Annotation of imach/src/imach.c, revision 1.229
1.229 ! brouard 1: /* $Id: imach.c,v 1.228 2016/07/22 17:45:30 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.229 ! brouard 4: Revision 1.228 2016/07/22 17:45:30 brouard
! 5: Summary: Fixing some arrays, still debugging
! 6:
1.227 brouard 7: Revision 1.226 2016/07/12 18:42:34 brouard
8: Summary: temp
9:
1.226 brouard 10: Revision 1.225 2016/07/12 08:40:03 brouard
11: Summary: saving but not running
12:
1.225 brouard 13: Revision 1.224 2016/07/01 13:16:01 brouard
14: Summary: Fixes
15:
1.224 brouard 16: Revision 1.223 2016/02/19 09:23:35 brouard
17: Summary: temporary
18:
1.223 brouard 19: Revision 1.222 2016/02/17 08:14:50 brouard
20: Summary: Probably last 0.98 stable version 0.98r6
21:
1.222 brouard 22: Revision 1.221 2016/02/15 23:35:36 brouard
23: Summary: minor bug
24:
1.220 brouard 25: Revision 1.219 2016/02/15 00:48:12 brouard
26: *** empty log message ***
27:
1.219 brouard 28: Revision 1.218 2016/02/12 11:29:23 brouard
29: Summary: 0.99 Back projections
30:
1.218 brouard 31: Revision 1.217 2015/12/23 17:18:31 brouard
32: Summary: Experimental backcast
33:
1.217 brouard 34: Revision 1.216 2015/12/18 17:32:11 brouard
35: Summary: 0.98r4 Warning and status=-2
36:
37: Version 0.98r4 is now:
38: - displaying an error when status is -1, date of interview unknown and date of death known;
39: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
40: Older changes concerning s=-2, dating from 2005 have been supersed.
41:
1.216 brouard 42: Revision 1.215 2015/12/16 08:52:24 brouard
43: Summary: 0.98r4 working
44:
1.215 brouard 45: Revision 1.214 2015/12/16 06:57:54 brouard
46: Summary: temporary not working
47:
1.214 brouard 48: Revision 1.213 2015/12/11 18:22:17 brouard
49: Summary: 0.98r4
50:
1.213 brouard 51: Revision 1.212 2015/11/21 12:47:24 brouard
52: Summary: minor typo
53:
1.212 brouard 54: Revision 1.211 2015/11/21 12:41:11 brouard
55: Summary: 0.98r3 with some graph of projected cross-sectional
56:
57: Author: Nicolas Brouard
58:
1.211 brouard 59: Revision 1.210 2015/11/18 17:41:20 brouard
60: Summary: Start working on projected prevalences
61:
1.210 brouard 62: Revision 1.209 2015/11/17 22:12:03 brouard
63: Summary: Adding ftolpl parameter
64: Author: N Brouard
65:
66: We had difficulties to get smoothed confidence intervals. It was due
67: to the period prevalence which wasn't computed accurately. The inner
68: parameter ftolpl is now an outer parameter of the .imach parameter
69: file after estepm. If ftolpl is small 1.e-4 and estepm too,
70: computation are long.
71:
1.209 brouard 72: Revision 1.208 2015/11/17 14:31:57 brouard
73: Summary: temporary
74:
1.208 brouard 75: Revision 1.207 2015/10/27 17:36:57 brouard
76: *** empty log message ***
77:
1.207 brouard 78: Revision 1.206 2015/10/24 07:14:11 brouard
79: *** empty log message ***
80:
1.206 brouard 81: Revision 1.205 2015/10/23 15:50:53 brouard
82: Summary: 0.98r3 some clarification for graphs on likelihood contributions
83:
1.205 brouard 84: Revision 1.204 2015/10/01 16:20:26 brouard
85: Summary: Some new graphs of contribution to likelihood
86:
1.204 brouard 87: Revision 1.203 2015/09/30 17:45:14 brouard
88: Summary: looking at better estimation of the hessian
89:
90: Also a better criteria for convergence to the period prevalence And
91: therefore adding the number of years needed to converge. (The
92: prevalence in any alive state shold sum to one
93:
1.203 brouard 94: Revision 1.202 2015/09/22 19:45:16 brouard
95: Summary: Adding some overall graph on contribution to likelihood. Might change
96:
1.202 brouard 97: Revision 1.201 2015/09/15 17:34:58 brouard
98: Summary: 0.98r0
99:
100: - Some new graphs like suvival functions
101: - Some bugs fixed like model=1+age+V2.
102:
1.201 brouard 103: Revision 1.200 2015/09/09 16:53:55 brouard
104: Summary: Big bug thanks to Flavia
105:
106: Even model=1+age+V2. did not work anymore
107:
1.200 brouard 108: Revision 1.199 2015/09/07 14:09:23 brouard
109: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
110:
1.199 brouard 111: Revision 1.198 2015/09/03 07:14:39 brouard
112: Summary: 0.98q5 Flavia
113:
1.198 brouard 114: Revision 1.197 2015/09/01 18:24:39 brouard
115: *** empty log message ***
116:
1.197 brouard 117: Revision 1.196 2015/08/18 23:17:52 brouard
118: Summary: 0.98q5
119:
1.196 brouard 120: Revision 1.195 2015/08/18 16:28:39 brouard
121: Summary: Adding a hack for testing purpose
122:
123: After reading the title, ftol and model lines, if the comment line has
124: a q, starting with #q, the answer at the end of the run is quit. It
125: permits to run test files in batch with ctest. The former workaround was
126: $ echo q | imach foo.imach
127:
1.195 brouard 128: Revision 1.194 2015/08/18 13:32:00 brouard
129: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
130:
1.194 brouard 131: Revision 1.193 2015/08/04 07:17:42 brouard
132: Summary: 0.98q4
133:
1.193 brouard 134: Revision 1.192 2015/07/16 16:49:02 brouard
135: Summary: Fixing some outputs
136:
1.192 brouard 137: Revision 1.191 2015/07/14 10:00:33 brouard
138: Summary: Some fixes
139:
1.191 brouard 140: Revision 1.190 2015/05/05 08:51:13 brouard
141: Summary: Adding digits in output parameters (7 digits instead of 6)
142:
143: Fix 1+age+.
144:
1.190 brouard 145: Revision 1.189 2015/04/30 14:45:16 brouard
146: Summary: 0.98q2
147:
1.189 brouard 148: Revision 1.188 2015/04/30 08:27:53 brouard
149: *** empty log message ***
150:
1.188 brouard 151: Revision 1.187 2015/04/29 09:11:15 brouard
152: *** empty log message ***
153:
1.187 brouard 154: Revision 1.186 2015/04/23 12:01:52 brouard
155: Summary: V1*age is working now, version 0.98q1
156:
157: Some codes had been disabled in order to simplify and Vn*age was
158: working in the optimization phase, ie, giving correct MLE parameters,
159: but, as usual, outputs were not correct and program core dumped.
160:
1.186 brouard 161: Revision 1.185 2015/03/11 13:26:42 brouard
162: Summary: Inclusion of compile and links command line for Intel Compiler
163:
1.185 brouard 164: Revision 1.184 2015/03/11 11:52:39 brouard
165: Summary: Back from Windows 8. Intel Compiler
166:
1.184 brouard 167: Revision 1.183 2015/03/10 20:34:32 brouard
168: Summary: 0.98q0, trying with directest, mnbrak fixed
169:
170: We use directest instead of original Powell test; probably no
171: incidence on the results, but better justifications;
172: We fixed Numerical Recipes mnbrak routine which was wrong and gave
173: wrong results.
