: return( GLOCK_ERROR_GETCWD );
1044: }
1045: /* got dirc from getcwd*/
1046: printf(" DIRC = %s \n",dirc);
1.205 brouard 1047: } else { /* strip directory from path */
1.126 brouard 1048: ss++; /* after this, the filename */
1049: l2 = strlen( ss ); /* length of filename */
1050: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1051: strcpy( name, ss ); /* save file name */
1052: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1053: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1054: printf(" DIRC2 = %s \n",dirc);
1055: }
1056: /* We add a separator at the end of dirc if not exists */
1057: l1 = strlen( dirc ); /* length of directory */
1058: if( dirc[l1-1] != DIRSEPARATOR ){
1059: dirc[l1] = DIRSEPARATOR;
1060: dirc[l1+1] = 0;
1061: printf(" DIRC3 = %s \n",dirc);
1062: }
1063: ss = strrchr( name, '.' ); /* find last / */
1064: if (ss >0){
1065: ss++;
1066: strcpy(ext,ss); /* save extension */
1067: l1= strlen( name);
1068: l2= strlen(ss)+1;
1069: strncpy( finame, name, l1-l2);
1070: finame[l1-l2]= 0;
1071: }
1072:
1073: return( 0 ); /* we're done */
1074: }
1075:
1076:
1077: /******************************************/
1078:
1079: void replace_back_to_slash(char *s, char*t)
1080: {
1081: int i;
1082: int lg=0;
1083: i=0;
1084: lg=strlen(t);
1085: for(i=0; i<= lg; i++) {
1086: (s[i] = t[i]);
1087: if (t[i]== '\\') s[i]='/';
1088: }
1089: }
1090:
1.132 brouard 1091: char *trimbb(char *out, char *in)
1.137 brouard 1092: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1093: char *s;
1094: s=out;
1095: while (*in != '\0'){
1.137 brouard 1096: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1097: in++;
1098: }
1099: *out++ = *in++;
1100: }
1101: *out='\0';
1102: return s;
1103: }
1104:
1.187 brouard 1105: /* char *substrchaine(char *out, char *in, char *chain) */
1106: /* { */
1107: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1108: /* char *s, *t; */
1109: /* t=in;s=out; */
1110: /* while ((*in != *chain) && (*in != '\0')){ */
1111: /* *out++ = *in++; */
1112: /* } */
1113:
1114: /* /\* *in matches *chain *\/ */
1115: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1116: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1117: /* } */
1118: /* in--; chain--; */
1119: /* while ( (*in != '\0')){ */
1120: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1121: /* *out++ = *in++; */
1122: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1123: /* } */
1124: /* *out='\0'; */
1125: /* out=s; */
1126: /* return out; */
1127: /* } */
1128: char *substrchaine(char *out, char *in, char *chain)
1129: {
1130: /* Substract chain 'chain' from 'in', return and output 'out' */
1131: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1132:
1133: char *strloc;
1134:
1135: strcpy (out, in);
1136: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1137: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1138: if(strloc != NULL){
1139: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1140: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1141: /* strcpy (strloc, strloc +strlen(chain));*/
1142: }
1143: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1144: return out;
1145: }
1146:
1147:
1.145 brouard 1148: char *cutl(char *blocc, char *alocc, char *in, char occ)
1149: {
1.187 brouard 1150: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1151: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1152: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1153: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1154: */
1.160 brouard 1155: char *s, *t;
1.145 brouard 1156: t=in;s=in;
1157: while ((*in != occ) && (*in != '\0')){
1158: *alocc++ = *in++;
1159: }
1160: if( *in == occ){
1161: *(alocc)='\0';
1162: s=++in;
1163: }
1164:
1165: if (s == t) {/* occ not found */
1166: *(alocc-(in-s))='\0';
1167: in=s;
1168: }
1169: while ( *in != '\0'){
1170: *blocc++ = *in++;
1171: }
1172:
1173: *blocc='\0';
1174: return t;
1175: }
1.137 brouard 1176: char *cutv(char *blocc, char *alocc, char *in, char occ)
1177: {
1.187 brouard 1178: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1179: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1180: gives blocc="abcdef2ghi" and alocc="j".
1181: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1182: */
1183: char *s, *t;
1184: t=in;s=in;
1185: while (*in != '\0'){
1186: while( *in == occ){
1187: *blocc++ = *in++;
1188: s=in;
1189: }
1190: *blocc++ = *in++;
1191: }
1192: if (s == t) /* occ not found */
1193: *(blocc-(in-s))='\0';
1194: else
1195: *(blocc-(in-s)-1)='\0';
1196: in=s;
1197: while ( *in != '\0'){
1198: *alocc++ = *in++;
1199: }
1200:
1201: *alocc='\0';
1202: return s;
1203: }
1204:
1.126 brouard 1205: int nbocc(char *s, char occ)
1206: {
1207: int i,j=0;
1208: int lg=20;
1209: i=0;
1210: lg=strlen(s);
1211: for(i=0; i<= lg; i++) {
1212: if (s[i] == occ ) j++;
1213: }
1214: return j;
1215: }
1216:
1.137 brouard 1217: /* void cutv(char *u,char *v, char*t, char occ) */
1218: /* { */
1219: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1220: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1221: /* gives u="abcdef2ghi" and v="j" *\/ */
1222: /* int i,lg,j,p=0; */
1223: /* i=0; */
1224: /* lg=strlen(t); */
1225: /* for(j=0; j<=lg-1; j++) { */
1226: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1227: /* } */
1.126 brouard 1228:
1.137 brouard 1229: /* for(j=0; j<p; j++) { */
1230: /* (u[j] = t[j]); */
1231: /* } */
1232: /* u[p]='\0'; */
1.126 brouard 1233:
1.137 brouard 1234: /* for(j=0; j<= lg; j++) { */
1235: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1236: /* } */
1237: /* } */
1.126 brouard 1238:
1.160 brouard 1239: #ifdef _WIN32
1240: char * strsep(char **pp, const char *delim)
1241: {
1242: char *p, *q;
1243:
1244: if ((p = *pp) == NULL)
1245: return 0;
1246: if ((q = strpbrk (p, delim)) != NULL)
1247: {
1248: *pp = q + 1;
1249: *q = '\0';
1250: }
1251: else
1252: *pp = 0;
1253: return p;
1254: }
1255: #endif
1256:
1.126 brouard 1257: /********************** nrerror ********************/
1258:
1259: void nrerror(char error_text[])
1260: {
1261: fprintf(stderr,"ERREUR ...\n");
1262: fprintf(stderr,"%s\n",error_text);
1263: exit(EXIT_FAILURE);
1264: }
1265: /*********************** vector *******************/
1266: double *vector(int nl, int nh)
1267: {
1268: double *v;
1269: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1270: if (!v) nrerror("allocation failure in vector");
1271: return v-nl+NR_END;
1272: }
1273:
1274: /************************ free vector ******************/
1275: void free_vector(double*v, int nl, int nh)
1276: {
1277: free((FREE_ARG)(v+nl-NR_END));
1278: }
1279:
1280: /************************ivector *******************************/
1281: int *ivector(long nl,long nh)
1282: {
1283: int *v;
1284: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1285: if (!v) nrerror("allocation failure in ivector");
1286: return v-nl+NR_END;
1287: }
1288:
1289: /******************free ivector **************************/
1290: void free_ivector(int *v, long nl, long nh)
1291: {
1292: free((FREE_ARG)(v+nl-NR_END));
1293: }
1294:
1295: /************************lvector *******************************/
1296: long *lvector(long nl,long nh)
1297: {
1298: long *v;
1299: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1300: if (!v) nrerror("allocation failure in ivector");
1301: return v-nl+NR_END;
1302: }
1303:
1304: /******************free lvector **************************/
1305: void free_lvector(long *v, long nl, long nh)
1306: {
1307: free((FREE_ARG)(v+nl-NR_END));
1308: }
1309:
1310: /******************* imatrix *******************************/
1311: int **imatrix(long nrl, long nrh, long ncl, long nch)
1312: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1313: {
1314: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1315: int **m;
1316:
1317: /* allocate pointers to rows */
1318: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1319: if (!m) nrerror("allocation failure 1 in matrix()");
1320: m += NR_END;
1321: m -= nrl;
1322:
1323:
1324: /* allocate rows and set pointers to them */
1325: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1326: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1327: m[nrl] += NR_END;
1328: m[nrl] -= ncl;
1329:
1330: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1331:
1332: /* return pointer to array of pointers to rows */
1333: return m;
1334: }
1335:
1336: /****************** free_imatrix *************************/
1337: void free_imatrix(m,nrl,nrh,ncl,nch)
1338: int **m;
1339: long nch,ncl,nrh,nrl;
1340: /* free an int matrix allocated by imatrix() */
1341: {
1342: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1343: free((FREE_ARG) (m+nrl-NR_END));
1344: }
1345:
1346: /******************* matrix *******************************/
1347: double **matrix(long nrl, long nrh, long ncl, long nch)
1348: {
1349: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1350: double **m;
1351:
1352: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1353: if (!m) nrerror("allocation failure 1 in matrix()");
1354: m += NR_END;
1355: m -= nrl;
1356:
1357: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1358: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1359: m[nrl] += NR_END;
1360: m[nrl] -= ncl;
1361:
1362: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1363: return m;
1.145 brouard 1364: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1365: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1366: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1367: */
1368: }
1369:
1370: /*************************free matrix ************************/
1371: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1372: {
1373: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1374: free((FREE_ARG)(m+nrl-NR_END));
1375: }
1376:
1377: /******************* ma3x *******************************/
1378: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1379: {
1380: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1381: double ***m;
1382:
1383: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1384: if (!m) nrerror("allocation failure 1 in matrix()");
1385: m += NR_END;
1386: m -= nrl;
1387:
1388: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1389: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1390: m[nrl] += NR_END;
1391: m[nrl] -= ncl;
1392:
1393: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1394:
1395: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1396: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1397: m[nrl][ncl] += NR_END;
1398: m[nrl][ncl] -= nll;
1399: for (j=ncl+1; j<=nch; j++)
1400: m[nrl][j]=m[nrl][j-1]+nlay;
1401:
1402: for (i=nrl+1; i<=nrh; i++) {
1403: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1404: for (j=ncl+1; j<=nch; j++)
1405: m[i][j]=m[i][j-1]+nlay;
1406: }
1407: return m;
1408: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1409: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1410: */
1411: }
1412:
1413: /*************************free ma3x ************************/
1414: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1415: {
1416: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1417: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1418: free((FREE_ARG)(m+nrl-NR_END));
1419: }
1420:
1421: /*************** function subdirf ***********/
1422: char *subdirf(char fileres[])
1423: {
1424: /* Caution optionfilefiname is hidden */
1425: strcpy(tmpout,optionfilefiname);
1426: strcat(tmpout,"/"); /* Add to the right */
1427: strcat(tmpout,fileres);
1428: return tmpout;
1429: }
1430:
1431: /*************** function subdirf2 ***********/
1432: char *subdirf2(char fileres[], char *preop)
1433: {
1434:
1435: /* Caution optionfilefiname is hidden */
1436: strcpy(tmpout,optionfilefiname);
1437: strcat(tmpout,"/");
1438: strcat(tmpout,preop);
1439: strcat(tmpout,fileres);
1440: return tmpout;
1441: }
1442:
1443: /*************** function subdirf3 ***********/
1444: char *subdirf3(char fileres[], char *preop, char *preop2)
1445: {
1446:
1447: /* Caution optionfilefiname is hidden */
1448: strcpy(tmpout,optionfilefiname);
1449: strcat(tmpout,"/");
1450: strcat(tmpout,preop);
1451: strcat(tmpout,preop2);
1452: strcat(tmpout,fileres);
1453: return tmpout;
1454: }
1.213 brouard 1455:
1456: /*************** function subdirfext ***********/
1457: char *subdirfext(char fileres[], char *preop, char *postop)
1458: {
1459:
1460: strcpy(tmpout,preop);
1461: strcat(tmpout,fileres);
1462: strcat(tmpout,postop);
1463: return tmpout;
1464: }
1.126 brouard 1465:
1.213 brouard 1466: /*************** function subdirfext3 ***********/
1467: char *subdirfext3(char fileres[], char *preop, char *postop)
1468: {
1469:
1470: /* Caution optionfilefiname is hidden */
1471: strcpy(tmpout,optionfilefiname);
1472: strcat(tmpout,"/");
1473: strcat(tmpout,preop);
1474: strcat(tmpout,fileres);
1475: strcat(tmpout,postop);
1476: return tmpout;
1477: }
1478:
1.162 brouard 1479: char *asc_diff_time(long time_sec, char ascdiff[])
1480: {
1481: long sec_left, days, hours, minutes;
1482: days = (time_sec) / (60*60*24);
1483: sec_left = (time_sec) % (60*60*24);
1484: hours = (sec_left) / (60*60) ;
1485: sec_left = (sec_left) %(60*60);
1486: minutes = (sec_left) /60;
1487: sec_left = (sec_left) % (60);
1488: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1489: return ascdiff;
1490: }
1491:
1.126 brouard 1492: /***************** f1dim *************************/
1493: extern int ncom;
1494: extern double *pcom,*xicom;
1495: extern double (*nrfunc)(double []);
1496:
1497: double f1dim(double x)
1498: {
1499: int j;
1500: double f;
1501: double *xt;
1502:
1503: xt=vector(1,ncom);
1504: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1505: f=(*nrfunc)(xt);
1506: free_vector(xt,1,ncom);
1507: return f;
1508: }
1509:
1510: /*****************brent *************************/
1511: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1512: {
1513: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1514: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1515: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1516: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1517: * returned function value.
1518: */
1.126 brouard 1519: int iter;
1520: double a,b,d,etemp;
1.159 brouard 1521: double fu=0,fv,fw,fx;
1.164 brouard 1522: double ftemp=0.;
1.126 brouard 1523: double p,q,r,tol1,tol2,u,v,w,x,xm;
1524: double e=0.0;
1525:
1526: a=(ax < cx ? ax : cx);
1527: b=(ax > cx ? ax : cx);
1528: x=w=v=bx;
1529: fw=fv=fx=(*f)(x);
1530: for (iter=1;iter<=ITMAX;iter++) {
1531: xm=0.5*(a+b);
1532: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1533: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1534: printf(".");fflush(stdout);
1535: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1536: #ifdef DEBUGBRENT
1.126 brouard 1537: 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);
1538: 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);
1539: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1540: #endif
1541: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1542: *xmin=x;
1543: return fx;
1544: }
1545: ftemp=fu;
1546: if (fabs(e) > tol1) {
1547: r=(x-w)*(fx-fv);
1548: q=(x-v)*(fx-fw);
1549: p=(x-v)*q-(x-w)*r;
1550: q=2.0*(q-r);
1551: if (q > 0.0) p = -p;
1552: q=fabs(q);
1553: etemp=e;
1554: e=d;
1555: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1.224 ! brouard 1556: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1.126 brouard 1557: else {
1.224 ! brouard 1558: d=p/q;
! 1559: u=x+d;
! 1560: if (u-a < tol2 || b-u < tol2)
! 1561: d=SIGN(tol1,xm-x);
1.126 brouard 1562: }
1563: } else {
1564: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1565: }
1566: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1567: fu=(*f)(u);
1568: if (fu <= fx) {
1569: if (u >= x) a=x; else b=x;
1570: SHFT(v,w,x,u)
1.183 brouard 1571: SHFT(fv,fw,fx,fu)
1572: } else {
1573: if (u < x) a=u; else b=u;
1574: if (fu <= fw || w == x) {
1.224 ! brouard 1575: v=w;
! 1576: w=u;
! 1577: fv=fw;
! 1578: fw=fu;
1.183 brouard 1579: } else if (fu <= fv || v == x || v == w) {
1.224 ! brouard 1580: v=u;
! 1581: fv=fu;
1.183 brouard 1582: }
1583: }
1.126 brouard 1584: }
1585: nrerror("Too many iterations in brent");
1586: *xmin=x;
1587: return fx;
1588: }
1589:
1590: /****************** mnbrak ***********************/
1591:
1592: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1593: double (*func)(double))
1.183 brouard 1594: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1595: the downhill direction (defined by the function as evaluated at the initial points) and returns
1596: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1597: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1598: */
1.126 brouard 1599: double ulim,u,r,q, dum;
1600: double fu;
1.187 brouard 1601:
1602: double scale=10.;
1603: int iterscale=0;
1604:
1605: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1606: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1607:
1608:
1609: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1610: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1611: /* *bx = *ax - (*ax - *bx)/scale; */
1612: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1613: /* } */
1614:
1.126 brouard 1615: if (*fb > *fa) {
1616: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1617: SHFT(dum,*fb,*fa,dum)
1618: }
1.126 brouard 1619: *cx=(*bx)+GOLD*(*bx-*ax);
1620: *fc=(*func)(*cx);
1.183 brouard 1621: #ifdef DEBUG
1.224 ! brouard 1622: printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
! 1623: fprintf(ficlog,"mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
1.183 brouard 1624: #endif
1.224 ! brouard 1625: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc. If fc=inf it exits and if flat fb=fc it exits too.*/
1.126 brouard 1626: r=(*bx-*ax)*(*fb-*fc);
1.224 ! brouard 1627: q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
1.126 brouard 1628: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1629: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1630: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1631: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1632: fu=(*func)(u);
1.163 brouard 1633: #ifdef DEBUG
1634: /* f(x)=A(x-u)**2+f(u) */
1635: double A, fparabu;
1636: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1637: fparabu= *fa - A*(*ax-u)*(*ax-u);
1.224 ! brouard 1638: printf("\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
! 1639: fprintf(ficlog,"\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
1.183 brouard 1640: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1641: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1642: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1643: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1644: #endif
1.184 brouard 1645: #ifdef MNBRAKORIGINAL
1.183 brouard 1646: #else
1.191 brouard 1647: /* if (fu > *fc) { */
1648: /* #ifdef DEBUG */
1649: /* printf("mnbrak4 fu > fc \n"); */
1650: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1651: /* #endif */
1652: /* /\* 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 *\\/ *\/ */
1653: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1654: /* dum=u; /\* Shifting c and u *\/ */
1655: /* u = *cx; */
1656: /* *cx = dum; */
1657: /* dum = fu; */
1658: /* fu = *fc; */
1659: /* *fc =dum; */
1660: /* } else { /\* end *\/ */
1661: /* #ifdef DEBUG */
1662: /* printf("mnbrak3 fu < fc \n"); */
1663: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1664: /* #endif */
1665: /* dum=u; /\* Shifting c and u *\/ */
1666: /* u = *cx; */
1667: /* *cx = dum; */
1668: /* dum = fu; */
1669: /* fu = *fc; */
1670: /* *fc =dum; */
1671: /* } */
1.224 ! brouard 1672: #ifdef DEBUGMNBRAK
! 1673: double A, fparabu;
! 1674: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
! 1675: fparabu= *fa - A*(*ax-u)*(*ax-u);
! 1676: printf("\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
! 1677: fprintf(ficlog,"\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
1.183 brouard 1678: #endif
1.191 brouard 1679: dum=u; /* Shifting c and u */
1680: u = *cx;
1681: *cx = dum;
1682: dum = fu;
1683: fu = *fc;
1684: *fc =dum;
1.183 brouard 1685: #endif
1.162 brouard 1686: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1687: #ifdef DEBUG
1.224 ! brouard 1688: printf("\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
! 1689: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1.183 brouard 1690: #endif
1.126 brouard 1691: fu=(*func)(u);
1692: if (fu < *fc) {
1.183 brouard 1693: #ifdef DEBUG
1.224 ! brouard 1694: printf("\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
! 1695: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
! 1696: #endif
! 1697: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
! 1698: SHFT(*fb,*fc,fu,(*func)(u))
! 1699: #ifdef DEBUG
! 1700: printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
1.183 brouard 1701: #endif
1702: }
1.162 brouard 1703: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1704: #ifdef DEBUG
1.224 ! brouard 1705: printf("\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
! 1706: fprintf(ficlog,"\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1.183 brouard 1707: #endif
1.126 brouard 1708: u=ulim;
1709: fu=(*func)(u);
1.183 brouard 1710: } else { /* u could be left to b (if r > q parabola has a maximum) */
1711: #ifdef DEBUG
1.224 ! brouard 1712: printf("\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
! 1713: fprintf(ficlog,"\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
1.183 brouard 1714: #endif
1.126 brouard 1715: u=(*cx)+GOLD*(*cx-*bx);
1716: fu=(*func)(u);
1.224 ! brouard 1717: #ifdef DEBUG
! 1718: printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
! 1719: fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
! 1720: #endif
1.183 brouard 1721: } /* end tests */
1.126 brouard 1722: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1723: SHFT(*fa,*fb,*fc,fu)
1724: #ifdef DEBUG
1.224 ! brouard 1725: printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
! 1726: fprintf(ficlog, "\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
1.183 brouard 1727: #endif
1728: } /* 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 1729: }
1730:
1731: /*************** linmin ************************/
1.162 brouard 1732: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1733: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1734: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1735: the value of func at the returned location p . This is actually all accomplished by calling the
1736: routines mnbrak and brent .*/
1.126 brouard 1737: int ncom;
1738: double *pcom,*xicom;
1739: double (*nrfunc)(double []);
1740:
1.224 ! brouard 1741: #ifdef LINMINORIGINAL
1.126 brouard 1742: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1.224 ! brouard 1743: #else
! 1744: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat)
! 1745: #endif
1.126 brouard 1746: {
1747: double brent(double ax, double bx, double cx,
1748: double (*f)(double), double tol, double *xmin);
1749: double f1dim(double x);
1750: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1751: double *fc, double (*func)(double));
1752: int j;
1753: double xx,xmin,bx,ax;
1754: double fx,fb,fa;
1.187 brouard 1755:
1.203 brouard 1756: #ifdef LINMINORIGINAL
1757: #else
1758: double scale=10., axs, xxs; /* Scale added for infinity */
1759: #endif
1760:
1.126 brouard 1761: ncom=n;
1762: pcom=vector(1,n);
1763: xicom=vector(1,n);
1764: nrfunc=func;
1765: for (j=1;j<=n;j++) {
1766: pcom[j]=p[j];
1.202 brouard 1767: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1768: }
1.187 brouard 1769:
1.203 brouard 1770: #ifdef LINMINORIGINAL
1771: xx=1.;
1772: #else
1773: axs=0.0;
1774: xxs=1.;
1775: do{
1776: xx= xxs;
1777: #endif
1.187 brouard 1778: ax=0.;
1779: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1780: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1781: /* 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)) */
1782: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1783: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1784: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1785: /* 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 1786: #ifdef LINMINORIGINAL
1787: #else
1788: if (fx != fx){
1.224 ! brouard 1789: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
! 1790: printf("|");
! 1791: fprintf(ficlog,"|");
1.203 brouard 1792: #ifdef DEBUGLINMIN
1.224 ! brouard 1793: printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n", axs, xxs, fx,fb, fa, xx, ax, bx);
1.203 brouard 1794: #endif
1795: }
1.224 ! brouard 1796: }while(fx != fx && xxs > 1.e-5);
1.203 brouard 1797: #endif
1798:
1.191 brouard 1799: #ifdef DEBUGLINMIN
1800: 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 1801: 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 1802: #endif
1.224 ! brouard 1803: #ifdef LINMINORIGINAL
! 1804: #else
! 1805: if(fb == fx){ /* Flat function in the direction */
! 1806: xmin=xx;
! 1807: *flat=1;
! 1808: }else{
! 1809: *flat=0;
! 1810: #endif
! 1811: /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
1.187 brouard 1812: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1813: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1814: /* fmin = f(p[j] + xmin * xi[j]) */
1815: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1816: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1817: #ifdef DEBUG
1.224 ! brouard 1818: printf("retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
! 1819: fprintf(ficlog,"retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
! 1820: #endif
! 1821: #ifdef LINMINORIGINAL
! 1822: #else
! 1823: }
1.126 brouard 1824: #endif
1.191 brouard 1825: #ifdef DEBUGLINMIN
1826: printf("linmin end ");
1.202 brouard 1827: fprintf(ficlog,"linmin end ");
1.191 brouard 1828: #endif
1.126 brouard 1829: for (j=1;j<=n;j++) {
1.203 brouard 1830: #ifdef LINMINORIGINAL
1831: xi[j] *= xmin;
1832: #else
1833: #ifdef DEBUGLINMIN
1834: if(xxs <1.0)
1835: printf(" before xi[%d]=%12.8f", j,xi[j]);
1836: #endif
1837: 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) */
1838: #ifdef DEBUGLINMIN
1839: if(xxs <1.0)
1840: 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 );
1841: #endif
1842: #endif
1.187 brouard 1843: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1844: }
1.191 brouard 1845: #ifdef DEBUGLINMIN
1.203 brouard 1846: printf("\n");
1.191 brouard 1847: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 1848: 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 1849: for (j=1;j<=n;j++) {
1.202 brouard 1850: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1851: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1852: if(j % ncovmodel == 0){
1.191 brouard 1853: printf("\n");
1.202 brouard 1854: fprintf(ficlog,"\n");
1855: }
1.191 brouard 1856: }
1.203 brouard 1857: #else
1.191 brouard 1858: #endif
1.126 brouard 1859: free_vector(xicom,1,n);
1860: free_vector(pcom,1,n);
1861: }
1862:
1863:
1864: /*************** powell ************************/
1.162 brouard 1865: /*
1866: Minimization of a function func of n variables. Input consists of an initial starting point
1867: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1868: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1869: such that failure to decrease by more than this amount on one iteration signals doneness. On
1870: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1871: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1872: */
1.224 ! brouard 1873: #ifdef LINMINORIGINAL
! 1874: #else
! 1875: int *flatdir; /* Function is vanishing in that direction */
! 1876: int flat=0; /* Function is vanishing in that direction */
! 1877: #endif
1.126 brouard 1878: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1879: double (*func)(double []))
1880: {
1.224 ! brouard 1881: #ifdef LINMINORIGINAL
! 1882: void linmin(double p[], double xi[], int n, double *fret,
1.126 brouard 1883: double (*func)(double []));
1.224 ! brouard 1884: #else
! 1885: void linmin(double p[], double xi[], int n, double *fret,
! 1886: double (*func)(double []),int *flat);
! 1887: #endif
1.126 brouard 1888: int i,ibig,j;
1889: double del,t,*pt,*ptt,*xit;
1.181 brouard 1890: double directest;
1.126 brouard 1891: double fp,fptt;
1892: double *xits;
1893: int niterf, itmp;
1.224 ! brouard 1894: #ifdef LINMINORIGINAL
! 1895: #else
! 1896:
! 1897: flatdir=ivector(1,n);
! 1898: for (j=1;j<=n;j++) flatdir[j]=0;
! 1899: #endif
1.126 brouard 1900:
1901: pt=vector(1,n);
1902: ptt=vector(1,n);
1903: xit=vector(1,n);
1904: xits=vector(1,n);
1905: *fret=(*func)(p);
1906: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 1907: rcurr_time = time(NULL);
1.126 brouard 1908: for (*iter=1;;++(*iter)) {
1.187 brouard 1909: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1910: ibig=0;
1911: del=0.0;
1.157 brouard 1912: rlast_time=rcurr_time;
1913: /* (void) gettimeofday(&curr_time,&tzp); */
1914: rcurr_time = time(NULL);
1915: curr_time = *localtime(&rcurr_time);
1916: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1917: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1918: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1919: for (i=1;i<=n;i++) {
1.126 brouard 1920: printf(" %d %.12f",i, p[i]);
1921: fprintf(ficlog," %d %.12lf",i, p[i]);
1922: fprintf(ficrespow," %.12lf", p[i]);
1923: }
1924: printf("\n");
1925: fprintf(ficlog,"\n");
1926: fprintf(ficrespow,"\n");fflush(ficrespow);
1927: if(*iter <=3){
1.157 brouard 1928: tml = *localtime(&rcurr_time);
1929: strcpy(strcurr,asctime(&tml));
1930: rforecast_time=rcurr_time;
1.126 brouard 1931: itmp = strlen(strcurr);
1932: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.224 ! brouard 1933: strcurr[itmp-1]='\0';
1.162 brouard 1934: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1935: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1936: for(niterf=10;niterf<=30;niterf+=10){
1.224 ! brouard 1937: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
! 1938: forecast_time = *localtime(&rforecast_time);
! 1939: strcpy(strfor,asctime(&forecast_time));
! 1940: itmp = strlen(strfor);
! 1941: if(strfor[itmp-1]=='\n')
! 1942: strfor[itmp-1]='\0';
! 1943: 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);
! 1944: 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 1945: }
1946: }
1.187 brouard 1947: for (i=1;i<=n;i++) { /* For each direction i */
1948: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1949: fptt=(*fret);
1950: #ifdef DEBUG
1.203 brouard 1951: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1952: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1953: #endif
1.203 brouard 1954: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1955: fprintf(ficlog,"%d",i);fflush(ficlog);
1.224 ! brouard 1956: #ifdef LINMINORIGINAL
1.188 brouard 1957: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1.224 ! brouard 1958: #else
! 1959: linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
! 1960: flatdir[i]=flat; /* Function is vanishing in that direction i */
! 1961: #endif
! 1962: /* Outputs are fret(new point p) p is updated and xit rescaled */
1.188 brouard 1963: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1.224 ! brouard 1964: /* because that direction will be replaced unless the gain del is small */
! 1965: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
! 1966: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
! 1967: /* with the new direction. */
! 1968: del=fabs(fptt-(*fret));
! 1969: ibig=i;
1.126 brouard 1970: }
1971: #ifdef DEBUG
1972: printf("%d %.12e",i,(*fret));
1973: fprintf(ficlog,"%d %.12e",i,(*fret));
1974: for (j=1;j<=n;j++) {
1.224 ! brouard 1975: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
! 1976: printf(" x(%d)=%.12e",j,xit[j]);
! 1977: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1.126 brouard 1978: }
1979: for(j=1;j<=n;j++) {
1.224 ! brouard 1980: printf(" p(%d)=%lf ",j,p[j]);
! 1981: fprintf(ficlog," p(%d)=%lf ",j,p[j]);
1.126 brouard 1982: }
1983: printf("\n");
1984: fprintf(ficlog,"\n");
1985: #endif
1.187 brouard 1986: } /* end loop on each direction i */
1987: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1988: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1989: /* New value of last point Pn is not computed, P(n-1) */
1.224 ! brouard 1990: for(j=1;j<=n;j++) {
! 1991: printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
! 1992: fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
! 1993: }
! 1994: printf("\n");
! 1995: fprintf(ficlog,"\n");
! 1996:
1.182 brouard 1997: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1998: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1999: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
2000: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
2001: /* decreased of more than 3.84 */
2002: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
2003: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
2004: /* By adding 10 parameters more the gain should be 18.31 */
1.224 ! brouard 2005:
1.188 brouard 2006: /* Starting the program with initial values given by a former maximization will simply change */
2007: /* the scales of the directions and the directions, because the are reset to canonical directions */
2008: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
2009: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 2010: #ifdef DEBUG
2011: int k[2],l;
2012: k[0]=1;
2013: k[1]=-1;
2014: printf("Max: %.12e",(*func)(p));
2015: fprintf(ficlog,"Max: %.12e",(*func)(p));
2016: for (j=1;j<=n;j++) {
2017: printf(" %.12e",p[j]);
2018: fprintf(ficlog," %.12e",p[j]);
2019: }
2020: printf("\n");
2021: fprintf(ficlog,"\n");
2022: for(l=0;l<=1;l++) {
2023: for (j=1;j<=n;j++) {
2024: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
2025: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2026: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2027: }
2028: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2029: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2030: }
2031: #endif
2032:
1.224 ! brouard 2033: #ifdef LINMINORIGINAL
! 2034: #else
! 2035: free_ivector(flatdir,1,n);
! 2036: #endif
1.126 brouard 2037: free_vector(xit,1,n);
2038: free_vector(xits,1,n);
2039: free_vector(ptt,1,n);
2040: free_vector(pt,1,n);
2041: return;
1.192 brouard 2042: } /* enough precision */
1.126 brouard 2043: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 2044: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 2045: ptt[j]=2.0*p[j]-pt[j];
2046: xit[j]=p[j]-pt[j];
2047: pt[j]=p[j];
2048: }
1.181 brouard 2049: fptt=(*func)(ptt); /* f_3 */
1.224 ! brouard 2050: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
! 2051: if (*iter <=4) {
! 2052: #else
! 2053: #ifdef POWELLNOF3INFF1TEST /* skips test F3 <F1 */
1.192 brouard 2054: #else
1.161 brouard 2055: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 2056: #endif
1.162 brouard 2057: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 2058: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 2059: /* Let f"(x2) be the 2nd derivative equal everywhere. */
2060: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
2061: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.224 ! brouard 2062: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
! 2063: /* also lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
! 2064: /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
1.161 brouard 2065: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.224 ! brouard 2066: /* Even if f3 <f1, directest can be negative and t >0 */
! 2067: /* mu² and del² are equal when f3=f1 */
! 2068: /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
! 2069: /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
! 2070: /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0 */
! 2071: /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0 */
1.183 brouard 2072: #ifdef NRCORIGINAL
2073: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
2074: #else
2075: 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 2076: t= t- del*SQR(fp-fptt);
1.183 brouard 2077: #endif
1.202 brouard 2078: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 2079: #ifdef DEBUG
1.181 brouard 2080: 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);
2081: 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 2082: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2083: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2084: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2085: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2086: 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);
2087: 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);
2088: #endif
1.183 brouard 2089: #ifdef POWELLORIGINAL
2090: if (t < 0.0) { /* Then we use it for new direction */
2091: #else
1.182 brouard 2092: if (directest*t < 0.0) { /* Contradiction between both tests */
1.224 ! brouard 2093: 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 2094: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1.224 ! brouard 2095: fprintf(ficlog,"directest= %.12lf (if directest<0 or t<0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1.192 brouard 2096: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
2097: }
1.181 brouard 2098: if (directest < 0.0) { /* Then we use it for new direction */
2099: #endif
1.191 brouard 2100: #ifdef DEBUGLINMIN
1.224 ! brouard 2101: printf("Before linmin in direction P%d-P0\n",n);
! 2102: for (j=1;j<=n;j++) {
! 2103: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
! 2104: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
! 2105: if(j % ncovmodel == 0){
! 2106: printf("\n");
! 2107: fprintf(ficlog,"\n");
! 2108: }
! 2109: }
! 2110: #endif
! 2111: #ifdef LINMINORIGINAL
! 2112: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
! 2113: #else
! 2114: linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
! 2115: flatdir[i]=flat; /* Function is vanishing in that direction i */
1.191 brouard 2116: #endif
1.224 ! brouard 2117:
1.191 brouard 2118: #ifdef DEBUGLINMIN
1.224 ! brouard 2119: for (j=1;j<=n;j++) {
! 2120: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
! 2121: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
! 2122: if(j % ncovmodel == 0){
! 2123: printf("\n");
! 2124: fprintf(ficlog,"\n");
! 2125: }
! 2126: }
! 2127: #endif
! 2128: for (j=1;j<=n;j++) {
! 2129: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
! 2130: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
! 2131: }
! 2132: #ifdef LINMINORIGINAL
! 2133: #else
! 2134: printf("Flat directions\n");
! 2135: fprintf(ficlog,"Flat directions\n");
! 2136: for (j=1;j<=n;j++) {
! 2137: printf("flatdir[%d]=%d ",j,flatdir[j]);
! 2138: fprintf(ficlog,"flatdir[%d]=%d ",j,flatdir[j]);
! 2139: }
! 2140: printf("\n");
! 2141: fprintf(ficlog,"\n");
1.191 brouard 2142: #endif
1.224 ! brouard 2143: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
! 2144: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
! 2145:
1.126 brouard 2146: #ifdef DEBUG
1.224 ! brouard 2147: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
! 2148: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
! 2149: for(j=1;j<=n;j++){
! 2150: printf(" %lf",xit[j]);
! 2151: fprintf(ficlog," %lf",xit[j]);
! 2152: }
! 2153: printf("\n");
! 2154: fprintf(ficlog,"\n");
1.126 brouard 2155: #endif
1.192 brouard 2156: } /* end of t or directest negative */
1.224 ! brouard 2157: #ifdef POWELLNOF3INFF1TEST
1.192 brouard 2158: #else
1.162 brouard 2159: } /* end if (fptt < fp) */
1.192 brouard 2160: #endif
1.224 ! brouard 2161: } /*NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done */
! 2162: #endif
1.192 brouard 2163: } /* loop iteration */
1.126 brouard 2164: }
2165:
2166: /**** Prevalence limit (stable or period prevalence) ****************/
2167:
1.203 brouard 2168: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
1.126 brouard 2169: {
1.218 brouard 2170: /* Computes the prevalence limit in each live state at age x and for covariate ij by left multiplying the unit
1.203 brouard 2171: matrix by transitions matrix until convergence is reached with precision ftolpl */
1.206 brouard 2172: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2173: /* Wx is row vector: population in state 1, population in state 2, population dead */
2174: /* or prevalence in state 1, prevalence in state 2, 0 */
2175: /* newm is the matrix after multiplications, its rows are identical at a factor */
2176: /* Initial matrix pimij */
2177: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2178: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2179: /* 0, 0 , 1} */
2180: /*
2181: * and after some iteration: */
2182: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2183: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2184: /* 0, 0 , 1} */
2185: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2186: /* {0.51571254859325999, 0.4842874514067399, */
2187: /* 0.51326036147820708, 0.48673963852179264} */
2188: /* If we start from prlim again, prlim tends to a constant matrix */
2189:
1.126 brouard 2190: int i, ii,j,k;
1.209 brouard 2191: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2192: /* double **matprod2(); */ /* test */
1.218 brouard 2193: double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126 brouard 2194: double **newm;
1.209 brouard 2195: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2196: int ncvloop=0;
1.169 brouard 2197:
1.209 brouard 2198: min=vector(1,nlstate);
2199: max=vector(1,nlstate);
2200: meandiff=vector(1,nlstate);
2201:
1.218 brouard 2202: /* Starting with matrix unity */
1.126 brouard 2203: for (ii=1;ii<=nlstate+ndeath;ii++)
2204: for (j=1;j<=nlstate+ndeath;j++){
2205: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2206: }
1.169 brouard 2207:
2208: cov[1]=1.;
2209:
2210: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2211: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2212: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2213: ncvloop++;
1.126 brouard 2214: newm=savm;
2215: /* Covariates have to be included here again */
1.138 brouard 2216: cov[2]=agefin;
1.187 brouard 2217: if(nagesqr==1)
2218: cov[3]= agefin*agefin;;
1.138 brouard 2219: for (k=1; k<=cptcovn;k++) {
1.200 brouard 2220: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.218 brouard 2221: /* Here comes the value of the covariate 'ij' */
1.200 brouard 2222: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
1.198 brouard 2223: /* 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 2224: }
1.186 brouard 2225: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2226: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2227: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
1.186 brouard 2228: for (k=1; k<=cptcovprod;k++) /* Useless */
1.200 brouard 2229: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2230: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.138 brouard 2231:
2232: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2233: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2234: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2235: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2236: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2237: /* age and covariate values of ij are in 'cov' */
1.142 brouard 2238: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2239:
1.126 brouard 2240: savm=oldm;
2241: oldm=newm;
1.209 brouard 2242:
2243: for(j=1; j<=nlstate; j++){
2244: max[j]=0.;
2245: min[j]=1.;
2246: }
2247: for(i=1;i<=nlstate;i++){
2248: sumnew=0;
2249: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2250: for(j=1; j<=nlstate; j++){
2251: prlim[i][j]= newm[i][j]/(1-sumnew);
2252: max[j]=FMAX(max[j],prlim[i][j]);
2253: min[j]=FMIN(min[j],prlim[i][j]);
2254: }
2255: }
2256:
1.126 brouard 2257: maxmax=0.;
1.209 brouard 2258: for(j=1; j<=nlstate; j++){
2259: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2260: maxmax=FMAX(maxmax,meandiff[j]);
2261: /* 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 2262: } /* j loop */
1.203 brouard 2263: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2264: /* 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 2265: if(maxmax < ftolpl){
1.209 brouard 2266: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2267: free_vector(min,1,nlstate);
2268: free_vector(max,1,nlstate);
2269: free_vector(meandiff,1,nlstate);
1.126 brouard 2270: return prlim;
2271: }
1.169 brouard 2272: } /* age loop */
1.208 brouard 2273: /* After some age loop it doesn't converge */
1.209 brouard 2274: 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 2275: 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 2276: /* 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); */
2277: free_vector(min,1,nlstate);
2278: free_vector(max,1,nlstate);
2279: free_vector(meandiff,1,nlstate);
1.208 brouard 2280:
1.169 brouard 2281: return prlim; /* should not reach here */
1.126 brouard 2282: }
2283:
1.217 brouard 2284:
2285: /**** Back Prevalence limit (stable or period prevalence) ****************/
2286:
1.218 brouard 2287: /* 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) */
2288: /* 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) */
2289: double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij)
1.217 brouard 2290: {
1.218 brouard 2291: /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit
1.217 brouard 2292: matrix by transitions matrix until convergence is reached with precision ftolpl */
2293: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2294: /* Wx is row vector: population in state 1, population in state 2, population dead */
2295: /* or prevalence in state 1, prevalence in state 2, 0 */
2296: /* newm is the matrix after multiplications, its rows are identical at a factor */
2297: /* Initial matrix pimij */
2298: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2299: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2300: /* 0, 0 , 1} */
2301: /*
2302: * and after some iteration: */
2303: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2304: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2305: /* 0, 0 , 1} */
2306: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2307: /* {0.51571254859325999, 0.4842874514067399, */
2308: /* 0.51326036147820708, 0.48673963852179264} */
2309: /* If we start from prlim again, prlim tends to a constant matrix */
2310:
2311: int i, ii,j,k;
2312: double *min, *max, *meandiff, maxmax,sumnew=0.;
2313: /* double **matprod2(); */ /* test */
2314: double **out, cov[NCOVMAX+1], **bmij();
2315: double **newm;
1.218 brouard 2316: double **dnewm, **doldm, **dsavm; /* for use */
2317: double **oldm, **savm; /* for use */
2318:
1.217 brouard 2319: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
2320: int ncvloop=0;
2321:
2322: min=vector(1,nlstate);
2323: max=vector(1,nlstate);
2324: meandiff=vector(1,nlstate);
2325:
1.218 brouard 2326: dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
2327: oldm=oldms; savm=savms;
2328:
2329: /* Starting with matrix unity */
2330: for (ii=1;ii<=nlstate+ndeath;ii++)
2331: for (j=1;j<=nlstate+ndeath;j++){
1.217 brouard 2332: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2333: }
2334:
2335: cov[1]=1.;
2336:
2337: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2338: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218 brouard 2339: /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
2340: for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217 brouard 2341: ncvloop++;
1.218 brouard 2342: newm=savm; /* oldm should be kept from previous iteration or unity at start */
2343: /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217 brouard 2344: /* Covariates have to be included here again */
2345: cov[2]=agefin;
2346: if(nagesqr==1)
2347: cov[3]= agefin*agefin;;
2348: for (k=1; k<=cptcovn;k++) {
2349: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
2350: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2351: /* 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])]); */
2352: }
2353: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2354: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2355: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
2356: for (k=1; k<=cptcovprod;k++) /* Useless */
2357: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2358: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2359:
2360: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2361: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2362: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
2363: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2364: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2365: /* ij should be linked to the correct index of cov */
2366: /* age and covariate values ij are in 'cov', but we need to pass
2367: * ij for the observed prevalence at age and status and covariate
2368: * number: prevacurrent[(int)agefin][ii][ij]
2369: */
2370: /* 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 *\/ */
2371: /* 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 *\/ */
2372: 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 2373: savm=oldm;
2374: oldm=newm;
2375: for(j=1; j<=nlstate; j++){
2376: max[j]=0.;
2377: min[j]=1.;
2378: }
2379: for(j=1; j<=nlstate; j++){
2380: for(i=1;i<=nlstate;i++){
1.218 brouard 2381: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
2382: bprlim[i][j]= newm[i][j];
2383: max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
2384: min[i]=FMIN(min[i],bprlim[i][j]);
1.217 brouard 2385: }
2386: }
1.218 brouard 2387:
1.217 brouard 2388: maxmax=0.;
2389: for(i=1; i<=nlstate; i++){
2390: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
2391: maxmax=FMAX(maxmax,meandiff[i]);
2392: /* 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); */
2393: } /* j loop */
2394: *ncvyear= -( (int)age- (int)agefin);
1.218 brouard 2395: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/
1.217 brouard 2396: if(maxmax < ftolpl){
1.220 brouard 2397: /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2398: free_vector(min,1,nlstate);
2399: free_vector(max,1,nlstate);
2400: free_vector(meandiff,1,nlstate);
2401: return bprlim;
2402: }
2403: } /* age loop */
2404: /* After some age loop it doesn't converge */
2405: 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\
2406: 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);
2407: /* 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); */
2408: free_vector(min,1,nlstate);
2409: free_vector(max,1,nlstate);
2410: free_vector(meandiff,1,nlstate);
2411:
2412: return bprlim; /* should not reach here */
2413: }
2414:
1.126 brouard 2415: /*************** transition probabilities ***************/
2416:
2417: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2418: {
1.138 brouard 2419: /* According to parameters values stored in x and the covariate's values stored in cov,
2420: computes the probability to be observed in state j being in state i by appying the
2421: model to the ncovmodel covariates (including constant and age).