174:
1.183 brouard 175: Revision 1.182 2015/02/12 08:19:57 brouard
176: Summary: Trying to keep directest which seems simpler and more general
177: Author: Nicolas Brouard
178:
1.182 brouard 179: Revision 1.181 2015/02/11 23:22:24 brouard
180: Summary: Comments on Powell added
181:
182: Author:
183:
1.181 brouard 184: Revision 1.180 2015/02/11 17:33:45 brouard
185: Summary: Finishing move from main to function (hpijx and prevalence_limit)
186:
1.180 brouard 187: Revision 1.179 2015/01/04 09:57:06 brouard
188: Summary: back to OS/X
189:
1.179 brouard 190: Revision 1.178 2015/01/04 09:35:48 brouard
191: *** empty log message ***
192:
1.178 brouard 193: Revision 1.177 2015/01/03 18:40:56 brouard
194: Summary: Still testing ilc32 on OSX
195:
1.177 brouard 196: Revision 1.176 2015/01/03 16:45:04 brouard
197: *** empty log message ***
198:
1.176 brouard 199: Revision 1.175 2015/01/03 16:33:42 brouard
200: *** empty log message ***
201:
1.175 brouard 202: Revision 1.174 2015/01/03 16:15:49 brouard
203: Summary: Still in cross-compilation
204:
1.174 brouard 205: Revision 1.173 2015/01/03 12:06:26 brouard
206: Summary: trying to detect cross-compilation
207:
1.173 brouard 208: Revision 1.172 2014/12/27 12:07:47 brouard
209: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
210:
1.172 brouard 211: Revision 1.171 2014/12/23 13:26:59 brouard
212: Summary: Back from Visual C
213:
214: Still problem with utsname.h on Windows
215:
1.171 brouard 216: Revision 1.170 2014/12/23 11:17:12 brouard
217: Summary: Cleaning some \%% back to %%
218:
219: The escape was mandatory for a specific compiler (which one?), but too many warnings.
220:
1.170 brouard 221: Revision 1.169 2014/12/22 23:08:31 brouard
222: Summary: 0.98p
223:
224: Outputs some informations on compiler used, OS etc. Testing on different platforms.
225:
1.169 brouard 226: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 227: Summary: update
1.169 brouard 228:
1.168 brouard 229: Revision 1.167 2014/12/22 13:50:56 brouard
230: Summary: Testing uname and compiler version and if compiled 32 or 64
231:
232: Testing on Linux 64
233:
1.167 brouard 234: Revision 1.166 2014/12/22 11:40:47 brouard
235: *** empty log message ***
236:
1.166 brouard 237: Revision 1.165 2014/12/16 11:20:36 brouard
238: Summary: After compiling on Visual C
239:
240: * imach.c (Module): Merging 1.61 to 1.162
241:
1.165 brouard 242: Revision 1.164 2014/12/16 10:52:11 brouard
243: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
244:
245: * imach.c (Module): Merging 1.61 to 1.162
246:
1.164 brouard 247: Revision 1.163 2014/12/16 10:30:11 brouard
248: * imach.c (Module): Merging 1.61 to 1.162
249:
1.163 brouard 250: Revision 1.162 2014/09/25 11:43:39 brouard
251: Summary: temporary backup 0.99!
252:
1.162 brouard 253: Revision 1.1 2014/09/16 11:06:58 brouard
254: Summary: With some code (wrong) for nlopt
255:
256: Author:
257:
258: Revision 1.161 2014/09/15 20:41:41 brouard
259: Summary: Problem with macro SQR on Intel compiler
260:
1.161 brouard 261: Revision 1.160 2014/09/02 09:24:05 brouard
262: *** empty log message ***
263:
1.160 brouard 264: Revision 1.159 2014/09/01 10:34:10 brouard
265: Summary: WIN32
266: Author: Brouard
267:
1.159 brouard 268: Revision 1.158 2014/08/27 17:11:51 brouard
269: *** empty log message ***
270:
1.158 brouard 271: Revision 1.157 2014/08/27 16:26:55 brouard
272: Summary: Preparing windows Visual studio version
273: Author: Brouard
274:
275: In order to compile on Visual studio, time.h is now correct and time_t
276: and tm struct should be used. difftime should be used but sometimes I
277: just make the differences in raw time format (time(&now).
278: Trying to suppress #ifdef LINUX
279: Add xdg-open for __linux in order to open default browser.
280:
1.157 brouard 281: Revision 1.156 2014/08/25 20:10:10 brouard
282: *** empty log message ***
283:
1.156 brouard 284: Revision 1.155 2014/08/25 18:32:34 brouard
285: Summary: New compile, minor changes
286: Author: Brouard
287:
1.155 brouard 288: Revision 1.154 2014/06/20 17:32:08 brouard
289: Summary: Outputs now all graphs of convergence to period prevalence
290:
1.154 brouard 291: Revision 1.153 2014/06/20 16:45:46 brouard
292: Summary: If 3 live state, convergence to period prevalence on same graph
293: Author: Brouard
294:
1.153 brouard 295: Revision 1.152 2014/06/18 17:54:09 brouard
296: Summary: open browser, use gnuplot on same dir than imach if not found in the path
297:
1.152 brouard 298: Revision 1.151 2014/06/18 16:43:30 brouard
299: *** empty log message ***
300:
1.151 brouard 301: Revision 1.150 2014/06/18 16:42:35 brouard
302: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
303: Author: brouard
304:
1.150 brouard 305: Revision 1.149 2014/06/18 15:51:14 brouard
306: Summary: Some fixes in parameter files errors
307: Author: Nicolas Brouard
308:
1.149 brouard 309: Revision 1.148 2014/06/17 17:38:48 brouard
310: Summary: Nothing new
311: Author: Brouard
312:
313: Just a new packaging for OS/X version 0.98nS
314:
1.148 brouard 315: Revision 1.147 2014/06/16 10:33:11 brouard
316: *** empty log message ***
317:
1.147 brouard 318: Revision 1.146 2014/06/16 10:20:28 brouard
319: Summary: Merge
320: Author: Brouard
321:
322: Merge, before building revised version.
323:
1.146 brouard 324: Revision 1.145 2014/06/10 21:23:15 brouard
325: Summary: Debugging with valgrind
326: Author: Nicolas Brouard
327:
328: Lot of changes in order to output the results with some covariates
329: After the Edimburgh REVES conference 2014, it seems mandatory to
330: improve the code.
331: No more memory valgrind error but a lot has to be done in order to
332: continue the work of splitting the code into subroutines.
333: Also, decodemodel has been improved. Tricode is still not
334: optimal. nbcode should be improved. Documentation has been added in
335: the source code.
336:
1.144 brouard 337: Revision 1.143 2014/01/26 09:45:38 brouard
338: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
339:
340: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
341: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
342:
1.143 brouard 343: Revision 1.142 2014/01/26 03:57:36 brouard
344: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
345:
346: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
347:
1.142 brouard 348: Revision 1.141 2014/01/26 02:42:01 brouard
349: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
350:
1.141 brouard 351: Revision 1.140 2011/09/02 10:37:54 brouard
352: Summary: times.h is ok with mingw32 now.
353:
1.140 brouard 354: Revision 1.139 2010/06/14 07:50:17 brouard
355: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
356: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
357:
1.139 brouard 358: Revision 1.138 2010/04/30 18:19:40 brouard
359: *** empty log message ***
360:
1.138 brouard 361: Revision 1.137 2010/04/29 18:11:38 brouard
362: (Module): Checking covariates for more complex models
363: than V1+V2. A lot of change to be done. Unstable.
364:
1.137 brouard 365: Revision 1.136 2010/04/26 20:30:53 brouard
366: (Module): merging some libgsl code. Fixing computation
367: of likelione (using inter/intrapolation if mle = 0) in order to
368: get same likelihood as if mle=1.
369: Some cleaning of code and comments added.
370:
1.136 brouard 371: Revision 1.135 2009/10/29 15:33:14 brouard
372: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
373:
1.135 brouard 374: Revision 1.134 2009/10/29 13:18:53 brouard
375: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
376:
1.134 brouard 377: Revision 1.133 2009/07/06 10:21:25 brouard
378: just nforces
379:
1.133 brouard 380: Revision 1.132 2009/07/06 08:22:05 brouard
381: Many tings
382:
1.132 brouard 383: Revision 1.131 2009/06/20 16:22:47 brouard
384: Some dimensions resccaled
385:
1.131 brouard 386: Revision 1.130 2009/05/26 06:44:34 brouard
387: (Module): Max Covariate is now set to 20 instead of 8. A
388: lot of cleaning with variables initialized to 0. Trying to make
389: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
390:
1.130 brouard 391: Revision 1.129 2007/08/31 13:49:27 lievre
392: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
393:
1.129 lievre 394: Revision 1.128 2006/06/30 13:02:05 brouard
395: (Module): Clarifications on computing e.j
396:
1.128 brouard 397: Revision 1.127 2006/04/28 18:11:50 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: (Module): In order to speed up (in case of numerous covariates) we
402: compute health expectancies (without variances) in a first step
403: and then all the health expectancies with variances or standard
404: deviation (needs data from the Hessian matrices) which slows the
405: computation.
406: In the future we should be able to stop the program is only health
407: expectancies and graph are needed without standard deviations.
408:
1.127 brouard 409: Revision 1.126 2006/04/28 17:23:28 brouard
410: (Module): Yes the sum of survivors was wrong since
411: imach-114 because nhstepm was no more computed in the age
412: loop. Now we define nhstepma in the age loop.
413: Version 0.98h
414:
1.126 brouard 415: Revision 1.125 2006/04/04 15:20:31 lievre
416: Errors in calculation of health expectancies. Age was not initialized.
417: Forecasting file added.
418:
419: Revision 1.124 2006/03/22 17:13:53 lievre
420: Parameters are printed with %lf instead of %f (more numbers after the comma).
421: The log-likelihood is printed in the log file
422:
423: Revision 1.123 2006/03/20 10:52:43 brouard
424: * imach.c (Module): <title> changed, corresponds to .htm file
425: name. <head> headers where missing.
426:
427: * imach.c (Module): Weights can have a decimal point as for
428: English (a comma might work with a correct LC_NUMERIC environment,
429: otherwise the weight is truncated).
430: Modification of warning when the covariates values are not 0 or
431: 1.
432: Version 0.98g
433:
434: Revision 1.122 2006/03/20 09:45:41 brouard
435: (Module): Weights can have a decimal point as for
436: English (a comma might work with a correct LC_NUMERIC environment,
437: otherwise the weight is truncated).
438: Modification of warning when the covariates values are not 0 or
439: 1.
440: Version 0.98g
441:
442: Revision 1.121 2006/03/16 17:45:01 lievre
443: * imach.c (Module): Comments concerning covariates added
444:
445: * imach.c (Module): refinements in the computation of lli if
446: status=-2 in order to have more reliable computation if stepm is
447: not 1 month. Version 0.98f
448:
449: Revision 1.120 2006/03/16 15:10:38 lievre
450: (Module): refinements in the computation of lli if
451: status=-2 in order to have more reliable computation if stepm is
452: not 1 month. Version 0.98f
453:
454: Revision 1.119 2006/03/15 17:42:26 brouard
455: (Module): Bug if status = -2, the loglikelihood was
456: computed as likelihood omitting the logarithm. Version O.98e
457:
458: Revision 1.118 2006/03/14 18:20:07 brouard
459: (Module): varevsij Comments added explaining the second
460: table of variances if popbased=1 .
461: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
462: (Module): Function pstamp added
463: (Module): Version 0.98d
464:
465: Revision 1.117 2006/03/14 17:16:22 brouard
466: (Module): varevsij Comments added explaining the second
467: table of variances if popbased=1 .
468: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
469: (Module): Function pstamp added
470: (Module): Version 0.98d
471:
472: Revision 1.116 2006/03/06 10:29:27 brouard
473: (Module): Variance-covariance wrong links and
474: varian-covariance of ej. is needed (Saito).
475:
476: Revision 1.115 2006/02/27 12:17:45 brouard
477: (Module): One freematrix added in mlikeli! 0.98c
478:
479: Revision 1.114 2006/02/26 12:57:58 brouard
480: (Module): Some improvements in processing parameter
481: filename with strsep.
482:
483: Revision 1.113 2006/02/24 14:20:24 brouard
484: (Module): Memory leaks checks with valgrind and:
485: datafile was not closed, some imatrix were not freed and on matrix
486: allocation too.
487:
488: Revision 1.112 2006/01/30 09:55:26 brouard
489: (Module): Back to gnuplot.exe instead of wgnuplot.exe
490:
491: Revision 1.111 2006/01/25 20:38:18 brouard
492: (Module): Lots of cleaning and bugs added (Gompertz)
493: (Module): Comments can be added in data file. Missing date values
494: can be a simple dot '.'.
495:
496: Revision 1.110 2006/01/25 00:51:50 brouard
497: (Module): Lots of cleaning and bugs added (Gompertz)
498:
499: Revision 1.109 2006/01/24 19:37:15 brouard
500: (Module): Comments (lines starting with a #) are allowed in data.
501:
502: Revision 1.108 2006/01/19 18:05:42 lievre
503: Gnuplot problem appeared...
504: To be fixed
505:
506: Revision 1.107 2006/01/19 16:20:37 brouard
507: Test existence of gnuplot in imach path
508:
509: Revision 1.106 2006/01/19 13:24:36 brouard
510: Some cleaning and links added in html output
511:
512: Revision 1.105 2006/01/05 20:23:19 lievre
513: *** empty log message ***
514:
515: Revision 1.104 2005/09/30 16:11:43 lievre
516: (Module): sump fixed, loop imx fixed, and simplifications.
517: (Module): If the status is missing at the last wave but we know
518: that the person is alive, then we can code his/her status as -2
519: (instead of missing=-1 in earlier versions) and his/her
520: contributions to the likelihood is 1 - Prob of dying from last
521: health status (= 1-p13= p11+p12 in the easiest case of somebody in
522: the healthy state at last known wave). Version is 0.98
523:
524: Revision 1.103 2005/09/30 15:54:49 lievre
525: (Module): sump fixed, loop imx fixed, and simplifications.
526:
527: Revision 1.102 2004/09/15 17:31:30 brouard
528: Add the possibility to read data file including tab characters.
529:
530: Revision 1.101 2004/09/15 10:38:38 brouard
531: Fix on curr_time
532:
533: Revision 1.100 2004/07/12 18:29:06 brouard
534: Add version for Mac OS X. Just define UNIX in Makefile
535:
536: Revision 1.99 2004/06/05 08:57:40 brouard
537: *** empty log message ***
538:
539: Revision 1.98 2004/05/16 15:05:56 brouard
540: New version 0.97 . First attempt to estimate force of mortality
541: directly from the data i.e. without the need of knowing the health
542: state at each age, but using a Gompertz model: log u =a + b*age .
543: This is the basic analysis of mortality and should be done before any
544: other analysis, in order to test if the mortality estimated from the
545: cross-longitudinal survey is different from the mortality estimated
546: from other sources like vital statistic data.
547:
548: The same imach parameter file can be used but the option for mle should be -3.
549:
1.133 brouard 550: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 551: former routines in order to include the new code within the former code.
552:
553: The output is very simple: only an estimate of the intercept and of
554: the slope with 95% confident intervals.
555:
556: Current limitations:
557: A) Even if you enter covariates, i.e. with the
558: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
559: B) There is no computation of Life Expectancy nor Life Table.
560:
561: Revision 1.97 2004/02/20 13:25:42 lievre
562: Version 0.96d. Population forecasting command line is (temporarily)
563: suppressed.
564:
565: Revision 1.96 2003/07/15 15:38:55 brouard
566: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
567: rewritten within the same printf. Workaround: many printfs.
568:
569: Revision 1.95 2003/07/08 07:54:34 brouard
570: * imach.c (Repository):
571: (Repository): Using imachwizard code to output a more meaningful covariance
572: matrix (cov(a12,c31) instead of numbers.
573:
574: Revision 1.94 2003/06/27 13:00:02 brouard
575: Just cleaning
576:
577: Revision 1.93 2003/06/25 16:33:55 brouard
578: (Module): On windows (cygwin) function asctime_r doesn't
579: exist so I changed back to asctime which exists.
580: (Module): Version 0.96b
581:
582: Revision 1.92 2003/06/25 16:30:45 brouard
583: (Module): On windows (cygwin) function asctime_r doesn't
584: exist so I changed back to asctime which exists.
585:
586: Revision 1.91 2003/06/25 15:30:29 brouard
587: * imach.c (Repository): Duplicated warning errors corrected.
588: (Repository): Elapsed time after each iteration is now output. It
589: helps to forecast when convergence will be reached. Elapsed time
590: is stamped in powell. We created a new html file for the graphs
591: concerning matrix of covariance. It has extension -cov.htm.