2422: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2423: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2424: ncth covariate in the global vector x is given by the formula:
2425: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2426: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2427: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2428: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2429: Outputs ps[i][j] the probability to be observed in j being in j according to
2430: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2431: */
2432: double s1, lnpijopii;
1.126 brouard 2433: /*double t34;*/
1.164 brouard 2434: int i,j, nc, ii, jj;
1.126 brouard 2435:
1.223 brouard 2436: for(i=1; i<= nlstate; i++){
2437: for(j=1; j<i;j++){
2438: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2439: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2440: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2441: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2442: }
2443: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2444: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2445: }
2446: for(j=i+1; j<=nlstate+ndeath;j++){
2447: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2448: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2449: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2450: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2451: }
2452: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2453: }
2454: }
1.218 brouard 2455:
1.223 brouard 2456: for(i=1; i<= nlstate; i++){
2457: s1=0;
2458: for(j=1; j<i; j++){
2459: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2460: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2461: }
2462: for(j=i+1; j<=nlstate+ndeath; j++){
2463: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2464: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2465: }
2466: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2467: ps[i][i]=1./(s1+1.);
2468: /* Computing other pijs */
2469: for(j=1; j<i; j++)
2470: ps[i][j]= exp(ps[i][j])*ps[i][i];
2471: for(j=i+1; j<=nlstate+ndeath; j++)
2472: ps[i][j]= exp(ps[i][j])*ps[i][i];
2473: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2474: } /* end i */
1.218 brouard 2475:
1.223 brouard 2476: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2477: for(jj=1; jj<= nlstate+ndeath; jj++){
2478: ps[ii][jj]=0;
2479: ps[ii][ii]=1;
2480: }
2481: }
1.218 brouard 2482:
2483:
1.223 brouard 2484: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2485: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2486: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2487: /* } */
2488: /* printf("\n "); */
2489: /* } */
2490: /* printf("\n ");printf("%lf ",cov[2]);*/
2491: /*
2492: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1.218 brouard 2493: goto end;*/
1.223 brouard 2494: return ps;
1.126 brouard 2495: }
2496:
1.218 brouard 2497: /*************** backward transition probabilities ***************/
2498:
2499: /* 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 ) */
2500: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
2501: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij )
2502: {
1.222 brouard 2503: /* Computes the backward probability at age agefin and covariate ij
2504: * and returns in **ps as well as **bmij.
2505: */
1.218 brouard 2506: int i, ii, j,k;
1.222 brouard 2507:
2508: double **out, **pmij();
2509: double sumnew=0.;
1.218 brouard 2510: double agefin;
1.222 brouard 2511:
2512: double **dnewm, **dsavm, **doldm;
2513: double **bbmij;
2514:
1.218 brouard 2515: doldm=ddoldms; /* global pointers */
1.222 brouard 2516: dnewm=ddnewms;
2517: dsavm=ddsavms;
2518:
2519: agefin=cov[2];
2520: /* bmij *//* age is cov[2], ij is included in cov, but we need for
2521: the observed prevalence (with this covariate ij) */
2522: dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
2523: /* We do have the matrix Px in savm and we need pij */
2524: for (j=1;j<=nlstate+ndeath;j++){
2525: sumnew=0.; /* w1 p11 + w2 p21 only on live states */
2526: for (ii=1;ii<=nlstate;ii++){
2527: sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
2528: } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
2529: for (ii=1;ii<=nlstate+ndeath;ii++){
2530: if(sumnew >= 1.e-10){
2531: /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
2532: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
2533: /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
2534: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
2535: /* }else */
2536: doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
2537: }else{
2538: 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);
2539: }
2540: } /*End ii */
2541: } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
2542: /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
2543: bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
2544: /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
2545: /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
2546: /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
2547: /* left Product of this matrix by diag matrix of prevalences (savm) */
2548: for (j=1;j<=nlstate+ndeath;j++){
2549: for (ii=1;ii<=nlstate+ndeath;ii++){
2550: dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
2551: }
2552: } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
2553: ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
2554: /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
2555: /* end bmij */
2556: return ps;
1.218 brouard 2557: }
1.217 brouard 2558: /*************** transition probabilities ***************/
2559:
1.218 brouard 2560: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217 brouard 2561: {
2562: /* According to parameters values stored in x and the covariate's values stored in cov,
2563: computes the probability to be observed in state j being in state i by appying the
2564: model to the ncovmodel covariates (including constant and age).
2565: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2566: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2567: ncth covariate in the global vector x is given by the formula:
2568: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2569: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2570: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2571: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2572: Outputs ps[i][j] the probability to be observed in j being in j according to
2573: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2574: */
2575: double s1, lnpijopii;
2576: /*double t34;*/
2577: int i,j, nc, ii, jj;
2578:
1.218 brouard 2579: for(i=1; i<= nlstate; i++){
2580: for(j=1; j<i;j++){
2581: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2582: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2583: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2584: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2585: }
2586: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2587: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2588: }
2589: for(j=i+1; j<=nlstate+ndeath;j++){
2590: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2591: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2592: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2593: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2594: }
2595: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2596: }
2597: }
2598:
2599: for(i=1; i<= nlstate; i++){
2600: s1=0;
2601: for(j=1; j<i; j++){
2602: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2603: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2604: }
2605: for(j=i+1; j<=nlstate+ndeath; j++){
2606: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2607: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2608: }
2609: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2610: ps[i][i]=1./(s1+1.);
2611: /* Computing other pijs */
2612: for(j=1; j<i; j++)
2613: ps[i][j]= exp(ps[i][j])*ps[i][i];
2614: for(j=i+1; j<=nlstate+ndeath; j++)
2615: ps[i][j]= exp(ps[i][j])*ps[i][i];
2616: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2617: } /* end i */
2618:
2619: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2620: for(jj=1; jj<= nlstate+ndeath; jj++){
2621: ps[ii][jj]=0;
2622: ps[ii][ii]=1;
2623: }
2624: }
2625: /* Added for backcast */ /* Transposed matrix too */
2626: for(jj=1; jj<= nlstate+ndeath; jj++){
2627: s1=0.;
2628: for(ii=1; ii<= nlstate+ndeath; ii++){
2629: s1+=ps[ii][jj];
2630: }
2631: for(ii=1; ii<= nlstate; ii++){
2632: ps[ii][jj]=ps[ii][jj]/s1;
2633: }
2634: }
2635: /* Transposition */
2636: for(jj=1; jj<= nlstate+ndeath; jj++){
2637: for(ii=jj; ii<= nlstate+ndeath; ii++){
2638: s1=ps[ii][jj];
2639: ps[ii][jj]=ps[jj][ii];
2640: ps[jj][ii]=s1;
2641: }
2642: }
2643: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2644: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2645: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2646: /* } */
2647: /* printf("\n "); */
2648: /* } */
2649: /* printf("\n ");printf("%lf ",cov[2]);*/
2650: /*
2651: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2652: goto end;*/
2653: return ps;
1.217 brouard 2654: }
2655:
2656:
1.126 brouard 2657: /**************** Product of 2 matrices ******************/
2658:
1.145 brouard 2659: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2660: {
2661: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2662: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2663: /* in, b, out are matrice of pointers which should have been initialized
2664: before: only the contents of out is modified. The function returns
2665: a pointer to pointers identical to out */
1.145 brouard 2666: int i, j, k;
1.126 brouard 2667: for(i=nrl; i<= nrh; i++)
1.145 brouard 2668: for(k=ncolol; k<=ncoloh; k++){
2669: out[i][k]=0.;
2670: for(j=ncl; j<=nch; j++)
2671: out[i][k] +=in[i][j]*b[j][k];
2672: }
1.126 brouard 2673: return out;
2674: }
2675:
2676:
2677: /************* Higher Matrix Product ***************/
2678:
2679: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2680: {
1.218 brouard 2681: /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
1.126 brouard 2682: 'nhstepm*hstepm*stepm' months (i.e. until
2683: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2684: nhstepm*hstepm matrices.
2685: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2686: (typically every 2 years instead of every month which is too big
2687: for the memory).
2688: Model is determined by parameters x and covariates have to be
2689: included manually here.
2690:
2691: */
2692:
2693: int i, j, d, h, k;
1.131 brouard 2694: double **out, cov[NCOVMAX+1];
1.126 brouard 2695: double **newm;
1.187 brouard 2696: double agexact;
1.214 brouard 2697: double agebegin, ageend;
1.126 brouard 2698:
2699: /* Hstepm could be zero and should return the unit matrix */
2700: for (i=1;i<=nlstate+ndeath;i++)
2701: for (j=1;j<=nlstate+ndeath;j++){
2702: oldm[i][j]=(i==j ? 1.0 : 0.0);
2703: po[i][j][0]=(i==j ? 1.0 : 0.0);
2704: }
2705: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2706: for(h=1; h <=nhstepm; h++){
2707: for(d=1; d <=hstepm; d++){
2708: newm=savm;
2709: /* Covariates have to be included here again */
2710: cov[1]=1.;
1.214 brouard 2711: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 2712: cov[2]=agexact;
2713: if(nagesqr==1)
1.218 brouard 2714: cov[3]= agexact*agexact;
1.131 brouard 2715: for (k=1; k<=cptcovn;k++)
1.218 brouard 2716: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2717: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.186 brouard 2718: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1.218 brouard 2719: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2720: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2721: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.145 brouard 2722: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.218 brouard 2723: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2724: /* 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 2725:
2726:
2727: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2728: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 2729: /* right multiplication of oldm by the current matrix */
1.126 brouard 2730: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2731: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 brouard 2732: /* if((int)age == 70){ */
2733: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
2734: /* for(i=1; i<=nlstate+ndeath; i++) { */
2735: /* printf("%d pmmij ",i); */
2736: /* for(j=1;j<=nlstate+ndeath;j++) { */
2737: /* printf("%f ",pmmij[i][j]); */
2738: /* } */
2739: /* printf(" oldm "); */
2740: /* for(j=1;j<=nlstate+ndeath;j++) { */
2741: /* printf("%f ",oldm[i][j]); */
2742: /* } */
2743: /* printf("\n"); */
2744: /* } */
2745: /* } */
1.126 brouard 2746: savm=oldm;
2747: oldm=newm;
2748: }
2749: for(i=1; i<=nlstate+ndeath; i++)
2750: for(j=1;j<=nlstate+ndeath;j++) {
1.218 brouard 2751: po[i][j][h]=newm[i][j];
2752: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2753: }
1.128 brouard 2754: /*printf("h=%d ",h);*/
1.126 brouard 2755: } /* end h */
1.218 brouard 2756: /* printf("\n H=%d \n",h); */
1.126 brouard 2757: return po;
2758: }
2759:
1.217 brouard 2760: /************* Higher Back Matrix Product ***************/
1.218 brouard 2761: /* 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 2762: double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )
1.217 brouard 2763: {
1.218 brouard 2764: /* Computes the transition matrix starting at age 'age' over
1.217 brouard 2765: 'nhstepm*hstepm*stepm' months (i.e. until
1.218 brouard 2766: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2767: nhstepm*hstepm matrices.
2768: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2769: (typically every 2 years instead of every month which is too big
1.217 brouard 2770: for the memory).
1.218 brouard 2771: Model is determined by parameters x and covariates have to be
2772: included manually here.
1.217 brouard 2773:
1.222 brouard 2774: */
1.217 brouard 2775:
2776: int i, j, d, h, k;
2777: double **out, cov[NCOVMAX+1];
2778: double **newm;
2779: double agexact;
2780: double agebegin, ageend;
1.222 brouard 2781: double **oldm, **savm;
1.217 brouard 2782:
1.222 brouard 2783: oldm=oldms;savm=savms;
1.217 brouard 2784: /* Hstepm could be zero and should return the unit matrix */
2785: for (i=1;i<=nlstate+ndeath;i++)
2786: for (j=1;j<=nlstate+ndeath;j++){
2787: oldm[i][j]=(i==j ? 1.0 : 0.0);
2788: po[i][j][0]=(i==j ? 1.0 : 0.0);
2789: }
2790: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2791: for(h=1; h <=nhstepm; h++){
2792: for(d=1; d <=hstepm; d++){
2793: newm=savm;
2794: /* Covariates have to be included here again */
2795: cov[1]=1.;
2796: agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
2797: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
2798: cov[2]=agexact;
2799: if(nagesqr==1)
1.222 brouard 2800: cov[3]= agexact*agexact;
1.218 brouard 2801: for (k=1; k<=cptcovn;k++)
1.222 brouard 2802: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2803: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.217 brouard 2804: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1.222 brouard 2805: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2806: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2807: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.217 brouard 2808: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.222 brouard 2809: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2810: /* 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 2811:
2812:
1.217 brouard 2813: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2814: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 2815: /* Careful transposed matrix */
1.222 brouard 2816: /* age is in cov[2] */
1.218 brouard 2817: /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
1.222 brouard 2818: /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
1.218 brouard 2819: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1.222 brouard 2820: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217 brouard 2821: /* if((int)age == 70){ */
2822: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
2823: /* for(i=1; i<=nlstate+ndeath; i++) { */
2824: /* printf("%d pmmij ",i); */
2825: /* for(j=1;j<=nlstate+ndeath;j++) { */
2826: /* printf("%f ",pmmij[i][j]); */
2827: /* } */
2828: /* printf(" oldm "); */
2829: /* for(j=1;j<=nlstate+ndeath;j++) { */
2830: /* printf("%f ",oldm[i][j]); */
2831: /* } */
2832: /* printf("\n"); */
2833: /* } */
2834: /* } */
2835: savm=oldm;
2836: oldm=newm;
2837: }
2838: for(i=1; i<=nlstate+ndeath; i++)
2839: for(j=1;j<=nlstate+ndeath;j++) {
1.222 brouard 2840: po[i][j][h]=newm[i][j];
2841: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.217 brouard 2842: }
2843: /*printf("h=%d ",h);*/
2844: } /* end h */
1.222 brouard 2845: /* printf("\n H=%d \n",h); */
1.217 brouard 2846: return po;
2847: }
2848:
2849:
1.162 brouard 2850: #ifdef NLOPT
2851: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2852: double fret;
2853: double *xt;
2854: int j;
2855: myfunc_data *d2 = (myfunc_data *) pd;
2856: /* xt = (p1-1); */
2857: xt=vector(1,n);
2858: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2859:
2860: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2861: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2862: printf("Function = %.12lf ",fret);
2863: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2864: printf("\n");
2865: free_vector(xt,1,n);
2866: return fret;
2867: }
2868: #endif
1.126 brouard 2869:
2870: /*************** log-likelihood *************/
2871: double func( double *x)
2872: {
1.224 ! brouard 2873: int i, ii, j, k, mi, d, kk;
! 2874: int ioffset=0;
! 2875: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
! 2876: double **out;
! 2877: double sw; /* Sum of weights */
! 2878: double lli; /* Individual log likelihood */
! 2879: int s1, s2;
! 2880: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate */
! 2881: double bbh, survp;
! 2882: long ipmx;
! 2883: double agexact;
! 2884: /*extern weight */
! 2885: /* We are differentiating ll according to initial status */
! 2886: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
! 2887: /*for(i=1;i<imx;i++)
! 2888: printf(" %d\n",s[4][i]);
! 2889: */
1.162 brouard 2890:
1.224 ! brouard 2891: ++countcallfunc;
1.162 brouard 2892:
1.224 ! brouard 2893: cov[1]=1.;
1.126 brouard 2894:
1.224 ! brouard 2895: for(k=1; k<=nlstate; k++) ll[k]=0.;
! 2896: ioffset=0;
! 2897: if(mle==1){
! 2898: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
! 2899: /* Computes the values of the ncovmodel covariates of the model
! 2900: depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
! 2901: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
! 2902: to be observed in j being in i according to the model.
! 2903: */
! 2904: ioffset=2+nagesqr+cptcovage;
! 2905: /* for (k=1; k<=cptcovn;k++){ /\* Simple and product covariates without age* products *\/ */
! 2906: for (k=1; k<=ncoveff;k++){ /* Simple and product covariates without age* products */
! 2907: cov[++ioffset]=covar[Tvar[k]][i];
! 2908: }
! 2909: for(iqv=1; iqv <= nqveff; iqv++){ /* Quantitatives covariates */
! 2910: cov[++ioffset]=coqvar[iqv][i];
! 2911: }
1.126 brouard 2912:
1.224 ! brouard 2913: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
! 2914: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
! 2915: has been calculated etc */
! 2916: /* For an individual i, wav[i] gives the number of effective waves */
! 2917: /* We compute the contribution to Likelihood of each effective transition
! 2918: mw[mi][i] is real wave of the mi th effectve wave */
! 2919: /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
! 2920: s2=s[mw[mi+1][i]][i];
! 2921: And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
! 2922: But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
! 2923: meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
! 2924: */
! 2925: for(mi=1; mi<= wav[i]-1; mi++){
! 2926: for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
! 2927: cov[ioffset+itv]=cotvar[mw[mi][i]][itv][i];
! 2928: }
! 2929: for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
! 2930: cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i];
! 2931: }
! 2932: /* ioffset=2+nagesqr+cptcovn+nqv+ntv+nqtv; */
! 2933: for (ii=1;ii<=nlstate+ndeath;ii++)
! 2934: for (j=1;j<=nlstate+ndeath;j++){
! 2935: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 2936: savm[ii][j]=(ii==j ? 1.0 : 0.0);
! 2937: }
! 2938: for(d=0; d<dh[mi][i]; d++){
! 2939: newm=savm;
! 2940: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 2941: cov[2]=agexact;
! 2942: if(nagesqr==1)
! 2943: cov[3]= agexact*agexact; /* Should be changed here */
! 2944: for (kk=1; kk<=cptcovage;kk++) {
! 2945: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
! 2946: }
! 2947: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
! 2948: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
! 2949: savm=oldm;
! 2950: oldm=newm;
! 2951: } /* end mult */
! 2952:
! 2953: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
! 2954: /* But now since version 0.9 we anticipate for bias at large stepm.
! 2955: * If stepm is larger than one month (smallest stepm) and if the exact delay
! 2956: * (in months) between two waves is not a multiple of stepm, we rounded to
! 2957: * the nearest (and in case of equal distance, to the lowest) interval but now
! 2958: * we keep into memory the bias bh[mi][i] and also the previous matrix product
! 2959: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
! 2960: * probability in order to take into account the bias as a fraction of the way
! 2961: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
! 2962: * -stepm/2 to stepm/2 .
! 2963: * For stepm=1 the results are the same as for previous versions of Imach.
! 2964: * For stepm > 1 the results are less biased than in previous versions.
! 2965: */
! 2966: s1=s[mw[mi][i]][i];
! 2967: s2=s[mw[mi+1][i]][i];
! 2968: bbh=(double)bh[mi][i]/(double)stepm;
! 2969: /* bias bh is positive if real duration
! 2970: * is higher than the multiple of stepm and negative otherwise.
! 2971: */
! 2972: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
! 2973: if( s2 > nlstate){
! 2974: /* i.e. if s2 is a death state and if the date of death is known
! 2975: then the contribution to the likelihood is the probability to
! 2976: die between last step unit time and current step unit time,
! 2977: which is also equal to probability to die before dh
! 2978: minus probability to die before dh-stepm .
! 2979: In version up to 0.92 likelihood was computed
! 2980: as if date of death was unknown. Death was treated as any other
! 2981: health state: the date of the interview describes the actual state
! 2982: and not the date of a change in health state. The former idea was
! 2983: to consider that at each interview the state was recorded
! 2984: (healthy, disable or death) and IMaCh was corrected; but when we
! 2985: introduced the exact date of death then we should have modified
! 2986: the contribution of an exact death to the likelihood. This new
! 2987: contribution is smaller and very dependent of the step unit
! 2988: stepm. It is no more the probability to die between last interview
! 2989: and month of death but the probability to survive from last
! 2990: interview up to one month before death multiplied by the
! 2991: probability to die within a month. Thanks to Chris
! 2992: Jackson for correcting this bug. Former versions increased
! 2993: mortality artificially. The bad side is that we add another loop
! 2994: which slows down the processing. The difference can be up to 10%
! 2995: lower mortality.
! 2996: */
! 2997: /* If, at the beginning of the maximization mostly, the
! 2998: cumulative probability or probability to be dead is
! 2999: constant (ie = 1) over time d, the difference is equal to
! 3000: 0. out[s1][3] = savm[s1][3]: probability, being at state
! 3001: s1 at precedent wave, to be dead a month before current
! 3002: wave is equal to probability, being at state s1 at
! 3003: precedent wave, to be dead at mont of the current
! 3004: wave. Then the observed probability (that this person died)
! 3005: is null according to current estimated parameter. In fact,
! 3006: it should be very low but not zero otherwise the log go to
! 3007: infinity.
! 3008: */
1.183 brouard 3009: /* #ifdef INFINITYORIGINAL */
3010: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3011: /* #else */
3012: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
3013: /* lli=log(mytinydouble); */
3014: /* else */
3015: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3016: /* #endif */
1.224 ! brouard 3017: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3018:
1.224 ! brouard 3019: } else if ( s2==-1 ) { /* alive */
! 3020: for (j=1,survp=0. ; j<=nlstate; j++)
! 3021: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
! 3022: /*survp += out[s1][j]; */
! 3023: lli= log(survp);
! 3024: }
! 3025: else if (s2==-4) {
! 3026: for (j=3,survp=0. ; j<=nlstate; j++)
! 3027: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
! 3028: lli= log(survp);
! 3029: }
! 3030: else if (s2==-5) {
! 3031: for (j=1,survp=0. ; j<=2; j++)
! 3032: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
! 3033: lli= log(survp);
! 3034: }
! 3035: else{
! 3036: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
! 3037: /* 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 */
! 3038: }
! 3039: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
! 3040: /*if(lli ==000.0)*/
! 3041: /*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); */
! 3042: ipmx +=1;
! 3043: sw += weight[i];
! 3044: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
! 3045: /* if (lli < log(mytinydouble)){ */
! 3046: /* 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); */
! 3047: /* 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]); */
! 3048: /* } */
! 3049: } /* end of wave */
! 3050: } /* end of individual */
! 3051: } else if(mle==2){
! 3052: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
! 3053: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
! 3054: for(mi=1; mi<= wav[i]-1; mi++){
! 3055: for (ii=1;ii<=nlstate+ndeath;ii++)
! 3056: for (j=1;j<=nlstate+ndeath;j++){
! 3057: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 3058: savm[ii][j]=(ii==j ? 1.0 : 0.0);
! 3059: }
! 3060: for(d=0; d<=dh[mi][i]; d++){
! 3061: newm=savm;
! 3062: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 3063: cov[2]=agexact;
! 3064: if(nagesqr==1)
! 3065: cov[3]= agexact*agexact;
! 3066: for (kk=1; kk<=cptcovage;kk++) {
! 3067: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
! 3068: }
! 3069: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
! 3070: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
! 3071: savm=oldm;
! 3072: oldm=newm;
! 3073: } /* end mult */
! 3074:
! 3075: s1=s[mw[mi][i]][i];
! 3076: s2=s[mw[mi+1][i]][i];
! 3077: bbh=(double)bh[mi][i]/(double)stepm;
! 3078: 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 */
! 3079: ipmx +=1;
! 3080: sw += weight[i];
! 3081: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
! 3082: } /* end of wave */
! 3083: } /* end of individual */
! 3084: } else if(mle==3){ /* exponential inter-extrapolation */
! 3085: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
! 3086: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
! 3087: for(mi=1; mi<= wav[i]-1; mi++){
! 3088: for (ii=1;ii<=nlstate+ndeath;ii++)
! 3089: for (j=1;j<=nlstate+ndeath;j++){
! 3090: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 3091: savm[ii][j]=(ii==j ? 1.0 : 0.0);
! 3092: }
! 3093: for(d=0; d<dh[mi][i]; d++){
! 3094: newm=savm;
! 3095: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 3096: cov[2]=agexact;
! 3097: if(nagesqr==1)
! 3098: cov[3]= agexact*agexact;
! 3099: for (kk=1; kk<=cptcovage;kk++) {
! 3100: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
! 3101: }
! 3102: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
! 3103: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
! 3104: savm=oldm;
! 3105: oldm=newm;
! 3106: } /* end mult */
! 3107:
! 3108: s1=s[mw[mi][i]][i];
! 3109: s2=s[mw[mi+1][i]][i];
! 3110: bbh=(double)bh[mi][i]/(double)stepm;
! 3111: 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 */
! 3112: ipmx +=1;
! 3113: sw += weight[i];
! 3114: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
! 3115: } /* end of wave */
! 3116: } /* end of individual */
! 3117: }else if (mle==4){ /* ml=4 no inter-extrapolation */
! 3118: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
! 3119: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
! 3120: for(mi=1; mi<= wav[i]-1; mi++){
! 3121: for (ii=1;ii<=nlstate+ndeath;ii++)
! 3122: for (j=1;j<=nlstate+ndeath;j++){
! 3123: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 3124: savm[ii][j]=(ii==j ? 1.0 : 0.0);
! 3125: }
! 3126: for(d=0; d<dh[mi][i]; d++){
! 3127: newm=savm;
! 3128: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 3129: cov[2]=agexact;
! 3130: if(nagesqr==1)
! 3131: cov[3]= agexact*agexact;
! 3132: for (kk=1; kk<=cptcovage;kk++) {
! 3133: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
! 3134: }
1.126 brouard 3135:
1.224 ! brouard 3136: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
! 3137: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
! 3138: savm=oldm;
! 3139: oldm=newm;
! 3140: } /* end mult */
! 3141:
! 3142: s1=s[mw[mi][i]][i];
! 3143: s2=s[mw[mi+1][i]][i];
! 3144: if( s2 > nlstate){
! 3145: lli=log(out[s1][s2] - savm[s1][s2]);
! 3146: } else if ( s2==-1 ) { /* alive */
! 3147: for (j=1,survp=0. ; j<=nlstate; j++)
! 3148: survp += out[s1][j];
! 3149: lli= log(survp);
! 3150: }else{
! 3151: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
! 3152: }
! 3153: ipmx +=1;
! 3154: sw += weight[i];
! 3155: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.126 brouard 3156: /* 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]); */
1.224 ! brouard 3157: } /* end of wave */
! 3158: } /* end of individual */
! 3159: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
! 3160: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
! 3161: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
! 3162: for(mi=1; mi<= wav[i]-1; mi++){
! 3163: for (ii=1;ii<=nlstate+ndeath;ii++)
! 3164: for (j=1;j<=nlstate+ndeath;j++){
! 3165: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 3166: savm[ii][j]=(ii==j ? 1.0 : 0.0);
! 3167: }
! 3168: for(d=0; d<dh[mi][i]; d++){
! 3169: newm=savm;
! 3170: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 3171: cov[2]=agexact;
! 3172: if(nagesqr==1)
! 3173: cov[3]= agexact*agexact;
! 3174: for (kk=1; kk<=cptcovage;kk++) {
! 3175: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
! 3176: }
1.126 brouard 3177:
1.224 ! brouard 3178: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
! 3179: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
! 3180: savm=oldm;
! 3181: oldm=newm;
! 3182: } /* end mult */
! 3183:
! 3184: s1=s[mw[mi][i]][i];
! 3185: s2=s[mw[mi+1][i]][i];
! 3186: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
! 3187: ipmx +=1;
! 3188: sw += weight[i];
! 3189: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
! 3190: /*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]);*/
! 3191: } /* end of wave */
! 3192: } /* end of individual */
! 3193: } /* End of if */
! 3194: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
! 3195: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
! 3196: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
! 3197: return -l;
1.126 brouard 3198: }
3199:
3200: /*************** log-likelihood *************/
3201: double funcone( double *x)
3202: {
3203: /* Same as likeli but slower because of a lot of printf and if */
3204: int i, ii, j, k, mi, d, kk;
1.224 ! brouard 3205: int ioffset=0;
1.131 brouard 3206: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 3207: double **out;
3208: double lli; /* Individual log likelihood */
3209: double llt;
3210: int s1, s2;
1.224 ! brouard 3211: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate */
1.126 brouard 3212: double bbh, survp;
1.187 brouard 3213: double agexact;
1.214 brouard 3214: double agebegin, ageend;
1.126 brouard 3215: /*extern weight */
3216: /* We are differentiating ll according to initial status */
3217: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3218: /*for(i=1;i<imx;i++)
3219: printf(" %d\n",s[4][i]);
3220: */
3221: cov[1]=1.;
3222:
3223: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 ! brouard 3224: ioffset=0;
! 3225: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
! 3226: ioffset=2+nagesqr+cptcovage;
! 3227: /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
! 3228: for (k=1; k<=ncoveff;k++){ /* Simple and product covariates without age* products */
! 3229: cov[++ioffset]=covar[Tvar[k]][i];
! 3230: }
! 3231: for(iqv=1; iqv <= nqveff; iqv++){ /* Quantitatives covariates */
! 3232: cov[++ioffset]=coqvar[iqv][i];
! 3233: }
1.126 brouard 3234:
3235: for(mi=1; mi<= wav[i]-1; mi++){
1.224 ! brouard 3236: for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
! 3237: cov[ioffset+itv]=cotvar[mw[mi][i]][itv][i];
! 3238: }
! 3239: for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
! 3240: cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i];
! 3241: }
1.126 brouard 3242: for (ii=1;ii<=nlstate+ndeath;ii++)
1.224 ! brouard 3243: for (j=1;j<=nlstate+ndeath;j++){
! 3244: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 3245: savm[ii][j]=(ii==j ? 1.0 : 0.0);
! 3246: }
1.214 brouard 3247:
3248: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
3249: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
3250: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
1.224 ! brouard 3251: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
! 3252: and mw[mi+1][i]. dh depends on stepm.*/
! 3253: newm=savm;
! 3254: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 3255: cov[2]=agexact;
! 3256: if(nagesqr==1)
! 3257: cov[3]= agexact*agexact;
! 3258: for (kk=1; kk<=cptcovage;kk++) {
! 3259: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
! 3260: }
! 3261:
! 3262: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
! 3263: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
! 3264: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
! 3265: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
! 3266: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
! 3267: savm=oldm;
! 3268: oldm=newm;
1.126 brouard 3269: } /* end mult */
3270:
3271: s1=s[mw[mi][i]][i];
3272: s2=s[mw[mi+1][i]][i];
1.217 brouard 3273: /* if(s2==-1){ */
3274: /* printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */
3275: /* /\* exit(1); *\/ */
3276: /* } */
1.126 brouard 3277: bbh=(double)bh[mi][i]/(double)stepm;
3278: /* bias is positive if real duration
3279: * is higher than the multiple of stepm and negative otherwise.
3280: */
3281: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1.224 ! brouard 3282: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3283: } else if ( s2==-1 ) { /* alive */
1.224 ! brouard 3284: for (j=1,survp=0. ; j<=nlstate; j++)
! 3285: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
! 3286: lli= log(survp);
1.126 brouard 3287: }else if (mle==1){
1.224 ! brouard 3288: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1.126 brouard 3289: } else if(mle==2){
1.224 ! brouard 3290: lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
1.126 brouard 3291: } else if(mle==3){ /* exponential inter-extrapolation */
1.224 ! brouard 3292: lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
1.126 brouard 3293: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1.224 ! brouard 3294: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 3295: } else{ /* mle=0 back to 1 */
1.224 ! brouard 3296: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
! 3297: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 3298: } /* End of if */
3299: ipmx +=1;
3300: sw += weight[i];
3301: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 3302: /*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 3303: if(globpr){
1.224 ! brouard 3304: fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
1.126 brouard 3305: %11.6f %11.6f %11.6f ", \
1.224 ! brouard 3306: num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
! 3307: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
! 3308: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
! 3309: llt +=ll[k]*gipmx/gsw;
! 3310: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
! 3311: }
! 3312: fprintf(ficresilk," %10.6f\n", -llt);
1.126 brouard 3313: }
3314: } /* end of wave */
3315: } /* end of individual */
3316: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3317: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3318: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3319: if(globpr==0){ /* First time we count the contributions and weights */
3320: gipmx=ipmx;
3321: gsw=sw;
3322: }
3323: return -l;
3324: }
3325:
3326:
3327: /*************** function likelione ***********/
3328: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
3329: {
3330: /* This routine should help understanding what is done with
3331: the selection of individuals/waves and
3332: to check the exact contribution to the likelihood.