592:
593: Revision 1.90 2003/06/24 12:34:15 brouard
594: (Module): Some bugs corrected for windows. Also, when
595: mle=-1 a template is output in file "or"mypar.txt with the design
596: of the covariance matrix to be input.
597:
598: Revision 1.89 2003/06/24 12:30:52 brouard
599: (Module): Some bugs corrected for windows. Also, when
600: mle=-1 a template is output in file "or"mypar.txt with the design
601: of the covariance matrix to be input.
602:
603: Revision 1.88 2003/06/23 17:54:56 brouard
604: * 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.
605:
606: Revision 1.87 2003/06/18 12:26:01 brouard
607: Version 0.96
608:
609: Revision 1.86 2003/06/17 20:04:08 brouard
610: (Module): Change position of html and gnuplot routines and added
611: routine fileappend.
612:
613: Revision 1.85 2003/06/17 13:12:43 brouard
614: * imach.c (Repository): Check when date of death was earlier that
615: current date of interview. It may happen when the death was just
616: prior to the death. In this case, dh was negative and likelihood
617: was wrong (infinity). We still send an "Error" but patch by
618: assuming that the date of death was just one stepm after the
619: interview.
620: (Repository): Because some people have very long ID (first column)
621: we changed int to long in num[] and we added a new lvector for
622: memory allocation. But we also truncated to 8 characters (left
623: truncation)
624: (Repository): No more line truncation errors.
625:
626: Revision 1.84 2003/06/13 21:44:43 brouard
627: * imach.c (Repository): Replace "freqsummary" at a correct
628: place. It differs from routine "prevalence" which may be called
629: many times. Probs is memory consuming and must be used with
630: parcimony.
631: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
632:
633: Revision 1.83 2003/06/10 13:39:11 lievre
634: *** empty log message ***
635:
636: Revision 1.82 2003/06/05 15:57:20 brouard
637: Add log in imach.c and fullversion number is now printed.
638:
639: */
640: /*
641: Interpolated Markov Chain
642:
643: Short summary of the programme:
644:
1.227 brouard 645: This program computes Healthy Life Expectancies or State-specific
646: (if states aren't health statuses) Expectancies from
647: cross-longitudinal data. Cross-longitudinal data consist in:
648:
649: -1- a first survey ("cross") where individuals from different ages
650: are interviewed on their health status or degree of disability (in
651: the case of a health survey which is our main interest)
652:
653: -2- at least a second wave of interviews ("longitudinal") which
654: measure each change (if any) in individual health status. Health
655: expectancies are computed from the time spent in each health state
656: according to a model. More health states you consider, more time is
657: necessary to reach the Maximum Likelihood of the parameters involved
658: in the model. The simplest model is the multinomial logistic model
659: where pij is the probability to be observed in state j at the second
660: wave conditional to be observed in state i at the first
661: wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
662: etc , where 'age' is age and 'sex' is a covariate. If you want to
663: have a more complex model than "constant and age", you should modify
664: the program where the markup *Covariates have to be included here
665: again* invites you to do it. More covariates you add, slower the
1.126 brouard 666: convergence.
667:
668: The advantage of this computer programme, compared to a simple
669: multinomial logistic model, is clear when the delay between waves is not
670: identical for each individual. Also, if a individual missed an
671: intermediate interview, the information is lost, but taken into
672: account using an interpolation or extrapolation.
673:
674: hPijx is the probability to be observed in state i at age x+h
675: conditional to the observed state i at age x. The delay 'h' can be
676: split into an exact number (nh*stepm) of unobserved intermediate
677: states. This elementary transition (by month, quarter,
678: semester or year) is modelled as a multinomial logistic. The hPx
679: matrix is simply the matrix product of nh*stepm elementary matrices
680: and the contribution of each individual to the likelihood is simply
681: hPijx.
682:
683: Also this programme outputs the covariance matrix of the parameters but also
1.218 brouard 684: of the life expectancies. It also computes the period (stable) prevalence.
685:
686: Back prevalence and projections:
1.227 brouard 687:
688: - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
689: double agemaxpar, double ftolpl, int *ncvyearp, double
690: dateprev1,double dateprev2, int firstpass, int lastpass, int
691: mobilavproj)
692:
693: Computes the back prevalence limit for any combination of
694: covariate values k at any age between ageminpar and agemaxpar and
695: returns it in **bprlim. In the loops,
696:
697: - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
698: **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
699:
700: - hBijx Back Probability to be in state i at age x-h being in j at x
1.218 brouard 701: Computes for any combination of covariates k and any age between bage and fage
702: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
703: oldm=oldms;savm=savms;
1.227 brouard 704:
705: - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.218 brouard 706: Computes the transition matrix starting at age 'age' over
707: 'nhstepm*hstepm*stepm' months (i.e. until
708: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1.227 brouard 709: nhstepm*hstepm matrices.
710:
711: Returns p3mat[i][j][h] after calling
712: p3mat[i][j][h]=matprod2(newm,
713: bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
714: dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
715: oldm);
1.226 brouard 716:
717: Important routines
718:
719: - func (or funcone), computes logit (pij) distinguishing
720: o fixed variables (single or product dummies or quantitative);
721: o varying variables by:
722: (1) wave (single, product dummies, quantitative),
723: (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
724: % fixed dummy (treated) or quantitative (not done because time-consuming);
725: % varying dummy (not done) or quantitative (not done);
726: - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
727: and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
728: - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
729: o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
730: race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
1.218 brouard 731:
1.226 brouard 732:
733:
1.133 brouard 734: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
735: Institut national d'études démographiques, Paris.
1.126 brouard 736: This software have been partly granted by Euro-REVES, a concerted action
737: from the European Union.
738: It is copyrighted identically to a GNU software product, ie programme and
739: software can be distributed freely for non commercial use. Latest version
740: can be accessed at http://euroreves.ined.fr/imach .
741:
742: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
743: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
744:
745: **********************************************************************/
746: /*
747: main
748: read parameterfile
749: read datafile
750: concatwav
751: freqsummary
752: if (mle >= 1)
753: mlikeli
754: print results files
755: if mle==1
756: computes hessian
757: read end of parameter file: agemin, agemax, bage, fage, estepm
758: begin-prev-date,...
759: open gnuplot file
760: open html file
1.145 brouard 761: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
762: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
763: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
764: freexexit2 possible for memory heap.
765:
766: h Pij x | pij_nom ficrestpij
767: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
768: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
769: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
770:
771: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
772: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
773: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
774: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
775: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
776:
1.126 brouard 777: forecasting if prevfcast==1 prevforecast call prevalence()
778: health expectancies
779: Variance-covariance of DFLE
780: prevalence()
781: movingaverage()
782: varevsij()
783: if popbased==1 varevsij(,popbased)
784: total life expectancies
785: Variance of period (stable) prevalence
786: end
787: */
788:
1.187 brouard 789: /* #define DEBUG */
790: /* #define DEBUGBRENT */
1.203 brouard 791: /* #define DEBUGLINMIN */
792: /* #define DEBUGHESS */
793: #define DEBUGHESSIJ
1.224 brouard 794: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan) *\/ */
1.165 brouard 795: #define POWELL /* Instead of NLOPT */
1.224 brouard 796: #define POWELLNOF3INFF1TEST /* Skip test */
1.186 brouard 797: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
798: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 799:
800: #include <math.h>
801: #include <stdio.h>
802: #include <stdlib.h>
803: #include <string.h>
1.226 brouard 804: #include <ctype.h>
1.159 brouard 805:
806: #ifdef _WIN32
807: #include <io.h>
1.172 brouard 808: #include <windows.h>
809: #include <tchar.h>
1.159 brouard 810: #else
1.126 brouard 811: #include <unistd.h>
1.159 brouard 812: #endif
1.126 brouard 813:
814: #include <limits.h>
815: #include <sys/types.h>
1.171 brouard 816:
817: #if defined(__GNUC__)
818: #include <sys/utsname.h> /* Doesn't work on Windows */
819: #endif
820:
1.126 brouard 821: #include <sys/stat.h>
822: #include <errno.h>
1.159 brouard 823: /* extern int errno; */
1.126 brouard 824:
1.157 brouard 825: /* #ifdef LINUX */
826: /* #include <time.h> */
827: /* #include "timeval.h" */
828: /* #else */
829: /* #include <sys/time.h> */
830: /* #endif */
831:
1.126 brouard 832: #include <time.h>
833:
1.136 brouard 834: #ifdef GSL
835: #include <gsl/gsl_errno.h>
836: #include <gsl/gsl_multimin.h>
837: #endif
838:
1.167 brouard 839:
1.162 brouard 840: #ifdef NLOPT
841: #include <nlopt.h>
842: typedef struct {
843: double (* function)(double [] );
844: } myfunc_data ;
845: #endif
846:
1.126 brouard 847: /* #include <libintl.h> */
848: /* #define _(String) gettext (String) */
849:
1.141 brouard 850: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 851:
852: #define GNUPLOTPROGRAM "gnuplot"
853: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
854: #define FILENAMELENGTH 132
855:
856: #define GLOCK_ERROR_NOPATH -1 /* empty path */
857: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
858:
1.144 brouard 859: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
860: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 861:
862: #define NINTERVMAX 8
1.144 brouard 863: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
864: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
865: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 866: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 867: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
868: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.126 brouard 869: #define MAXN 20000
1.144 brouard 870: #define YEARM 12. /**< Number of months per year */
1.218 brouard 871: /* #define AGESUP 130 */
872: #define AGESUP 150
873: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126 brouard 874: #define AGEBASE 40
1.194 brouard 875: #define AGEOVERFLOW 1.e20
1.164 brouard 876: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 877: #ifdef _WIN32
878: #define DIRSEPARATOR '\\'
879: #define CHARSEPARATOR "\\"
880: #define ODIRSEPARATOR '/'
881: #else
1.126 brouard 882: #define DIRSEPARATOR '/'
883: #define CHARSEPARATOR "/"
884: #define ODIRSEPARATOR '\\'
885: #endif
886:
1.229 ! brouard 887: /* $Id: imach.c,v 1.228 2016/07/22 17:45:30 brouard Exp $ */
1.126 brouard 888: /* $State: Exp $ */
1.196 brouard 889: #include "version.h"
890: char version[]=__IMACH_VERSION__;
1.224 brouard 891: char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";
1.229 ! brouard 892: char fullversion[]="$Revision: 1.228 $ $Date: 2016/07/22 17:45:30 $";
1.126 brouard 893: char strstart[80];
894: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 895: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 896: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 897: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
898: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
899: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
1.225 brouard 900: int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
901: int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
1.145 brouard 902: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
903: int cptcovprodnoage=0; /**< Number of covariate products without age */
904: int cptcoveff=0; /* Total number of covariates to vary for printing results */
1.224 brouard 905: int ncoveff=0; /* Total number of effective covariates in the model */
1.225 brouard 906: int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
1.224 brouard 907: int ntveff=0; /**< ntveff number of effective time varying variables */
908: int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
1.145 brouard 909: int cptcov=0; /* Working variable */
1.218 brouard 910: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.126 brouard 911: int npar=NPARMAX;
912: int nlstate=2; /* Number of live states */
913: int ndeath=1; /* Number of dead states */
1.130 brouard 914: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.223 brouard 915: int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
1.126 brouard 916: int popbased=0;
917:
918: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 919: int maxwav=0; /* Maxim number of waves */
920: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
921: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
922: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 923: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 924: int mle=1, weightopt=0;
1.126 brouard 925: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
926: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
927: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
928: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 929: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 930: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 931: double **matprod2(); /* test */
1.126 brouard 932: double **oldm, **newm, **savm; /* Working pointers to matrices */
933: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218 brouard 934: double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
935:
1.136 brouard 936: /*FILE *fic ; */ /* Used in readdata only */
1.217 brouard 937: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 938: FILE *ficlog, *ficrespow;
1.130 brouard 939: int globpr=0; /* Global variable for printing or not */
1.126 brouard 940: double fretone; /* Only one call to likelihood */
1.130 brouard 941: long ipmx=0; /* Number of contributions */
1.126 brouard 942: double sw; /* Sum of weights */
943: char filerespow[FILENAMELENGTH];
944: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
945: FILE *ficresilk;
946: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
947: FILE *ficresprobmorprev;
948: FILE *fichtm, *fichtmcov; /* Html File */
949: FILE *ficreseij;
950: char filerese[FILENAMELENGTH];
951: FILE *ficresstdeij;
952: char fileresstde[FILENAMELENGTH];
953: FILE *ficrescveij;
954: char filerescve[FILENAMELENGTH];
955: FILE *ficresvij;
956: char fileresv[FILENAMELENGTH];
957: FILE *ficresvpl;
958: char fileresvpl[FILENAMELENGTH];
959: char title[MAXLINE];
1.217 brouard 960: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 961: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
962: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
963: char command[FILENAMELENGTH];
964: int outcmd=0;
965:
1.217 brouard 966: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 967: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 968: char filelog[FILENAMELENGTH]; /* Log file */
969: char filerest[FILENAMELENGTH];
970: char fileregp[FILENAMELENGTH];
971: char popfile[FILENAMELENGTH];
972:
973: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
974:
1.157 brouard 975: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
976: /* struct timezone tzp; */
977: /* extern int gettimeofday(); */
978: struct tm tml, *gmtime(), *localtime();
979:
980: extern time_t time();
981:
982: struct tm start_time, end_time, curr_time, last_time, forecast_time;
983: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
984: struct tm tm;
985:
1.126 brouard 986: char strcurr[80], strfor[80];
987:
988: char *endptr;
989: long lval;
990: double dval;
991:
992: #define NR_END 1
993: #define FREE_ARG char*
994: #define FTOL 1.0e-10
995:
996: #define NRANSI
997: #define ITMAX 200
998:
999: #define TOL 2.0e-4
1000:
1001: #define CGOLD 0.3819660
1002: #define ZEPS 1.0e-10
1003: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
1004:
1005: #define GOLD 1.618034
1006: #define GLIMIT 100.0
1007: #define TINY 1.0e-20