3333: Plotting could be done.
3334: */
3335: int k;
3336:
3337: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 3338: strcpy(fileresilk,"ILK_");
1.202 brouard 3339: strcat(fileresilk,fileresu);
1.126 brouard 3340: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
3341: printf("Problem with resultfile: %s\n", fileresilk);
3342: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
3343: }
1.214 brouard 3344: 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");
3345: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 3346: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
3347: for(k=1; k<=nlstate; k++)
3348: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
3349: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
3350: }
3351:
3352: *fretone=(*funcone)(p);
3353: if(*globpri !=0){
3354: fclose(ficresilk);
1.205 brouard 3355: if (mle ==0)
3356: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
3357: else if(mle >=1)
3358: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
3359: 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 3360:
1.208 brouard 3361:
3362: for (k=1; k<= nlstate ; k++) {
1.211 brouard 3363: 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 3364: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
3365: }
1.207 brouard 3366: 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 3367: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3368: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 3369: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3370: fflush(fichtm);
1.205 brouard 3371: }
1.126 brouard 3372: return;
3373: }
3374:
3375:
3376: /*********** Maximum Likelihood Estimation ***************/
3377:
3378: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
3379: {
1.165 brouard 3380: int i,j, iter=0;
1.126 brouard 3381: double **xi;
3382: double fret;
3383: double fretone; /* Only one call to likelihood */
3384: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 3385:
3386: #ifdef NLOPT
3387: int creturn;
3388: nlopt_opt opt;
3389: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
3390: double *lb;
3391: double minf; /* the minimum objective value, upon return */
3392: double * p1; /* Shifted parameters from 0 instead of 1 */
3393: myfunc_data dinst, *d = &dinst;
3394: #endif
3395:
3396:
1.126 brouard 3397: xi=matrix(1,npar,1,npar);
3398: for (i=1;i<=npar;i++)
3399: for (j=1;j<=npar;j++)
3400: xi[i][j]=(i==j ? 1.0 : 0.0);
3401: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 3402: strcpy(filerespow,"POW_");
1.126 brouard 3403: strcat(filerespow,fileres);
3404: if((ficrespow=fopen(filerespow,"w"))==NULL) {
3405: printf("Problem with resultfile: %s\n", filerespow);
3406: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
3407: }
3408: fprintf(ficrespow,"# Powell\n# iter -2*LL");
3409: for (i=1;i<=nlstate;i++)
3410: for(j=1;j<=nlstate+ndeath;j++)
3411: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
3412: fprintf(ficrespow,"\n");
1.162 brouard 3413: #ifdef POWELL
1.126 brouard 3414: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 3415: #endif
1.126 brouard 3416:
1.162 brouard 3417: #ifdef NLOPT
3418: #ifdef NEWUOA
3419: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
3420: #else
3421: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
3422: #endif
3423: lb=vector(0,npar-1);
3424: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
3425: nlopt_set_lower_bounds(opt, lb);
3426: nlopt_set_initial_step1(opt, 0.1);
3427:
3428: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
3429: d->function = func;
3430: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
3431: nlopt_set_min_objective(opt, myfunc, d);
3432: nlopt_set_xtol_rel(opt, ftol);
3433: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
3434: printf("nlopt failed! %d\n",creturn);
3435: }
3436: else {
3437: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
3438: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
3439: iter=1; /* not equal */
3440: }
3441: nlopt_destroy(opt);
3442: #endif
1.126 brouard 3443: free_matrix(xi,1,npar,1,npar);
3444: fclose(ficrespow);
1.203 brouard 3445: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
3446: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 3447: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 3448:
3449: }
3450:
3451: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 3452: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 3453: {
3454: double **a,**y,*x,pd;
1.203 brouard 3455: /* double **hess; */
1.164 brouard 3456: int i, j;
1.126 brouard 3457: int *indx;
3458:
3459: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 3460: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 3461: void lubksb(double **a, int npar, int *indx, double b[]) ;
3462: void ludcmp(double **a, int npar, int *indx, double *d) ;
3463: double gompertz(double p[]);
1.203 brouard 3464: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 3465:
3466: printf("\nCalculation of the hessian matrix. Wait...\n");
3467: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
3468: for (i=1;i<=npar;i++){
1.203 brouard 3469: printf("%d-",i);fflush(stdout);
3470: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 3471:
3472: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
3473:
3474: /* printf(" %f ",p[i]);
3475: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
3476: }
3477:
3478: for (i=1;i<=npar;i++) {
3479: for (j=1;j<=npar;j++) {
3480: if (j>i) {
1.203 brouard 3481: printf(".%d-%d",i,j);fflush(stdout);
3482: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
3483: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 3484:
3485: hess[j][i]=hess[i][j];
3486: /*printf(" %lf ",hess[i][j]);*/
3487: }
3488: }
3489: }
3490: printf("\n");
3491: fprintf(ficlog,"\n");
3492:
3493: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
3494: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
3495:
3496: a=matrix(1,npar,1,npar);
3497: y=matrix(1,npar,1,npar);
3498: x=vector(1,npar);
3499: indx=ivector(1,npar);
3500: for (i=1;i<=npar;i++)
3501: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
3502: ludcmp(a,npar,indx,&pd);
3503:
3504: for (j=1;j<=npar;j++) {
3505: for (i=1;i<=npar;i++) x[i]=0;
3506: x[j]=1;
3507: lubksb(a,npar,indx,x);
3508: for (i=1;i<=npar;i++){
3509: matcov[i][j]=x[i];
3510: }
3511: }
3512:
3513: printf("\n#Hessian matrix#\n");
3514: fprintf(ficlog,"\n#Hessian matrix#\n");
3515: for (i=1;i<=npar;i++) {
3516: for (j=1;j<=npar;j++) {
1.203 brouard 3517: printf("%.6e ",hess[i][j]);
3518: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 3519: }
3520: printf("\n");
3521: fprintf(ficlog,"\n");
3522: }
3523:
1.203 brouard 3524: /* printf("\n#Covariance matrix#\n"); */
3525: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
3526: /* for (i=1;i<=npar;i++) { */
3527: /* for (j=1;j<=npar;j++) { */
3528: /* printf("%.6e ",matcov[i][j]); */
3529: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
3530: /* } */
3531: /* printf("\n"); */
3532: /* fprintf(ficlog,"\n"); */
3533: /* } */
3534:
1.126 brouard 3535: /* Recompute Inverse */
1.203 brouard 3536: /* for (i=1;i<=npar;i++) */
3537: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
3538: /* ludcmp(a,npar,indx,&pd); */
3539:
3540: /* printf("\n#Hessian matrix recomputed#\n"); */
3541:
3542: /* for (j=1;j<=npar;j++) { */
3543: /* for (i=1;i<=npar;i++) x[i]=0; */
3544: /* x[j]=1; */
3545: /* lubksb(a,npar,indx,x); */
3546: /* for (i=1;i<=npar;i++){ */
3547: /* y[i][j]=x[i]; */
3548: /* printf("%.3e ",y[i][j]); */
3549: /* fprintf(ficlog,"%.3e ",y[i][j]); */
3550: /* } */
3551: /* printf("\n"); */
3552: /* fprintf(ficlog,"\n"); */
3553: /* } */
3554:
3555: /* Verifying the inverse matrix */
3556: #ifdef DEBUGHESS
3557: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 3558:
1.203 brouard 3559: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
3560: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 3561:
3562: for (j=1;j<=npar;j++) {
3563: for (i=1;i<=npar;i++){
1.203 brouard 3564: printf("%.2f ",y[i][j]);
3565: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 3566: }
3567: printf("\n");
3568: fprintf(ficlog,"\n");
3569: }
1.203 brouard 3570: #endif
1.126 brouard 3571:
3572: free_matrix(a,1,npar,1,npar);
3573: free_matrix(y,1,npar,1,npar);
3574: free_vector(x,1,npar);
3575: free_ivector(indx,1,npar);
1.203 brouard 3576: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 3577:
3578:
3579: }
3580:
3581: /*************** hessian matrix ****************/
3582: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 3583: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 3584: int i;
3585: int l=1, lmax=20;
1.203 brouard 3586: double k1,k2, res, fx;
1.132 brouard 3587: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 3588: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
3589: int k=0,kmax=10;
3590: double l1;
3591:
3592: fx=func(x);
3593: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 3594: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 3595: l1=pow(10,l);
3596: delts=delt;
3597: for(k=1 ; k <kmax; k=k+1){
3598: delt = delta*(l1*k);
3599: p2[theta]=x[theta] +delt;
1.145 brouard 3600: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 3601: p2[theta]=x[theta]-delt;
3602: k2=func(p2)-fx;
3603: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 3604: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 3605:
1.203 brouard 3606: #ifdef DEBUGHESSII
1.126 brouard 3607: 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);
3608: 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);
3609: #endif
3610: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
3611: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
3612: k=kmax;
3613: }
3614: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 3615: k=kmax; l=lmax*10;
1.126 brouard 3616: }
3617: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
3618: delts=delt;
3619: }
1.203 brouard 3620: } /* End loop k */
1.126 brouard 3621: }
3622: delti[theta]=delts;
3623: return res;
3624:
3625: }
3626:
1.203 brouard 3627: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 3628: {
3629: int i;
1.164 brouard 3630: int l=1, lmax=20;
1.126 brouard 3631: double k1,k2,k3,k4,res,fx;
1.132 brouard 3632: double p2[MAXPARM+1];
1.203 brouard 3633: int k, kmax=1;
3634: double v1, v2, cv12, lc1, lc2;
1.208 brouard 3635:
3636: int firstime=0;
1.203 brouard 3637:
1.126 brouard 3638: fx=func(x);
1.203 brouard 3639: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 3640: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 3641: p2[thetai]=x[thetai]+delti[thetai]*k;
3642: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3643: k1=func(p2)-fx;
3644:
1.203 brouard 3645: p2[thetai]=x[thetai]+delti[thetai]*k;
3646: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3647: k2=func(p2)-fx;
3648:
1.203 brouard 3649: p2[thetai]=x[thetai]-delti[thetai]*k;
3650: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3651: k3=func(p2)-fx;
3652:
1.203 brouard 3653: p2[thetai]=x[thetai]-delti[thetai]*k;
3654: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3655: k4=func(p2)-fx;
1.203 brouard 3656: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
3657: if(k1*k2*k3*k4 <0.){
1.208 brouard 3658: firstime=1;
1.203 brouard 3659: kmax=kmax+10;
1.208 brouard 3660: }
3661: if(kmax >=10 || firstime ==1){
1.218 brouard 3662: 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);
3663: 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 3664: 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);
3665: 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);
3666: }
3667: #ifdef DEBUGHESSIJ
3668: v1=hess[thetai][thetai];
3669: v2=hess[thetaj][thetaj];
3670: cv12=res;
3671: /* Computing eigen value of Hessian matrix */
3672: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3673: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3674: if ((lc2 <0) || (lc1 <0) ){
3675: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3676: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3677: 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);
3678: 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);
3679: }
1.126 brouard 3680: #endif
3681: }
3682: return res;
3683: }
3684:
1.203 brouard 3685: /* Not done yet: Was supposed to fix if not exactly at the maximum */
3686: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
3687: /* { */
3688: /* int i; */
3689: /* int l=1, lmax=20; */
3690: /* double k1,k2,k3,k4,res,fx; */
3691: /* double p2[MAXPARM+1]; */
3692: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
3693: /* int k=0,kmax=10; */
3694: /* double l1; */
3695:
3696: /* fx=func(x); */
3697: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
3698: /* l1=pow(10,l); */
3699: /* delts=delt; */
3700: /* for(k=1 ; k <kmax; k=k+1){ */
3701: /* delt = delti*(l1*k); */
3702: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
3703: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3704: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3705: /* k1=func(p2)-fx; */
3706:
3707: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3708: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3709: /* k2=func(p2)-fx; */
3710:
3711: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3712: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3713: /* k3=func(p2)-fx; */
3714:
3715: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3716: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3717: /* k4=func(p2)-fx; */
3718: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
3719: /* #ifdef DEBUGHESSIJ */
3720: /* 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); */
3721: /* 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); */
3722: /* #endif */
3723: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
3724: /* k=kmax; */
3725: /* } */
3726: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
3727: /* k=kmax; l=lmax*10; */
3728: /* } */
3729: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
3730: /* delts=delt; */
3731: /* } */
3732: /* } /\* End loop k *\/ */
3733: /* } */
3734: /* delti[theta]=delts; */
3735: /* return res; */
3736: /* } */
3737:
3738:
1.126 brouard 3739: /************** Inverse of matrix **************/
3740: void ludcmp(double **a, int n, int *indx, double *d)
3741: {
3742: int i,imax,j,k;
3743: double big,dum,sum,temp;
3744: double *vv;
3745:
3746: vv=vector(1,n);
3747: *d=1.0;
3748: for (i=1;i<=n;i++) {
3749: big=0.0;
3750: for (j=1;j<=n;j++)
3751: if ((temp=fabs(a[i][j])) > big) big=temp;
3752: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
3753: vv[i]=1.0/big;
3754: }
3755: for (j=1;j<=n;j++) {
3756: for (i=1;i<j;i++) {
3757: sum=a[i][j];
3758: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
3759: a[i][j]=sum;
3760: }
3761: big=0.0;
3762: for (i=j;i<=n;i++) {
3763: sum=a[i][j];
3764: for (k=1;k<j;k++)
3765: sum -= a[i][k]*a[k][j];
3766: a[i][j]=sum;
3767: if ( (dum=vv[i]*fabs(sum)) >= big) {
3768: big=dum;
3769: imax=i;
3770: }
3771: }
3772: if (j != imax) {
3773: for (k=1;k<=n;k++) {
3774: dum=a[imax][k];
3775: a[imax][k]=a[j][k];
3776: a[j][k]=dum;
3777: }
3778: *d = -(*d);
3779: vv[imax]=vv[j];
3780: }
3781: indx[j]=imax;
3782: if (a[j][j] == 0.0) a[j][j]=TINY;
3783: if (j != n) {
3784: dum=1.0/(a[j][j]);
3785: for (i=j+1;i<=n;i++) a[i][j] *= dum;
3786: }
3787: }
3788: free_vector(vv,1,n); /* Doesn't work */
3789: ;
3790: }
3791:
3792: void lubksb(double **a, int n, int *indx, double b[])
3793: {
3794: int i,ii=0,ip,j;
3795: double sum;
3796:
3797: for (i=1;i<=n;i++) {
3798: ip=indx[i];
3799: sum=b[ip];
3800: b[ip]=b[i];
3801: if (ii)
3802: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
3803: else if (sum) ii=i;
3804: b[i]=sum;
3805: }
3806: for (i=n;i>=1;i--) {
3807: sum=b[i];
3808: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
3809: b[i]=sum/a[i][i];
3810: }
3811: }
3812:
3813: void pstamp(FILE *fichier)
3814: {
1.196 brouard 3815: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 3816: }
3817:
3818: /************ Frequencies ********************/
1.220 brouard 3819: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
3820: int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
3821: int firstpass, int lastpass, int stepm, int weightopt, char model[])
3822: { /* Some frequencies */
3823:
3824: int i, m, jk, j1, bool, z1,j;
3825: int iind=0, iage=0;
3826: int mi; /* Effective wave */
3827: int first;
3828: double ***freq; /* Frequencies */
1.224 ! brouard 3829: double *meanq;
! 3830: double **meanqt;
1.220 brouard 3831: double *pp, **prop, *posprop, *pospropt;
3832: double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
3833: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
3834: double agebegin, ageend;
3835:
3836: pp=vector(1,nlstate);
3837: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
3838: posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
3839: pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
3840: /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
1.224 ! brouard 3841: meanq=vector(1,nqveff);
! 3842: meanqt=matrix(1,lastpass,1,nqtveff);
1.220 brouard 3843: strcpy(fileresp,"P_");
3844: strcat(fileresp,fileresu);
3845: /*strcat(fileresphtm,fileresu);*/
3846: if((ficresp=fopen(fileresp,"w"))==NULL) {
3847: printf("Problem with prevalence resultfile: %s\n", fileresp);
3848: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
3849: exit(0);
3850: }
1.214 brouard 3851:
1.220 brouard 3852: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
3853: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
3854: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3855: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3856: fflush(ficlog);
3857: exit(70);
3858: }
3859: else{
3860: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.214 brouard 3861: <hr size=\"2\" color=\"#EC5E5E\"> \n\
3862: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.220 brouard 3863: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
3864: }
3865: 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 3866:
1.220 brouard 3867: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
3868: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
3869: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
3870: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
3871: fflush(ficlog);
3872: exit(70);
3873: }
3874: else{
3875: 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 3876: <hr size=\"2\" color=\"#EC5E5E\"> \n\
3877: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.220 brouard 3878: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
3879: }
3880: 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 3881:
1.220 brouard 3882: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
3883: j1=0;
1.126 brouard 3884:
1.224 ! brouard 3885: j=ncoveff;
1.220 brouard 3886: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3887:
3888: first=1;
3889:
3890: /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
3891: reference=low_education V1=0,V2=0
3892: med_educ V1=1 V2=0,
3893: high_educ V1=0 V2=1
3894: Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
3895: */
1.126 brouard 3896:
1.224 ! brouard 3897: for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination excluding varying and quantitatives */
1.220 brouard 3898: posproptt=0.;
3899: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
3900: scanf("%d", i);*/
3901: for (i=-5; i<=nlstate+ndeath; i++)
3902: for (jk=-5; jk<=nlstate+ndeath; jk++)
3903: for(m=iagemin; m <= iagemax+3; m++)
3904: freq[i][jk][m]=0;
3905:
3906: for (i=1; i<=nlstate; i++) {
3907: for(m=iagemin; m <= iagemax+3; m++)
3908: prop[i][m]=0;
3909: posprop[i]=0;
3910: pospropt[i]=0;
3911: }
1.224 ! brouard 3912: for (z1=1; z1<= nqveff; z1++) {
! 3913: meanq[z1]+=0.;
! 3914: for(m=1;m<=lastpass;m++){
! 3915: meanqt[m][z1]=0.;
! 3916: }
! 3917: }
1.220 brouard 3918:
3919: dateintsum=0;
3920: k2cpt=0;
1.224 ! brouard 3921: /* For that comination of covariate j1, we count and print the frequencies */
1.220 brouard 3922: for (iind=1; iind<=imx; iind++) { /* For each individual iind */
3923: bool=1;
1.224 ! brouard 3924: if (nqveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
! 3925: for (z1=1; z1<= nqveff; z1++) {
! 3926: meanq[z1]+=coqvar[Tvar[z1]][iind];
! 3927: }
! 3928: for (z1=1; z1<=ncoveff; z1++) {
! 3929: /* if(Tvaraff[z1] ==-20){ */
! 3930: /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
! 3931: /* }else if(Tvaraff[z1] ==-10){ */
! 3932: /* /\* sumnew+=coqvar[z1][iind]; *\/ */
! 3933: /* }else */
1.220 brouard 3934: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
1.224 ! brouard 3935: /* Tests if this individual i responded to j1 (V4=1 V3=0) */
1.220 brouard 3936: bool=0;
3937: /* 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 3938: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
3939: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
1.220 brouard 3940: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
3941: }
3942: } /* end z1 */
3943: } /* cptcovn > 0 */
3944:
1.224 ! brouard 3945: if (bool==1){ /* We selected an individual iin satisfying combination j1 */
1.220 brouard 3946: /* for(m=firstpass; m<=lastpass; m++){ */
3947: for(mi=1; mi<wav[iind];mi++){
3948: m=mw[mi][iind];
3949: /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
3950: and mw[mi+1][iind]. dh depends on stepm. */
3951: agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
3952: ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
3953: if(m >=firstpass && m <=lastpass){
3954: k2=anint[m][iind]+(mint[m][iind]/12.);
3955: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
3956: if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
3957: if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
3958: if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
3959: prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
3960: if (m<lastpass) {
3961: /* if(s[m][iind]==4 && s[m+1][iind]==4) */
3962: /* 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]); */
3963: if(s[m][iind]==-1)
3964: 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.));
3965: freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
3966: /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
3967: 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 */
3968: }
3969: }
3970: if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
3971: dateintsum=dateintsum+k2;
3972: k2cpt++;
3973: /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
3974: }
3975: /*}*/
3976: } /* end m */
3977: } /* end bool */
3978: } /* end iind = 1 to imx */
3979: /* prop[s][age] is feeded for any initial and valid live state as well as
3980: freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
3981:
3982:
3983: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
3984: pstamp(ficresp);
1.224 ! brouard 3985: if (ncoveff>0) {
1.220 brouard 3986: fprintf(ficresp, "\n#********** Variable ");
3987: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
3988: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
1.224 ! brouard 3989: for (z1=1; z1<=ncoveff; z1++){
1.220 brouard 3990: fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
3991: fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
3992: fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
3993: }
3994: fprintf(ficresp, "**********\n#");
3995: fprintf(ficresphtm, "**********</h3>\n");
3996: fprintf(ficresphtmfr, "**********</h3>\n");
3997: fprintf(ficlog, "\n#********** Variable ");
1.224 ! brouard 3998: for (z1=1; z1<=ncoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.220 brouard 3999: fprintf(ficlog, "**********\n");
4000: }
4001: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
4002: for(i=1; i<=nlstate;i++) {
4003: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
4004: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
4005: }
4006: fprintf(ficresp, "\n");
4007: fprintf(ficresphtm, "\n");
4008:
4009: /* Header of frequency table by age */
4010: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
4011: fprintf(ficresphtmfr,"<th>Age</th> ");
4012: for(jk=-1; jk <=nlstate+ndeath; jk++){
4013: for(m=-1; m <=nlstate+ndeath; m++){
4014: if(jk!=0 && m!=0)
4015: fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
4016: }
4017: }
4018: fprintf(ficresphtmfr, "\n");
1.214 brouard 4019:
1.220 brouard 4020: /* For each age */
4021: for(iage=iagemin; iage <= iagemax+3; iage++){
4022: fprintf(ficresphtm,"<tr>");
4023: if(iage==iagemax+1){
4024: fprintf(ficlog,"1");
4025: fprintf(ficresphtmfr,"<tr><th>0</th> ");
4026: }else if(iage==iagemax+2){
4027: fprintf(ficlog,"0");
4028: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
4029: }else if(iage==iagemax+3){
4030: fprintf(ficlog,"Total");
4031: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
4032: }else{
4033: if(first==1){
4034: first=0;
4035: printf("See log file for details...\n");
4036: }
4037: fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
4038: fprintf(ficlog,"Age %d", iage);
4039: }
4040: for(jk=1; jk <=nlstate ; jk++){
4041: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
4042: pp[jk] += freq[jk][m][iage];
4043: }
4044: for(jk=1; jk <=nlstate ; jk++){
4045: for(m=-1, pos=0; m <=0 ; m++)
4046: pos += freq[jk][m][iage];
4047: if(pp[jk]>=1.e-10){
4048: if(first==1){
4049: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
4050: }
4051: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
4052: }else{
4053: if(first==1)
4054: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
4055: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
4056: }
4057: }
4058:
4059: for(jk=1; jk <=nlstate ; jk++){
4060: /* posprop[jk]=0; */
4061: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
4062: pp[jk] += freq[jk][m][iage];
4063: } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
4064:
4065: for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
4066: pos += pp[jk]; /* pos is the total number of transitions until this age */
4067: posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
4068: from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4069: pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
4070: from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4071: }
4072: for(jk=1; jk <=nlstate ; jk++){
4073: if(pos>=1.e-5){
4074: if(first==1)
4075: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
4076: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
4077: }else{
4078: if(first==1)
4079: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
4080: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
4081: }
4082: if( iage <= iagemax){
4083: if(pos>=1.e-5){
4084: fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
4085: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
4086: /*probs[iage][jk][j1]= pp[jk]/pos;*/
4087: /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
4088: }
4089: else{
4090: fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
4091: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
4092: }
4093: }
4094: pospropt[jk] +=posprop[jk];
4095: } /* end loop jk */
4096: /* pospropt=0.; */
4097: for(jk=-1; jk <=nlstate+ndeath; jk++){
4098: for(m=-1; m <=nlstate+ndeath; m++){
4099: if(freq[jk][m][iage] !=0 ) { /* minimizing output */
4100: if(first==1){
4101: printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
4102: }
4103: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
4104: }
4105: if(jk!=0 && m!=0)
4106: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
4107: }
4108: } /* end loop jk */
4109: posproptt=0.;
4110: for(jk=1; jk <=nlstate; jk++){
4111: posproptt += pospropt[jk];
4112: }
4113: fprintf(ficresphtmfr,"</tr>\n ");
4114: if(iage <= iagemax){
4115: fprintf(ficresp,"\n");
4116: fprintf(ficresphtm,"</tr>\n");
4117: }
4118: if(first==1)
4119: printf("Others in log...\n");
4120: fprintf(ficlog,"\n");
4121: } /* end loop age iage */
4122: fprintf(ficresphtm,"<tr><th>Tot</th>");
4123: for(jk=1; jk <=nlstate ; jk++){
4124: if(posproptt < 1.e-5){
1.221 brouard 4125: fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);
4126: }else{
1.220 brouard 4127: fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);
4128: }
4129: }
4130: fprintf(ficresphtm,"</tr>\n");
4131: fprintf(ficresphtm,"</table>\n");
4132: fprintf(ficresphtmfr,"</table>\n");
4133: if(posproptt < 1.e-5){
4134: fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4135: fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4136: fprintf(ficres,"\n This combination (%d) is not valid and no result will be produced\n\n",j1);
4137: invalidvarcomb[j1]=1;
4138: }else{
4139: fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
4140: invalidvarcomb[j1]=0;
4141: }
4142: fprintf(ficresphtmfr,"</table>\n");
4143: } /* end selected combination of covariate j1 */
4144: dateintmean=dateintsum/k2cpt;
4145:
4146: fclose(ficresp);
4147: fclose(ficresphtm);
4148: fclose(ficresphtmfr);
1.224 ! brouard 4149: free_vector(meanq,1,nqveff);
! 4150: free_matrix(meanqt,1,lastpass,1,nqtveff);
1.220 brouard 4151: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
4152: free_vector(pospropt,1,nlstate);
4153: free_vector(posprop,1,nlstate);
4154: free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
4155: free_vector(pp,1,nlstate);
1.224 ! brouard 4156: /* End of freqsummary */
1.220 brouard 4157: }
1.126 brouard 4158:
4159: /************ Prevalence ********************/
1.222 brouard 4160: 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)
4161: {
4162: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
4163: in each health status at the date of interview (if between dateprev1 and dateprev2).
4164: We still use firstpass and lastpass as another selection.
4165: */
1.126 brouard 4166:
1.222 brouard 4167: int i, m, jk, j1, bool, z1,j;
4168: int mi; /* Effective wave */
4169: int iage;
4170: double agebegin, ageend;
4171:
4172: double **prop;
4173: double posprop;
4174: double y2; /* in fractional years */
4175: int iagemin, iagemax;
4176: int first; /** to stop verbosity which is redirected to log file */
4177:
4178: iagemin= (int) agemin;
4179: iagemax= (int) agemax;
4180: /*pp=vector(1,nlstate);*/
4181: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
4182: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
4183: j1=0;
4184:
4185: /*j=cptcoveff;*/
4186: if (cptcovn<1) {j=1;ncodemax[1]=1;}
4187:
4188: first=1;
1.224 ! brouard 4189: for(j1=1; j1<= (int) pow(2,nqveff);j1++){ /* For each combination of covariate */
1.222 brouard 4190: for (i=1; i<=nlstate; i++)
4191: for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
4192: prop[i][iage]=0.0;
4193:
4194: for (i=1; i<=imx; i++) { /* Each individual */
4195: bool=1;
4196: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
1.224 ! brouard 4197: for (z1=1; z1<=nqveff; 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*/
1.222 brouard 4198: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
4199: bool=0;
4200: }
4201: if (bool==1) { /* For this combination of covariates values, this individual fits */
4202: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
4203: for(mi=1; mi<wav[i];mi++){
4204: m=mw[mi][i];
4205: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
4206: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
4207: if(m >=firstpass && m <=lastpass){
4208: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
4209: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
4210: if(agev[m][i]==0) agev[m][i]=iagemax+1;
4211: if(agev[m][i]==1) agev[m][i]=iagemax+2;
4212: if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
4213: 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);
4214: exit(1);
4215: }
4216: if (s[m][i]>0 && s[m][i]<=nlstate) {
4217: /*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]]);*/
4218: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
4219: prop[s[m][i]][iagemax+3] += weight[i];
4220: } /* end valid statuses */
4221: } /* end selection of dates */
4222: } /* end selection of waves */
4223: } /* end effective waves */
4224: } /* end bool */
4225: }
4226: for(i=iagemin; i <= iagemax+3; i++){
4227: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
4228: posprop += prop[jk][i];
4229: }
4230:
4231: for(jk=1; jk <=nlstate ; jk++){
4232: if( i <= iagemax){
4233: if(posprop>=1.e-5){
4234: probs[i][jk][j1]= prop[jk][i]/posprop;
4235: } else{
4236: if(first==1){
4237: first=0;
4238: 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]);
4239: }
4240: }
4241: }
4242: }/* end jk */
4243: }/* end i */
4244: /*} *//* end i1 */
4245: } /* end j1 */
4246:
4247: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
4248: /*free_vector(pp,1,nlstate);*/
4249: free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
4250: } /* End of prevalence */
1.126 brouard 4251:
4252: /************* Waves Concatenation ***************/
4253:
4254: 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)
4255: {
4256: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
4257: Death is a valid wave (if date is known).
4258: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
4259: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
4260: and mw[mi+1][i]. dh depends on stepm.
4261: */
4262:
1.224 ! brouard 4263: int i=0, mi=0, m=0, mli=0;
1.126 brouard 4264: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
4265: double sum=0., jmean=0.;*/
1.224 ! brouard 4266: int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
1.126 brouard 4267: int j, k=0,jk, ju, jl;
4268: double sum=0.;
4269: first=0;
1.214 brouard 4270: firstwo=0;
1.217 brouard 4271: firsthree=0;
1.218 brouard 4272: firstfour=0;
1.164 brouard 4273: jmin=100000;
1.126 brouard 4274: jmax=-1;
4275: jmean=0.;
1.224 ! brouard 4276:
! 4277: /* Treating live states */
1.214 brouard 4278: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.224 ! brouard 4279: mi=0; /* First valid wave */
! 4280: mli=0; /* Last valid wave */
1.126 brouard 4281: m=firstpass;
1.214 brouard 4282: while(s[m][i] <= nlstate){ /* a live state */
1.224 ! brouard 4283: if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */
! 4284: mli=m-1;/* mw[++mi][i]=m-1; */
! 4285: }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
1.223 brouard 4286: mw[++mi][i]=m;
1.224 ! brouard 4287: mli=m;
! 4288: } /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
! 4289: if(m < lastpass){ /* m < lastpass, standard case */
! 4290: m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
1.216 brouard 4291: }
1.224 ! brouard 4292: else{ /* m >= lastpass, eventual special issue with warning */
! 4293: #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
! 4294: break;
! 4295: #else
1.223 brouard 4296: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
4297: if(firsthree == 0){
1.224 ! brouard 4298: printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
1.223 brouard 4299: firsthree=1;
4300: }
1.224 ! brouard 4301: fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
1.223 brouard 4302: mw[++mi][i]=m;
1.224 ! brouard 4303: mli=m;
1.223 brouard 4304: }
4305: if(s[m][i]==-2){ /* Vital status is really unknown */
4306: nbwarn++;
4307: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */
4308: 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);
1.224 ! brouard 4309: fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
1.223 brouard 4310: }
4311: break;
4312: }
4313: break;
1.224 ! brouard 4314: #endif
! 4315: }/* End m >= lastpass */
1.126 brouard 4316: }/* end while */
1.224 ! brouard 4317:
! 4318: /* mi is the last effective wave, m is lastpass, mw[j][i] gives the # of j-th effective wave for individual i */
1.216 brouard 4319: /* After last pass */
1.224 ! brouard 4320: /* Treating death states */
1.214 brouard 4321: if (s[m][i] > nlstate){ /* In a death state */
1.224 ! brouard 4322: /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
! 4323: /* } */
1.126 brouard 4324: mi++; /* Death is another wave */
4325: /* if(mi==0) never been interviewed correctly before death */
1.223 brouard 4326: /* Only death is a correct wave */
1.126 brouard 4327: mw[mi][i]=m;
1.224 ! brouard 4328: }
! 4329: #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
! 4330: else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */
1.216 brouard 4331: /* m++; */
4332: /* mi++; */
4333: /* s[m][i]=nlstate+1; /\* We are setting the status to the last of non live state *\/ */
4334: /* mw[mi][i]=m; */
1.218 brouard 4335: if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
1.224 ! brouard 4336: if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */
! 4337: nbwarn++;
! 4338: if(firstfiv==0){
! 4339: printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
! 4340: firstfiv=1;
! 4341: }else{
! 4342: fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
! 4343: }
! 4344: }else{ /* Death occured afer last wave potential bias */
! 4345: nberr++;
! 4346: if(firstwo==0){
! 4347: printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
! 4348: firstwo=1;
! 4349: }
! 4350: fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
1.223 brouard 4351: }
1.218 brouard 4352: }else{ /* end date of interview is known */
1.223 brouard 4353: /* death is known but not confirmed by death status at any wave */
4354: if(firstfour==0){
4355: 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 );
4356: firstfour=1;
4357: }
4358: 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 4359: }
1.224 ! brouard 4360: } /* end if date of death is known */
! 4361: #endif
! 4362: wav[i]=mi; /* mi should be the last effective wave (or mli) */
! 4363: /* wav[i]=mw[mi][i]; */
1.126 brouard 4364: if(mi==0){
4365: nbwarn++;
4366: if(first==0){
1.223 brouard 4367: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
4368: first=1;
1.126 brouard 4369: }
4370: if(first==1){
1.223 brouard 4371: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.126 brouard 4372: }
4373: } /* end mi==0 */
4374: } /* End individuals */
1.214 brouard 4375: /* wav and mw are no more changed */
1.223 brouard 4376:
1.214 brouard 4377:
1.126 brouard 4378: for(i=1; i<=imx; i++){
4379: for(mi=1; mi<wav[i];mi++){
4380: if (stepm <=0)
1.223 brouard 4381: dh[mi][i]=1;
1.126 brouard 4382: else{
1.223 brouard 4383: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
4384: if (agedc[i] < 2*AGESUP) {
4385: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
4386: if(j==0) j=1; /* Survives at least one month after exam */
4387: else if(j<0){
4388: nberr++;
4389: 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]);
4390: j=1; /* Temporary Dangerous patch */
4391: 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);
4392: 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]);
4393: 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);
4394: }
4395: k=k+1;
4396: if (j >= jmax){
4397: jmax=j;
4398: ijmax=i;
4399: }
4400: if (j <= jmin){
4401: jmin=j;
4402: ijmin=i;
4403: }
4404: sum=sum+j;
4405: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
4406: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
4407: }
4408: }
4409: else{
4410: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.126 brouard 4411: /* if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
1.223 brouard 4412:
4413: k=k+1;
4414: if (j >= jmax) {
4415: jmax=j;
4416: ijmax=i;
4417: }
4418: else if (j <= jmin){
4419: jmin=j;
4420: ijmin=i;
4421: }
4422: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
4423: /*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]);*/
4424: if(j<0){
4425: nberr++;
4426: 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]);
4427: 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]);
4428: }
4429: sum=sum+j;
4430: }
4431: jk= j/stepm;
4432: jl= j -jk*stepm;
4433: ju= j -(jk+1)*stepm;
4434: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
4435: if(jl==0){
4436: dh[mi][i]=jk;
4437: bh[mi][i]=0;
4438: }else{ /* We want a negative bias in order to only have interpolation ie
4439: * to avoid the price of an extra matrix product in likelihood */
4440: dh[mi][i]=jk+1;
4441: bh[mi][i]=ju;
4442: }
4443: }else{
4444: if(jl <= -ju){
4445: dh[mi][i]=jk;
4446: bh[mi][i]=jl; /* bias is positive if real duration
4447: * is higher than the multiple of stepm and negative otherwise.
4448: */
4449: }
4450: else{
4451: dh[mi][i]=jk+1;
4452: bh[mi][i]=ju;
4453: }
4454: if(dh[mi][i]==0){
4455: dh[mi][i]=1; /* At least one step */
4456: bh[mi][i]=ju; /* At least one step */
4457: /* 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);*/
4458: }
4459: } /* end if mle */
1.126 brouard 4460: }
4461: } /* end wave */
4462: }
4463: jmean=sum/k;
4464: 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 4465: 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 4466: }
4467:
4468: /*********** Tricode ****************************/
1.220 brouard 4469: void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 4470: {
1.144 brouard 4471: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
4472: /* 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 4473: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.224 ! brouard 4474: * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
! 4475: * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
1.144 brouard 4476: */
1.130 brouard 4477:
1.145 brouard 4478: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 4479: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 4480: int cptcode=0; /* Modality max of covariates j */
4481: int modmincovj=0; /* Modality min of covariates j */
4482:
4483:
1.220 brouard 4484: /* cptcoveff=0; */
1.224 ! brouard 4485: /* *cptcov=0; */
1.126 brouard 4486:
1.144 brouard 4487: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 4488:
1.224 ! brouard 4489: /* Loop on covariates without age and products and no quantitative variable */
! 4490: /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
! 4491: for (j=1; j<=(*cptcov); j++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
1.192 brouard 4492: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.186 brouard 4493: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.224 ! brouard 4494: modality of this covariate Vj*/
! 4495: if(Tvar[j] >=1 && Tvar[j] <= *cptcov){ /* A real fixed covariate */
! 4496: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
! 4497: * If product of Vn*Vm, still boolean *:
! 4498: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
! 4499: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
! 4500: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
! 4501: modality of the nth covariate of individual i. */
! 4502: if (ij > modmaxcovj)
! 4503: modmaxcovj=ij;
! 4504: else if (ij < modmincovj)
! 4505: modmincovj=ij;
! 4506: if ((ij < -1) && (ij > NCOVMAX)){
! 4507: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
! 4508: exit(1);
! 4509: }else
! 4510: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 4511: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 4512: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 4513: /* getting the maximum value of the modality of the covariate
1.224 ! brouard 4514: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
! 4515: female ies 1, then modmaxcovj=1.*/
! 4516: }
! 4517: } /* end for loop on individuals i */
1.145 brouard 4518: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.192 brouard 4519: 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 4520: cptcode=modmaxcovj;
1.137 brouard 4521: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.224 ! brouard 4522: /*for (i=0; i<=cptcode; i++) {*/
1.192 brouard 4523: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
4524: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
4525: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
4526: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
1.219 brouard 4527: if( k != -1){
4528: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
4529: covariate for which somebody answered excluding
4530: undefined. Usually 2: 0 and 1. */
4531: }
4532: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
4533: covariate for which somebody answered including
4534: undefined. Usually 3: -1, 0 and 1. */
1.145 brouard 4535: }
4536: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
1.224 ! brouard 4537: * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 4538: } /* Ndum[-1] number of undefined modalities */
1.219 brouard 4539:
1.136 brouard 4540: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 4541: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
4542: 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 4543: modmincovj=3; modmaxcovj = 7;
1.186 brouard 4544: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
4545: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
4546: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 4547: nbcode[Tvar[j]][ij]=k;
4548: nbcode[Tvar[j]][1]=0;
4549: nbcode[Tvar[j]][2]=1;
4550: nbcode[Tvar[j]][3]=2;
1.197 brouard 4551: To be continued (not working yet).