1008:
1009: static double maxarg1,maxarg2;
1010: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
1011: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
1012:
1013: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
1014: #define rint(a) floor(a+0.5)
1.166 brouard 1015: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 1016: #define mytinydouble 1.0e-16
1.166 brouard 1017: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
1018: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
1019: /* static double dsqrarg; */
1020: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 1021: static double sqrarg;
1022: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
1023: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1024: int agegomp= AGEGOMP;
1025:
1026: int imx;
1027: int stepm=1;
1028: /* Stepm, step in month: minimum step interpolation*/
1029:
1030: int estepm;
1031: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
1032:
1033: int m,nb;
1034: long *num;
1.197 brouard 1035: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 1036: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
1037: covariate for which somebody answered excluding
1038: undefined. Usually 2: 0 and 1. */
1039: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
1040: covariate for which somebody answered including
1041: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 1042: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218 brouard 1043: double **pmmij, ***probs; /* Global pointer */
1.219 brouard 1044: double ***mobaverage, ***mobaverages; /* New global variable */
1.126 brouard 1045: double *ageexmed,*agecens;
1046: double dateintmean=0;
1047:
1048: double *weight;
1049: int **s; /* Status */
1.141 brouard 1050: double *agedc;
1.145 brouard 1051: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 1052: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 1053: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.225 brouard 1054: double **coqvar; /* Fixed quantitative covariate iqv */
1055: double ***cotvar; /* Time varying covariate itv */
1056: double ***cotqvar; /* Time varying quantitative covariate itqv */
1.141 brouard 1057: double idx;
1058: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.226 brouard 1059: int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
1.227 brouard 1060: int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
1061: int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */
1.197 brouard 1062: int *Tage;
1.227 brouard 1063: int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
1.228 brouard 1064: int *Tmodelind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1065: int *TmodelInvind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1066: int *TmodelInvQind; /** Tmodelqind[1]=1 for V5(quantitative varying) position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.145 brouard 1067: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 1068: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.227 brouard 1069: int **Tvard;
1070: int *Tprod;/**< Gives the k position of the k1 product */
1071: int *Tposprod; /**< Gives the k1 product from the k position */
1072: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
1073: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
1074: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
1075: */
1076: int cptcovprod, *Tvaraff, *invalidvarcomb;
1.126 brouard 1077: double *lsurv, *lpop, *tpop;
1078:
1.143 brouard 1079: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
1080: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 1081:
1082: /**************** split *************************/
1083: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1084: {
1085: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1086: the name of the file (name), its extension only (ext) and its first part of the name (finame)
1087: */
1088: char *ss; /* pointer */
1.186 brouard 1089: int l1=0, l2=0; /* length counters */
1.126 brouard 1090:
1091: l1 = strlen(path ); /* length of path */
1092: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1093: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1094: if ( ss == NULL ) { /* no directory, so determine current directory */
1095: strcpy( name, path ); /* we got the fullname name because no directory */
1096: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
1097: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1098: /* get current working directory */
1099: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 1100: #ifdef WIN32
1101: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
1102: #else
1103: if (getcwd(dirc, FILENAME_MAX) == NULL) {
1104: #endif
1.126 brouard 1105: return( GLOCK_ERROR_GETCWD );
1106: }
1107: /* got dirc from getcwd*/
1108: printf(" DIRC = %s \n",dirc);
1.205 brouard 1109: } else { /* strip directory from path */
1.126 brouard 1110: ss++; /* after this, the filename */
1111: l2 = strlen( ss ); /* length of filename */
1112: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1113: strcpy( name, ss ); /* save file name */
1114: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1115: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1116: printf(" DIRC2 = %s \n",dirc);
1117: }
1118: /* We add a separator at the end of dirc if not exists */
1119: l1 = strlen( dirc ); /* length of directory */
1120: if( dirc[l1-1] != DIRSEPARATOR ){
1121: dirc[l1] = DIRSEPARATOR;
1122: dirc[l1+1] = 0;
1123: printf(" DIRC3 = %s \n",dirc);
1124: }
1125: ss = strrchr( name, '.' ); /* find last / */
1126: if (ss >0){
1127: ss++;
1128: strcpy(ext,ss); /* save extension */
1129: l1= strlen( name);
1130: l2= strlen(ss)+1;
1131: strncpy( finame, name, l1-l2);
1132: finame[l1-l2]= 0;
1133: }
1134:
1135: return( 0 ); /* we're done */
1136: }
1137:
1138:
1139: /******************************************/
1140:
1141: void replace_back_to_slash(char *s, char*t)
1142: {
1143: int i;
1144: int lg=0;
1145: i=0;
1146: lg=strlen(t);
1147: for(i=0; i<= lg; i++) {
1148: (s[i] = t[i]);
1149: if (t[i]== '\\') s[i]='/';
1150: }
1151: }
1152:
1.132 brouard 1153: char *trimbb(char *out, char *in)
1.137 brouard 1154: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1155: char *s;
1156: s=out;
1157: while (*in != '\0'){
1.137 brouard 1158: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1159: in++;
1160: }
1161: *out++ = *in++;
1162: }
1163: *out='\0';
1164: return s;
1165: }
1166:
1.187 brouard 1167: /* char *substrchaine(char *out, char *in, char *chain) */
1168: /* { */
1169: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1170: /* char *s, *t; */
1171: /* t=in;s=out; */
1172: /* while ((*in != *chain) && (*in != '\0')){ */
1173: /* *out++ = *in++; */
1174: /* } */
1175:
1176: /* /\* *in matches *chain *\/ */
1177: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1178: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1179: /* } */
1180: /* in--; chain--; */
1181: /* while ( (*in != '\0')){ */
1182: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1183: /* *out++ = *in++; */
1184: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1185: /* } */
1186: /* *out='\0'; */
1187: /* out=s; */
1188: /* return out; */
1189: /* } */
1190: char *substrchaine(char *out, char *in, char *chain)
1191: {
1192: /* Substract chain 'chain' from 'in', return and output 'out' */
1193: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1194:
1195: char *strloc;
1196:
1197: strcpy (out, in);
1198: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1199: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1200: if(strloc != NULL){
1201: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1202: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1203: /* strcpy (strloc, strloc +strlen(chain));*/
1204: }
1205: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1206: return out;
1207: }
1208:
1209:
1.145 brouard 1210: char *cutl(char *blocc, char *alocc, char *in, char occ)
1211: {
1.187 brouard 1212: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1213: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1214: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1215: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1216: */
1.160 brouard 1217: char *s, *t;
1.145 brouard 1218: t=in;s=in;
1219: while ((*in != occ) && (*in != '\0')){
1220: *alocc++ = *in++;
1221: }
1222: if( *in == occ){
1223: *(alocc)='\0';
1224: s=++in;
1225: }
1226:
1227: if (s == t) {/* occ not found */
1228: *(alocc-(in-s))='\0';
1229: in=s;
1230: }
1231: while ( *in != '\0'){
1232: *blocc++ = *in++;
1233: }
1234:
1235: *blocc='\0';
1236: return t;
1237: }
1.137 brouard 1238: char *cutv(char *blocc, char *alocc, char *in, char occ)
1239: {
1.187 brouard 1240: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1241: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1242: gives blocc="abcdef2ghi" and alocc="j".
1243: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1244: */
1245: char *s, *t;
1246: t=in;s=in;
1247: while (*in != '\0'){
1248: while( *in == occ){
1249: *blocc++ = *in++;
1250: s=in;
1251: }
1252: *blocc++ = *in++;
1253: }
1254: if (s == t) /* occ not found */
1255: *(blocc-(in-s))='\0';
1256: else
1257: *(blocc-(in-s)-1)='\0';
1258: in=s;
1259: while ( *in != '\0'){
1260: *alocc++ = *in++;
1261: }
1262:
1263: *alocc='\0';
1264: return s;
1265: }
1266:
1.126 brouard 1267: int nbocc(char *s, char occ)
1268: {
1269: int i,j=0;
1270: int lg=20;