1.145 brouard 4552: */
1.197 brouard 4553: ij=0; /* ij is similar to i but can jump over null modalities */
4554: 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*/
4555: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
1.219 brouard 4556: break;
4557: }
1.224 ! brouard 4558: ij++;
! 4559: 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.*/
! 4560: cptcode = ij; /* New max modality for covar j */
1.192 brouard 4561: } /* end of loop on modality i=-1 to 1 or more */
1.224 ! brouard 4562:
1.192 brouard 4563: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
4564: /* /\*recode from 0 *\/ */
4565: /* k is a modality. If we have model=V1+V1*sex */
4566: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
4567: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
4568: /* } */
4569: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
4570: /* if (ij > ncodemax[j]) { */
4571: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4572: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4573: /* break; */
4574: /* } */
4575: /* } /\* end of loop on modality k *\/ */
1.137 brouard 4576: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
4577:
1.219 brouard 4578: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 4579:
1.187 brouard 4580: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.219 brouard 4581: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
4582: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
4583: Ndum[ij]++; /* Might be supersed V1 + V1*age */
1.224 ! brouard 4584: } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
1.219 brouard 4585:
4586: ij=0;
4587: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
4588: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
4589: if((Ndum[i]!=0) && (i<=ncovcol)){
4590: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
1.224 ! brouard 4591: Tvaraff[++ij]=i; /*For printing (unclear) */
! 4592: }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){
! 4593: Tvaraff[++ij]=-10; /* Dont'n know how to treat quantitative variables yet */
! 4594: }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){
! 4595: Tvaraff[++ij]=i; /*For printing (unclear) */
! 4596: }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){
! 4597: Tvaraff[++ij]=-20; /* Dont'n know how to treat quantitative variables yet */
1.219 brouard 4598: }
1.224 ! brouard 4599: } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
1.219 brouard 4600: /* ij--; */
1.220 brouard 4601: /* cptcoveff=ij; /\*Number of total covariates*\/ */
1.224 ! brouard 4602: *cptcov=ij; /*Number of total real effective covariates: effective
! 4603: * because they can be excluded from the model and real
! 4604: * if in the model but excluded because missing values*/
1.126 brouard 4605: }
4606:
1.145 brouard 4607:
1.126 brouard 4608: /*********** Health Expectancies ****************/
4609:
1.127 brouard 4610: 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 4611:
4612: {
4613: /* Health expectancies, no variances */
1.164 brouard 4614: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 4615: int nhstepma, nstepma; /* Decreasing with age */
4616: double age, agelim, hf;
4617: double ***p3mat;
4618: double eip;
4619:
4620: pstamp(ficreseij);
4621: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
4622: fprintf(ficreseij,"# Age");
4623: for(i=1; i<=nlstate;i++){
4624: for(j=1; j<=nlstate;j++){
4625: fprintf(ficreseij," e%1d%1d ",i,j);
4626: }
4627: fprintf(ficreseij," e%1d. ",i);
4628: }
4629: fprintf(ficreseij,"\n");
4630:
4631:
4632: if(estepm < stepm){
4633: printf ("Problem %d lower than %d\n",estepm, stepm);
4634: }
4635: else hstepm=estepm;
4636: /* We compute the life expectancy from trapezoids spaced every estepm months
4637: * This is mainly to measure the difference between two models: for example
4638: * if stepm=24 months pijx are given only every 2 years and by summing them
4639: * we are calculating an estimate of the Life Expectancy assuming a linear
4640: * progression in between and thus overestimating or underestimating according
4641: * to the curvature of the survival function. If, for the same date, we
4642: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4643: * to compare the new estimate of Life expectancy with the same linear
4644: * hypothesis. A more precise result, taking into account a more precise
4645: * curvature will be obtained if estepm is as small as stepm. */
4646:
4647: /* For example we decided to compute the life expectancy with the smallest unit */
4648: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4649: nhstepm is the number of hstepm from age to agelim
4650: nstepm is the number of stepm from age to agelin.
4651: Look at hpijx to understand the reason of that which relies in memory size
4652: and note for a fixed period like estepm months */
4653: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4654: survival function given by stepm (the optimization length). Unfortunately it
4655: means that if the survival funtion is printed only each two years of age and if
4656: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4657: results. So we changed our mind and took the option of the best precision.
4658: */
4659: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4660:
4661: agelim=AGESUP;
4662: /* If stepm=6 months */
4663: /* Computed by stepm unit matrices, product of hstepm matrices, stored
4664: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
4665:
4666: /* nhstepm age range expressed in number of stepm */
4667: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4668: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4669: /* if (stepm >= YEARM) hstepm=1;*/
4670: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4671: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4672:
4673: for (age=bage; age<=fage; age ++){
4674: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4675: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4676: /* if (stepm >= YEARM) hstepm=1;*/
4677: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
4678:
4679: /* If stepm=6 months */
4680: /* Computed by stepm unit matrices, product of hstepma matrices, stored
4681: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
4682:
4683: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
4684:
4685: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4686:
4687: printf("%d|",(int)age);fflush(stdout);
4688: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
4689:
4690: /* Computing expectancies */
4691: for(i=1; i<=nlstate;i++)
4692: for(j=1; j<=nlstate;j++)
4693: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
4694: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
4695:
4696: /* 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]);*/
4697:
4698: }
4699:
4700: fprintf(ficreseij,"%3.0f",age );
4701: for(i=1; i<=nlstate;i++){
4702: eip=0;
4703: for(j=1; j<=nlstate;j++){
4704: eip +=eij[i][j][(int)age];
4705: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
4706: }
4707: fprintf(ficreseij,"%9.4f", eip );
4708: }
4709: fprintf(ficreseij,"\n");
4710:
4711: }
4712: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4713: printf("\n");
4714: fprintf(ficlog,"\n");
4715:
4716: }
4717:
1.127 brouard 4718: 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 4719:
4720: {
4721: /* Covariances of health expectancies eij and of total life expectancies according
1.222 brouard 4722: to initial status i, ei. .
1.126 brouard 4723: */
4724: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
4725: int nhstepma, nstepma; /* Decreasing with age */
4726: double age, agelim, hf;
4727: double ***p3matp, ***p3matm, ***varhe;
4728: double **dnewm,**doldm;
4729: double *xp, *xm;
4730: double **gp, **gm;
4731: double ***gradg, ***trgradg;
4732: int theta;
4733:
4734: double eip, vip;
4735:
4736: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
4737: xp=vector(1,npar);
4738: xm=vector(1,npar);
4739: dnewm=matrix(1,nlstate*nlstate,1,npar);
4740: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
4741:
4742: pstamp(ficresstdeij);
4743: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
4744: fprintf(ficresstdeij,"# Age");
4745: for(i=1; i<=nlstate;i++){
4746: for(j=1; j<=nlstate;j++)
4747: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
4748: fprintf(ficresstdeij," e%1d. ",i);
4749: }
4750: fprintf(ficresstdeij,"\n");
4751:
4752: pstamp(ficrescveij);
4753: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
4754: fprintf(ficrescveij,"# Age");
4755: for(i=1; i<=nlstate;i++)
4756: for(j=1; j<=nlstate;j++){
4757: cptj= (j-1)*nlstate+i;
4758: for(i2=1; i2<=nlstate;i2++)
4759: for(j2=1; j2<=nlstate;j2++){
4760: cptj2= (j2-1)*nlstate+i2;
4761: if(cptj2 <= cptj)
4762: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
4763: }
4764: }
4765: fprintf(ficrescveij,"\n");
4766:
4767: if(estepm < stepm){
4768: printf ("Problem %d lower than %d\n",estepm, stepm);
4769: }
4770: else hstepm=estepm;
4771: /* We compute the life expectancy from trapezoids spaced every estepm months
4772: * This is mainly to measure the difference between two models: for example
4773: * if stepm=24 months pijx are given only every 2 years and by summing them
4774: * we are calculating an estimate of the Life Expectancy assuming a linear
4775: * progression in between and thus overestimating or underestimating according
4776: * to the curvature of the survival function. If, for the same date, we
4777: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4778: * to compare the new estimate of Life expectancy with the same linear
4779: * hypothesis. A more precise result, taking into account a more precise
4780: * curvature will be obtained if estepm is as small as stepm. */
4781:
4782: /* For example we decided to compute the life expectancy with the smallest unit */
4783: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4784: nhstepm is the number of hstepm from age to agelim
4785: nstepm is the number of stepm from age to agelin.
4786: Look at hpijx to understand the reason of that which relies in memory size
4787: and note for a fixed period like estepm months */
4788: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4789: survival function given by stepm (the optimization length). Unfortunately it
4790: means that if the survival funtion is printed only each two years of age and if
4791: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4792: results. So we changed our mind and took the option of the best precision.
4793: */
4794: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4795:
4796: /* If stepm=6 months */
4797: /* nhstepm age range expressed in number of stepm */
4798: agelim=AGESUP;
4799: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
4800: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4801: /* if (stepm >= YEARM) hstepm=1;*/
4802: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4803:
4804: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4805: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4806: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
4807: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
4808: gp=matrix(0,nhstepm,1,nlstate*nlstate);
4809: gm=matrix(0,nhstepm,1,nlstate*nlstate);
4810:
4811: for (age=bage; age<=fage; age ++){
4812: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4813: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4814: /* if (stepm >= YEARM) hstepm=1;*/
4815: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218 brouard 4816:
1.126 brouard 4817: /* If stepm=6 months */
4818: /* Computed by stepm unit matrices, product of hstepma matrices, stored
4819: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
4820:
4821: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.218 brouard 4822:
1.126 brouard 4823: /* Computing Variances of health expectancies */
4824: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
4825: decrease memory allocation */
4826: for(theta=1; theta <=npar; theta++){
4827: for(i=1; i<=npar; i++){
1.222 brouard 4828: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4829: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126 brouard 4830: }
4831: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
4832: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
1.218 brouard 4833:
1.126 brouard 4834: for(j=1; j<= nlstate; j++){
1.222 brouard 4835: for(i=1; i<=nlstate; i++){
4836: for(h=0; h<=nhstepm-1; h++){
4837: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
4838: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
4839: }
4840: }
1.126 brouard 4841: }
1.218 brouard 4842:
1.126 brouard 4843: for(ij=1; ij<= nlstate*nlstate; ij++)
1.222 brouard 4844: for(h=0; h<=nhstepm-1; h++){
4845: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
4846: }
1.126 brouard 4847: }/* End theta */
4848:
4849:
4850: for(h=0; h<=nhstepm-1; h++)
4851: for(j=1; j<=nlstate*nlstate;j++)
1.222 brouard 4852: for(theta=1; theta <=npar; theta++)
4853: trgradg[h][j][theta]=gradg[h][theta][j];
1.126 brouard 4854:
1.218 brouard 4855:
1.222 brouard 4856: for(ij=1;ij<=nlstate*nlstate;ij++)
1.126 brouard 4857: for(ji=1;ji<=nlstate*nlstate;ji++)
1.222 brouard 4858: varhe[ij][ji][(int)age] =0.;
1.218 brouard 4859:
1.222 brouard 4860: printf("%d|",(int)age);fflush(stdout);
4861: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
4862: for(h=0;h<=nhstepm-1;h++){
1.126 brouard 4863: for(k=0;k<=nhstepm-1;k++){
1.222 brouard 4864: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
4865: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
4866: for(ij=1;ij<=nlstate*nlstate;ij++)
4867: for(ji=1;ji<=nlstate*nlstate;ji++)
4868: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126 brouard 4869: }
4870: }
1.218 brouard 4871:
1.126 brouard 4872: /* Computing expectancies */
4873: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
4874: for(i=1; i<=nlstate;i++)
4875: for(j=1; j<=nlstate;j++)
1.222 brouard 4876: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
4877: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.218 brouard 4878:
1.222 brouard 4879: /* 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 4880:
1.222 brouard 4881: }
1.218 brouard 4882:
1.126 brouard 4883: fprintf(ficresstdeij,"%3.0f",age );
4884: for(i=1; i<=nlstate;i++){
4885: eip=0.;
4886: vip=0.;
4887: for(j=1; j<=nlstate;j++){
1.222 brouard 4888: eip += eij[i][j][(int)age];
4889: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
4890: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
4891: 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 4892: }
4893: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
4894: }
4895: fprintf(ficresstdeij,"\n");
1.218 brouard 4896:
1.126 brouard 4897: fprintf(ficrescveij,"%3.0f",age );
4898: for(i=1; i<=nlstate;i++)
4899: for(j=1; j<=nlstate;j++){
1.222 brouard 4900: cptj= (j-1)*nlstate+i;
4901: for(i2=1; i2<=nlstate;i2++)
4902: for(j2=1; j2<=nlstate;j2++){
4903: cptj2= (j2-1)*nlstate+i2;
4904: if(cptj2 <= cptj)
4905: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
4906: }
1.126 brouard 4907: }
4908: fprintf(ficrescveij,"\n");
1.218 brouard 4909:
1.126 brouard 4910: }
4911: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
4912: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
4913: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
4914: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
4915: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4916: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4917: printf("\n");
4918: fprintf(ficlog,"\n");
1.218 brouard 4919:
1.126 brouard 4920: free_vector(xm,1,npar);
4921: free_vector(xp,1,npar);
4922: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
4923: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
4924: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
4925: }
1.218 brouard 4926:
1.126 brouard 4927: /************ Variance ******************/
1.209 brouard 4928: 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 4929: {
4930: /* Variance of health expectancies */
4931: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
4932: /* double **newm;*/
4933: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
4934:
4935: /* int movingaverage(); */
4936: double **dnewm,**doldm;
4937: double **dnewmp,**doldmp;
4938: int i, j, nhstepm, hstepm, h, nstepm ;
4939: int k;
4940: double *xp;
4941: double **gp, **gm; /* for var eij */
4942: double ***gradg, ***trgradg; /*for var eij */
4943: double **gradgp, **trgradgp; /* for var p point j */
4944: double *gpp, *gmp; /* for var p point j */
4945: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
4946: double ***p3mat;
4947: double age,agelim, hf;
4948: /* double ***mobaverage; */
4949: int theta;
4950: char digit[4];
4951: char digitp[25];
4952:
4953: char fileresprobmorprev[FILENAMELENGTH];
4954:
4955: if(popbased==1){
4956: if(mobilav!=0)
4957: strcpy(digitp,"-POPULBASED-MOBILAV_");
4958: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
4959: }
4960: else
4961: strcpy(digitp,"-STABLBASED_");
1.126 brouard 4962:
1.218 brouard 4963: /* if (mobilav!=0) { */
4964: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
4965: /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
4966: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
4967: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
4968: /* } */
4969: /* } */
4970:
4971: strcpy(fileresprobmorprev,"PRMORPREV-");
4972: sprintf(digit,"%-d",ij);
4973: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
4974: strcat(fileresprobmorprev,digit); /* Tvar to be done */
4975: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
4976: strcat(fileresprobmorprev,fileresu);
4977: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
4978: printf("Problem with resultfile: %s\n", fileresprobmorprev);
4979: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
4980: }
4981: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4982: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4983: pstamp(ficresprobmorprev);
4984: 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);
4985: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
4986: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4987: fprintf(ficresprobmorprev," p.%-d SE",j);
4988: for(i=1; i<=nlstate;i++)
4989: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
4990: }
4991: fprintf(ficresprobmorprev,"\n");
4992:
4993: fprintf(ficgp,"\n# Routine varevsij");
4994: fprintf(ficgp,"\nunset title \n");
4995: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
4996: 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");
4997: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
4998: /* } */
4999: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5000: pstamp(ficresvij);
5001: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
5002: if(popbased==1)
5003: 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);
5004: else
5005: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
5006: fprintf(ficresvij,"# Age");
5007: for(i=1; i<=nlstate;i++)
5008: for(j=1; j<=nlstate;j++)
5009: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
5010: fprintf(ficresvij,"\n");
5011:
5012: xp=vector(1,npar);
5013: dnewm=matrix(1,nlstate,1,npar);
5014: doldm=matrix(1,nlstate,1,nlstate);
5015: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
5016: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5017:
5018: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
5019: gpp=vector(nlstate+1,nlstate+ndeath);
5020: gmp=vector(nlstate+1,nlstate+ndeath);
5021: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126 brouard 5022:
1.218 brouard 5023: if(estepm < stepm){
5024: printf ("Problem %d lower than %d\n",estepm, stepm);
5025: }
5026: else hstepm=estepm;
5027: /* For example we decided to compute the life expectancy with the smallest unit */
5028: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5029: nhstepm is the number of hstepm from age to agelim
5030: nstepm is the number of stepm from age to agelim.
5031: Look at function hpijx to understand why because of memory size limitations,
5032: we decided (b) to get a life expectancy respecting the most precise curvature of the
5033: survival function given by stepm (the optimization length). Unfortunately it
5034: means that if the survival funtion is printed every two years of age and if
5035: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5036: results. So we changed our mind and took the option of the best precision.
5037: */
5038: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5039: agelim = AGESUP;
5040: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5041: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5042: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5043: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5044: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
5045: gp=matrix(0,nhstepm,1,nlstate);
5046: gm=matrix(0,nhstepm,1,nlstate);
5047:
5048:
5049: for(theta=1; theta <=npar; theta++){
5050: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
5051: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5052: }
5053:
5054: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5055:
5056: if (popbased==1) {
5057: if(mobilav ==0){
5058: for(i=1; i<=nlstate;i++)
5059: prlim[i][i]=probs[(int)age][i][ij];
5060: }else{ /* mobilav */
5061: for(i=1; i<=nlstate;i++)
5062: prlim[i][i]=mobaverage[(int)age][i][ij];
5063: }
5064: }
5065:
5066: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); /* Returns p3mat[i][j][h] for h=1 to nhstepm */
5067: for(j=1; j<= nlstate; j++){
5068: for(h=0; h<=nhstepm; h++){
5069: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
5070: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
5071: }
5072: }
5073: /* Next for computing probability of death (h=1 means
5074: computed over hstepm matrices product = hstepm*stepm months)
5075: as a weighted average of prlim.
5076: */
5077: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5078: for(i=1,gpp[j]=0.; i<= nlstate; i++)
5079: gpp[j] += prlim[i][i]*p3mat[i][j][1];
5080: }
5081: /* end probability of death */
5082:
5083: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
5084: xp[i] = x[i] - (i==theta ?delti[theta]:0);
5085:
5086: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
5087:
5088: if (popbased==1) {
5089: if(mobilav ==0){
5090: for(i=1; i<=nlstate;i++)
5091: prlim[i][i]=probs[(int)age][i][ij];
5092: }else{ /* mobilav */
5093: for(i=1; i<=nlstate;i++)
5094: prlim[i][i]=mobaverage[(int)age][i][ij];
5095: }
5096: }
5097:
5098: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
5099:
5100: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
5101: for(h=0; h<=nhstepm; h++){
5102: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
5103: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
5104: }
5105: }
5106: /* This for computing probability of death (h=1 means
5107: computed over hstepm matrices product = hstepm*stepm months)
5108: as a weighted average of prlim.
5109: */
5110: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5111: for(i=1,gmp[j]=0.; i<= nlstate; i++)
5112: gmp[j] += prlim[i][i]*p3mat[i][j][1];
5113: }
5114: /* end probability of death */
5115:
5116: for(j=1; j<= nlstate; j++) /* vareij */
5117: for(h=0; h<=nhstepm; h++){
5118: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
5119: }
5120:
5121: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
5122: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
5123: }
5124:
5125: } /* End theta */
5126:
5127: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
5128:
5129: for(h=0; h<=nhstepm; h++) /* veij */
5130: for(j=1; j<=nlstate;j++)
5131: for(theta=1; theta <=npar; theta++)
5132: trgradg[h][j][theta]=gradg[h][theta][j];
5133:
5134: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
5135: for(theta=1; theta <=npar; theta++)
5136: trgradgp[j][theta]=gradgp[theta][j];
5137:
5138:
5139: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
5140: for(i=1;i<=nlstate;i++)
5141: for(j=1;j<=nlstate;j++)
5142: vareij[i][j][(int)age] =0.;
5143:
5144: for(h=0;h<=nhstepm;h++){
5145: for(k=0;k<=nhstepm;k++){
5146: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
5147: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
5148: for(i=1;i<=nlstate;i++)
5149: for(j=1;j<=nlstate;j++)
5150: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
5151: }
5152: }
5153:
5154: /* pptj */
5155: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
5156: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
5157: for(j=nlstate+1;j<=nlstate+ndeath;j++)
5158: for(i=nlstate+1;i<=nlstate+ndeath;i++)
5159: varppt[j][i]=doldmp[j][i];
5160: /* end ppptj */
5161: /* x centered again */
5162:
5163: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
5164:
5165: if (popbased==1) {
5166: if(mobilav ==0){
5167: for(i=1; i<=nlstate;i++)
5168: prlim[i][i]=probs[(int)age][i][ij];
5169: }else{ /* mobilav */
5170: for(i=1; i<=nlstate;i++)
5171: prlim[i][i]=mobaverage[(int)age][i][ij];
5172: }
5173: }
5174:
5175: /* This for computing probability of death (h=1 means
5176: computed over hstepm (estepm) matrices product = hstepm*stepm months)
5177: as a weighted average of prlim.
5178: */
5179: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
5180: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5181: for(i=1,gmp[j]=0.;i<= nlstate; i++)
5182: gmp[j] += prlim[i][i]*p3mat[i][j][1];
5183: }
5184: /* end probability of death */
5185:
5186: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
5187: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
5188: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
5189: for(i=1; i<=nlstate;i++){
5190: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
5191: }
5192: }
5193: fprintf(ficresprobmorprev,"\n");
5194:
5195: fprintf(ficresvij,"%.0f ",age );
5196: for(i=1; i<=nlstate;i++)
5197: for(j=1; j<=nlstate;j++){
5198: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
5199: }
5200: fprintf(ficresvij,"\n");
5201: free_matrix(gp,0,nhstepm,1,nlstate);
5202: free_matrix(gm,0,nhstepm,1,nlstate);
5203: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
5204: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
5205: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5206: } /* End age */
5207: free_vector(gpp,nlstate+1,nlstate+ndeath);
5208: free_vector(gmp,nlstate+1,nlstate+ndeath);
5209: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
5210: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
5211: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
5212: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
5213: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
5214: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
5215: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
5216: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
5217: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
5218: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
5219: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
5220: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
5221: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
5222: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
5223: 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);
5224: /* 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 5225: */
1.218 brouard 5226: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
5227: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 5228:
1.218 brouard 5229: free_vector(xp,1,npar);
5230: free_matrix(doldm,1,nlstate,1,nlstate);
5231: free_matrix(dnewm,1,nlstate,1,npar);
5232: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5233: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
5234: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5235: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5236: fclose(ficresprobmorprev);
5237: fflush(ficgp);
5238: fflush(fichtm);
5239: } /* end varevsij */
1.126 brouard 5240:
5241: /************ Variance of prevlim ******************/
1.209 brouard 5242: 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 5243: {
1.205 brouard 5244: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 5245: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 5246:
1.126 brouard 5247: double **dnewm,**doldm;
5248: int i, j, nhstepm, hstepm;
5249: double *xp;
5250: double *gp, *gm;
5251: double **gradg, **trgradg;
1.208 brouard 5252: double **mgm, **mgp;
1.126 brouard 5253: double age,agelim;
5254: int theta;
5255:
5256: pstamp(ficresvpl);
5257: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
5258: fprintf(ficresvpl,"# Age");
5259: for(i=1; i<=nlstate;i++)
5260: fprintf(ficresvpl," %1d-%1d",i,i);
5261: fprintf(ficresvpl,"\n");
5262:
5263: xp=vector(1,npar);
5264: dnewm=matrix(1,nlstate,1,npar);
5265: doldm=matrix(1,nlstate,1,nlstate);
5266:
5267: hstepm=1*YEARM; /* Every year of age */
5268: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
5269: agelim = AGESUP;
5270: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5271: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5272: if (stepm >= YEARM) hstepm=1;
5273: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5274: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 5275: mgp=matrix(1,npar,1,nlstate);
5276: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 5277: gp=vector(1,nlstate);
5278: gm=vector(1,nlstate);
5279:
5280: for(theta=1; theta <=npar; theta++){
5281: for(i=1; i<=npar; i++){ /* Computes gradient */
5282: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5283: }
1.209 brouard 5284: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
5285: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5286: else
5287: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 5288: for(i=1;i<=nlstate;i++){
1.126 brouard 5289: gp[i] = prlim[i][i];
1.208 brouard 5290: mgp[theta][i] = prlim[i][i];
5291: }
1.126 brouard 5292: for(i=1; i<=npar; i++) /* Computes gradient */
5293: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 5294: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
5295: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5296: else
5297: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 5298: for(i=1;i<=nlstate;i++){
1.126 brouard 5299: gm[i] = prlim[i][i];
1.208 brouard 5300: mgm[theta][i] = prlim[i][i];
5301: }
1.126 brouard 5302: for(i=1;i<=nlstate;i++)
5303: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 5304: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 5305: } /* End theta */
5306:
5307: trgradg =matrix(1,nlstate,1,npar);
5308:
5309: for(j=1; j<=nlstate;j++)
5310: for(theta=1; theta <=npar; theta++)
5311: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 5312: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5313: /* printf("\nmgm mgp %d ",(int)age); */
5314: /* for(j=1; j<=nlstate;j++){ */
5315: /* printf(" %d ",j); */
5316: /* for(theta=1; theta <=npar; theta++) */
5317: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
5318: /* printf("\n "); */
5319: /* } */
5320: /* } */
5321: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5322: /* printf("\n gradg %d ",(int)age); */
5323: /* for(j=1; j<=nlstate;j++){ */
5324: /* printf("%d ",j); */
5325: /* for(theta=1; theta <=npar; theta++) */
5326: /* printf("%d %lf ",theta,gradg[theta][j]); */
5327: /* printf("\n "); */
5328: /* } */
5329: /* } */
1.126 brouard 5330:
5331: for(i=1;i<=nlstate;i++)
5332: varpl[i][(int)age] =0.;
1.209 brouard 5333: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.205 brouard 5334: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5335: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
5336: }else{
1.126 brouard 5337: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5338: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 5339: }
1.126 brouard 5340: for(i=1;i<=nlstate;i++)
5341: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
5342:
5343: fprintf(ficresvpl,"%.0f ",age );
5344: for(i=1; i<=nlstate;i++)
5345: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
5346: fprintf(ficresvpl,"\n");
5347: free_vector(gp,1,nlstate);
5348: free_vector(gm,1,nlstate);
1.208 brouard 5349: free_matrix(mgm,1,npar,1,nlstate);
5350: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 5351: free_matrix(gradg,1,npar,1,nlstate);
5352: free_matrix(trgradg,1,nlstate,1,npar);
5353: } /* End age */
5354:
5355: free_vector(xp,1,npar);
5356: free_matrix(doldm,1,nlstate,1,npar);
5357: free_matrix(dnewm,1,nlstate,1,nlstate);
5358:
5359: }
5360:
5361: /************ Variance of one-step probabilities ******************/
5362: 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 5363: {
5364: int i, j=0, k1, l1, tj;
5365: int k2, l2, j1, z1;
5366: int k=0, l;
5367: int first=1, first1, first2;
5368: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
5369: double **dnewm,**doldm;
5370: double *xp;
5371: double *gp, *gm;
5372: double **gradg, **trgradg;
5373: double **mu;
5374: double age, cov[NCOVMAX+1];
5375: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
5376: int theta;
5377: char fileresprob[FILENAMELENGTH];
5378: char fileresprobcov[FILENAMELENGTH];
5379: char fileresprobcor[FILENAMELENGTH];
5380: double ***varpij;
5381:
5382: strcpy(fileresprob,"PROB_");
5383: strcat(fileresprob,fileres);
5384: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
5385: printf("Problem with resultfile: %s\n", fileresprob);
5386: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
5387: }
5388: strcpy(fileresprobcov,"PROBCOV_");
5389: strcat(fileresprobcov,fileresu);
5390: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
5391: printf("Problem with resultfile: %s\n", fileresprobcov);
5392: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
5393: }
5394: strcpy(fileresprobcor,"PROBCOR_");
5395: strcat(fileresprobcor,fileresu);
5396: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
5397: printf("Problem with resultfile: %s\n", fileresprobcor);
5398: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
5399: }
5400: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
5401: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
5402: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
5403: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
5404: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
5405: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
5406: pstamp(ficresprob);
5407: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
5408: fprintf(ficresprob,"# Age");
5409: pstamp(ficresprobcov);
5410: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
5411: fprintf(ficresprobcov,"# Age");
5412: pstamp(ficresprobcor);
5413: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
5414: fprintf(ficresprobcor,"# Age");
1.126 brouard 5415:
5416:
1.222 brouard 5417: for(i=1; i<=nlstate;i++)
5418: for(j=1; j<=(nlstate+ndeath);j++){
5419: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
5420: fprintf(ficresprobcov," p%1d-%1d ",i,j);
5421: fprintf(ficresprobcor," p%1d-%1d ",i,j);
5422: }
5423: /* fprintf(ficresprob,"\n");
5424: fprintf(ficresprobcov,"\n");
5425: fprintf(ficresprobcor,"\n");
5426: */
5427: xp=vector(1,npar);
5428: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
5429: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
5430: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
5431: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
5432: first=1;
5433: fprintf(ficgp,"\n# Routine varprob");
5434: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
5435: fprintf(fichtm,"\n");
5436:
5437: 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);
5438: 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);
5439: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 5440: and drawn. It helps understanding how is the covariance between two incidences.\
5441: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.222 brouard 5442: 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 5443: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
5444: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
5445: standard deviations wide on each axis. <br>\
5446: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
5447: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
5448: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
5449:
1.222 brouard 5450: cov[1]=1;
5451: /* tj=cptcoveff; */
1.224 ! brouard 5452: tj = (int) pow(2,nqveff);
1.222 brouard 5453: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
5454: j1=0;
1.224 ! brouard 5455: for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/
1.222 brouard 5456: if (cptcovn>0) {
5457: fprintf(ficresprob, "\n#********** Variable ");
1.224 ! brouard 5458: for (z1=1; z1<=nqveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5459: fprintf(ficresprob, "**********\n#\n");
5460: fprintf(ficresprobcov, "\n#********** Variable ");
1.224 ! brouard 5461: for (z1=1; z1<=nqveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5462: fprintf(ficresprobcov, "**********\n#\n");
1.220 brouard 5463:
1.222 brouard 5464: fprintf(ficgp, "\n#********** Variable ");
1.224 ! brouard 5465: for (z1=1; z1<=nqveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5466: fprintf(ficgp, "**********\n#\n");
1.220 brouard 5467:
5468:
1.222 brouard 5469: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.224 ! brouard 5470: for (z1=1; z1<=nqveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5471: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 5472:
1.222 brouard 5473: fprintf(ficresprobcor, "\n#********** Variable ");
1.224 ! brouard 5474: for (z1=1; z1<=nqveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5475: fprintf(ficresprobcor, "**********\n#");
5476: if(invalidvarcomb[j1]){
5477: fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
5478: fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
5479: continue;
5480: }
5481: }
5482: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
5483: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
5484: gp=vector(1,(nlstate)*(nlstate+ndeath));
5485: gm=vector(1,(nlstate)*(nlstate+ndeath));
5486: for (age=bage; age<=fage; age ++){
5487: cov[2]=age;
5488: if(nagesqr==1)
5489: cov[3]= age*age;
5490: for (k=1; k<=cptcovn;k++) {
5491: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
5492: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
5493: * 1 1 1 1 1
5494: * 2 2 1 1 1
5495: * 3 1 2 1 1
5496: */
5497: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
5498: }
5499: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5500: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
5501: for (k=1; k<=cptcovprod;k++)
5502: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.220 brouard 5503:
5504:
1.222 brouard 5505: for(theta=1; theta <=npar; theta++){
5506: for(i=1; i<=npar; i++)
5507: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.220 brouard 5508:
1.222 brouard 5509: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1.220 brouard 5510:
1.222 brouard 5511: k=0;
5512: for(i=1; i<= (nlstate); i++){
5513: for(j=1; j<=(nlstate+ndeath);j++){
5514: k=k+1;
5515: gp[k]=pmmij[i][j];
5516: }
5517: }
1.220 brouard 5518:
1.222 brouard 5519: for(i=1; i<=npar; i++)
5520: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.220 brouard 5521:
1.222 brouard 5522: pmij(pmmij,cov,ncovmodel,xp,nlstate);
5523: k=0;
5524: for(i=1; i<=(nlstate); i++){
5525: for(j=1; j<=(nlstate+ndeath);j++){
5526: k=k+1;
5527: gm[k]=pmmij[i][j];
5528: }
5529: }
1.220 brouard 5530:
1.222 brouard 5531: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
5532: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
5533: }
1.126 brouard 5534:
1.222 brouard 5535: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
5536: for(theta=1; theta <=npar; theta++)
5537: trgradg[j][theta]=gradg[theta][j];
1.220 brouard 5538:
1.222 brouard 5539: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
5540: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.220 brouard 5541:
1.222 brouard 5542: pmij(pmmij,cov,ncovmodel,x,nlstate);
1.220 brouard 5543:
1.222 brouard 5544: k=0;
5545: for(i=1; i<=(nlstate); i++){
5546: for(j=1; j<=(nlstate+ndeath);j++){
5547: k=k+1;
5548: mu[k][(int) age]=pmmij[i][j];
5549: }
5550: }
5551: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
5552: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
5553: varpij[i][j][(int)age] = doldm[i][j];
1.220 brouard 5554:
1.222 brouard 5555: /*printf("\n%d ",(int)age);
5556: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
5557: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
5558: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
5559: }*/
1.220 brouard 5560:
1.222 brouard 5561: fprintf(ficresprob,"\n%d ",(int)age);
5562: fprintf(ficresprobcov,"\n%d ",(int)age);
5563: fprintf(ficresprobcor,"\n%d ",(int)age);
1.220 brouard 5564:
1.222 brouard 5565: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
5566: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
5567: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
5568: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
5569: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
5570: }
5571: i=0;
5572: for (k=1; k<=(nlstate);k++){
5573: for (l=1; l<=(nlstate+ndeath);l++){
5574: i++;
5575: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
5576: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
5577: for (j=1; j<=i;j++){
5578: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
5579: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
5580: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
5581: }
5582: }
5583: }/* end of loop for state */
5584: } /* end of loop for age */
5585: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
5586: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
5587: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
5588: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
5589:
5590: /* Confidence intervalle of pij */
5591: /*
5592: fprintf(ficgp,"\nunset parametric;unset label");
5593: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
5594: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
5595: 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);
5596: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
5597: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
5598: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
5599: */
5600:
5601: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
5602: first1=1;first2=2;
5603: for (k2=1; k2<=(nlstate);k2++){
5604: for (l2=1; l2<=(nlstate+ndeath);l2++){
5605: if(l2==k2) continue;
5606: j=(k2-1)*(nlstate+ndeath)+l2;
5607: for (k1=1; k1<=(nlstate);k1++){
5608: for (l1=1; l1<=(nlstate+ndeath);l1++){
5609: if(l1==k1) continue;
5610: i=(k1-1)*(nlstate+ndeath)+l1;
5611: if(i<=j) continue;
5612: for (age=bage; age<=fage; age ++){
5613: if ((int)age %5==0){
5614: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
5615: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
5616: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
5617: mu1=mu[i][(int) age]/stepm*YEARM ;
5618: mu2=mu[j][(int) age]/stepm*YEARM;
5619: c12=cv12/sqrt(v1*v2);
5620: /* Computing eigen value of matrix of covariance */
5621: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
5622: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
5623: if ((lc2 <0) || (lc1 <0) ){
5624: if(first2==1){
5625: first1=0;
5626: 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);
5627: }
5628: 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);
5629: /* lc1=fabs(lc1); */ /* If we want to have them positive */
5630: /* lc2=fabs(lc2); */
5631: }
1.220 brouard 5632:
1.222 brouard 5633: /* Eigen vectors */
5634: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
5635: /*v21=sqrt(1.-v11*v11); *//* error */
5636: v21=(lc1-v1)/cv12*v11;
5637: v12=-v21;
5638: v22=v11;
5639: tnalp=v21/v11;
5640: if(first1==1){
5641: first1=0;
5642: 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);
5643: }
5644: 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);
5645: /*printf(fignu*/
5646: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
5647: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
5648: if(first==1){
5649: first=0;
5650: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
5651: fprintf(ficgp,"\nset parametric;unset label");
5652: 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);
5653: fprintf(ficgp,"\nset ter svg size 640, 480");
5654: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.220 brouard 5655: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
1.201 brouard 5656: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.222 brouard 5657: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
5658: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5659: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5660: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
5661: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5662: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
5663: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
5664: 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", \