1271: i=0;
1272: lg=strlen(s);
1273: for(i=0; i<= lg; i++) {
1274: if (s[i] == occ ) j++;
1275: }
1276: return j;
1277: }
1278:
1.137 brouard 1279: /* void cutv(char *u,char *v, char*t, char occ) */
1280: /* { */
1281: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1282: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1283: /* gives u="abcdef2ghi" and v="j" *\/ */
1284: /* int i,lg,j,p=0; */
1285: /* i=0; */
1286: /* lg=strlen(t); */
1287: /* for(j=0; j<=lg-1; j++) { */
1288: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1289: /* } */
1.126 brouard 1290:
1.137 brouard 1291: /* for(j=0; j<p; j++) { */
1292: /* (u[j] = t[j]); */
1293: /* } */
1294: /* u[p]='\0'; */
1.126 brouard 1295:
1.137 brouard 1296: /* for(j=0; j<= lg; j++) { */
1297: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1298: /* } */
1299: /* } */
1.126 brouard 1300:
1.160 brouard 1301: #ifdef _WIN32
1302: char * strsep(char **pp, const char *delim)
1303: {
1304: char *p, *q;
1305:
1306: if ((p = *pp) == NULL)
1307: return 0;
1308: if ((q = strpbrk (p, delim)) != NULL)
1309: {
1310: *pp = q + 1;
1311: *q = '\0';
1312: }
1313: else
1314: *pp = 0;
1315: return p;
1316: }
1317: #endif
1318:
1.126 brouard 1319: /********************** nrerror ********************/
1320:
1321: void nrerror(char error_text[])
1322: {
1323: fprintf(stderr,"ERREUR ...\n");
1324: fprintf(stderr,"%s\n",error_text);
1325: exit(EXIT_FAILURE);
1326: }
1327: /*********************** vector *******************/
1328: double *vector(int nl, int nh)
1329: {
1330: double *v;
1331: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1332: if (!v) nrerror("allocation failure in vector");
1333: return v-nl+NR_END;
1334: }
1335:
1336: /************************ free vector ******************/
1337: void free_vector(double*v, int nl, int nh)
1338: {
1339: free((FREE_ARG)(v+nl-NR_END));
1340: }
1341:
1342: /************************ivector *******************************/
1343: int *ivector(long nl,long nh)
1344: {
1345: int *v;
1346: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1347: if (!v) nrerror("allocation failure in ivector");
1348: return v-nl+NR_END;
1349: }
1350:
1351: /******************free ivector **************************/
1352: void free_ivector(int *v, long nl, long nh)
1353: {
1354: free((FREE_ARG)(v+nl-NR_END));
1355: }
1356:
1357: /************************lvector *******************************/
1358: long *lvector(long nl,long nh)
1359: {
1360: long *v;
1361: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1362: if (!v) nrerror("allocation failure in ivector");
1363: return v-nl+NR_END;
1364: }
1365:
1366: /******************free lvector **************************/
1367: void free_lvector(long *v, long nl, long nh)
1368: {
1369: free((FREE_ARG)(v+nl-NR_END));
1370: }
1371:
1372: /******************* imatrix *******************************/
1373: int **imatrix(long nrl, long nrh, long ncl, long nch)
1374: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1375: {
1376: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1377: int **m;
1378:
1379: /* allocate pointers to rows */
1380: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1381: if (!m) nrerror("allocation failure 1 in matrix()");
1382: m += NR_END;
1383: m -= nrl;
1384:
1385:
1386: /* allocate rows and set pointers to them */
1387: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1388: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1389: m[nrl] += NR_END;
1390: m[nrl] -= ncl;
1391:
1392: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1393:
1394: /* return pointer to array of pointers to rows */
1395: return m;
1396: }
1397:
1398: /****************** free_imatrix *************************/
1399: void free_imatrix(m,nrl,nrh,ncl,nch)
1400: int **m;
1401: long nch,ncl,nrh,nrl;
1402: /* free an int matrix allocated by imatrix() */
1403: {
1404: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1405: free((FREE_ARG) (m+nrl-NR_END));
1406: }
1407:
1408: /******************* matrix *******************************/
1409: double **matrix(long nrl, long nrh, long ncl, long nch)
1410: {
1411: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1412: double **m;
1413:
1414: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1415: if (!m) nrerror("allocation failure 1 in matrix()");
1416: m += NR_END;
1417: m -= nrl;
1418:
1419: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1420: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1421: m[nrl] += NR_END;
1422: m[nrl] -= ncl;
1423:
1424: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1425: return m;
1.145 brouard 1426: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1427: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1428: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1429: */
1430: }
1431:
1432: /*************************free matrix ************************/
1433: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1434: {
1435: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1436: free((FREE_ARG)(m+nrl-NR_END));
1437: }
1438:
1439: /******************* ma3x *******************************/
1440: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1441: {
1442: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1443: double ***m;
1444:
1445: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1446: if (!m) nrerror("allocation failure 1 in matrix()");
1447: m += NR_END;
1448: m -= nrl;
1449:
1450: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1451: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1452: m[nrl] += NR_END;
1453: m[nrl] -= ncl;
1454:
1455: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1456:
1457: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1458: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1459: m[nrl][ncl] += NR_END;
1460: m[nrl][ncl] -= nll;
1461: for (j=ncl+1; j<=nch; j++)
1462: m[nrl][j]=m[nrl][j-1]+nlay;
1463:
1464: for (i=nrl+1; i<=nrh; i++) {
1465: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1466: for (j=ncl+1; j<=nch; j++)
1467: m[i][j]=m[i][j-1]+nlay;
1468: }
1469: return m;
1470: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1471: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1472: */
1473: }
1474:
1475: /*************************free ma3x ************************/
1476: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1477: {
1478: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1479: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1480: free((FREE_ARG)(m+nrl-NR_END));
1481: }
1482:
1483: /*************** function subdirf ***********/
1484: char *subdirf(char fileres[])
1485: {
1486: /* Caution optionfilefiname is hidden */
1487: strcpy(tmpout,optionfilefiname);
1488: strcat(tmpout,"/"); /* Add to the right */
1489: strcat(tmpout,fileres);
1490: return tmpout;
1491: }
1492:
1493: /*************** function subdirf2 ***********/
1494: char *subdirf2(char fileres[], char *preop)
1495: {
1496:
1497: /* Caution optionfilefiname is hidden */
1498: strcpy(tmpout,optionfilefiname);
1499: strcat(tmpout,"/");
1500: strcat(tmpout,preop);
1501: strcat(tmpout,fileres);
1502: return tmpout;
1503: }
1504:
1505: /*************** function subdirf3 ***********/
1506: char *subdirf3(char fileres[], char *preop, char *preop2)
1507: {
1508:
1509: /* Caution optionfilefiname is hidden */
1510: strcpy(tmpout,optionfilefiname);
1511: strcat(tmpout,"/");
1512: strcat(tmpout,preop);
1513: strcat(tmpout,preop2);
1514: strcat(tmpout,fileres);
1515: return tmpout;
1516: }
1.213 brouard 1517:
1518: /*************** function subdirfext ***********/
1519: char *subdirfext(char fileres[], char *preop, char *postop)
1520: {
1521:
1522: strcpy(tmpout,preop);
1523: strcat(tmpout,fileres);
1524: strcat(tmpout,postop);
1525: return tmpout;
1526: }
1.126 brouard 1527:
1.213 brouard 1528: /*************** function subdirfext3 ***********/
1529: char *subdirfext3(char fileres[], char *preop, char *postop)
1530: {
1531:
1532: /* Caution optionfilefiname is hidden */
1533: strcpy(tmpout,optionfilefiname);
1534: strcat(tmpout,"/");
1535: strcat(tmpout,preop);
1536: strcat(tmpout,fileres);
1537: strcat(tmpout,postop);
1538: return tmpout;
1539: }
1540:
1.162 brouard 1541: char *asc_diff_time(long time_sec, char ascdiff[])
1542: {
1543: long sec_left, days, hours, minutes;
1544: days = (time_sec) / (60*60*24);
1545: sec_left = (time_sec) % (60*60*24);
1546: hours = (sec_left) / (60*60) ;
1547: sec_left = (sec_left) %(60*60);
1548: minutes = (sec_left) /60;
1549: sec_left = (sec_left) % (60);
1550: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1551: return ascdiff;
1552: }
1553:
1.126 brouard 1554: /***************** f1dim *************************/
1555: extern int ncom;
1556: extern double *pcom,*xicom;
1557: extern double (*nrfunc)(double []);
1558:
1559: double f1dim(double x)
1560: {
1561: int j;
1562: double f;
1563: double *xt;
1564:
1565: xt=vector(1,ncom);
1566: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1567: f=(*nrfunc)(xt);
1568: free_vector(xt,1,ncom);
1569: return f;
1570: }
1571:
1572: /*****************brent *************************/
1573: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1574: {
1575: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1576: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1577: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1578: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1579: * returned function value.