5665: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
5666: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
5667: }else{
5668: first=0;
5669: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
5670: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
5671: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
5672: 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", \
5673: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
5674: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
5675: }/* if first */
5676: } /* age mod 5 */
5677: } /* end loop age */
5678: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5679: first=1;
5680: } /*l12 */
5681: } /* k12 */
5682: } /*l1 */
5683: }/* k1 */
5684: } /* loop on combination of covariates j1 */
5685: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
5686: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
5687: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
5688: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
5689: free_vector(xp,1,npar);
5690: fclose(ficresprob);
5691: fclose(ficresprobcov);
5692: fclose(ficresprobcor);
5693: fflush(ficgp);
5694: fflush(fichtmcov);
5695: }
1.126 brouard 5696:
5697:
5698: /******************* Printing html file ***********/
1.201 brouard 5699: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 5700: int lastpass, int stepm, int weightopt, char model[],\
5701: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.217 brouard 5702: int popforecast, int prevfcast, int backcast, int estepm , \
1.213 brouard 5703: double jprev1, double mprev1,double anprev1, double dateprev1, \
5704: double jprev2, double mprev2,double anprev2, double dateprev2){
1.126 brouard 5705: int jj1, k1, i1, cpt;
5706:
5707: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
5708: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
5709: </ul>");
1.214 brouard 5710: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
5711: 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",
5712: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
5713: 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 5714: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
5715: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 5716: fprintf(fichtm,"\
5717: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 5718: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 5719: fprintf(fichtm,"\
1.217 brouard 5720: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
5721: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
5722: fprintf(fichtm,"\
1.126 brouard 5723: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5724: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 5725: fprintf(fichtm,"\
1.217 brouard 5726: - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
5727: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
5728: fprintf(fichtm,"\
1.211 brouard 5729: - (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 5730: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5731: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 5732: if(prevfcast==1){
5733: fprintf(fichtm,"\
5734: - Prevalence projections by age and states: \
1.201 brouard 5735: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 5736: }
1.126 brouard 5737:
1.222 brouard 5738: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
1.126 brouard 5739:
1.224 ! brouard 5740: m=pow(2,nqveff);
1.222 brouard 5741: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 5742:
1.222 brouard 5743: jj1=0;
5744: for(k1=1; k1<=m;k1++){
1.220 brouard 5745:
1.222 brouard 5746: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
5747: jj1++;
5748: if (cptcovn > 0) {
5749: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.224 ! brouard 5750: for (cpt=1; cpt<=nqveff;cpt++){
1.222 brouard 5751: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
5752: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
5753: }
5754: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
5755: if(invalidvarcomb[k1]){
5756: fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
5757: printf("\nCombination (%d) ignored because no cases \n",k1);
5758: continue;
5759: }
5760: }
5761: /* aij, bij */
5762: 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 5763: <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 5764: /* Pij */
5765: 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 5766: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 5767: /* Quasi-incidences */
5768: 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 5769: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211 brouard 5770: incidence (rates) are the limit when h tends to zero of the ratio of the probability <sub>h</sub>P<sub>ij</sub> \
5771: 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 5772: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 5773: /* Survival functions (period) in state j */
5774: for(cpt=1; cpt<=nlstate;cpt++){
5775: 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 5776: <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 5777: }
5778: /* State specific survival functions (period) */
5779: for(cpt=1; cpt<=nlstate;cpt++){
5780: fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
1.220 brouard 5781: Or probability to survive in various states (1 to %d) being in state %d at different ages. \
1.201 brouard 5782: <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 5783: }
5784: /* Period (stable) prevalence in each health state */
5785: for(cpt=1; cpt<=nlstate;cpt++){
5786: 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 5787: <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 5788: }
5789: if(backcast==1){
5790: /* Period (stable) back prevalence in each health state */
5791: for(cpt=1; cpt<=nlstate;cpt++){
5792: 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 5793: <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 5794: }
1.217 brouard 5795: }
1.222 brouard 5796: if(prevfcast==1){
5797: /* Projection of prevalence up to period (stable) prevalence in each health state */
5798: for(cpt=1; cpt<=nlstate;cpt++){
5799: 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 5800: <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 5801: }
5802: }
1.220 brouard 5803:
1.222 brouard 5804: for(cpt=1; cpt<=nlstate;cpt++) {
5805: 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 5806: <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 5807: }
5808: /* } /\* end i1 *\/ */
5809: }/* End k1 */
5810: fprintf(fichtm,"</ul>");
1.126 brouard 5811:
1.222 brouard 5812: fprintf(fichtm,"\
1.126 brouard 5813: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 5814: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 5815: - 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 5816: But because parameters are usually highly correlated (a higher incidence of disability \
5817: and a higher incidence of recovery can give very close observed transition) it might \
5818: be very useful to look not only at linear confidence intervals estimated from the \
5819: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
5820: (parameters) of the logistic regression, it might be more meaningful to visualize the \
5821: covariance matrix of the one-step probabilities. \
5822: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 5823:
1.222 brouard 5824: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
5825: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
5826: fprintf(fichtm,"\
1.126 brouard 5827: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 5828: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 5829:
1.222 brouard 5830: fprintf(fichtm,"\
1.126 brouard 5831: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 5832: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
5833: fprintf(fichtm,"\
1.126 brouard 5834: - 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): \
5835: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5836: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.222 brouard 5837: fprintf(fichtm,"\
1.126 brouard 5838: - (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): \
5839: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5840: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.222 brouard 5841: fprintf(fichtm,"\
1.128 brouard 5842: - 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 5843: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
5844: fprintf(fichtm,"\
1.128 brouard 5845: - 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 5846: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
5847: fprintf(fichtm,"\
1.126 brouard 5848: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.222 brouard 5849: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 5850:
5851: /* if(popforecast==1) fprintf(fichtm,"\n */
5852: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
5853: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
5854: /* <br>",fileres,fileres,fileres,fileres); */
5855: /* else */
5856: /* 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 5857: fflush(fichtm);
5858: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.126 brouard 5859:
1.224 ! brouard 5860: m=pow(2,nqveff);
1.222 brouard 5861: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 5862:
1.222 brouard 5863: jj1=0;
5864: for(k1=1; k1<=m;k1++){
5865: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
5866: jj1++;
1.126 brouard 5867: if (cptcovn > 0) {
5868: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.224 ! brouard 5869: for (cpt=1; cpt<=nqveff;cpt++)
1.222 brouard 5870: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 5871: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 5872:
1.222 brouard 5873: if(invalidvarcomb[k1]){
5874: fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
5875: continue;
5876: }
1.126 brouard 5877: }
5878: for(cpt=1; cpt<=nlstate;cpt++) {
1.218 brouard 5879: fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
5880: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d.svg\"> %s_%d-%d.svg</a>\n <br>\
1.205 brouard 5881: <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 5882: }
5883: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 5884: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
5885: true period expectancies (those weighted with period prevalences are also\
5886: drawn in addition to the population based expectancies computed using\
1.218 brouard 5887: observed and cahotic prevalences: <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\
1.205 brouard 5888: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.222 brouard 5889: /* } /\* end i1 *\/ */
5890: }/* End k1 */
5891: fprintf(fichtm,"</ul>");
5892: fflush(fichtm);
1.126 brouard 5893: }
5894:
5895: /******************* Gnuplot file **************/
1.223 brouard 5896: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
1.126 brouard 5897:
5898: char dirfileres[132],optfileres[132];
1.223 brouard 5899: char gplotcondition[132];
1.164 brouard 5900: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.211 brouard 5901: int lv=0, vlv=0, kl=0;
1.130 brouard 5902: int ng=0;
1.201 brouard 5903: int vpopbased;
1.223 brouard 5904: int ioffset; /* variable offset for columns */
1.219 brouard 5905:
1.126 brouard 5906: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
5907: /* printf("Problem with file %s",optionfilegnuplot); */
5908: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
5909: /* } */
5910:
5911: /*#ifdef windows */
5912: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.223 brouard 5913: /*#endif */
1.224 ! brouard 5914: m=pow(2,nqveff);
1.126 brouard 5915:
1.202 brouard 5916: /* Contribution to likelihood */
5917: /* Plot the probability implied in the likelihood */
1.223 brouard 5918: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
5919: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
5920: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
5921: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 5922: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 5923: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
5924: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
1.223 brouard 5925: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
5926: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
5927: 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));
5928: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
5929: 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));
5930: for (i=1; i<= nlstate ; i ++) {
5931: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
5932: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
5933: 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);
5934: for (j=2; j<= nlstate+ndeath ; j ++) {
5935: 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);
5936: }
5937: fprintf(ficgp,";\nset out; unset ylabel;\n");
5938: }
5939: /* 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 */
5940: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
5941: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
5942: fprintf(ficgp,"\nset out;unset log\n");
5943: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
1.202 brouard 5944:
1.126 brouard 5945: strcpy(dirfileres,optionfilefiname);
5946: strcpy(optfileres,"vpl");
1.223 brouard 5947: /* 1eme*/
1.211 brouard 5948: for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
1.220 brouard 5949: for (k1=1; k1<= m ; k1 ++) { /* For each valid combination of covariate */
1.211 brouard 5950: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
5951: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
1.224 ! brouard 5952: for (k=1; k<=nqveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
! 5953: lv= decodtabm(k1,k,nqveff); /* Should be the value of the covariate corresponding to k1 combination */
1.223 brouard 5954: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5955: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5956: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5957: vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
5958: /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
5959: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 5960: }
5961: fprintf(ficgp,"\n#\n");
1.223 brouard 5962: if(invalidvarcomb[k1]){
5963: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
5964: continue;
5965: }
1.211 brouard 5966:
1.223 brouard 5967: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
5968: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
5969: fprintf(ficgp,"set xlabel \"Age\" \n\
1.219 brouard 5970: set ylabel \"Probability\" \n \
5971: set ter svg size 640, 480\n \
1.201 brouard 5972: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.219 brouard 5973:
1.223 brouard 5974: for (i=1; i<= nlstate ; i ++) {
5975: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5976: else fprintf(ficgp," %%*lf (%%*lf)");
5977: }
5978: 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);
5979: for (i=1; i<= nlstate ; i ++) {
5980: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5981: else fprintf(ficgp," %%*lf (%%*lf)");
5982: }
5983: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
5984: for (i=1; i<= nlstate ; i ++) {
5985: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5986: else fprintf(ficgp," %%*lf (%%*lf)");
5987: }
5988: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
5989: if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
5990: /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
5991: fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
1.224 ! brouard 5992: if(nqveff ==0){
1.223 brouard 5993: fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ", 2+(cpt-1), cpt );
5994: }else{
5995: kl=0;
1.224 ! brouard 5996: for (k=1; k<=nqveff; k++){ /* For each combination of covariate */
! 5997: lv= decodtabm(k1,k,nqveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
1.223 brouard 5998: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5999: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6000: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6001: vlv= nbcode[Tvaraff[k]][lv];
6002: kl++;
6003: /* 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 *\/ */
6004: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
6005: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
6006: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
1.224 ! brouard 6007: if(k==nqveff){
1.223 brouard 6008: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
6009: 6+(cpt-1), cpt );
6010: }else{
6011: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
6012: kl++;
6013: }
6014: } /* end covariate */
6015: } /* end if no covariate */
6016: } /* end if backcast */
6017: fprintf(ficgp,"\nset out \n");
1.201 brouard 6018: } /* k1 */
6019: } /* cpt */
1.126 brouard 6020: /*2 eme*/
6021: for (k1=1; k1<= m ; k1 ++) {
1.220 brouard 6022:
1.223 brouard 6023: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
1.224 ! brouard 6024: for (k=1; k<=nqveff; k++){ /* For each covariate and each value */
! 6025: lv= decodtabm(k1,k,nqveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 6026: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6027: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6028: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6029: vlv= nbcode[Tvaraff[k]][lv];
6030: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6031: }
6032: fprintf(ficgp,"\n#\n");
6033: if(invalidvarcomb[k1]){
6034: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6035: continue;
6036: }
1.219 brouard 6037:
1.223 brouard 6038: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
6039: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6040: if(vpopbased==0)
6041: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
6042: else
6043: fprintf(ficgp,"\nreplot ");
6044: for (i=1; i<= nlstate+1 ; i ++) {
6045: k=2*i;
6046: 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);
6047: for (j=1; j<= nlstate+1 ; j ++) {
6048: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6049: else fprintf(ficgp," %%*lf (%%*lf)");
6050: }
6051: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
6052: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
6053: 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);
6054: for (j=1; j<= nlstate+1 ; j ++) {
6055: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6056: else fprintf(ficgp," %%*lf (%%*lf)");
6057: }
6058: fprintf(ficgp,"\" t\"\" w l lt 0,");
6059: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
6060: for (j=1; j<= nlstate+1 ; j ++) {
6061: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6062: else fprintf(ficgp," %%*lf (%%*lf)");
6063: }
6064: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
6065: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
6066: } /* state */
6067: } /* vpopbased */
6068: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
1.201 brouard 6069: } /* k1 */
1.219 brouard 6070:
6071:
1.126 brouard 6072: /*3eme*/
6073: for (k1=1; k1<= m ; k1 ++) {
1.220 brouard 6074:
1.126 brouard 6075: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.211 brouard 6076: fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt);
1.224 ! brouard 6077: for (k=1; k<=nqveff; k++){ /* For each covariate and each value */
! 6078: lv= decodtabm(k1,k,nqveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 6079: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6080: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6081: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6082: vlv= nbcode[Tvaraff[k]][lv];
6083: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6084: }
6085: fprintf(ficgp,"\n#\n");
1.223 brouard 6086: if(invalidvarcomb[k1]){
6087: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6088: continue;
6089: }
1.219 brouard 6090:
1.126 brouard 6091: /* k=2+nlstate*(2*cpt-2); */
6092: k=2+(nlstate+1)*(cpt-1);
1.201 brouard 6093: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
1.199 brouard 6094: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 6095: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.126 brouard 6096: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
1.223 brouard 6097: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
6098: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
6099: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
6100: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
6101: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
1.219 brouard 6102:
1.126 brouard 6103: */
6104: for (i=1; i< nlstate ; i ++) {
1.223 brouard 6105: 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);
6106: /* fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
1.219 brouard 6107:
1.126 brouard 6108: }
1.201 brouard 6109: 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 6110: }
6111: }
6112:
1.223 brouard 6113: /* 4eme */
1.201 brouard 6114: /* Survival functions (period) from state i in state j by initial state i */
6115: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
1.220 brouard 6116:
1.201 brouard 6117: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.211 brouard 6118: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
1.224 ! brouard 6119: for (k=1; k<=nqveff; k++){ /* For each covariate and each value */
! 6120: lv= decodtabm(k1,k,nqveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 6121: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6122: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6123: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6124: vlv= nbcode[Tvaraff[k]][lv];
6125: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6126: }
6127: fprintf(ficgp,"\n#\n");
1.223 brouard 6128: if(invalidvarcomb[k1]){
6129: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6130: continue;
6131: }
1.220 brouard 6132:
1.201 brouard 6133: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
6134: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
1.220 brouard 6135: set ter svg size 640, 480\n \
6136: unset log y\n \
1.201 brouard 6137: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6138: k=3;
1.201 brouard 6139: for (i=1; i<= nlstate ; i ++){
1.223 brouard 6140: if(i==1){
6141: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6142: }else{
6143: fprintf(ficgp,", '' ");
6144: }
6145: l=(nlstate+ndeath)*(i-1)+1;
6146: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
6147: for (j=2; j<= nlstate+ndeath ; j ++)
6148: fprintf(ficgp,"+$%d",k+l+j-1);
6149: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
1.201 brouard 6150: } /* nlstate */
6151: fprintf(ficgp,"\nset out\n");
6152: } /* end cpt state*/
6153: } /* end covariate */
1.220 brouard 6154:
6155: /* 5eme */
1.201 brouard 6156: /* Survival functions (period) from state i in state j by final state j */
1.202 brouard 6157: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.201 brouard 6158: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
1.223 brouard 6159:
1.201 brouard 6160: 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);
1.224 ! brouard 6161: for (k=1; k<=nqveff; k++){ /* For each covariate and each value */
! 6162: lv= decodtabm(k1,k,nqveff); /* Should be the covariate number corresponding to k1 combination */
1.220 brouard 6163: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6164: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6165: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6166: vlv= nbcode[Tvaraff[k]][lv];
6167: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6168: }
6169: fprintf(ficgp,"\n#\n");
1.223 brouard 6170: if(invalidvarcomb[k1]){
6171: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6172: continue;
6173: }
1.220 brouard 6174:
1.201 brouard 6175: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
6176: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
1.220 brouard 6177: set ter svg size 640, 480\n \
6178: unset log y\n \
1.201 brouard 6179: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6180: k=3;
1.201 brouard 6181: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
1.220 brouard 6182: if(j==1)
6183: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6184: else
6185: fprintf(ficgp,", '' ");
6186: l=(nlstate+ndeath)*(cpt-1) +j;
6187: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
6188: /* for (i=2; i<= nlstate+ndeath ; i ++) */
6189: /* fprintf(ficgp,"+$%d",k+l+i-1); */
6190: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
1.201 brouard 6191: } /* nlstate */
6192: fprintf(ficgp,", '' ");
6193: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
6194: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
1.220 brouard 6195: l=(nlstate+ndeath)*(cpt-1) +j;
6196: if(j < nlstate)
6197: fprintf(ficgp,"$%d +",k+l);
6198: else
6199: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
1.201 brouard 6200: }
6201: fprintf(ficgp,"\nset out\n");
6202: } /* end cpt state*/
6203: } /* end covariate */
1.220 brouard 6204:
6205: /* 6eme */
1.202 brouard 6206: /* CV preval stable (period) for each covariate */
1.211 brouard 6207: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.153 brouard 6208: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.223 brouard 6209:
1.211 brouard 6210: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
1.224 ! brouard 6211: for (k=1; k<=nqveff; k++){ /* For each covariate and each value */
! 6212: lv= decodtabm(k1,k,nqveff); /* Should be the covariate number corresponding to k1 combination */
1.220 brouard 6213: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6214: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6215: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6216: vlv= nbcode[Tvaraff[k]][lv];
6217: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6218: }
6219: fprintf(ficgp,"\n#\n");
1.223 brouard 6220: if(invalidvarcomb[k1]){
6221: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6222: continue;
6223: }
6224:
1.201 brouard 6225: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 6226: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.223 brouard 6227: set ter svg size 640, 480\n \
6228: unset log y\n \
1.153 brouard 6229: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6230: k=3; /* Offset */
1.153 brouard 6231: for (i=1; i<= nlstate ; i ++){
1.220 brouard 6232: if(i==1)
6233: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6234: else
6235: fprintf(ficgp,", '' ");
6236: l=(nlstate+ndeath)*(i-1)+1;
6237: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
6238: for (j=2; j<= nlstate ; j ++)
6239: fprintf(ficgp,"+$%d",k+l+j-1);
6240: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153 brouard 6241: } /* nlstate */
1.201 brouard 6242: fprintf(ficgp,"\nset out\n");
1.153 brouard 6243: } /* end cpt state*/
6244: } /* end covariate */
1.223 brouard 6245:
6246:
1.220 brouard 6247: /* 7eme */
1.218 brouard 6248: if(backcast == 1){
1.217 brouard 6249: /* CV back preval stable (period) for each covariate */
1.218 brouard 6250: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
6251: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.220 brouard 6252: fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
1.224 ! brouard 6253: for (k=1; k<=nqveff; k++){ /* For each covariate and each value */
! 6254: lv= decodtabm(k1,k,nqveff); /* Should be the covariate number corresponding to k1 combination */
1.220 brouard 6255: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6256: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
1.223 brouard 6257: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.220 brouard 6258: vlv= nbcode[Tvaraff[k]][lv];
6259: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6260: }
6261: fprintf(ficgp,"\n#\n");
6262: if(invalidvarcomb[k1]){
1.223 brouard 6263: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6264: continue;
1.220 brouard 6265: }
6266:
6267: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
6268: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
6269: set ter svg size 640, 480\n \
6270: unset log y\n \
1.218 brouard 6271: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.220 brouard 6272: k=3; /* Offset */
6273: for (i=1; i<= nlstate ; i ++){
6274: if(i==1)
6275: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
6276: else
6277: fprintf(ficgp,", '' ");
6278: /* l=(nlstate+ndeath)*(i-1)+1; */
6279: l=(nlstate+ndeath)*(cpt-1)+1;
6280: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
6281: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
6282: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
6283: /* for (j=2; j<= nlstate ; j ++) */
6284: /* fprintf(ficgp,"+$%d",k+l+j-1); */
6285: /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
6286: fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
6287: } /* nlstate */
6288: fprintf(ficgp,"\nset out\n");
1.218 brouard 6289: } /* end cpt state*/
6290: } /* end covariate */
6291: } /* End if backcast */
6292:
1.223 brouard 6293: /* 8eme */
1.218 brouard 6294: if(prevfcast==1){
6295: /* Projection from cross-sectional to stable (period) for each covariate */
6296:
6297: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.211 brouard 6298: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.219 brouard 6299: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
1.224 ! brouard 6300: for (k=1; k<=nqveff; k++){ /* For each correspondig covariate value */
! 6301: lv= decodtabm(k1,k,nqveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
1.219 brouard 6302: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6303: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6304: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6305: vlv= nbcode[Tvaraff[k]][lv];
1.220 brouard 6306: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.219 brouard 6307: }
6308: fprintf(ficgp,"\n#\n");
1.220 brouard 6309: if(invalidvarcomb[k1]){
1.223 brouard 6310: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6311: continue;
1.220 brouard 6312: }
1.219 brouard 6313:
6314: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
6315: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
6316: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
1.223 brouard 6317: set ter svg size 640, 480\n \
6318: unset log y\n \
1.219 brouard 6319: plot [%.f:%.f] ", ageminpar, agemaxpar);
6320: for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
6321: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6322: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6323: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6324: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6325: if(i==1){
6326: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
6327: }else{
6328: fprintf(ficgp,",\\\n '' ");
6329: }
1.224 ! brouard 6330: if(nqveff ==0){ /* No covariate */
1.219 brouard 6331: ioffset=2; /* Age is in 2 */
6332: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
6333: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
6334: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
6335: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
6336: fprintf(ficgp," u %d:(", ioffset);
6337: if(i==nlstate+1)
6338: fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ", \
6339: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
6340: else
6341: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
6342: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
6343: }else{ /* more than 2 covariates */
1.224 ! brouard 6344: if(nqveff ==1){
1.219 brouard 6345: ioffset=4; /* Age is in 4 */
6346: }else{
6347: ioffset=6; /* Age is in 6 */
1.223 brouard 6348: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6349: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
1.219 brouard 6350: }
1.220 brouard 6351: fprintf(ficgp," u %d:(",ioffset);
1.219 brouard 6352: kl=0;
1.220 brouard 6353: strcpy(gplotcondition,"(");
1.224 ! brouard 6354: for (k=1; k<=nqveff; k++){ /* For each covariate writing the chain of conditions */
! 6355: lv= decodtabm(k1,k,nqveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
1.219 brouard 6356: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6357: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6358: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.220 brouard 6359: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
6360: kl++;
6361: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
1.219 brouard 6362: kl++;
1.224 ! brouard 6363: if(k <nqveff && nqveff>1)
1.220 brouard 6364: sprintf(gplotcondition+strlen(gplotcondition)," && ");
6365: }
6366: strcpy(gplotcondition+strlen(gplotcondition),")");
6367: /* 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 *\/ */
6368: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
6369: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
6370: /* '' 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*/
6371: if(i==nlstate+1){
6372: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
6373: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
6374: }else{
1.223 brouard 6375: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
6376: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
1.220 brouard 6377: }
1.219 brouard 6378: } /* end if covariate */
6379: } /* nlstate */
6380: fprintf(ficgp,"\nset out\n");
1.223 brouard 6381: } /* end cpt state*/
6382: } /* end covariate */
6383: } /* End if prevfcast */
1.219 brouard 6384:
1.211 brouard 6385:
1.223 brouard 6386: /* proba elementaires */
6387: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 6388: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 6389: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 6390: for(k=1; k <=(nlstate+ndeath); k++){
6391: if (k != i) {
1.223 brouard 6392: fprintf(ficgp,"# current state %d\n",k);
6393: for(j=1; j <=ncovmodel; j++){
6394: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
6395: jk++;
6396: }
6397: fprintf(ficgp,"\n");
1.126 brouard 6398: }
6399: }
1.223 brouard 6400: }
1.187 brouard 6401: fprintf(ficgp,"##############\n#\n");
1.223 brouard 6402:
1.145 brouard 6403: /*goto avoid;*/
1.200 brouard 6404: fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
1.187 brouard 6405: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
6406: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
6407: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
6408: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
6409: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6410: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
6411: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6412: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
6413: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
6414: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6415: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
6416: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
6417: fprintf(ficgp,"#\n");
1.223 brouard 6418: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
6419: fprintf(ficgp,"# ng=%d\n",ng);
1.224 ! brouard 6420: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",nqveff,m);
1.223 brouard 6421: for(jk=1; jk <=m; jk++) {
6422: fprintf(ficgp,"# jk=%d\n",jk);
6423: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
6424: fprintf(ficgp,"\nset ter svg size 640, 480 ");
6425: if (ng==1){
6426: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
6427: fprintf(ficgp,"\nunset log y");
6428: }else if (ng==2){
6429: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
6430: fprintf(ficgp,"\nset log y");
6431: }else if (ng==3){
6432: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
6433: fprintf(ficgp,"\nset log y");
6434: }else
6435: fprintf(ficgp,"\nunset title ");
6436: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
6437: i=1;
6438: for(k2=1; k2<=nlstate; k2++) {
6439: k3=i;
6440: for(k=1; k<=(nlstate+ndeath); k++) {
6441: if (k != k2){
6442: switch( ng) {
6443: case 1:
6444: if(nagesqr==0)
6445: fprintf(ficgp," p%d+p%d*x",i,i+1);
6446: else /* nagesqr =1 */
6447: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
6448: break;
6449: case 2: /* ng=2 */
6450: if(nagesqr==0)
6451: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
6452: else /* nagesqr =1 */
6453: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
6454: break;
6455: case 3:
6456: if(nagesqr==0)
6457: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
6458: else /* nagesqr =1 */
6459: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
6460: break;
6461: }
6462: ij=1;/* To be checked else nbcode[0][0] wrong */
6463: for(j=3; j <=ncovmodel-nagesqr; j++) {
6464: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
6465: if(ij <=cptcovage) { /* Bug valgrind */
6466: if((j-2)==Tage[ij]) { /* Bug valgrind */
6467: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
6468: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
6469: ij++;
6470: }
6471: }
6472: else
6473: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
6474: }
6475: }else{
6476: i=i-ncovmodel;
6477: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
6478: fprintf(ficgp," (1.");
6479: }
1.217 brouard 6480:
1.223 brouard 6481: if(ng != 1){
6482: fprintf(ficgp,")/(1");
1.126 brouard 6483:
1.223 brouard 6484: for(k1=1; k1 <=nlstate; k1++){
6485: if(nagesqr==0)
6486: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
6487: else /* nagesqr =1 */
6488: fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
1.217 brouard 6489:
1.223 brouard 6490: ij=1;
6491: for(j=3; j <=ncovmodel-nagesqr; j++){
6492: if(ij <=cptcovage) { /* Bug valgrind */
6493: if((j-2)==Tage[ij]) { /* Bug valgrind */
6494: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
6495: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
6496: ij++;
6497: }
6498: }
6499: else
6500: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
6501: }
6502: fprintf(ficgp,")");
6503: }
6504: fprintf(ficgp,")");
6505: if(ng ==2)
6506: fprintf(ficgp," t \"p%d%d\" ", k2,k);
6507: else /* ng= 3 */
6508: fprintf(ficgp," t \"i%d%d\" ", k2,k);
6509: }else{ /* end ng <> 1 */
6510: if( k !=k2) /* logit p11 is hard to draw */
6511: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
6512: }
6513: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
6514: fprintf(ficgp,",");
6515: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
6516: fprintf(ficgp,",");
6517: i=i+ncovmodel;
6518: } /* end k */
6519: } /* end k2 */
6520: fprintf(ficgp,"\n set out\n");
6521: } /* end jk */
6522: } /* end ng */
6523: /* avoid: */
6524: fflush(ficgp);
1.126 brouard 6525: } /* end gnuplot */
6526:
6527:
6528: /*************** Moving average **************/
1.219 brouard 6529: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.222 brouard 6530: int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
1.218 brouard 6531:
1.222 brouard 6532: int i, cpt, cptcod;
6533: int modcovmax =1;
6534: int mobilavrange, mob;
6535: int iage=0;
6536:
6537: double sum=0.;
6538: double age;
6539: double *sumnewp, *sumnewm;
6540: double *agemingood, *agemaxgood; /* Currently identical for all covariates */
6541:
6542:
1.224 ! brouard 6543: /* modcovmax=2*nqveff;/\* Max number of modalities. We suppose */
1.222 brouard 6544: /* a covariate has 2 modalities, should be equal to ncovcombmax *\/ */
6545:
6546: sumnewp = vector(1,ncovcombmax);
6547: sumnewm = vector(1,ncovcombmax);
6548: agemingood = vector(1,ncovcombmax);
6549: agemaxgood = vector(1,ncovcombmax);
6550:
6551: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
6552: sumnewm[cptcod]=0.;
6553: sumnewp[cptcod]=0.;
6554: agemingood[cptcod]=0;
6555: agemaxgood[cptcod]=0;
6556: }
6557: if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
6558:
6559: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
6560: if(mobilav==1) mobilavrange=5; /* default */
6561: else mobilavrange=mobilav;
6562: for (age=bage; age<=fage; age++)
6563: for (i=1; i<=nlstate;i++)
6564: for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
6565: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
6566: /* We keep the original values on the extreme ages bage, fage and for
6567: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
6568: we use a 5 terms etc. until the borders are no more concerned.
6569: */
6570: for (mob=3;mob <=mobilavrange;mob=mob+2){
6571: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
6572: for (i=1; i<=nlstate;i++){
6573: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
6574: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
6575: for (cpt=1;cpt<=(mob-1)/2;cpt++){
6576: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
6577: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
6578: }
6579: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
6580: }
6581: }
6582: }/* end age */
6583: }/* end mob */
6584: }else
6585: return -1;
6586: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
6587: /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
6588: if(invalidvarcomb[cptcod]){
6589: printf("\nCombination (%d) ignored because no cases \n",cptcod);
6590: continue;
6591: }
1.219 brouard 6592:
1.222 brouard 6593: agemingood[cptcod]=fage-(mob-1)/2;
6594: for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
6595: sumnewm[cptcod]=0.;
6596: for (i=1; i<=nlstate;i++){
6597: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6598: }
6599: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
6600: agemingood[cptcod]=age;
6601: }else{ /* bad */
6602: for (i=1; i<=nlstate;i++){
6603: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6604: } /* i */
6605: } /* end bad */
6606: }/* age */
6607: sum=0.;
6608: for (i=1; i<=nlstate;i++){
6609: sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6610: }
6611: if(fabs(sum - 1.) > 1.e-3) { /* bad */
6612: 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);
6613: /* for (i=1; i<=nlstate;i++){ */
6614: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
6615: /* } /\* i *\/ */
6616: } /* end bad */
6617: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
6618: /* From youngest, finding the oldest wrong */
6619: agemaxgood[cptcod]=bage+(mob-1)/2;
6620: for (age=bage+(mob-1)/2; age<=fage; age++){
6621: sumnewm[cptcod]=0.;
6622: for (i=1; i<=nlstate;i++){
6623: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6624: }
6625: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
6626: agemaxgood[cptcod]=age;
6627: }else{ /* bad */
6628: for (i=1; i<=nlstate;i++){
6629: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6630: } /* i */
6631: } /* end bad */
6632: }/* age */
6633: sum=0.;
6634: for (i=1; i<=nlstate;i++){
6635: sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6636: }
6637: if(fabs(sum - 1.) > 1.e-3) { /* bad */
6638: 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);
6639: /* for (i=1; i<=nlstate;i++){ */
6640: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
6641: /* } /\* i *\/ */
6642: } /* end bad */
6643:
6644: for (age=bage; age<=fage; age++){
6645: printf("%d %d ", cptcod, (int)age);
6646: sumnewp[cptcod]=0.;
6647: sumnewm[cptcod]=0.;
6648: for (i=1; i<=nlstate;i++){
6649: sumnewp[cptcod]+=probs[(int)age][i][cptcod];
6650: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6651: /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
6652: }
6653: /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
6654: }
6655: /* printf("\n"); */
6656: /* } */
6657: /* brutal averaging */
6658: for (i=1; i<=nlstate;i++){
6659: for (age=1; age<=bage; age++){
6660: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6661: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
6662: }
6663: for (age=fage; age<=AGESUP; age++){
6664: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6665: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
6666: }
6667: } /* end i status */
6668: for (i=nlstate+1; i<=nlstate+ndeath;i++){
6669: for (age=1; age<=AGESUP; age++){
6670: /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
6671: mobaverage[(int)age][i][cptcod]=0.;
6672: }
6673: }
6674: }/* end cptcod */
6675: free_vector(sumnewm,1, ncovcombmax);
6676: free_vector(sumnewp,1, ncovcombmax);
6677: free_vector(agemaxgood,1, ncovcombmax);
6678: free_vector(agemingood,1, ncovcombmax);
6679: return 0;
6680: }/* End movingaverage */
1.218 brouard 6681:
1.126 brouard 6682:
6683: /************** Forecasting ******************/
1.224 ! brouard 6684: 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 nqveff){
1.126 brouard 6685: /* proj1, year, month, day of starting projection
6686: agemin, agemax range of age
6687: dateprev1 dateprev2 range of dates during which prevalence is computed
6688: anproj2 year of en of projection (same day and month as proj1).
6689: */
1.164 brouard 6690: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 6691: double agec; /* generic age */
6692: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
6693: double *popeffectif,*popcount;
6694: double ***p3mat;
1.218 brouard 6695: /* double ***mobaverage; */
1.126 brouard 6696: char fileresf[FILENAMELENGTH];
6697:
6698: agelim=AGESUP;
1.211 brouard 6699: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
6700: in each health status at the date of interview (if between dateprev1 and dateprev2).
6701: We still use firstpass and lastpass as another selection.
6702: */
1.214 brouard 6703: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
6704: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 6705:
1.201 brouard 6706: strcpy(fileresf,"F_");
6707: strcat(fileresf,fileresu);
1.126 brouard 6708: if((ficresf=fopen(fileresf,"w"))==NULL) {
6709: printf("Problem with forecast resultfile: %s\n", fileresf);
6710: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
6711: }
1.215 brouard 6712: printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
6713: fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 6714:
1.224 ! brouard 6715: if (nqveff==0) ncodemax[nqveff]=1;
1.126 brouard 6716:
6717:
6718: stepsize=(int) (stepm+YEARM-1)/YEARM;
6719: if (stepm<=12) stepsize=1;
6720: if(estepm < stepm){
6721: printf ("Problem %d lower than %d\n",estepm, stepm);
6722: }
6723: else hstepm=estepm;
6724:
6725: hstepm=hstepm/stepm;
6726: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
6727: fractional in yp1 */
6728: anprojmean=yp;
6729: yp2=modf((yp1*12),&yp);
6730: mprojmean=yp;
6731: yp1=modf((yp2*30.5),&yp);
6732: jprojmean=yp;
6733: if(jprojmean==0) jprojmean=1;
6734: if(mprojmean==0) jprojmean=1;
6735:
1.224 ! brouard 6736: i1=nqveff;
1.126 brouard 6737: if (cptcovn < 1){i1=1;}
6738:
6739: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
6740:
6741: fprintf(ficresf,"#****** Routine prevforecast **\n");
6742:
6743: /* if (h==(int)(YEARM*yearp)){ */
6744: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
1.224 ! brouard 6745: for(cptcod=1;cptcod<=ncodemax[nqveff];cptcod++){
1.126 brouard 6746: k=k+1;
1.211 brouard 6747: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
1.224 ! brouard 6748: for(j=1;j<=nqveff;j++) {
1.219 brouard 6749: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 6750: }
1.211 brouard 6751: fprintf(ficresf," yearproj age");
1.126 brouard 6752: for(j=1; j<=nlstate+ndeath;j++){
1.219 brouard 6753: for(i=1; i<=nlstate;i++)
1.126 brouard 6754: fprintf(ficresf," p%d%d",i,j);
1.219 brouard 6755: fprintf(ficresf," wp.%d",j);
1.126 brouard 6756: }
1.217 brouard 6757: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.219 brouard 6758: fprintf(ficresf,"\n");
6759: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
6760: for (agec=fage; agec>=(ageminpar-1); agec--){
6761: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
6762: nhstepm = nhstepm/hstepm;
6763: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6764: oldm=oldms;savm=savms;
6765: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
6766:
6767: for (h=0; h<=nhstepm; h++){
6768: if (h*hstepm/YEARM*stepm ==yearp) {
1.126 brouard 6769: fprintf(ficresf,"\n");
1.224 ! brouard 6770: for(j=1;j<=nqveff;j++)
1.198 brouard 6771: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.219 brouard 6772: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
6773: }
6774: for(j=1; j<=nlstate+ndeath;j++) {
6775: ppij=0.;
6776: for(i=1; i<=nlstate;i++) {
6777: if (mobilav==1)
6778: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
6779: else {
6780: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
6781: }
6782: if (h*hstepm/YEARM*stepm== yearp) {
6783: fprintf(ficresf," %.3f", p3mat[i][j][h]);
6784: }
6785: } /* end i */
6786: if (h*hstepm/YEARM*stepm==yearp) {
6787: fprintf(ficresf," %.3f", ppij);
6788: }
6789: }/* end j */
6790: } /* end h */
6791: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6792: } /* end agec */
1.126 brouard 6793: } /* end yearp */
6794: } /* end cptcod */
6795: } /* end cptcov */
1.219 brouard 6796:
1.126 brouard 6797: fclose(ficresf);
1.215 brouard 6798: printf("End of Computing forecasting \n");
6799: fprintf(ficlog,"End of Computing forecasting\n");
6800:
1.126 brouard 6801: }
6802:
1.218 brouard 6803: /* /\************** Back Forecasting ******************\/ */
1.224 ! brouard 6804: /* 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 nqveff){ */
1.218 brouard 6805: /* /\* back1, year, month, day of starting backection */
6806: /* agemin, agemax range of age */
6807: /* dateprev1 dateprev2 range of dates during which prevalence is computed */
6808: /* anback2 year of en of backection (same day and month as back1). */
6809: /* *\/ */
6810: /* int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */
6811: /* double agec; /\* generic age *\/ */
6812: /* double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */
6813: /* double *popeffectif,*popcount; */
6814: /* double ***p3mat; */
6815: /* /\* double ***mobaverage; *\/ */
6816: /* char fileresfb[FILENAMELENGTH]; */
6817:
6818: /* agelim=AGESUP; */
6819: /* /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */
6820: /* in each health status at the date of interview (if between dateprev1 and dateprev2). */
6821: /* We still use firstpass and lastpass as another selection. */
6822: /* *\/ */
6823: /* /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */
6824: /* /\* firstpass, lastpass, stepm, weightopt, model); *\/ */
6825: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
6826:
6827: /* strcpy(fileresfb,"FB_"); */
6828: /* strcat(fileresfb,fileresu); */
6829: /* if((ficresfb=fopen(fileresfb,"w"))==NULL) { */
6830: /* printf("Problem with back forecast resultfile: %s\n", fileresfb); */
6831: /* fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */
6832: /* } */
6833: /* printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
6834: /* fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
6835:
1.224 ! brouard 6836: /* if (nqveff==0) ncodemax[nqveff]=1; */
1.218 brouard 6837:
6838: /* /\* if (mobilav!=0) { *\/ */
6839: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
6840: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
6841: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
6842: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
6843: /* /\* } *\/ */
6844: /* /\* } *\/ */
6845:
6846: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
6847: /* if (stepm<=12) stepsize=1; */
6848: /* if(estepm < stepm){ */
6849: /* printf ("Problem %d lower than %d\n",estepm, stepm); */
6850: /* } */
6851: /* else hstepm=estepm; */
6852:
6853: /* hstepm=hstepm/stepm; */
6854: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
6855: /* fractional in yp1 *\/ */
6856: /* anprojmean=yp; */
6857: /* yp2=modf((yp1*12),&yp); */
6858: /* mprojmean=yp; */
6859: /* yp1=modf((yp2*30.5),&yp); */
6860: /* jprojmean=yp; */
6861: /* if(jprojmean==0) jprojmean=1; */
6862: /* if(mprojmean==0) jprojmean=1; */
6863:
1.224 ! brouard 6864: /* i1=nqveff; */
1.218 brouard 6865: /* if (cptcovn < 1){i1=1;} */
1.217 brouard 6866:
1.218 brouard 6867: /* fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); */
1.217 brouard 6868:
1.218 brouard 6869: /* fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */
6870:
6871: /* /\* if (h==(int)(YEARM*yearp)){ *\/ */
6872: /* for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
1.224 ! brouard 6873: /* for(cptcod=1;cptcod<=ncodemax[nqveff];cptcod++){ */
1.218 brouard 6874: /* k=k+1; */
6875: /* fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
1.224 ! brouard 6876: /* for(j=1;j<=nqveff;j++) { */
1.218 brouard 6877: /* fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
6878: /* } */
6879: /* fprintf(ficresfb," yearbproj age"); */
6880: /* for(j=1; j<=nlstate+ndeath;j++){ */
6881: /* for(i=1; i<=nlstate;i++) */
6882: /* fprintf(ficresfb," p%d%d",i,j); */
6883: /* fprintf(ficresfb," p.%d",j); */
6884: /* } */
6885: /* for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) { */
6886: /* /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { *\/ */
6887: /* fprintf(ficresfb,"\n"); */
6888: /* fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
6889: /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
6890: /* nhstepm=(int) rint((agelim-agec)*YEARM/stepm); */
6891: /* nhstepm = nhstepm/hstepm; */
6892: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
6893: /* oldm=oldms;savm=savms; */
6894: /* hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k); */
6895: /* for (h=0; h<=nhstepm; h++){ */
6896: /* if (h*hstepm/YEARM*stepm ==yearp) { */
6897: /* fprintf(ficresfb,"\n"); */
1.224 ! brouard 6898: /* for(j=1;j<=nqveff;j++) */
1.218 brouard 6899: /* fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
6900: /* fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */
6901: /* } */
6902: /* for(j=1; j<=nlstate+ndeath;j++) { */
6903: /* ppij=0.; */
6904: /* for(i=1; i<=nlstate;i++) { */
6905: /* if (mobilav==1) */
6906: /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */
6907: /* else { */
6908: /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */
6909: /* } */
6910: /* if (h*hstepm/YEARM*stepm== yearp) { */
6911: /* fprintf(ficresfb," %.3f", p3mat[i][j][h]); */
6912: /* } */
6913: /* } /\* end i *\/ */
6914: /* if (h*hstepm/YEARM*stepm==yearp) { */
6915: /* fprintf(ficresfb," %.3f", ppij); */
6916: /* } */
6917: /* }/\* end j *\/ */
6918: /* } /\* end h *\/ */
6919: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
6920: /* } /\* end agec *\/ */
6921: /* } /\* end yearp *\/ */
6922: /* } /\* end cptcod *\/ */
6923: /* } /\* end cptcov *\/ */
6924:
6925: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
6926:
6927: /* fclose(ficresfb); */
6928: /* printf("End of Computing Back forecasting \n"); */
6929: /* fprintf(ficlog,"End of Computing Back forecasting\n"); */
1.217 brouard 6930:
1.218 brouard 6931: /* } */
1.217 brouard 6932:
1.126 brouard 6933: /************** Forecasting *****not tested NB*************/
1.169 brouard 6934: 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 6935:
6936: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
6937: int *popage;
6938: double calagedatem, agelim, kk1, kk2;
6939: double *popeffectif,*popcount;
6940: double ***p3mat,***tabpop,***tabpopprev;
1.218 brouard 6941: /* double ***mobaverage; */
1.126 brouard 6942: char filerespop[FILENAMELENGTH];
6943:
6944: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6945: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6946: agelim=AGESUP;
6947: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
6948:
6949: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6950:
6951:
1.201 brouard 6952: strcpy(filerespop,"POP_");
6953: strcat(filerespop,fileresu);
1.126 brouard 6954: if((ficrespop=fopen(filerespop,"w"))==NULL) {
6955: printf("Problem with forecast resultfile: %s\n", filerespop);
6956: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
6957: }
6958: printf("Computing forecasting: result on file '%s' \n", filerespop);
6959: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
6960:
1.224 ! brouard 6961: if (nqveff==0) ncodemax[nqveff]=1;
1.126 brouard 6962:
1.218 brouard 6963: /* if (mobilav!=0) { */
6964: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
6965: /* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ */
6966: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
6967: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
6968: /* } */
6969: /* } */
1.126 brouard 6970:
6971: stepsize=(int) (stepm+YEARM-1)/YEARM;
6972: if (stepm<=12) stepsize=1;
6973:
6974: agelim=AGESUP;
6975:
6976: hstepm=1;
6977: hstepm=hstepm/stepm;
1.218 brouard 6978:
1.126 brouard 6979: if (popforecast==1) {
6980: if((ficpop=fopen(popfile,"r"))==NULL) {
6981: printf("Problem with population file : %s\n",popfile);exit(0);
6982: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
6983: }
6984: popage=ivector(0,AGESUP);
6985: popeffectif=vector(0,AGESUP);
6986: popcount=vector(0,AGESUP);
6987:
6988: i=1;
6989: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
1.218 brouard 6990:
1.126 brouard 6991: imx=i;
6992: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
6993: }
1.218 brouard 6994:
1.126 brouard 6995: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.224 ! brouard 6996: for(cptcod=1;cptcod<=ncodemax[nqveff];cptcod++){
1.126 brouard 6997: k=k+1;
6998: fprintf(ficrespop,"\n#******");
1.224 ! brouard 6999: for(j=1;j<=nqveff;j++) {
1.198 brouard 7000: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 7001: }
7002: fprintf(ficrespop,"******\n");
7003: fprintf(ficrespop,"# Age");
7004: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
7005: if (popforecast==1) fprintf(ficrespop," [Population]");
7006:
7007: for (cpt=0; cpt<=0;cpt++) {
7008: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
7009:
1.218 brouard 7010: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.126 brouard 7011: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
7012: nhstepm = nhstepm/hstepm;
7013:
7014: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
7015: oldm=oldms;savm=savms;
7016: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.218 brouard 7017:
1.126 brouard 7018: for (h=0; h<=nhstepm; h++){
7019: if (h==(int) (calagedatem+YEARM*cpt)) {
7020: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
7021: }
7022: for(j=1; j<=nlstate+ndeath;j++) {
7023: kk1=0.;kk2=0;
7024: for(i=1; i<=nlstate;i++) {
7025: if (mobilav==1)
7026: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
7027: else {
7028: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
7029: }
7030: }
7031: if (h==(int)(calagedatem+12*cpt)){
7032: tabpop[(int)(agedeb)][j][cptcod]=kk1;
1.218 brouard 7033: /*fprintf(ficrespop," %.3f", kk1);
7034: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
1.126 brouard 7035: }
7036: }
7037: for(i=1; i<=nlstate;i++){
7038: kk1=0.;
1.218 brouard 7039: for(j=1; j<=nlstate;j++){
7040: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
7041: }
7042: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.126 brouard 7043: }
1.218 brouard 7044:
7045: if (h==(int)(calagedatem+12*cpt))
7046: for(j=1; j<=nlstate;j++)
7047: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
1.126 brouard 7048: }
7049: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
7050: }
7051: }
1.218 brouard 7052:
7053: /******/
7054:
1.126 brouard 7055: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
7056: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
7057: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
7058: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
7059: nhstepm = nhstepm/hstepm;
7060:
7061: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
7062: oldm=oldms;savm=savms;
7063: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
7064: for (h=0; h<=nhstepm; h++){
7065: if (h==(int) (calagedatem+YEARM*cpt)) {
7066: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
7067: }
7068: for(j=1; j<=nlstate+ndeath;j++) {
7069: kk1=0.;kk2=0;
7070: for(i=1; i<=nlstate;i++) {
7071: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
7072: }
7073: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
7074: }
7075: }
7076: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
7077: }
7078: }
1.218 brouard 7079: }
1.126 brouard 7080: }
1.218 brouard 7081:
7082: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7083:
1.126 brouard 7084: if (popforecast==1) {
7085: free_ivector(popage,0,AGESUP);
7086: free_vector(popeffectif,0,AGESUP);
7087: free_vector(popcount,0,AGESUP);
7088: }
7089: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7090: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7091: fclose(ficrespop);
7092: } /* End of popforecast */
1.218 brouard 7093:
1.126 brouard 7094: int fileappend(FILE *fichier, char *optionfich)
7095: {
7096: if((fichier=fopen(optionfich,"a"))==NULL) {
7097: printf("Problem with file: %s\n", optionfich);
7098: fprintf(ficlog,"Problem with file: %s\n", optionfich);
7099: return (0);
7100: }
7101: fflush(fichier);
7102: return (1);
7103: }
7104:
7105:
7106: /**************** function prwizard **********************/
7107: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
7108: {
7109:
7110: /* Wizard to print covariance matrix template */
7111:
1.164 brouard 7112: char ca[32], cb[32];
7113: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 7114: int numlinepar;
7115:
7116: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7117: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7118: for(i=1; i <=nlstate; i++){
7119: jj=0;
7120: for(j=1; j <=nlstate+ndeath; j++){
7121: if(j==i) continue;
7122: jj++;
7123: /*ca[0]= k+'a'-1;ca[1]='\0';*/
7124: printf("%1d%1d",i,j);
7125: fprintf(ficparo,"%1d%1d",i,j);
7126: for(k=1; k<=ncovmodel;k++){
7127: /* printf(" %lf",param[i][j][k]); */
7128: /* fprintf(ficparo," %lf",param[i][j][k]); */
7129: printf(" 0.");
7130: fprintf(ficparo," 0.");
7131: }
7132: printf("\n");
7133: fprintf(ficparo,"\n");
7134: }
7135: }
7136: printf("# Scales (for hessian or gradient estimation)\n");
7137: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
7138: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
7139: for(i=1; i <=nlstate; i++){
7140: jj=0;
7141: for(j=1; j <=nlstate+ndeath; j++){
7142: if(j==i) continue;
7143: jj++;
7144: fprintf(ficparo,"%1d%1d",i,j);
7145: printf("%1d%1d",i,j);
7146: fflush(stdout);
7147: for(k=1; k<=ncovmodel;k++){
7148: /* printf(" %le",delti3[i][j][k]); */
7149: /* fprintf(ficparo," %le",delti3[i][j][k]); */
7150: printf(" 0.");
7151: fprintf(ficparo," 0.");
7152: }
7153: numlinepar++;
7154: printf("\n");
7155: fprintf(ficparo,"\n");
7156: }
7157: }
7158: printf("# Covariance matrix\n");
7159: /* # 121 Var(a12)\n\ */
7160: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7161: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7162: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7163: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7164: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7165: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7166: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7167: fflush(stdout);
7168: fprintf(ficparo,"# Covariance matrix\n");
7169: /* # 121 Var(a12)\n\ */
7170: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7171: /* # ...\n\ */
7172: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7173:
7174: for(itimes=1;itimes<=2;itimes++){
7175: jj=0;
7176: for(i=1; i <=nlstate; i++){
7177: for(j=1; j <=nlstate+ndeath; j++){
7178: if(j==i) continue;
7179: for(k=1; k<=ncovmodel;k++){
7180: jj++;
7181: ca[0]= k+'a'-1;ca[1]='\0';
7182: if(itimes==1){
7183: printf("#%1d%1d%d",i,j,k);
7184: fprintf(ficparo,"#%1d%1d%d",i,j,k);
7185: }else{
7186: printf("%1d%1d%d",i,j,k);
7187: fprintf(ficparo,"%1d%1d%d",i,j,k);
7188: /* printf(" %.5le",matcov[i][j]); */
7189: }
7190: ll=0;
7191: for(li=1;li <=nlstate; li++){
7192: for(lj=1;lj <=nlstate+ndeath; lj++){
7193: if(lj==li) continue;
7194: for(lk=1;lk<=ncovmodel;lk++){
7195: ll++;
7196: if(ll<=jj){
7197: cb[0]= lk +'a'-1;cb[1]='\0';
7198: if(ll<jj){
7199: if(itimes==1){
7200: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7201: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7202: }else{
7203: printf(" 0.");
7204: fprintf(ficparo," 0.");
7205: }
7206: }else{
7207: if(itimes==1){
7208: printf(" Var(%s%1d%1d)",ca,i,j);
7209: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
7210: }else{
7211: printf(" 0.");
7212: fprintf(ficparo," 0.");
7213: }
7214: }
7215: }
7216: } /* end lk */
7217: } /* end lj */
7218: } /* end li */
7219: printf("\n");
7220: fprintf(ficparo,"\n");
7221: numlinepar++;
7222: } /* end k*/
7223: } /*end j */
7224: } /* end i */
7225: } /* end itimes */
7226:
7227: } /* end of prwizard */
7228: /******************* Gompertz Likelihood ******************************/
7229: double gompertz(double x[])
7230: {
7231: double A,B,L=0.0,sump=0.,num=0.;
7232: int i,n=0; /* n is the size of the sample */
7233:
1.220 brouard 7234: for (i=1;i<=imx ; i++) {
1.126 brouard 7235: sump=sump+weight[i];
7236: /* sump=sump+1;*/
7237: num=num+1;
7238: }
7239:
7240:
7241: /* for (i=0; i<=imx; i++)
7242: 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]);*/
7243:
7244: for (i=1;i<=imx ; i++)
7245: {
7246: if (cens[i] == 1 && wav[i]>1)
7247: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
7248:
7249: if (cens[i] == 0 && wav[i]>1)
7250: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
7251: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
7252:
7253: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
7254: if (wav[i] > 1 ) { /* ??? */
7255: L=L+A*weight[i];
7256: /* 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]);*/
7257: }
7258: }
7259:
7260: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
7261:
7262: return -2*L*num/sump;
7263: }
7264:
1.136 brouard 7265: #ifdef GSL
7266: /******************* Gompertz_f Likelihood ******************************/
7267: double gompertz_f(const gsl_vector *v, void *params)
7268: {
7269: double A,B,LL=0.0,sump=0.,num=0.;
7270: double *x= (double *) v->data;
7271: int i,n=0; /* n is the size of the sample */
7272:
7273: for (i=0;i<=imx-1 ; i++) {
7274: sump=sump+weight[i];
7275: /* sump=sump+1;*/
7276: num=num+1;
7277: }
7278:
7279:
7280: /* for (i=0; i<=imx; i++)
7281: 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]);*/
7282: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
7283: for (i=1;i<=imx ; i++)
7284: {
7285: if (cens[i] == 1 && wav[i]>1)
7286: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
7287:
7288: if (cens[i] == 0 && wav[i]>1)
7289: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
7290: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
7291:
7292: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
7293: if (wav[i] > 1 ) { /* ??? */
7294: LL=LL+A*weight[i];
7295: /* 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]);*/
7296: }
7297: }
7298:
7299: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
7300: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
7301:
7302: return -2*LL*num/sump;
7303: }
7304: #endif
7305:
1.126 brouard 7306: /******************* Printing html file ***********/
1.201 brouard 7307: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 7308: int lastpass, int stepm, int weightopt, char model[],\
7309: int imx, double p[],double **matcov,double agemortsup){
7310: int i,k;
7311:
7312: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
7313: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
7314: for (i=1;i<=2;i++)
7315: 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 7316: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 7317: fprintf(fichtm,"</ul>");
7318:
7319: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
7320:
7321: 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>");
7322:
7323: for (k=agegomp;k<(agemortsup-2);k++)
7324: 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]);
7325:
7326:
7327: fflush(fichtm);
7328: }
7329:
7330: /******************* Gnuplot file **************/
1.201 brouard 7331: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 7332:
7333: char dirfileres[132],optfileres[132];
1.164 brouard 7334:
1.126 brouard 7335: int ng;
7336:
7337:
7338: /*#ifdef windows */
7339: fprintf(ficgp,"cd \"%s\" \n",pathc);
7340: /*#endif */
7341:
7342:
7343: strcpy(dirfileres,optionfilefiname);
7344: strcpy(optfileres,"vpl");
1.199 brouard 7345: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 7346: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 7347: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 7348: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 7349: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
7350:
7351: }
7352:
1.136 brouard 7353: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
7354: {
1.126 brouard 7355:
1.136 brouard 7356: /*-------- data file ----------*/
7357: FILE *fic;
7358: char dummy[]=" ";
1.223 brouard 7359: int i=0, j=0, n=0, iv=0;
7360: int lstra;
1.136 brouard 7361: int linei, month, year,iout;
7362: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 7363: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 7364: char *stratrunc;
1.223 brouard 7365:
1.126 brouard 7366:
7367:
1.136 brouard 7368: if((fic=fopen(datafile,"r"))==NULL) {
1.218 brouard 7369: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
7370: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136 brouard 7371: }
1.126 brouard 7372:
1.136 brouard 7373: i=1;
7374: linei=0;
7375: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
7376: linei=linei+1;
7377: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
7378: if(line[j] == '\t')
7379: line[j] = ' ';
7380: }
7381: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
7382: ;
7383: };
7384: line[j+1]=0; /* Trims blanks at end of line */
7385: if(line[0]=='#'){
7386: fprintf(ficlog,"Comment line\n%s\n",line);
7387: printf("Comment line\n%s\n",line);
7388: continue;
7389: }
7390: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 7391: strcpy(line, linetmp);
1.223 brouard 7392:
7393: /* Loops on waves */
7394: for (j=maxwav;j>=1;j--){
7395: for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */
7396: cutv(stra, strb, line, ' ');
7397: if(strb[0]=='.') { /* Missing value */
7398: lval=-1;
7399: }else{
7400: errno=0;
7401: /* what_kind_of_number(strb); */
7402: dval=strtod(strb,&endptr);
7403: /* if( strb[0]=='\0' || (*endptr != '\0')){ */
7404: /* if(strb != endptr && *endptr == '\0') */
7405: /* dval=dlval; */
7406: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
7407: if( strb[0]=='\0' || (*endptr != '\0')){
7408: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav);
7409: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog);
7410: return 1;
7411: }
7412: cotqvar[j][iv][i]=dval;
7413: }
7414: strcpy(line,stra);
7415: }/* end loop ntqv */
7416:
7417: for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */
7418: cutv(stra, strb, line, ' ');
7419: if(strb[0]=='.') { /* Missing value */
7420: lval=-1;
7421: }else{
7422: errno=0;
7423: lval=strtol(strb,&endptr,10);
7424: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
7425: if( strb[0]=='\0' || (*endptr != '\0')){
7426: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav);
7427: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);fflush(ficlog);
7428: return 1;
7429: }
7430: }
7431: if(lval <-1 || lval >1){
7432: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
7433: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7434: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
7435: For example, for multinomial values like 1, 2 and 3,\n \
7436: build V1=0 V2=0 for the reference value (1),\n \
7437: V1=1 V2=0 for (2) \n \
7438: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
7439: output of IMaCh is often meaningless.\n \
7440: Exiting.\n",lval,linei, i,line,j);
7441: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
7442: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7443: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
7444: For example, for multinomial values like 1, 2 and 3,\n \
7445: build V1=0 V2=0 for the reference value (1),\n \
7446: V1=1 V2=0 for (2) \n \
7447: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
7448: output of IMaCh is often meaningless.\n \
7449: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
7450: return 1;
7451: }
7452: cotvar[j][iv][i]=(double)(lval);
7453: strcpy(line,stra);
7454: }/* end loop ntv */
1.126 brouard 7455:
1.223 brouard 7456: /* Statuses at wave */
1.137 brouard 7457: cutv(stra, strb, line, ' ');
1.223 brouard 7458: if(strb[0]=='.') { /* Missing value */
7459: lval=-1;
1.136 brouard 7460: }else{
1.223 brouard 7461: errno=0;
7462: lval=strtol(strb,&endptr,10);
7463: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
7464: if( strb[0]=='\0' || (*endptr != '\0')){
7465: 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);
7466: 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);
7467: return 1;
7468: }
1.136 brouard 7469: }
1.223 brouard 7470:
1.136 brouard 7471: s[j][i]=lval;
1.223 brouard 7472:
7473: /* Date of Interview */
1.136 brouard 7474: strcpy(line,stra);
7475: cutv(stra, strb,line,' ');
1.169 brouard 7476: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7477: }
1.169 brouard 7478: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.223 brouard 7479: month=99;
7480: year=9999;
1.136 brouard 7481: }else{
1.223 brouard 7482: 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);
7483: 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);
7484: return 1;
1.136 brouard 7485: }
7486: anint[j][i]= (double) year;
7487: mint[j][i]= (double)month;
7488: strcpy(line,stra);
1.223 brouard 7489: } /* End loop on waves */
7490:
7491: /* Date of death */
1.136 brouard 7492: cutv(stra, strb,line,' ');
1.169 brouard 7493: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7494: }
1.169 brouard 7495: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 7496: month=99;
7497: year=9999;
7498: }else{
1.141 brouard 7499: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
1.223 brouard 7500: 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);
7501: return 1;
1.136 brouard 7502: }
7503: andc[i]=(double) year;
7504: moisdc[i]=(double) month;
7505: strcpy(line,stra);
7506:
1.223 brouard 7507: /* Date of birth */
1.136 brouard 7508: cutv(stra, strb,line,' ');
1.169 brouard 7509: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7510: }
1.169 brouard 7511: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 7512: month=99;
7513: year=9999;
7514: }else{
1.141 brouard 7515: 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);
7516: 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);
1.223 brouard 7517: return 1;
1.136 brouard 7518: }
7519: if (year==9999) {
1.141 brouard 7520: 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);
7521: 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);
1.223 brouard 7522: return 1;
1.126 brouard 7523:
1.136 brouard 7524: }
7525: annais[i]=(double)(year);
7526: moisnais[i]=(double)(month);
7527: strcpy(line,stra);
1.223 brouard 7528:
7529: /* Sample weight */
1.136 brouard 7530: cutv(stra, strb,line,' ');
7531: errno=0;
7532: dval=strtod(strb,&endptr);
7533: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 7534: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
7535: 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 7536: fflush(ficlog);
7537: return 1;
7538: }
7539: weight[i]=dval;
7540: strcpy(line,stra);
1.223 brouard 7541:
7542: for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */
7543: cutv(stra, strb, line, ' ');
7544: if(strb[0]=='.') { /* Missing value */
7545: lval=-1;
7546: }else{
7547: errno=0;
7548: /* what_kind_of_number(strb); */
7549: dval=strtod(strb,&endptr);
7550: /* if(strb != endptr && *endptr == '\0') */
7551: /* dval=dlval; */
7552: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
7553: if( strb[0]=='\0' || (*endptr != '\0')){
7554: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);
7555: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);fflush(ficlog);
7556: return 1;
7557: }
7558: coqvar[iv][i]=dval;
7559: }
7560: strcpy(line,stra);
7561: }/* end loop nqv */
1.136 brouard 7562:
1.223 brouard 7563: /* Covariate values */
1.136 brouard 7564: for (j=ncovcol;j>=1;j--){
7565: cutv(stra, strb,line,' ');
1.223 brouard 7566: if(strb[0]=='.') { /* Missing covariate value */
7567: lval=-1;
1.136 brouard 7568: }else{
1.223 brouard 7569: errno=0;
7570: lval=strtol(strb,&endptr,10);
7571: if( strb[0]=='\0' || (*endptr != '\0')){
7572: 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);
7573: 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);
7574: return 1;
7575: }
1.136 brouard 7576: }
7577: if(lval <-1 || lval >1){
1.223 brouard 7578: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 7579: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7580: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
7581: For example, for multinomial values like 1, 2 and 3,\n \
7582: build V1=0 V2=0 for the reference value (1),\n \
7583: V1=1 V2=0 for (2) \n \
7584: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
7585: output of IMaCh is often meaningless.\n \
7586: Exiting.\n",lval,linei, i,line,j);
1.223 brouard 7587: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 7588: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7589: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
7590: For example, for multinomial values like 1, 2 and 3,\n \
7591: build V1=0 V2=0 for the reference value (1),\n \
7592: V1=1 V2=0 for (2) \n \
7593: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
7594: output of IMaCh is often meaningless.\n \
7595: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.223 brouard 7596: return 1;
1.136 brouard 7597: }
7598: covar[j][i]=(double)(lval);
7599: strcpy(line,stra);
7600: }
7601: lstra=strlen(stra);
7602:
7603: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
7604: stratrunc = &(stra[lstra-9]);
7605: num[i]=atol(stratrunc);
7606: }
7607: else
7608: num[i]=atol(stra);
7609: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
7610: 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;}*/
7611:
7612: i=i+1;
7613: } /* End loop reading data */
1.126 brouard 7614:
1.136 brouard 7615: *imax=i-1; /* Number of individuals */
7616: fclose(fic);
7617:
7618: return (0);
1.164 brouard 7619: /* endread: */
1.223 brouard 7620: printf("Exiting readdata: ");
7621: fclose(fic);
7622: return (1);
7623: }
1.126 brouard 7624:
1.145 brouard 7625: void removespace(char *str) {
7626: char *p1 = str, *p2 = str;
7627: do
7628: while (*p2 == ' ')
7629: p2++;
1.169 brouard 7630: while (*p1++ == *p2++);
1.145 brouard 7631: }
7632:
1.224 ! brouard 7633: int decodemodel ( char model[], int lastobs)
! 7634: /**< This routine decode the model and returns:
! 7635: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
! 7636: * - nagesqr = 1 if age*age in the model, otherwise 0.
! 7637: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
! 7638: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
! 7639: * - cptcovage number of covariates with age*products =2
! 7640: * - cptcovs number of simple covariates
! 7641: * - 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
! 7642: * which is a new column after the 9 (ncovcol) variables.
! 7643: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
! 7644: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
! 7645: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
! 7646: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
! 7647: */
1.136 brouard 7648: {
1.145 brouard 7649: int i, j, k, ks;
1.164 brouard 7650: int j1, k1, k2;
1.136 brouard 7651: char modelsav[80];
1.145 brouard 7652: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 7653: char *strpt;
1.136 brouard 7654:
1.145 brouard 7655: /*removespace(model);*/
1.136 brouard 7656: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 7657: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 7658: if (strstr(model,"AGE") !=0){
1.192 brouard 7659: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
7660: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 7661: return 1;
7662: }
1.141 brouard 7663: if (strstr(model,"v") !=0){
7664: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
7665: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
7666: return 1;
7667: }
1.187 brouard 7668: strcpy(modelsav,model);
7669: if ((strpt=strstr(model,"age*age")) !=0){
7670: printf(" strpt=%s, model=%s\n",strpt, model);
7671: if(strpt != model){
1.224 ! brouard 7672: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 7673: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 7674: corresponding column of parameters.\n",model);
1.224 ! brouard 7675: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 7676: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 7677: corresponding column of parameters.\n",model); fflush(ficlog);
1.224 ! brouard 7678: return 1;
! 7679: }
1.187 brouard 7680:
7681: nagesqr=1;
7682: if (strstr(model,"+age*age") !=0)
1.224 ! brouard 7683: substrchaine(modelsav, model, "+age*age");
1.187 brouard 7684: else if (strstr(model,"age*age+") !=0)
1.224 ! brouard 7685: substrchaine(modelsav, model, "age*age+");
1.187 brouard 7686: else
1.224 ! brouard 7687: substrchaine(modelsav, model, "age*age");
1.187 brouard 7688: }else
7689: nagesqr=0;
7690: if (strlen(modelsav) >1){
7691: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
7692: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
1.224 ! brouard 7693: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2 */
1.187 brouard 7694: cptcovt= j+1; /* Number of total covariates in the model, not including
1.224 ! brouard 7695: * cst, age and age*age
! 7696: * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
! 7697: /* including age products which are counted in cptcovage.
! 7698: * but the covariates which are products must be treated
! 7699: * separately: ncovn=4- 2=2 (V1+V3). */
1.187 brouard 7700: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
7701: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
7702:
7703:
7704: /* Design
7705: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
7706: * < ncovcol=8 >
7707: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
7708: * k= 1 2 3 4 5 6 7 8
7709: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
7710: * covar[k,i], value of kth covariate if not including age for individual i:
1.224 ! brouard 7711: * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
! 7712: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
1.187 brouard 7713: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
7714: * Tage[++cptcovage]=k
7715: * if products, new covar are created after ncovcol with k1
7716: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
7717: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
7718: * 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
7719: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
7720: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
7721: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
7722: * < ncovcol=8 >
7723: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
7724: * k= 1 2 3 4 5 6 7 8 9 10 11 12
7725: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
7726: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
7727: * p Tprod[1]@2={ 6, 5}
7728: *p Tvard[1][1]@4= {7, 8, 5, 6}
7729: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
7730: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
7731: *How to reorganize?
7732: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
7733: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
7734: * {2, 1, 4, 8, 5, 6, 3, 7}
7735: * Struct []
7736: */
1.145 brouard 7737:
1.187 brouard 7738: /* This loop fills the array Tvar from the string 'model'.*/
7739: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
7740: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
7741: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
7742: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
7743: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
7744: /* k=1 Tvar[1]=2 (from V2) */
7745: /* k=5 Tvar[5] */
7746: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 7747: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 7748: /* } */
1.198 brouard 7749: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 7750: /*
7751: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
7752: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 7753: Tvar[k]=0;
1.187 brouard 7754: cptcovage=0;
7755: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
1.223 brouard 7756: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
7757: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
7758: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
7759: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
7760: /*scanf("%d",i);*/
7761: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
7762: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
7763: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
7764: /* covar is not filled and then is empty */
7765: cptcovprod--;
7766: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
7767: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
7768: cptcovage++; /* Sums the number of covariates which include age as a product */
7769: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
7770: /*printf("stre=%s ", stre);*/
7771: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
7772: cptcovprod--;
7773: cutl(stre,strb,strc,'V');
7774: Tvar[k]=atoi(stre);
7775: cptcovage++;
7776: Tage[cptcovage]=k;
7777: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
7778: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
7779: cptcovn++;
7780: cptcovprodnoage++;k1++;
7781: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
7782: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
7783: because this model-covariate is a construction we invent a new column
7784: ncovcol + k1
7785: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
7786: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
7787: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
7788: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
7789: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
7790: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
7791: k2=k2+2;
7792: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
7793: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
7794: for (i=1; i<=lastobs;i++){
7795: /* Computes the new covariate which is a product of
7796: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
7797: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
7798: }
7799: } /* End age is not in the model */
7800: } /* End if model includes a product */
7801: else { /* no more sum */
7802: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
7803: /* scanf("%d",i);*/
7804: cutl(strd,strc,strb,'V');
7805: ks++; /**< Number of simple covariates */
7806: cptcovn++;
7807: Tvar[k]=atoi(strd);
7808: }
7809: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
7810: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
7811: scanf("%d",i);*/
1.187 brouard 7812: } /* end of loop + on total covariates */
7813: } /* end if strlen(modelsave == 0) age*age might exist */
7814: } /* end if strlen(model == 0) */
1.136 brouard 7815:
7816: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
7817: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
7818:
7819: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.224 ! brouard 7820: printf("cptcovprod=%d ", cptcovprod);
! 7821: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.136 brouard 7822:
1.224 ! brouard 7823: scanf("%d ",i);*/
! 7824: /* Dispatching in quantitative and time varying covariates */
1.136 brouard 7825:
1.224 ! brouard 7826: for(k=1, ncoveff=0, nqveff=0, ntveff=0, nqtveff=0;k<=cptcovn; k++){ /* or cptocvt */
! 7827: if (Tvar[k] <=ncovcol){
! 7828: ncoveff++;
! 7829: }else if( Tvar[k] <=ncovcol+nqv){
! 7830: nqveff++;
! 7831: }else if( Tvar[k] <=ncovcol+nqv+ntv){
! 7832: ntveff++;
! 7833: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
! 7834: nqtveff++;
! 7835: }else
! 7836: printf("Error in effective covariates \n");
! 7837: }
1.136 brouard 7838:
1.137 brouard 7839: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 7840: /*endread:*/
1.224 ! brouard 7841: printf("Exiting decodemodel: ");
! 7842: return (1);
1.136 brouard 7843: }
7844:
1.169 brouard 7845: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 7846: {
7847: int i, m;
1.218 brouard 7848: int firstone=0;
7849:
1.136 brouard 7850: for (i=1; i<=imx; i++) {
7851: for(m=2; (m<= maxwav); m++) {
7852: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
7853: anint[m][i]=9999;
1.216 brouard 7854: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
7855: s[m][i]=-1;
1.136 brouard 7856: }
7857: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 7858: *nberr = *nberr + 1;
1.218 brouard 7859: if(firstone == 0){
7860: firstone=1;
7861: 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);
7862: }
7863: 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 7864: s[m][i]=-1;
7865: }
7866: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 7867: (*nberr)++;
1.136 brouard 7868: 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]);
7869: 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]);
7870: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
7871: }
7872: }
7873: }
7874:
7875: for (i=1; i<=imx; i++) {
7876: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
7877: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 7878: 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 7879: if (s[m][i] >= nlstate+1) {
1.169 brouard 7880: if(agedc[i]>0){
7881: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 7882: agev[m][i]=agedc[i];
1.214 brouard 7883: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 7884: }else {
1.136 brouard 7885: if ((int)andc[i]!=9999){
7886: nbwarn++;
7887: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
7888: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
7889: agev[m][i]=-1;
7890: }
7891: }
1.169 brouard 7892: } /* agedc > 0 */
1.214 brouard 7893: } /* end if */
1.136 brouard 7894: else if(s[m][i] !=9){ /* Standard case, age in fractional
7895: years but with the precision of a month */
7896: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
7897: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
7898: agev[m][i]=1;
7899: else if(agev[m][i] < *agemin){
7900: *agemin=agev[m][i];
7901: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
7902: }
7903: else if(agev[m][i] >*agemax){
7904: *agemax=agev[m][i];
1.156 brouard 7905: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 7906: }
7907: /*agev[m][i]=anint[m][i]-annais[i];*/
7908: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 7909: } /* en if 9*/
1.136 brouard 7910: else { /* =9 */
1.214 brouard 7911: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 7912: agev[m][i]=1;
7913: s[m][i]=-1;
7914: }
7915: }
1.214 brouard 7916: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 7917: agev[m][i]=1;
1.214 brouard 7918: else{
7919: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
7920: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
7921: agev[m][i]=0;
7922: }
7923: } /* End for lastpass */
7924: }
1.136 brouard 7925:
7926: for (i=1; i<=imx; i++) {
7927: for(m=firstpass; (m<=lastpass); m++){
7928: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 7929: (*nberr)++;
1.136 brouard 7930: 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);
7931: 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);
7932: return 1;
7933: }
7934: }
7935: }
7936:
7937: /*for (i=1; i<=imx; i++){
7938: for (m=firstpass; (m<lastpass); m++){
7939: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
7940: }
7941:
7942: }*/
7943:
7944:
1.139 brouard 7945: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
7946: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 7947:
7948: return (0);
1.164 brouard 7949: /* endread:*/
1.136 brouard 7950: printf("Exiting calandcheckages: ");
7951: return (1);
7952: }
7953:
1.172 brouard 7954: #if defined(_MSC_VER)
7955: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
7956: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
7957: //#include "stdafx.h"
7958: //#include <stdio.h>
7959: //#include <tchar.h>
7960: //#include <windows.h>
7961: //#include <iostream>
7962: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
7963:
7964: LPFN_ISWOW64PROCESS fnIsWow64Process;
7965:
7966: BOOL IsWow64()
7967: {
7968: BOOL bIsWow64 = FALSE;
7969:
7970: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
7971: // (HANDLE, PBOOL);
7972:
7973: //LPFN_ISWOW64PROCESS fnIsWow64Process;
7974:
7975: HMODULE module = GetModuleHandle(_T("kernel32"));
7976: const char funcName[] = "IsWow64Process";
7977: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
7978: GetProcAddress(module, funcName);
7979:
7980: if (NULL != fnIsWow64Process)
7981: {
7982: if (!fnIsWow64Process(GetCurrentProcess(),
7983: &bIsWow64))
7984: //throw std::exception("Unknown error");
7985: printf("Unknown error\n");
7986: }
7987: return bIsWow64 != FALSE;
7988: }
7989: #endif
1.177 brouard 7990:
1.191 brouard 7991: void syscompilerinfo(int logged)
1.167 brouard 7992: {
7993: /* #include "syscompilerinfo.h"*/
1.185 brouard 7994: /* command line Intel compiler 32bit windows, XP compatible:*/
7995: /* /GS /W3 /Gy
7996: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
7997: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
7998: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 7999: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
8000: */
8001: /* 64 bits */
1.185 brouard 8002: /*
8003: /GS /W3 /Gy
8004: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
8005: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
8006: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
8007: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
8008: /* Optimization are useless and O3 is slower than O2 */
8009: /*
8010: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
8011: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
8012: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
8013: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
8014: */
1.186 brouard 8015: /* Link is */ /* /OUT:"visual studio
1.185 brouard 8016: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
8017: /PDB:"visual studio
8018: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
8019: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
8020: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
8021: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
8022: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
8023: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
8024: uiAccess='false'"
8025: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
8026: /NOLOGO /TLBID:1
8027: */
1.177 brouard 8028: #if defined __INTEL_COMPILER
1.178 brouard 8029: #if defined(__GNUC__)
8030: struct utsname sysInfo; /* For Intel on Linux and OS/X */
8031: #endif
1.177 brouard 8032: #elif defined(__GNUC__)
1.179 brouard 8033: #ifndef __APPLE__
1.174 brouard 8034: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 8035: #endif
1.177 brouard 8036: struct utsname sysInfo;
1.178 brouard 8037: int cross = CROSS;
8038: if (cross){
8039: printf("Cross-");
1.191 brouard 8040: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 8041: }
1.174 brouard 8042: #endif
8043:
1.171 brouard 8044: #include <stdint.h>
1.178 brouard 8045:
1.191 brouard 8046: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 8047: #if defined(__clang__)
1.191 brouard 8048: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 8049: #endif
8050: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 8051: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 8052: #endif
8053: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 8054: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 8055: #endif
8056: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 8057: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 8058: #endif
8059: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 8060: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 8061: #endif
8062: #if defined(_MSC_VER)
1.191 brouard 8063: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 8064: #endif
8065: #if defined(__PGI)
1.191 brouard 8066: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 8067: #endif
8068: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 8069: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 8070: #endif
1.191 brouard 8071: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 8072:
1.167 brouard 8073: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
8074: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
8075: // Windows (x64 and x86)
1.191 brouard 8076: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 8077: #elif __unix__ // all unices, not all compilers
8078: // Unix
1.191 brouard 8079: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 8080: #elif __linux__
8081: // linux
1.191 brouard 8082: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 8083: #elif __APPLE__
1.174 brouard 8084: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 8085: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 8086: #endif
8087:
8088: /* __MINGW32__ */
8089: /* __CYGWIN__ */
8090: /* __MINGW64__ */
8091: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
8092: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
8093: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
8094: /* _WIN64 // Defined for applications for Win64. */
8095: /* _M_X64 // Defined for compilations that target x64 processors. */
8096: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 8097:
1.167 brouard 8098: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 8099: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 8100: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 8101: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 8102: #else
1.191 brouard 8103: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 8104: #endif
8105:
1.169 brouard 8106: #if defined(__GNUC__)
8107: # if defined(__GNUC_PATCHLEVEL__)
8108: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
8109: + __GNUC_MINOR__ * 100 \
8110: + __GNUC_PATCHLEVEL__)
8111: # else
8112: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
8113: + __GNUC_MINOR__ * 100)
8114: # endif
1.174 brouard 8115: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 8116: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 8117:
8118: if (uname(&sysInfo) != -1) {
8119: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 8120: 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 8121: }
8122: else
8123: perror("uname() error");
1.179 brouard 8124: //#ifndef __INTEL_COMPILER
8125: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 8126: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 8127: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 8128: #endif
1.169 brouard 8129: #endif
1.172 brouard 8130:
8131: // void main()
8132: // {
1.169 brouard 8133: #if defined(_MSC_VER)
1.174 brouard 8134: if (IsWow64()){
1.191 brouard 8135: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
8136: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 8137: }
8138: else{
1.191 brouard 8139: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
8140: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 8141: }
1.172 brouard 8142: // printf("\nPress Enter to continue...");
8143: // getchar();
8144: // }
8145:
1.169 brouard 8146: #endif
8147:
1.167 brouard 8148:
1.219 brouard 8149: }
1.136 brouard 8150:
1.219 brouard 8151: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.180 brouard 8152: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
8153: int i, j, k, i1 ;
1.202 brouard 8154: /* double ftolpl = 1.e-10; */
1.180 brouard 8155: double age, agebase, agelim;
1.203 brouard 8156: double tot;
1.180 brouard 8157:
1.202 brouard 8158: strcpy(filerespl,"PL_");
8159: strcat(filerespl,fileresu);
8160: if((ficrespl=fopen(filerespl,"w"))==NULL) {
8161: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
8162: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
8163: }
8164: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
8165: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
8166: pstamp(ficrespl);
1.203 brouard 8167: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 8168: fprintf(ficrespl,"#Age ");
8169: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
8170: fprintf(ficrespl,"\n");
1.180 brouard 8171:
1.219 brouard 8172: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180 brouard 8173:
1.219 brouard 8174: agebase=ageminpar;
8175: agelim=agemaxpar;
1.180 brouard 8176:
1.224 ! brouard 8177: i1=pow(2,ncoveff);
1.219 brouard 8178: if (cptcovn < 1){i1=1;}
1.180 brouard 8179:
1.220 brouard 8180: for(k=1; k<=i1;k++){
8181: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
1.180 brouard 8182: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
1.219 brouard 8183: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.220 brouard 8184: /* k=k+1; */
1.219 brouard 8185: /* to clean */
8186: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
8187: fprintf(ficrespl,"#******");
8188: printf("#******");
8189: fprintf(ficlog,"#******");
1.224 ! brouard 8190: for(j=1;j<=nqveff;j++) {
1.219 brouard 8191: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8192: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8193: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8194: }
8195: fprintf(ficrespl,"******\n");
8196: printf("******\n");
8197: fprintf(ficlog,"******\n");
1.220 brouard 8198: if(invalidvarcomb[k]){
8199: printf("\nCombination (%d) ignored because no cases \n",k);
8200: fprintf(ficrespl,"#Combination (%d) ignored because no cases \n",k);
8201: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
8202: continue;
8203: }
1.219 brouard 8204:
8205: fprintf(ficrespl,"#Age ");
1.224 ! brouard 8206: for(j=1;j<=nqveff;j++) {
1.219 brouard 8207: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8208: }
8209: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
8210: fprintf(ficrespl,"Total Years_to_converge\n");
8211:
8212: for (age=agebase; age<=agelim; age++){
8213: /* for (age=agebase; age<=agebase; age++){ */
8214: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
8215: fprintf(ficrespl,"%.0f ",age );
1.224 ! brouard 8216: for(j=1;j<=nqveff;j++)
1.220 brouard 8217: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.219 brouard 8218: tot=0.;
8219: for(i=1; i<=nlstate;i++){
1.220 brouard 8220: tot += prlim[i][i];
8221: fprintf(ficrespl," %.5f", prlim[i][i]);
1.219 brouard 8222: }
8223: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
8224: } /* Age */
8225: /* was end of cptcod */
8226: } /* cptcov */
8227: return 0;
1.180 brouard 8228: }
8229:
1.218 brouard 8230: 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){
8231: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
8232:
8233: /* Computes the back prevalence limit for any combination of covariate values
8234: * at any age between ageminpar and agemaxpar
8235: */
1.217 brouard 8236: int i, j, k, i1 ;
8237: /* double ftolpl = 1.e-10; */
8238: double age, agebase, agelim;
8239: double tot;
1.218 brouard 8240: /* double ***mobaverage; */
8241: /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
1.217 brouard 8242:
8243: strcpy(fileresplb,"PLB_");
8244: strcat(fileresplb,fileresu);
8245: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
8246: printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
8247: fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
8248: }
8249: printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
8250: fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
8251: pstamp(ficresplb);
8252: fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
8253: fprintf(ficresplb,"#Age ");
8254: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
8255: fprintf(ficresplb,"\n");
8256:
1.218 brouard 8257:
8258: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
8259:
8260: agebase=ageminpar;
8261: agelim=agemaxpar;
8262:
8263:
1.224 ! brouard 8264: i1=pow(2,nqveff);
1.218 brouard 8265: if (cptcovn < 1){i1=1;}
1.220 brouard 8266:
8267: for(k=1; k<=i1;k++){
8268: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
1.217 brouard 8269: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
1.218 brouard 8270: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.220 brouard 8271: /* k=k+1; */
1.218 brouard 8272: /* to clean */
8273: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
8274: fprintf(ficresplb,"#******");
8275: printf("#******");
8276: fprintf(ficlog,"#******");
1.224 ! brouard 8277: for(j=1;j<=nqveff;j++) {
1.218 brouard 8278: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8279: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8280: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8281: }
8282: fprintf(ficresplb,"******\n");
8283: printf("******\n");
8284: fprintf(ficlog,"******\n");
1.220 brouard 8285: if(invalidvarcomb[k]){
8286: printf("\nCombination (%d) ignored because no cases \n",k);
8287: fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
8288: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
8289: continue;
8290: }
1.218 brouard 8291:
8292: fprintf(ficresplb,"#Age ");
1.224 ! brouard 8293: for(j=1;j<=nqveff;j++) {
1.218 brouard 8294: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8295: }
8296: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
8297: fprintf(ficresplb,"Total Years_to_converge\n");
8298:
8299:
8300: for (age=agebase; age<=agelim; age++){
8301: /* for (age=agebase; age<=agebase; age++){ */
8302: if(mobilavproj > 0){
8303: /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
8304: /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.219 brouard 8305: bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);
1.218 brouard 8306: }else if (mobilavproj == 0){
1.219 brouard 8307: 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);
8308: 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);
8309: exit(1);
1.218 brouard 8310: }else{
1.219 brouard 8311: /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
8312: bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);
1.218 brouard 8313: }
8314: fprintf(ficresplb,"%.0f ",age );
1.224 ! brouard 8315: for(j=1;j<=nqveff;j++)
1.219 brouard 8316: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.218 brouard 8317: tot=0.;
8318: for(i=1; i<=nlstate;i++){
1.219 brouard 8319: tot += bprlim[i][i];
8320: fprintf(ficresplb," %.5f", bprlim[i][i]);
1.218 brouard 8321: }
8322: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
8323: } /* Age */
8324: /* was end of cptcod */
8325: } /* cptcov */
8326:
8327: /* hBijx(p, bage, fage); */
8328: /* fclose(ficrespijb); */
8329:
8330: return 0;
1.217 brouard 8331: }
1.218 brouard 8332:
1.180 brouard 8333: int hPijx(double *p, int bage, int fage){
8334: /*------------- h Pij x at various ages ------------*/
8335:
8336: int stepsize;
8337: int agelim;
8338: int hstepm;
8339: int nhstepm;
8340: int h, i, i1, j, k;
8341:
8342: double agedeb;
8343: double ***p3mat;
8344:
1.201 brouard 8345: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 8346: if((ficrespij=fopen(filerespij,"w"))==NULL) {
8347: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
8348: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
8349: }
8350: printf("Computing pij: result on file '%s' \n", filerespij);
8351: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
8352:
8353: stepsize=(int) (stepm+YEARM-1)/YEARM;
8354: /*if (stepm<=24) stepsize=2;*/
8355:
8356: agelim=AGESUP;
8357: hstepm=stepsize*YEARM; /* Every year of age */
8358: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.218 brouard 8359:
1.180 brouard 8360: /* hstepm=1; aff par mois*/
8361: pstamp(ficrespij);
8362: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.224 ! brouard 8363: i1= pow(2,nqveff);
1.218 brouard 8364: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
8365: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
8366: /* k=k+1; */
1.224 ! brouard 8367: for (k=1; k <= (int) pow(2,nqveff); k++){
1.183 brouard 8368: fprintf(ficrespij,"\n#****** ");
1.224 ! brouard 8369: for(j=1;j<=nqveff;j++)
1.198 brouard 8370: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.183 brouard 8371: fprintf(ficrespij,"******\n");
8372:
8373: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
8374: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
8375: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
8376:
8377: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 8378:
1.183 brouard 8379: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8380: oldm=oldms;savm=savms;
8381: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
8382: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
8383: for(i=1; i<=nlstate;i++)
8384: for(j=1; j<=nlstate+ndeath;j++)
8385: fprintf(ficrespij," %1d-%1d",i,j);
8386: fprintf(ficrespij,"\n");
8387: for (h=0; h<=nhstepm; h++){
8388: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
8389: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 8390: for(i=1; i<=nlstate;i++)
8391: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 8392: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 8393: fprintf(ficrespij,"\n");
8394: }
1.183 brouard 8395: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8396: fprintf(ficrespij,"\n");
8397: }
1.180 brouard 8398: /*}*/
8399: }
1.218 brouard 8400: return 0;
1.180 brouard 8401: }
1.218 brouard 8402:
8403: int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217 brouard 8404: /*------------- h Bij x at various ages ------------*/
8405:
8406: int stepsize;
1.218 brouard 8407: /* int agelim; */
8408: int ageminl;
1.217 brouard 8409: int hstepm;
8410: int nhstepm;
8411: int h, i, i1, j, k;
1.218 brouard 8412:
1.217 brouard 8413: double agedeb;
8414: double ***p3mat;
1.218 brouard 8415:
8416: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
8417: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
8418: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
8419: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
8420: }
8421: printf("Computing pij back: result on file '%s' \n", filerespijb);
8422: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
8423:
8424: stepsize=(int) (stepm+YEARM-1)/YEARM;
8425: /*if (stepm<=24) stepsize=2;*/
1.217 brouard 8426:
1.218 brouard 8427: /* agelim=AGESUP; */
8428: ageminl=30;
8429: hstepm=stepsize*YEARM; /* Every year of age */
8430: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
8431:
8432: /* hstepm=1; aff par mois*/
8433: pstamp(ficrespijb);
8434: fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");
1.224 ! brouard 8435: i1= pow(2,nqveff);
1.218 brouard 8436: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
8437: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
8438: /* k=k+1; */
1.224 ! brouard 8439: for (k=1; k <= (int) pow(2,nqveff); k++){
1.218 brouard 8440: fprintf(ficrespijb,"\n#****** ");
1.224 ! brouard 8441: for(j=1;j<=nqveff;j++)
1.218 brouard 8442: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8443: fprintf(ficrespijb,"******\n");
1.222 brouard 8444: if(invalidvarcomb[k]){
8445: fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
8446: continue;
8447: }
1.218 brouard 8448:
8449: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
8450: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
8451: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
8452: nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
8453: nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
8454:
8455: /* nhstepm=nhstepm*YEARM; aff par mois*/
8456:
8457: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8458: /* oldm=oldms;savm=savms; */
8459: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
8460: hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
8461: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
8462: fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
8463: for(i=1; i<=nlstate;i++)
8464: for(j=1; j<=nlstate+ndeath;j++)
8465: fprintf(ficrespijb," %1d-%1d",i,j);
8466: fprintf(ficrespijb,"\n");
8467: for (h=0; h<=nhstepm; h++){
8468: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
8469: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
8470: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
1.217 brouard 8471: for(i=1; i<=nlstate;i++)
8472: for(j=1; j<=nlstate+ndeath;j++)
1.218 brouard 8473: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
1.217 brouard 8474: fprintf(ficrespijb,"\n");
8475: }
1.218 brouard 8476: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8477: fprintf(ficrespijb,"\n");
1.217 brouard 8478: }
1.218 brouard 8479: /*}*/
8480: }
8481: return 0;
8482: } /* hBijx */
1.217 brouard 8483:
1.180 brouard 8484:
1.136 brouard 8485: /***********************************************/
8486: /**************** Main Program *****************/
8487: /***********************************************/
8488:
8489: int main(int argc, char *argv[])
8490: {
8491: #ifdef GSL
8492: const gsl_multimin_fminimizer_type *T;
8493: size_t iteri = 0, it;
8494: int rval = GSL_CONTINUE;
8495: int status = GSL_SUCCESS;
8496: double ssval;
8497: #endif
8498: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 8499: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.209 brouard 8500: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 8501: int jj, ll, li, lj, lk;
1.136 brouard 8502: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 8503: int num_filled;
1.136 brouard 8504: int itimes;
8505: int NDIM=2;
8506: int vpopbased=0;
8507:
1.164 brouard 8508: char ca[32], cb[32];
1.136 brouard 8509: /* FILE *fichtm; *//* Html File */
8510: /* FILE *ficgp;*/ /*Gnuplot File */
8511: struct stat info;
1.191 brouard 8512: double agedeb=0.;
1.194 brouard 8513:
8514: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219 brouard 8515: double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136 brouard 8516:
1.165 brouard 8517: double fret;
1.191 brouard 8518: double dum=0.; /* Dummy variable */
1.136 brouard 8519: double ***p3mat;
1.218 brouard 8520: /* double ***mobaverage; */
1.164 brouard 8521:
8522: char line[MAXLINE];
1.197 brouard 8523: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
8524:
8525: char model[MAXLINE], modeltemp[MAXLINE];
1.136 brouard 8526: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 8527: char *tok, *val; /* pathtot */
1.136 brouard 8528: int firstobs=1, lastobs=10;
1.195 brouard 8529: int c, h , cpt, c2;
1.191 brouard 8530: int jl=0;
8531: int i1, j1, jk, stepsize=0;
1.194 brouard 8532: int count=0;
8533:
1.164 brouard 8534: int *tab;
1.136 brouard 8535: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.217 brouard 8536: int backcast=0;
1.136 brouard 8537: int mobilav=0,popforecast=0;
1.191 brouard 8538: int hstepm=0, nhstepm=0;
1.136 brouard 8539: int agemortsup;
8540: float sumlpop=0.;
8541: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
8542: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
8543:
1.191 brouard 8544: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 8545: double ftolpl=FTOL;
8546: double **prlim;
1.217 brouard 8547: double **bprlim;
1.136 brouard 8548: double ***param; /* Matrix of parameters */
8549: double *p;
8550: double **matcov; /* Matrix of covariance */
1.203 brouard 8551: double **hess; /* Hessian matrix */
1.136 brouard 8552: double ***delti3; /* Scale */
8553: double *delti; /* Scale */
8554: double ***eij, ***vareij;
8555: double **varpl; /* Variances of prevalence limits by age */
8556: double *epj, vepp;
1.164 brouard 8557:
1.136 brouard 8558: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.217 brouard 8559: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;
8560:
1.136 brouard 8561: double **ximort;
1.145 brouard 8562: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 8563: int *dcwave;
8564:
1.164 brouard 8565: char z[1]="c";
1.136 brouard 8566:
8567: /*char *strt;*/
8568: char strtend[80];
1.126 brouard 8569:
1.164 brouard 8570:
1.126 brouard 8571: /* setlocale (LC_ALL, ""); */
8572: /* bindtextdomain (PACKAGE, LOCALEDIR); */
8573: /* textdomain (PACKAGE); */
8574: /* setlocale (LC_CTYPE, ""); */
8575: /* setlocale (LC_MESSAGES, ""); */
8576:
8577: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 8578: rstart_time = time(NULL);
8579: /* (void) gettimeofday(&start_time,&tzp);*/
8580: start_time = *localtime(&rstart_time);
1.126 brouard 8581: curr_time=start_time;
1.157 brouard 8582: /*tml = *localtime(&start_time.tm_sec);*/
8583: /* strcpy(strstart,asctime(&tml)); */
8584: strcpy(strstart,asctime(&start_time));
1.126 brouard 8585:
8586: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 8587: /* tp.tm_sec = tp.tm_sec +86400; */
8588: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 8589: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
8590: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
8591: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 8592: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 8593: /* strt=asctime(&tmg); */
8594: /* printf("Time(after) =%s",strstart); */
8595: /* (void) time (&time_value);
8596: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
8597: * tm = *localtime(&time_value);
8598: * strstart=asctime(&tm);
8599: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
8600: */
8601:
8602: nberr=0; /* Number of errors and warnings */
8603: nbwarn=0;
1.184 brouard 8604: #ifdef WIN32
8605: _getcwd(pathcd, size);
8606: #else
1.126 brouard 8607: getcwd(pathcd, size);
1.184 brouard 8608: #endif
1.191 brouard 8609: syscompilerinfo(0);
1.196 brouard 8610: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 8611: if(argc <=1){
8612: printf("\nEnter the parameter file name: ");
1.205 brouard 8613: if(!fgets(pathr,FILENAMELENGTH,stdin)){
8614: printf("ERROR Empty parameter file name\n");
8615: goto end;
8616: }
1.126 brouard 8617: i=strlen(pathr);
8618: if(pathr[i-1]=='\n')
8619: pathr[i-1]='\0';
1.156 brouard 8620: i=strlen(pathr);
1.205 brouard 8621: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 8622: pathr[i-1]='\0';
1.205 brouard 8623: }
8624: i=strlen(pathr);
8625: if( i==0 ){
8626: printf("ERROR Empty parameter file name\n");
8627: goto end;
8628: }
8629: for (tok = pathr; tok != NULL; ){
1.126 brouard 8630: printf("Pathr |%s|\n",pathr);
8631: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
8632: printf("val= |%s| pathr=%s\n",val,pathr);
8633: strcpy (pathtot, val);
8634: if(pathr[0] == '\0') break; /* Dirty */
8635: }
8636: }
8637: else{
8638: strcpy(pathtot,argv[1]);
8639: }
8640: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
8641: /*cygwin_split_path(pathtot,path,optionfile);
8642: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
8643: /* cutv(path,optionfile,pathtot,'\\');*/
8644:
8645: /* Split argv[0], imach program to get pathimach */
8646: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
8647: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
8648: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
8649: /* strcpy(pathimach,argv[0]); */
8650: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
8651: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
8652: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 8653: #ifdef WIN32
8654: _chdir(path); /* Can be a relative path */
8655: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
8656: #else
1.126 brouard 8657: chdir(path); /* Can be a relative path */
1.184 brouard 8658: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
8659: #endif
8660: printf("Current directory %s!\n",pathcd);
1.126 brouard 8661: strcpy(command,"mkdir ");
8662: strcat(command,optionfilefiname);
8663: if((outcmd=system(command)) != 0){
1.169 brouard 8664: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 8665: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
8666: /* fclose(ficlog); */
8667: /* exit(1); */
8668: }
8669: /* if((imk=mkdir(optionfilefiname))<0){ */
8670: /* perror("mkdir"); */
8671: /* } */
8672:
8673: /*-------- arguments in the command line --------*/
8674:
1.186 brouard 8675: /* Main Log file */
1.126 brouard 8676: strcat(filelog, optionfilefiname);
8677: strcat(filelog,".log"); /* */
8678: if((ficlog=fopen(filelog,"w"))==NULL) {
8679: printf("Problem with logfile %s\n",filelog);
8680: goto end;
8681: }
8682: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 8683: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 8684: fprintf(ficlog,"\nEnter the parameter file name: \n");
8685: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
8686: path=%s \n\
8687: optionfile=%s\n\
8688: optionfilext=%s\n\
1.156 brouard 8689: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 8690:
1.197 brouard 8691: syscompilerinfo(1);
1.167 brouard 8692:
1.126 brouard 8693: printf("Local time (at start):%s",strstart);
8694: fprintf(ficlog,"Local time (at start): %s",strstart);
8695: fflush(ficlog);
8696: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 8697: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 8698:
8699: /* */
8700: strcpy(fileres,"r");
8701: strcat(fileres, optionfilefiname);
1.201 brouard 8702: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 8703: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 8704: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 8705:
1.186 brouard 8706: /* Main ---------arguments file --------*/
1.126 brouard 8707:
8708: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 8709: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
8710: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 8711: fflush(ficlog);
1.149 brouard 8712: /* goto end; */
8713: exit(70);
1.126 brouard 8714: }
8715:
8716:
8717:
8718: strcpy(filereso,"o");
1.201 brouard 8719: strcat(filereso,fileresu);
1.126 brouard 8720: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
8721: printf("Problem with Output resultfile: %s\n", filereso);
8722: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
8723: fflush(ficlog);
8724: goto end;
8725: }
8726:
8727: /* Reads comments: lines beginning with '#' */
8728: numlinepar=0;
1.197 brouard 8729:
8730: /* First parameter line */
8731: while(fgets(line, MAXLINE, ficpar)) {
8732: /* If line starts with a # it is a comment */
8733: if (line[0] == '#') {
8734: numlinepar++;
8735: fputs(line,stdout);
8736: fputs(line,ficparo);
8737: fputs(line,ficlog);
8738: continue;
8739: }else
8740: break;
8741: }
8742: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
8743: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
8744: if (num_filled != 5) {
8745: printf("Should be 5 parameters\n");
8746: }
1.126 brouard 8747: numlinepar++;
1.197 brouard 8748: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
8749: }
8750: /* Second parameter line */
8751: while(fgets(line, MAXLINE, ficpar)) {
8752: /* If line starts with a # it is a comment */
8753: if (line[0] == '#') {
8754: numlinepar++;
8755: fputs(line,stdout);
8756: fputs(line,ficparo);
8757: fputs(line,ficlog);
8758: continue;
8759: }else
8760: break;
8761: }
1.223 brouard 8762: if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
8763: &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
8764: if (num_filled != 11) {
8765: printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
1.209 brouard 8766: printf("but line=%s\n",line);
1.197 brouard 8767: }
1.223 brouard 8768: printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
1.126 brouard 8769: }
1.203 brouard 8770: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 8771: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 8772: /* Third parameter line */
8773: while(fgets(line, MAXLINE, ficpar)) {
8774: /* If line starts with a # it is a comment */
8775: if (line[0] == '#') {
8776: numlinepar++;
8777: fputs(line,stdout);
8778: fputs(line,ficparo);
8779: fputs(line,ficlog);
8780: continue;
8781: }else
8782: break;
8783: }
1.201 brouard 8784: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
8785: if (num_filled == 0)
8786: model[0]='\0';
8787: else if (num_filled != 1){
1.197 brouard 8788: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
8789: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
8790: model[0]='\0';
8791: goto end;
8792: }
8793: else{
8794: if (model[0]=='+'){
8795: for(i=1; i<=strlen(model);i++)
8796: modeltemp[i-1]=model[i];
1.201 brouard 8797: strcpy(model,modeltemp);
1.197 brouard 8798: }
8799: }
1.199 brouard 8800: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 8801: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 8802: }
8803: /* 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); */
8804: /* numlinepar=numlinepar+3; /\* In general *\/ */
8805: /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
1.223 brouard 8806: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
8807: fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
1.126 brouard 8808: fflush(ficlog);
1.190 brouard 8809: /* if(model[0]=='#'|| model[0]== '\0'){ */
8810: if(model[0]=='#'){
1.187 brouard 8811: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
8812: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
8813: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
8814: if(mle != -1){
8815: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
8816: exit(1);
8817: }
8818: }
1.126 brouard 8819: while((c=getc(ficpar))=='#' && c!= EOF){
8820: ungetc(c,ficpar);
8821: fgets(line, MAXLINE, ficpar);
8822: numlinepar++;
1.195 brouard 8823: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
8824: z[0]=line[1];
8825: }
8826: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 8827: fputs(line, stdout);
8828: //puts(line);
1.126 brouard 8829: fputs(line,ficparo);
8830: fputs(line,ficlog);
8831: }
8832: ungetc(c,ficpar);
8833:
8834:
1.145 brouard 8835: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.223 brouard 8836: coqvar=matrix(1,nqv,1,n); /**< used in readdata */
8837: cotvar=ma3x(1,maxwav,1,ntv,1,n); /**< used in readdata */
1.224 ! brouard 8838: cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /**< used in readdata */
1.136 brouard 8839: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
8840: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
8841: v1+v2*age+v2*v3 makes cptcovn = 3
8842: */
8843: if (strlen(model)>1)
1.187 brouard 8844: 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 8845: else
1.187 brouard 8846: ncovmodel=2; /* Constant and age */
1.133 brouard 8847: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
8848: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 8849: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
8850: 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);
8851: 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);
8852: fflush(stdout);
8853: fclose (ficlog);
8854: goto end;
8855: }
1.126 brouard 8856: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
8857: delti=delti3[1][1];
8858: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
8859: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
8860: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 8861: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
8862: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 8863: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8864: fclose (ficparo);
8865: fclose (ficlog);
8866: goto end;
8867: exit(0);
1.220 brouard 8868: } else if(mle==-5) { /* Main Wizard */
1.126 brouard 8869: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 8870: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
8871: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 8872: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
8873: matcov=matrix(1,npar,1,npar);
1.203 brouard 8874: hess=matrix(1,npar,1,npar);
1.220 brouard 8875: } else{ /* Begin of mle != -1 or -5 */
1.145 brouard 8876: /* Read guessed parameters */
1.126 brouard 8877: /* Reads comments: lines beginning with '#' */
8878: while((c=getc(ficpar))=='#' && c!= EOF){
8879: ungetc(c,ficpar);
8880: fgets(line, MAXLINE, ficpar);
8881: numlinepar++;
1.141 brouard 8882: fputs(line,stdout);
1.126 brouard 8883: fputs(line,ficparo);
8884: fputs(line,ficlog);
8885: }
8886: ungetc(c,ficpar);
8887:
8888: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
8889: for(i=1; i <=nlstate; i++){
1.220 brouard 8890: j=0;
1.126 brouard 8891: for(jj=1; jj <=nlstate+ndeath; jj++){
1.220 brouard 8892: if(jj==i) continue;
8893: j++;
8894: fscanf(ficpar,"%1d%1d",&i1,&j1);
8895: if ((i1 != i) || (j1 != jj)){
8896: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126 brouard 8897: It might be a problem of design; if ncovcol and the model are correct\n \
8898: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.220 brouard 8899: exit(1);
8900: }
8901: fprintf(ficparo,"%1d%1d",i1,j1);
8902: if(mle==1)
8903: printf("%1d%1d",i,jj);
8904: fprintf(ficlog,"%1d%1d",i,jj);
8905: for(k=1; k<=ncovmodel;k++){
8906: fscanf(ficpar," %lf",¶m[i][j][k]);
8907: if(mle==1){
8908: printf(" %lf",param[i][j][k]);
8909: fprintf(ficlog," %lf",param[i][j][k]);
8910: }
8911: else
8912: fprintf(ficlog," %lf",param[i][j][k]);
8913: fprintf(ficparo," %lf",param[i][j][k]);
8914: }
8915: fscanf(ficpar,"\n");
8916: numlinepar++;
8917: if(mle==1)
8918: printf("\n");
8919: fprintf(ficlog,"\n");
8920: fprintf(ficparo,"\n");
1.126 brouard 8921: }
8922: }
8923: fflush(ficlog);
8924:
1.145 brouard 8925: /* Reads scales values */
1.126 brouard 8926: p=param[1][1];
8927:
8928: /* Reads comments: lines beginning with '#' */
8929: while((c=getc(ficpar))=='#' && c!= EOF){
8930: ungetc(c,ficpar);
8931: fgets(line, MAXLINE, ficpar);
8932: numlinepar++;
1.141 brouard 8933: fputs(line,stdout);
1.126 brouard 8934: fputs(line,ficparo);
8935: fputs(line,ficlog);
8936: }
8937: ungetc(c,ficpar);
8938:
8939: for(i=1; i <=nlstate; i++){
8940: for(j=1; j <=nlstate+ndeath-1; j++){
1.220 brouard 8941: fscanf(ficpar,"%1d%1d",&i1,&j1);
8942: if ( (i1-i) * (j1-j) != 0){
8943: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
8944: exit(1);
8945: }
8946: printf("%1d%1d",i,j);
8947: fprintf(ficparo,"%1d%1d",i1,j1);
8948: fprintf(ficlog,"%1d%1d",i1,j1);
8949: for(k=1; k<=ncovmodel;k++){
8950: fscanf(ficpar,"%le",&delti3[i][j][k]);
8951: printf(" %le",delti3[i][j][k]);
8952: fprintf(ficparo," %le",delti3[i][j][k]);
8953: fprintf(ficlog," %le",delti3[i][j][k]);
8954: }
8955: fscanf(ficpar,"\n");
8956: numlinepar++;
8957: printf("\n");
8958: fprintf(ficparo,"\n");
8959: fprintf(ficlog,"\n");
1.126 brouard 8960: }
8961: }
8962: fflush(ficlog);
1.220 brouard 8963:
1.145 brouard 8964: /* Reads covariance matrix */
1.126 brouard 8965: delti=delti3[1][1];
1.220 brouard 8966:
8967:
1.126 brouard 8968: /* 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 8969:
1.126 brouard 8970: /* Reads comments: lines beginning with '#' */
8971: while((c=getc(ficpar))=='#' && c!= EOF){
8972: ungetc(c,ficpar);
8973: fgets(line, MAXLINE, ficpar);
8974: numlinepar++;
1.141 brouard 8975: fputs(line,stdout);
1.126 brouard 8976: fputs(line,ficparo);
8977: fputs(line,ficlog);
8978: }
8979: ungetc(c,ficpar);
1.220 brouard 8980:
1.126 brouard 8981: matcov=matrix(1,npar,1,npar);
1.203 brouard 8982: hess=matrix(1,npar,1,npar);
1.131 brouard 8983: for(i=1; i <=npar; i++)
8984: for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220 brouard 8985:
1.194 brouard 8986: /* Scans npar lines */
1.126 brouard 8987: for(i=1; i <=npar; i++){
1.194 brouard 8988: count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
8989: if(count != 3){
1.220 brouard 8990: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 8991: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
8992: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.220 brouard 8993: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 8994: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
8995: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.220 brouard 8996: exit(1);
8997: }else{
8998: if(mle==1)
8999: printf("%1d%1d%1d",i1,j1,jk);
9000: }
1.194 brouard 9001: fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
9002: fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
1.126 brouard 9003: for(j=1; j <=i; j++){
1.220 brouard 9004: fscanf(ficpar," %le",&matcov[i][j]);
9005: if(mle==1){
9006: printf(" %.5le",matcov[i][j]);
9007: }
9008: fprintf(ficlog," %.5le",matcov[i][j]);
9009: fprintf(ficparo," %.5le",matcov[i][j]);
1.126 brouard 9010: }
9011: fscanf(ficpar,"\n");
9012: numlinepar++;
9013: if(mle==1)
1.220 brouard 9014: printf("\n");
1.126 brouard 9015: fprintf(ficlog,"\n");
9016: fprintf(ficparo,"\n");
9017: }
1.194 brouard 9018: /* End of read covariance matrix npar lines */
1.126 brouard 9019: for(i=1; i <=npar; i++)
9020: for(j=i+1;j<=npar;j++)
1.220 brouard 9021: matcov[i][j]=matcov[j][i];
1.126 brouard 9022:
9023: if(mle==1)
9024: printf("\n");
9025: fprintf(ficlog,"\n");
9026:
9027: fflush(ficlog);
9028:
9029: /*-------- Rewriting parameter file ----------*/
9030: strcpy(rfileres,"r"); /* "Rparameterfile */
9031: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
9032: strcat(rfileres,"."); /* */
9033: strcat(rfileres,optionfilext); /* Other files have txt extension */
9034: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 9035: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
9036: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 9037: }
9038: fprintf(ficres,"#%s\n",version);
9039: } /* End of mle != -3 */
1.218 brouard 9040:
1.186 brouard 9041: /* Main data
9042: */
1.126 brouard 9043: n= lastobs;
9044: num=lvector(1,n);
9045: moisnais=vector(1,n);
9046: annais=vector(1,n);
9047: moisdc=vector(1,n);
9048: andc=vector(1,n);
1.220 brouard 9049: weight=vector(1,n);
1.126 brouard 9050: agedc=vector(1,n);
9051: cod=ivector(1,n);
1.220 brouard 9052: for(i=1;i<=n;i++){
9053: num[i]=0;
9054: moisnais[i]=0;
9055: annais[i]=0;
9056: moisdc[i]=0;
9057: andc[i]=0;
9058: agedc[i]=0;
9059: cod[i]=0;
9060: weight[i]=1.0; /* Equal weights, 1 by default */
9061: }
1.126 brouard 9062: mint=matrix(1,maxwav,1,n);
9063: anint=matrix(1,maxwav,1,n);
1.131 brouard 9064: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 9065: tab=ivector(1,NCOVMAX);
1.144 brouard 9066: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 9067: 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 9068:
1.136 brouard 9069: /* Reads data from file datafile */
9070: if (readdata(datafile, firstobs, lastobs, &imx)==1)
9071: goto end;
9072:
9073: /* Calculation of the number of parameters from char model */
1.137 brouard 9074: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
9075: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
9076: k=3 V4 Tvar[k=3]= 4 (from V4)
9077: k=2 V1 Tvar[k=2]= 1 (from V1)
9078: k=1 Tvar[1]=2 (from V2)
9079: */
9080: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
9081: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
9082: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
9083: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
9084: */
9085: /* For model-covariate k tells which data-covariate to use but
9086: because this model-covariate is a construction we invent a new column
9087: ncovcol + k1
9088: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
9089: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 9090: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 9091: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
9092: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
9093: */
1.145 brouard 9094: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
9095: 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 9096: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
9097: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 9098: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 9099: 4 covariates (3 plus signs)
9100: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
9101: */
1.136 brouard 9102:
1.186 brouard 9103: /* Main decodemodel */
9104:
1.187 brouard 9105:
1.223 brouard 9106: if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/
1.136 brouard 9107: goto end;
9108:
1.137 brouard 9109: if((double)(lastobs-imx)/(double)imx > 1.10){
9110: nbwarn++;
9111: 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);
9112: 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);
9113: }
1.136 brouard 9114: /* if(mle==1){*/
1.137 brouard 9115: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
9116: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 9117: }
9118:
9119: /*-calculation of age at interview from date of interview and age at death -*/
9120: agev=matrix(1,maxwav,1,imx);
9121:
9122: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
9123: goto end;
9124:
1.126 brouard 9125:
1.136 brouard 9126: agegomp=(int)agemin;
9127: free_vector(moisnais,1,n);
9128: free_vector(annais,1,n);
1.126 brouard 9129: /* free_matrix(mint,1,maxwav,1,n);
9130: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 9131: /* free_vector(moisdc,1,n); */
9132: /* free_vector(andc,1,n); */
1.145 brouard 9133: /* */
9134:
1.126 brouard 9135: wav=ivector(1,imx);
1.214 brouard 9136: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
9137: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
9138: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
9139: 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.*/
9140: bh=imatrix(1,lastpass-firstpass+2,1,imx);
9141: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 9142:
9143: /* Concatenates waves */
1.214 brouard 9144: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
9145: Death is a valid wave (if date is known).
9146: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
9147: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
9148: and mw[mi+1][i]. dh depends on stepm.
9149: */
9150:
1.126 brouard 9151: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 9152: /* */
9153:
1.215 brouard 9154: free_vector(moisdc,1,n);
9155: free_vector(andc,1,n);
9156:
1.126 brouard 9157: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
9158: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
9159: ncodemax[1]=1;
1.145 brouard 9160: Ndum =ivector(-1,NCOVMAX);
1.220 brouard 9161: cptcoveff=0;
9162: if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
9163: tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
9164: }
9165:
9166: ncovcombmax=pow(2,cptcoveff);
9167: invalidvarcomb=ivector(1, ncovcombmax);
9168: for(i=1;i<ncovcombmax;i++)
9169: invalidvarcomb[i]=0;
9170:
1.211 brouard 9171: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 9172: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 9173: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.145 brouard 9174:
1.200 brouard 9175: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 9176: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 9177: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 9178: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
9179: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
9180: * (currently 0 or 1) in the data.
9181: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
9182: * corresponding modality (h,j).
9183: */
9184:
1.145 brouard 9185: h=0;
9186: /*if (cptcovn > 0) */
1.126 brouard 9187: m=pow(2,cptcoveff);
9188:
1.144 brouard 9189: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 9190: * For k=4 covariates, h goes from 1 to m=2**k
9191: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
9192: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 9193: * h\k 1 2 3 4
1.143 brouard 9194: *______________________________
9195: * 1 i=1 1 i=1 1 i=1 1 i=1 1
9196: * 2 2 1 1 1
9197: * 3 i=2 1 2 1 1
9198: * 4 2 2 1 1
9199: * 5 i=3 1 i=2 1 2 1
9200: * 6 2 1 2 1
9201: * 7 i=4 1 2 2 1
9202: * 8 2 2 2 1
1.197 brouard 9203: * 9 i=5 1 i=3 1 i=2 1 2
9204: * 10 2 1 1 2
9205: * 11 i=6 1 2 1 2
9206: * 12 2 2 1 2
9207: * 13 i=7 1 i=4 1 2 2
9208: * 14 2 1 2 2
9209: * 15 i=8 1 2 2 2
9210: * 16 2 2 2 2
1.143 brouard 9211: */
1.212 brouard 9212: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 9213: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
9214: * and the value of each covariate?
9215: * V1=1, V2=1, V3=2, V4=1 ?
9216: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
9217: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
9218: * In order to get the real value in the data, we use nbcode
9219: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
9220: * We are keeping this crazy system in order to be able (in the future?)
9221: * to have more than 2 values (0 or 1) for a covariate.
9222: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
9223: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
9224: * bbbbbbbb
9225: * 76543210
9226: * h-1 00000101 (6-1=5)
1.219 brouard 9227: *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211 brouard 9228: * &
9229: * 1 00000001 (1)
1.219 brouard 9230: * 00000000 = 1 & ((h-1) >> (k-1))
9231: * +1= 00000001 =1
1.211 brouard 9232: *
9233: * h=14, k=3 => h'=h-1=13, k'=k-1=2
9234: * h' 1101 =2^3+2^2+0x2^1+2^0
9235: * >>k' 11
9236: * & 00000001
9237: * = 00000001
9238: * +1 = 00000010=2 = codtabm(14,3)
9239: * Reverse h=6 and m=16?
9240: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
9241: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
9242: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
9243: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
9244: * V3=decodtabm(14,3,2**4)=2
9245: * h'=13 1101 =2^3+2^2+0x2^1+2^0
9246: *(h-1) >> (j-1) 0011 =13 >> 2
9247: * &1 000000001
9248: * = 000000001
9249: * +1= 000000010 =2
9250: * 2211
9251: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
9252: * V3=2
1.220 brouard 9253: * codtabm and decodtabm are identical
1.211 brouard 9254: */
9255:
1.145 brouard 9256:
9257: free_ivector(Ndum,-1,NCOVMAX);
9258:
9259:
1.126 brouard 9260:
1.186 brouard 9261: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 9262: strcpy(optionfilegnuplot,optionfilefiname);
9263: if(mle==-3)
1.201 brouard 9264: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 9265: strcat(optionfilegnuplot,".gp");
9266:
9267: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
9268: printf("Problem with file %s",optionfilegnuplot);
9269: }
9270: else{
1.204 brouard 9271: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 9272: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 9273: //fprintf(ficgp,"set missing 'NaNq'\n");
9274: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 9275: }
9276: /* fclose(ficgp);*/
1.186 brouard 9277:
9278:
9279: /* Initialisation of --------- index.htm --------*/
1.126 brouard 9280:
9281: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
9282: if(mle==-3)
1.201 brouard 9283: strcat(optionfilehtm,"-MORT_");
1.126 brouard 9284: strcat(optionfilehtm,".htm");
9285: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 9286: printf("Problem with %s \n",optionfilehtm);
9287: exit(0);
1.126 brouard 9288: }
9289:
9290: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
9291: strcat(optionfilehtmcov,"-cov.htm");
9292: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
9293: printf("Problem with %s \n",optionfilehtmcov), exit(0);
9294: }
9295: else{
9296: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
9297: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 9298: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 9299: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
9300: }
9301:
1.213 brouard 9302: 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 9303: <hr size=\"2\" color=\"#EC5E5E\"> \n\
9304: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 9305: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 9306: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 9307: \n\
9308: <hr size=\"2\" color=\"#EC5E5E\">\
9309: <ul><li><h4>Parameter files</h4>\n\
9310: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
9311: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
9312: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
9313: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
9314: - Date and time at start: %s</ul>\n",\
9315: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
9316: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
9317: fileres,fileres,\
9318: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
9319: fflush(fichtm);
9320:
9321: strcpy(pathr,path);
9322: strcat(pathr,optionfilefiname);
1.184 brouard 9323: #ifdef WIN32
9324: _chdir(optionfilefiname); /* Move to directory named optionfile */
9325: #else
1.126 brouard 9326: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 9327: #endif
9328:
1.126 brouard 9329:
1.220 brouard 9330: /* Calculates basic frequencies. Computes observed prevalence at single age
9331: and for any valid combination of covariates
1.126 brouard 9332: and prints on file fileres'p'. */
1.220 brouard 9333: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
1.223 brouard 9334: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 9335:
9336: fprintf(fichtm,"\n");
9337: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
9338: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
9339: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
9340: imx,agemin,agemax,jmin,jmax,jmean);
9341: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.220 brouard 9342: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9343: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9344: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9345: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218 brouard 9346:
1.126 brouard 9347: /* For Powell, parameters are in a vector p[] starting at p[1]
9348: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
9349: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
9350:
9351: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 9352: /* For mortality only */
1.126 brouard 9353: if (mle==-3){
1.136 brouard 9354: ximort=matrix(1,NDIM,1,NDIM);
1.220 brouard 9355: for(i=1;i<=NDIM;i++)
9356: for(j=1;j<=NDIM;j++)
9357: ximort[i][j]=0.;
1.186 brouard 9358: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 9359: cens=ivector(1,n);
9360: ageexmed=vector(1,n);
9361: agecens=vector(1,n);
9362: dcwave=ivector(1,n);
1.223 brouard 9363:
1.126 brouard 9364: for (i=1; i<=imx; i++){
9365: dcwave[i]=-1;
9366: for (m=firstpass; m<=lastpass; m++)
1.218 brouard 9367: if (s[m][i]>nlstate) {
9368: dcwave[i]=m;
9369: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
9370: break;
9371: }
1.126 brouard 9372: }
1.218 brouard 9373:
1.126 brouard 9374: for (i=1; i<=imx; i++) {
9375: if (wav[i]>0){
1.218 brouard 9376: ageexmed[i]=agev[mw[1][i]][i];
9377: j=wav[i];
9378: agecens[i]=1.;
9379:
9380: if (ageexmed[i]> 1 && wav[i] > 0){
9381: agecens[i]=agev[mw[j][i]][i];
9382: cens[i]= 1;
9383: }else if (ageexmed[i]< 1)
9384: cens[i]= -1;
9385: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
9386: cens[i]=0 ;
1.126 brouard 9387: }
9388: else cens[i]=-1;
9389: }
9390:
9391: for (i=1;i<=NDIM;i++) {
9392: for (j=1;j<=NDIM;j++)
1.218 brouard 9393: ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126 brouard 9394: }
9395:
1.145 brouard 9396: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 9397: /*printf("%lf %lf", p[1], p[2]);*/
9398:
9399:
1.136 brouard 9400: #ifdef GSL
9401: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 9402: #else
1.126 brouard 9403: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 9404: #endif
1.201 brouard 9405: strcpy(filerespow,"POW-MORT_");
9406: strcat(filerespow,fileresu);
1.126 brouard 9407: if((ficrespow=fopen(filerespow,"w"))==NULL) {
9408: printf("Problem with resultfile: %s\n", filerespow);
9409: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
9410: }
1.136 brouard 9411: #ifdef GSL
9412: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 9413: #else
1.126 brouard 9414: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 9415: #endif
1.126 brouard 9416: /* for (i=1;i<=nlstate;i++)
9417: for(j=1;j<=nlstate+ndeath;j++)
9418: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
9419: */
9420: fprintf(ficrespow,"\n");
1.136 brouard 9421: #ifdef GSL
9422: /* gsl starts here */
9423: T = gsl_multimin_fminimizer_nmsimplex;
9424: gsl_multimin_fminimizer *sfm = NULL;
9425: gsl_vector *ss, *x;
9426: gsl_multimin_function minex_func;
9427:
9428: /* Initial vertex size vector */
9429: ss = gsl_vector_alloc (NDIM);
9430:
9431: if (ss == NULL){
9432: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
9433: }
9434: /* Set all step sizes to 1 */
9435: gsl_vector_set_all (ss, 0.001);
9436:
9437: /* Starting point */
1.126 brouard 9438:
1.136 brouard 9439: x = gsl_vector_alloc (NDIM);
9440:
9441: if (x == NULL){
9442: gsl_vector_free(ss);
9443: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
9444: }
9445:
9446: /* Initialize method and iterate */
9447: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 9448: /* gsl_vector_set(x, 0, 0.0268); */
9449: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 9450: gsl_vector_set(x, 0, p[1]);
9451: gsl_vector_set(x, 1, p[2]);
9452:
9453: minex_func.f = &gompertz_f;
9454: minex_func.n = NDIM;
9455: minex_func.params = (void *)&p; /* ??? */
9456:
9457: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
9458: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
9459:
9460: printf("Iterations beginning .....\n\n");
9461: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
9462:
9463: iteri=0;
9464: while (rval == GSL_CONTINUE){
9465: iteri++;
9466: status = gsl_multimin_fminimizer_iterate(sfm);
9467:
9468: if (status) printf("error: %s\n", gsl_strerror (status));
9469: fflush(0);
9470:
9471: if (status)
9472: break;
9473:
9474: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
9475: ssval = gsl_multimin_fminimizer_size (sfm);
9476:
9477: if (rval == GSL_SUCCESS)
9478: printf ("converged to a local maximum at\n");
9479:
9480: printf("%5d ", iteri);
9481: for (it = 0; it < NDIM; it++){
9482: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
9483: }
9484: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
9485: }
9486:
9487: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
9488:
9489: gsl_vector_free(x); /* initial values */
9490: gsl_vector_free(ss); /* inital step size */
9491: for (it=0; it<NDIM; it++){
9492: p[it+1]=gsl_vector_get(sfm->x,it);
9493: fprintf(ficrespow," %.12lf", p[it]);
9494: }
9495: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
9496: #endif
9497: #ifdef POWELL
9498: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
9499: #endif
1.126 brouard 9500: fclose(ficrespow);
9501:
1.203 brouard 9502: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 9503:
9504: for(i=1; i <=NDIM; i++)
9505: for(j=i+1;j<=NDIM;j++)
1.220 brouard 9506: matcov[i][j]=matcov[j][i];
1.126 brouard 9507:
9508: printf("\nCovariance matrix\n ");
1.203 brouard 9509: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 9510: for(i=1; i <=NDIM; i++) {
9511: for(j=1;j<=NDIM;j++){
1.220 brouard 9512: printf("%f ",matcov[i][j]);
9513: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 9514: }
1.203 brouard 9515: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 9516: }
9517:
9518: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 9519: for (i=1;i<=NDIM;i++) {
1.126 brouard 9520: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 9521: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
9522: }
1.126 brouard 9523: lsurv=vector(1,AGESUP);
9524: lpop=vector(1,AGESUP);
9525: tpop=vector(1,AGESUP);
9526: lsurv[agegomp]=100000;
9527:
9528: for (k=agegomp;k<=AGESUP;k++) {
9529: agemortsup=k;
9530: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
9531: }
9532:
9533: for (k=agegomp;k<agemortsup;k++)
9534: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
9535:
9536: for (k=agegomp;k<agemortsup;k++){
9537: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
9538: sumlpop=sumlpop+lpop[k];
9539: }
9540:
9541: tpop[agegomp]=sumlpop;
9542: for (k=agegomp;k<(agemortsup-3);k++){
9543: /* tpop[k+1]=2;*/
9544: tpop[k+1]=tpop[k]-lpop[k];
9545: }
9546:
9547:
9548: printf("\nAge lx qx dx Lx Tx e(x)\n");
9549: for (k=agegomp;k<(agemortsup-2);k++)
9550: 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]);
9551:
9552:
9553: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220 brouard 9554: ageminpar=50;
9555: agemaxpar=100;
1.194 brouard 9556: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
9557: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
9558: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9559: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
9560: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
9561: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9562: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 9563: }else{
9564: printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
9565: 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 9566: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220 brouard 9567: }
1.201 brouard 9568: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 9569: stepm, weightopt,\
9570: model,imx,p,matcov,agemortsup);
9571:
9572: free_vector(lsurv,1,AGESUP);
9573: free_vector(lpop,1,AGESUP);
9574: free_vector(tpop,1,AGESUP);
1.220 brouard 9575: free_matrix(ximort,1,NDIM,1,NDIM);
1.136 brouard 9576: free_ivector(cens,1,n);
9577: free_vector(agecens,1,n);
9578: free_ivector(dcwave,1,n);
1.220 brouard 9579: #ifdef GSL
1.136 brouard 9580: #endif
1.186 brouard 9581: } /* Endof if mle==-3 mortality only */
1.205 brouard 9582: /* Standard */
9583: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
9584: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
9585: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 9586: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 9587: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
9588: for (k=1; k<=npar;k++)
9589: printf(" %d %8.5f",k,p[k]);
9590: printf("\n");
1.205 brouard 9591: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
9592: /* mlikeli uses func not funcone */
9593: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
9594: }
9595: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
9596: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
9597: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
9598: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
9599: }
9600: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 9601: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
9602: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
9603: for (k=1; k<=npar;k++)
9604: printf(" %d %8.5f",k,p[k]);
9605: printf("\n");
9606:
9607: /*--------- results files --------------*/
1.224 ! brouard 9608: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model);
1.126 brouard 9609:
9610:
9611: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9612: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9613: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9614: for(i=1,jk=1; i <=nlstate; i++){
9615: for(k=1; k <=(nlstate+ndeath); k++){
1.220 brouard 9616: if (k != i) {
9617: printf("%d%d ",i,k);
9618: fprintf(ficlog,"%d%d ",i,k);
9619: fprintf(ficres,"%1d%1d ",i,k);
9620: for(j=1; j <=ncovmodel; j++){
9621: printf("%12.7f ",p[jk]);
9622: fprintf(ficlog,"%12.7f ",p[jk]);
9623: fprintf(ficres,"%12.7f ",p[jk]);
9624: jk++;
9625: }
9626: printf("\n");
9627: fprintf(ficlog,"\n");
9628: fprintf(ficres,"\n");
9629: }
1.126 brouard 9630: }
9631: }
1.203 brouard 9632: if(mle != 0){
9633: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 9634: ftolhess=ftol; /* Usually correct */
1.203 brouard 9635: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
9636: 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");
9637: 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");
9638: for(i=1,jk=1; i <=nlstate; i++){
1.220 brouard 9639: for(k=1; k <=(nlstate+ndeath); k++){
9640: if (k != i) {
9641: printf("%d%d ",i,k);
9642: fprintf(ficlog,"%d%d ",i,k);
9643: for(j=1; j <=ncovmodel; j++){
9644: 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]));
9645: 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]));
9646: jk++;
9647: }
9648: printf("\n");
9649: fprintf(ficlog,"\n");
9650: }
9651: }
1.193 brouard 9652: }
1.203 brouard 9653: } /* end of hesscov and Wald tests */
1.220 brouard 9654:
1.203 brouard 9655: /* */
1.126 brouard 9656: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
9657: printf("# Scales (for hessian or gradient estimation)\n");
9658: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
9659: for(i=1,jk=1; i <=nlstate; i++){
9660: for(j=1; j <=nlstate+ndeath; j++){
1.220 brouard 9661: if (j!=i) {
9662: fprintf(ficres,"%1d%1d",i,j);
9663: printf("%1d%1d",i,j);
9664: fprintf(ficlog,"%1d%1d",i,j);
9665: for(k=1; k<=ncovmodel;k++){
9666: printf(" %.5e",delti[jk]);
9667: fprintf(ficlog," %.5e",delti[jk]);
9668: fprintf(ficres," %.5e",delti[jk]);
9669: jk++;
9670: }
9671: printf("\n");
9672: fprintf(ficlog,"\n");
9673: fprintf(ficres,"\n");
9674: }
1.126 brouard 9675: }
9676: }
9677:
9678: 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 9679: if(mle >= 1) /* To big for the screen */
1.126 brouard 9680: 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");
9681: 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");
9682: /* # 121 Var(a12)\n\ */
9683: /* # 122 Cov(b12,a12) Var(b12)\n\ */
9684: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
9685: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
9686: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
9687: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
9688: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
9689: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
9690:
9691:
9692: /* Just to have a covariance matrix which will be more understandable
9693: even is we still don't want to manage dictionary of variables
9694: */
9695: for(itimes=1;itimes<=2;itimes++){
9696: jj=0;
9697: for(i=1; i <=nlstate; i++){
1.220 brouard 9698: for(j=1; j <=nlstate+ndeath; j++){
9699: if(j==i) continue;
9700: for(k=1; k<=ncovmodel;k++){
9701: jj++;
9702: ca[0]= k+'a'-1;ca[1]='\0';
9703: if(itimes==1){
9704: if(mle>=1)
9705: printf("#%1d%1d%d",i,j,k);
9706: fprintf(ficlog,"#%1d%1d%d",i,j,k);
9707: fprintf(ficres,"#%1d%1d%d",i,j,k);
9708: }else{
9709: if(mle>=1)
9710: printf("%1d%1d%d",i,j,k);
9711: fprintf(ficlog,"%1d%1d%d",i,j,k);
9712: fprintf(ficres,"%1d%1d%d",i,j,k);
9713: }
9714: ll=0;
9715: for(li=1;li <=nlstate; li++){
9716: for(lj=1;lj <=nlstate+ndeath; lj++){
9717: if(lj==li) continue;
9718: for(lk=1;lk<=ncovmodel;lk++){
9719: ll++;
9720: if(ll<=jj){
9721: cb[0]= lk +'a'-1;cb[1]='\0';
9722: if(ll<jj){
9723: if(itimes==1){
9724: if(mle>=1)
9725: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9726: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9727: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9728: }else{
9729: if(mle>=1)
9730: printf(" %.5e",matcov[jj][ll]);
9731: fprintf(ficlog," %.5e",matcov[jj][ll]);
9732: fprintf(ficres," %.5e",matcov[jj][ll]);
9733: }
9734: }else{
9735: if(itimes==1){
9736: if(mle>=1)
9737: printf(" Var(%s%1d%1d)",ca,i,j);
9738: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
9739: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
9740: }else{
9741: if(mle>=1)
9742: printf(" %.7e",matcov[jj][ll]);
9743: fprintf(ficlog," %.7e",matcov[jj][ll]);
9744: fprintf(ficres," %.7e",matcov[jj][ll]);
9745: }
9746: }
9747: }
9748: } /* end lk */
9749: } /* end lj */
9750: } /* end li */
9751: if(mle>=1)
9752: printf("\n");
9753: fprintf(ficlog,"\n");
9754: fprintf(ficres,"\n");
9755: numlinepar++;
9756: } /* end k*/
9757: } /*end j */
1.126 brouard 9758: } /* end i */
9759: } /* end itimes */
9760:
9761: fflush(ficlog);
9762: fflush(ficres);
1.220 brouard 9763: while(fgets(line, MAXLINE, ficpar)) {
9764: /* If line starts with a # it is a comment */
9765: if (line[0] == '#') {
9766: numlinepar++;
9767: fputs(line,stdout);
9768: fputs(line,ficparo);
9769: fputs(line,ficlog);
9770: continue;
9771: }else
9772: break;
9773: }
9774:
1.209 brouard 9775: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
9776: /* ungetc(c,ficpar); */
9777: /* fgets(line, MAXLINE, ficpar); */
9778: /* fputs(line,stdout); */
9779: /* fputs(line,ficparo); */
9780: /* } */
9781: /* ungetc(c,ficpar); */
1.126 brouard 9782:
9783: estepm=0;
1.209 brouard 9784: 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 9785:
9786: if (num_filled != 6) {
9787: 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);
9788: 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);
9789: goto end;
9790: }
9791: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
9792: }
9793: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
9794: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
9795:
1.209 brouard 9796: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 9797: if (estepm==0 || estepm < stepm) estepm=stepm;
9798: if (fage <= 2) {
9799: bage = ageminpar;
9800: fage = agemaxpar;
9801: }
9802:
9803: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 9804: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
9805: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220 brouard 9806:
1.186 brouard 9807: /* Other stuffs, more or less useful */
1.126 brouard 9808: while((c=getc(ficpar))=='#' && c!= EOF){
9809: ungetc(c,ficpar);
9810: fgets(line, MAXLINE, ficpar);
1.141 brouard 9811: fputs(line,stdout);
1.126 brouard 9812: fputs(line,ficparo);
9813: }
9814: ungetc(c,ficpar);
9815:
9816: 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);
9817: 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);
9818: 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);
9819: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
9820: 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);
9821:
9822: while((c=getc(ficpar))=='#' && c!= EOF){
9823: ungetc(c,ficpar);
9824: fgets(line, MAXLINE, ficpar);
1.141 brouard 9825: fputs(line,stdout);
1.126 brouard 9826: fputs(line,ficparo);
9827: }
9828: ungetc(c,ficpar);
9829:
9830:
9831: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
9832: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
9833:
9834: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 9835: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 9836: fprintf(ficparo,"pop_based=%d\n",popbased);
9837: fprintf(ficres,"pop_based=%d\n",popbased);
9838:
9839: while((c=getc(ficpar))=='#' && c!= EOF){
9840: ungetc(c,ficpar);
9841: fgets(line, MAXLINE, ficpar);
1.141 brouard 9842: fputs(line,stdout);
1.126 brouard 9843: fputs(line,ficparo);
9844: }
9845: ungetc(c,ficpar);
9846:
9847: 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);
9848: 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);
9849: 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);
9850: 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);
9851: 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);
9852: /* day and month of proj2 are not used but only year anproj2.*/
9853:
1.217 brouard 9854: while((c=getc(ficpar))=='#' && c!= EOF){
9855: ungetc(c,ficpar);
9856: fgets(line, MAXLINE, ficpar);
9857: fputs(line,stdout);
9858: fputs(line,ficparo);
9859: }
9860: ungetc(c,ficpar);
9861:
9862: fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);
1.223 brouard 9863: 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);
9864: 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);
9865: 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 9866: /* day and month of proj2 are not used but only year anproj2.*/
1.126 brouard 9867:
9868:
1.220 brouard 9869: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145 brouard 9870: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 9871:
9872: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 9873: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.220 brouard 9874: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 9875: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9876: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 9877: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 9878: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9879: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 9880: }else{
1.218 brouard 9881: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
1.220 brouard 9882: }
9883: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
9884: model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
9885: jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
9886:
9887: /*------------ free_vector -------------*/
9888: /* chdir(path); */
9889:
1.215 brouard 9890: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
9891: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
9892: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
9893: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.126 brouard 9894: free_lvector(num,1,n);
9895: free_vector(agedc,1,n);
9896: /*free_matrix(covar,0,NCOVMAX,1,n);*/
9897: /*free_matrix(covar,1,NCOVMAX,1,n);*/
9898: fclose(ficparo);
9899: fclose(ficres);
1.220 brouard 9900:
9901:
1.186 brouard 9902: /* Other results (useful)*/
1.220 brouard 9903:
9904:
1.126 brouard 9905: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 9906: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
9907: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 9908: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 9909: fclose(ficrespl);
9910:
9911: /*------------- h Pij x at various ages ------------*/
1.180 brouard 9912: /*#include "hpijx.h"*/
9913: hPijx(p, bage, fage);
1.145 brouard 9914: fclose(ficrespij);
1.126 brouard 9915:
1.220 brouard 9916: /* ncovcombmax= pow(2,cptcoveff); */
1.219 brouard 9917: /*-------------- Variance of one-step probabilities---*/
1.145 brouard 9918: k=1;
1.126 brouard 9919: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
9920:
1.219 brouard 9921: /* Prevalence for each covariates in probs[age][status][cov] */
1.218 brouard 9922: probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.126 brouard 9923: for(i=1;i<=AGESUP;i++)
1.219 brouard 9924: for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.218 brouard 9925: for(k=1;k<=ncovcombmax;k++)
9926: probs[i][j][k]=0.;
1.219 brouard 9927: prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
9928: if (mobilav!=0 ||mobilavproj !=0 ) {
9929: mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
9930: for(i=1;i<=AGESUP;i++)
9931: for(j=1;j<=nlstate;j++)
9932: for(k=1;k<=ncovcombmax;k++)
9933: mobaverages[i][j][k]=0.;
9934: mobaverage=mobaverages;
9935: if (mobilav!=0) {
1.218 brouard 9936: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
9937: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
9938: printf(" Error in movingaverage mobilav=%d\n",mobilav);
9939: }
1.219 brouard 9940: }
9941: /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
9942: /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
9943: else if (mobilavproj !=0) {
1.218 brouard 9944: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
9945: fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
9946: printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
9947: }
1.219 brouard 9948: }
9949: }/* end if moving average */
9950:
1.126 brouard 9951: /*---------- Forecasting ------------------*/
9952: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
9953: if(prevfcast==1){
9954: /* if(stepm ==1){*/
1.224 ! brouard 9955: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, nqveff);
1.126 brouard 9956: }
1.217 brouard 9957: if(backcast==1){
1.219 brouard 9958: ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
9959: ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
9960: ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
9961:
9962: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
9963:
9964: bprlim=matrix(1,nlstate,1,nlstate);
9965: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
9966: fclose(ficresplb);
9967:
1.222 brouard 9968: hBijx(p, bage, fage, mobaverage);
9969: fclose(ficrespijb);
1.219 brouard 9970: free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
9971:
9972: /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
1.224 ! brouard 9973: bage, fage, firstpass, lastpass, anback2, p, nqveff); */
1.219 brouard 9974: free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
9975: free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
9976: free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
9977: }
1.217 brouard 9978:
1.186 brouard 9979:
9980: /* ------ Other prevalence ratios------------ */
1.126 brouard 9981:
1.215 brouard 9982: free_ivector(wav,1,imx);
9983: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
9984: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
9985: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.218 brouard 9986:
9987:
1.127 brouard 9988: /*---------- Health expectancies, no variances ------------*/
1.218 brouard 9989:
1.201 brouard 9990: strcpy(filerese,"E_");
9991: strcat(filerese,fileresu);
1.126 brouard 9992: if((ficreseij=fopen(filerese,"w"))==NULL) {
9993: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
9994: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
9995: }
1.208 brouard 9996: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
9997: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.219 brouard 9998:
1.224 ! brouard 9999: for (k=1; k <= (int) pow(2,nqveff); k++){
1.219 brouard 10000: fprintf(ficreseij,"\n#****** ");
1.224 ! brouard 10001: for(j=1;j<=nqveff;j++) {
1.220 brouard 10002: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.219 brouard 10003: }
10004: fprintf(ficreseij,"******\n");
10005:
10006: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
10007: oldm=oldms;savm=savms;
10008: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
1.127 brouard 10009:
1.219 brouard 10010: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127 brouard 10011: }
10012: fclose(ficreseij);
1.208 brouard 10013: printf("done evsij\n");fflush(stdout);
10014: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.218 brouard 10015:
1.127 brouard 10016: /*---------- Health expectancies and variances ------------*/
1.218 brouard 10017:
10018:
1.201 brouard 10019: strcpy(filerest,"T_");
10020: strcat(filerest,fileresu);
1.127 brouard 10021: if((ficrest=fopen(filerest,"w"))==NULL) {
10022: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
10023: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
10024: }
1.208 brouard 10025: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
10026: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.218 brouard 10027:
1.126 brouard 10028:
1.201 brouard 10029: strcpy(fileresstde,"STDE_");
10030: strcat(fileresstde,fileresu);
1.126 brouard 10031: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
10032: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
10033: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
10034: }
1.208 brouard 10035: printf(" Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
10036: fprintf(ficlog," Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 10037:
1.201 brouard 10038: strcpy(filerescve,"CVE_");
10039: strcat(filerescve,fileresu);
1.126 brouard 10040: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
10041: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
10042: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
10043: }
1.208 brouard 10044: printf(" Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
10045: fprintf(ficlog," Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 10046:
1.201 brouard 10047: strcpy(fileresv,"V_");
10048: strcat(fileresv,fileresu);
1.126 brouard 10049: if((ficresvij=fopen(fileresv,"w"))==NULL) {
10050: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
10051: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
10052: }
1.208 brouard 10053: printf(" Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(stdout);
10054: fprintf(ficlog," Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 10055:
1.145 brouard 10056: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
10057: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
10058:
1.224 ! brouard 10059: for (k=1; k <= (int) pow(2,nqveff); k++){
1.208 brouard 10060: fprintf(ficrest,"\n#****** ");
1.224 ! brouard 10061: for(j=1;j<=nqveff;j++)
1.218 brouard 10062: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 10063: fprintf(ficrest,"******\n");
10064:
10065: fprintf(ficresstdeij,"\n#****** ");
10066: fprintf(ficrescveij,"\n#****** ");
1.224 ! brouard 10067: for(j=1;j<=nqveff;j++) {
1.218 brouard 10068: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10069: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 10070: }
10071: fprintf(ficresstdeij,"******\n");
10072: fprintf(ficrescveij,"******\n");
10073:
10074: fprintf(ficresvij,"\n#****** ");
1.224 ! brouard 10075: for(j=1;j<=nqveff;j++)
1.218 brouard 10076: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 10077: fprintf(ficresvij,"******\n");
10078:
10079: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
10080: oldm=oldms;savm=savms;
10081: printf(" cvevsij %d, ",k);
10082: fprintf(ficlog, " cvevsij %d, ",k);
10083: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
10084: printf(" end cvevsij \n ");
10085: fprintf(ficlog, " end cvevsij \n ");
10086:
10087: /*
10088: */
10089: /* goto endfree; */
10090:
10091: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
10092: pstamp(ficrest);
10093:
10094:
10095: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.220 brouard 10096: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
10097: cptcod= 0; /* To be deleted */
10098: printf("varevsij %d \n",vpopbased);
10099: fprintf(ficlog, "varevsij %d \n",vpopbased);
10100: 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 */
10101: 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 ");
10102: if(vpopbased==1)
10103: 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);
10104: else
10105: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
10106: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
10107: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
10108: fprintf(ficrest,"\n");
10109: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
10110: epj=vector(1,nlstate+1);
10111: printf("Computing age specific period (stable) prevalences in each health state \n");
10112: fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
10113: for(age=bage; age <=fage ;age++){
10114: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
10115: if (vpopbased==1) {
10116: if(mobilav ==0){
10117: for(i=1; i<=nlstate;i++)
10118: prlim[i][i]=probs[(int)age][i][k];
10119: }else{ /* mobilav */
10120: for(i=1; i<=nlstate;i++)
10121: prlim[i][i]=mobaverage[(int)age][i][k];
10122: }
10123: }
1.219 brouard 10124:
1.220 brouard 10125: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
10126: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
10127: /* printf(" age %4.0f ",age); */
10128: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
10129: for(i=1, epj[j]=0.;i <=nlstate;i++) {
10130: epj[j] += prlim[i][i]*eij[i][j][(int)age];
10131: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
10132: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
10133: }
10134: epj[nlstate+1] +=epj[j];
10135: }
10136: /* printf(" age %4.0f \n",age); */
1.219 brouard 10137:
1.220 brouard 10138: for(i=1, vepp=0.;i <=nlstate;i++)
10139: for(j=1;j <=nlstate;j++)
10140: vepp += vareij[i][j][(int)age];
10141: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
10142: for(j=1;j <=nlstate;j++){
10143: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
10144: }
10145: fprintf(ficrest,"\n");
10146: }
1.208 brouard 10147: } /* End vpopbased */
10148: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
10149: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
10150: free_vector(epj,1,nlstate+1);
10151: printf("done \n");fflush(stdout);
10152: fprintf(ficlog,"done\n");fflush(ficlog);
10153:
1.145 brouard 10154: /*}*/
1.208 brouard 10155: } /* End k */
1.126 brouard 10156: free_vector(weight,1,n);
1.145 brouard 10157: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 10158: free_imatrix(s,1,maxwav+1,1,n);
10159: free_matrix(anint,1,maxwav,1,n);
10160: free_matrix(mint,1,maxwav,1,n);
10161: free_ivector(cod,1,n);
10162: free_ivector(tab,1,NCOVMAX);
10163: fclose(ficresstdeij);
10164: fclose(ficrescveij);
10165: fclose(ficresvij);
10166: fclose(ficrest);
1.208 brouard 10167: printf("done Health expectancies\n");fflush(stdout);
10168: fprintf(ficlog,"done Health expectancies\n");fflush(ficlog);
1.126 brouard 10169: fclose(ficpar);
10170:
10171: /*------- Variance of period (stable) prevalence------*/
10172:
1.201 brouard 10173: strcpy(fileresvpl,"VPL_");
10174: strcat(fileresvpl,fileresu);
1.126 brouard 10175: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
10176: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
10177: exit(0);
10178: }
1.208 brouard 10179: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
10180: fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.126 brouard 10181:
1.145 brouard 10182: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
10183: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
10184:
1.224 ! brouard 10185: for (k=1; k <= (int) pow(2,nqveff); k++){
1.145 brouard 10186: fprintf(ficresvpl,"\n#****** ");
1.224 ! brouard 10187: for(j=1;j<=nqveff;j++)
1.218 brouard 10188: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10189: fprintf(ficresvpl,"******\n");
10190:
10191: varpl=matrix(1,nlstate,(int) bage, (int) fage);
10192: oldm=oldms;savm=savms;
10193: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
10194: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 10195: /*}*/
1.126 brouard 10196: }
1.218 brouard 10197:
1.126 brouard 10198: fclose(ficresvpl);
1.208 brouard 10199: printf("done variance-covariance of period prevalence\n");fflush(stdout);
10200: fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
1.126 brouard 10201:
10202: /*---------- End : free ----------------*/
1.219 brouard 10203: if (mobilav!=0 ||mobilavproj !=0)
10204: 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 10205: free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220 brouard 10206: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
10207: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126 brouard 10208: } /* mle==-3 arrives here for freeing */
1.164 brouard 10209: /* endfree:*/
1.126 brouard 10210: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
10211: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
10212: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.224 ! brouard 10213: free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
1.223 brouard 10214: free_ma3x(cotvar,1,maxwav,1,ntv,1,n);
10215: free_matrix(coqvar,1,maxwav,1,n);
1.126 brouard 10216: free_matrix(covar,0,NCOVMAX,1,n);
10217: free_matrix(matcov,1,npar,1,npar);
1.203 brouard 10218: free_matrix(hess,1,npar,1,npar);
1.126 brouard 10219: /*free_vector(delti,1,npar);*/
10220: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
10221: free_matrix(agev,1,maxwav,1,imx);
10222: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
10223:
1.145 brouard 10224: free_ivector(ncodemax,1,NCOVMAX);
1.192 brouard 10225: free_ivector(ncodemaxwundef,1,NCOVMAX);
1.145 brouard 10226: free_ivector(Tvar,1,NCOVMAX);
10227: free_ivector(Tprod,1,NCOVMAX);
10228: free_ivector(Tvaraff,1,NCOVMAX);
1.220 brouard 10229: free_ivector(invalidvarcomb,1,ncovcombmax);
1.145 brouard 10230: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 10231:
10232: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
1.200 brouard 10233: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 10234: fflush(fichtm);
10235: fflush(ficgp);
10236:
10237:
10238: if((nberr >0) || (nbwarn>0)){
1.216 brouard 10239: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
10240: 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 10241: }else{
10242: printf("End of Imach\n");
10243: fprintf(ficlog,"End of Imach\n");
10244: }
10245: printf("See log file on %s\n",filelog);
10246: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 10247: /*(void) gettimeofday(&end_time,&tzp);*/
10248: rend_time = time(NULL);
10249: end_time = *localtime(&rend_time);
10250: /* tml = *localtime(&end_time.tm_sec); */
10251: strcpy(strtend,asctime(&end_time));
1.126 brouard 10252: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
10253: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 10254: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 10255:
1.157 brouard 10256: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
10257: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
10258: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 10259: /* printf("Total time was %d uSec.\n", total_usecs);*/
10260: /* if(fileappend(fichtm,optionfilehtm)){ */
10261: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
10262: fclose(fichtm);
10263: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
10264: fclose(fichtmcov);
10265: fclose(ficgp);
10266: fclose(ficlog);
10267: /*------ End -----------*/
10268:
10269:
10270: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 10271: #ifdef WIN32
10272: if (_chdir(pathcd) != 0)
10273: printf("Can't move to directory %s!\n",path);
10274: if(_getcwd(pathcd,MAXLINE) > 0)
10275: #else
1.126 brouard 10276: if(chdir(pathcd) != 0)
1.184 brouard 10277: printf("Can't move to directory %s!\n", path);
10278: if (getcwd(pathcd, MAXLINE) > 0)
10279: #endif
1.126 brouard 10280: printf("Current directory %s!\n",pathcd);
10281: /*strcat(plotcmd,CHARSEPARATOR);*/
10282: sprintf(plotcmd,"gnuplot");
1.157 brouard 10283: #ifdef _WIN32
1.126 brouard 10284: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
10285: #endif
10286: if(!stat(plotcmd,&info)){
1.158 brouard 10287: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 10288: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 10289: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 10290: }else
10291: strcpy(pplotcmd,plotcmd);
1.157 brouard 10292: #ifdef __unix
1.126 brouard 10293: strcpy(plotcmd,GNUPLOTPROGRAM);
10294: if(!stat(plotcmd,&info)){
1.158 brouard 10295: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 10296: }else
10297: strcpy(pplotcmd,plotcmd);
10298: #endif
10299: }else
10300: strcpy(pplotcmd,plotcmd);
10301:
10302: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 10303: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 10304:
10305: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 10306: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 10307: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 10308: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 10309: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 10310: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 10311: }
1.158 brouard 10312: printf(" Successful, please wait...");
1.126 brouard 10313: while (z[0] != 'q') {
10314: /* chdir(path); */
1.154 brouard 10315: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 10316: scanf("%s",z);
10317: /* if (z[0] == 'c') system("./imach"); */
10318: if (z[0] == 'e') {
1.158 brouard 10319: #ifdef __APPLE__
1.152 brouard 10320: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 10321: #elif __linux
10322: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 10323: #else
1.152 brouard 10324: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 10325: #endif
10326: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
10327: system(pplotcmd);
1.126 brouard 10328: }
10329: else if (z[0] == 'g') system(plotcmd);
10330: else if (z[0] == 'q') exit(0);
10331: }
10332: end:
10333: while (z[0] != 'q') {
1.195 brouard 10334: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 10335: scanf("%s",z);
10336: }
10337: }
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