1580: */
1.126 brouard 1581: int iter;
1582: double a,b,d,etemp;
1.159 brouard 1583: double fu=0,fv,fw,fx;
1.164 brouard 1584: double ftemp=0.;
1.126 brouard 1585: double p,q,r,tol1,tol2,u,v,w,x,xm;
1586: double e=0.0;
1587:
1588: a=(ax < cx ? ax : cx);
1589: b=(ax > cx ? ax : cx);
1590: x=w=v=bx;
1591: fw=fv=fx=(*f)(x);
1592: for (iter=1;iter<=ITMAX;iter++) {
1593: xm=0.5*(a+b);
1594: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1595: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1596: printf(".");fflush(stdout);
1597: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1598: #ifdef DEBUGBRENT
1.126 brouard 1599: 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);
1600: 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);
1601: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1602: #endif
1603: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1604: *xmin=x;
1605: return fx;
1606: }
1607: ftemp=fu;
1608: if (fabs(e) > tol1) {
1609: r=(x-w)*(fx-fv);
1610: q=(x-v)*(fx-fw);
1611: p=(x-v)*q-(x-w)*r;
1612: q=2.0*(q-r);
1613: if (q > 0.0) p = -p;
1614: q=fabs(q);
1615: etemp=e;
1616: e=d;
1617: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1.224 brouard 1618: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1.126 brouard 1619: else {
1.224 brouard 1620: d=p/q;
1621: u=x+d;
1622: if (u-a < tol2 || b-u < tol2)
1623: d=SIGN(tol1,xm-x);
1.126 brouard 1624: }
1625: } else {
1626: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1627: }
1628: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1629: fu=(*f)(u);
1630: if (fu <= fx) {
1631: if (u >= x) a=x; else b=x;
1632: SHFT(v,w,x,u)
1.183 brouard 1633: SHFT(fv,fw,fx,fu)
1634: } else {
1635: if (u < x) a=u; else b=u;
1636: if (fu <= fw || w == x) {
1.224 brouard 1637: v=w;
1638: w=u;
1639: fv=fw;
1640: fw=fu;
1.183 brouard 1641: } else if (fu <= fv || v == x || v == w) {
1.224 brouard 1642: v=u;
1643: fv=fu;
1.183 brouard 1644: }
1645: }
1.126 brouard 1646: }
1647: nrerror("Too many iterations in brent");
1648: *xmin=x;
1649: return fx;
1650: }
1651:
1652: /****************** mnbrak ***********************/
1653:
1654: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1655: double (*func)(double))
1.183 brouard 1656: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1657: the downhill direction (defined by the function as evaluated at the initial points) and returns
1658: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1659: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1660: */
1.126 brouard 1661: double ulim,u,r,q, dum;
1662: double fu;
1.187 brouard 1663:
1664: double scale=10.;
1665: int iterscale=0;
1666:
1667: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1668: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1669:
1670:
1671: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1672: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1673: /* *bx = *ax - (*ax - *bx)/scale; */
1674: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1675: /* } */
1676:
1.126 brouard 1677: if (*fb > *fa) {
1678: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1679: SHFT(dum,*fb,*fa,dum)
1680: }
1.126 brouard 1681: *cx=(*bx)+GOLD*(*bx-*ax);
1682: *fc=(*func)(*cx);
1.183 brouard 1683: #ifdef DEBUG
1.224 brouard 1684: printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
1685: 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 1686: #endif
1.224 brouard 1687: 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 1688: r=(*bx-*ax)*(*fb-*fc);
1.224 brouard 1689: q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
1.126 brouard 1690: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1691: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1692: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1693: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1694: fu=(*func)(u);
1.163 brouard 1695: #ifdef DEBUG
1696: /* f(x)=A(x-u)**2+f(u) */
1697: double A, fparabu;
1698: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1699: fparabu= *fa - A*(*ax-u)*(*ax-u);
1.224 brouard 1700: 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);
1701: 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 1702: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1703: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1704: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1705: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1706: #endif
1.184 brouard 1707: #ifdef MNBRAKORIGINAL
1.183 brouard 1708: #else
1.191 brouard 1709: /* if (fu > *fc) { */
1710: /* #ifdef DEBUG */
1711: /* printf("mnbrak4 fu > fc \n"); */
1712: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1713: /* #endif */
1714: /* /\* 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 *\\/ *\/ */
1715: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1716: /* dum=u; /\* Shifting c and u *\/ */
1717: /* u = *cx; */
1718: /* *cx = dum; */
1719: /* dum = fu; */
1720: /* fu = *fc; */
1721: /* *fc =dum; */
1722: /* } else { /\* end *\/ */
1723: /* #ifdef DEBUG */
1724: /* printf("mnbrak3 fu < fc \n"); */
1725: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1726: /* #endif */
1727: /* dum=u; /\* Shifting c and u *\/ */
1728: /* u = *cx; */
1729: /* *cx = dum; */
1730: /* dum = fu; */
1731: /* fu = *fc; */
1732: /* *fc =dum; */
1733: /* } */
1.224 brouard 1734: #ifdef DEBUGMNBRAK
1735: double A, fparabu;
1736: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1737: fparabu= *fa - A*(*ax-u)*(*ax-u);
1738: 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);
1739: 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 1740: #endif
1.191 brouard 1741: dum=u; /* Shifting c and u */
1742: u = *cx;
1743: *cx = dum;
1744: dum = fu;
1745: fu = *fc;
1746: *fc =dum;
1.183 brouard 1747: #endif
1.162 brouard 1748: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1749: #ifdef DEBUG
1.224 brouard 1750: printf("\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1751: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1.183 brouard 1752: #endif
1.126 brouard 1753: fu=(*func)(u);
1754: if (fu < *fc) {
1.183 brouard 1755: #ifdef DEBUG
1.224 brouard 1756: printf("\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
1757: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
1758: #endif
1759: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1760: SHFT(*fb,*fc,fu,(*func)(u))
1761: #ifdef DEBUG
1762: printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
1.183 brouard 1763: #endif
1764: }
1.162 brouard 1765: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1766: #ifdef DEBUG
1.224 brouard 1767: printf("\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1768: fprintf(ficlog,"\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1.183 brouard 1769: #endif
1.126 brouard 1770: u=ulim;
1771: fu=(*func)(u);
1.183 brouard 1772: } else { /* u could be left to b (if r > q parabola has a maximum) */
1773: #ifdef DEBUG
1.224 brouard 1774: printf("\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
1775: 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 1776: #endif
1.126 brouard 1777: u=(*cx)+GOLD*(*cx-*bx);
1778: fu=(*func)(u);
1.224 brouard 1779: #ifdef DEBUG
1780: printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
1781: fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
1782: #endif
1.183 brouard 1783: } /* end tests */
1.126 brouard 1784: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1785: SHFT(*fa,*fb,*fc,fu)
1786: #ifdef DEBUG
1.224 brouard 1787: printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
1788: 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 1789: #endif
1790: } /* 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 1791: }
1792:
1793: /*************** linmin ************************/
1.162 brouard 1794: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1795: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1796: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1797: the value of func at the returned location p . This is actually all accomplished by calling the
1798: routines mnbrak and brent .*/
1.126 brouard 1799: int ncom;
1800: double *pcom,*xicom;
1801: double (*nrfunc)(double []);
1802:
1.224 brouard 1803: #ifdef LINMINORIGINAL
1.126 brouard 1804: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1.224 brouard 1805: #else
1806: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat)
1807: #endif
1.126 brouard 1808: {
1809: double brent(double ax, double bx, double cx,
1810: double (*f)(double), double tol, double *xmin);
1811: double f1dim(double x);
1812: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1813: double *fc, double (*func)(double));
1814: int j;
1815: double xx,xmin,bx,ax;
1816: double fx,fb,fa;
1.187 brouard 1817:
1.203 brouard 1818: #ifdef LINMINORIGINAL
1819: #else
1820: double scale=10., axs, xxs; /* Scale added for infinity */
1821: #endif
1822:
1.126 brouard 1823: ncom=n;
1824: pcom=vector(1,n);
1825: xicom=vector(1,n);
1826: nrfunc=func;
1827: for (j=1;j<=n;j++) {
1828: pcom[j]=p[j];
1.202 brouard 1829: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1830: }
1.187 brouard 1831:
1.203 brouard 1832: #ifdef LINMINORIGINAL
1833: xx=1.;
1834: #else
1835: axs=0.0;
1836: xxs=1.;
1837: do{
1838: xx= xxs;
1839: #endif
1.187 brouard 1840: ax=0.;
1841: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1842: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1843: /* 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)) */
1844: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1845: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1846: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1847: /* 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 1848: #ifdef LINMINORIGINAL
1849: #else
1850: if (fx != fx){
1.224 brouard 1851: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1852: printf("|");
1853: fprintf(ficlog,"|");
1.203 brouard 1854: #ifdef DEBUGLINMIN
1.224 brouard 1855: 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 1856: #endif
1857: }
1.224 brouard 1858: }while(fx != fx && xxs > 1.e-5);
1.203 brouard 1859: #endif
1860:
1.191 brouard 1861: #ifdef DEBUGLINMIN
1862: 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 1863: 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 1864: #endif
1.224 brouard 1865: #ifdef LINMINORIGINAL
1866: #else
1867: if(fb == fx){ /* Flat function in the direction */
1868: xmin=xx;
1869: *flat=1;
1870: }else{
1871: *flat=0;
1872: #endif
1873: /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
1.187 brouard 1874: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1875: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1876: /* fmin = f(p[j] + xmin * xi[j]) */
1877: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1878: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1879: #ifdef DEBUG
1.224 brouard 1880: 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);
1881: 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);
1882: #endif
1883: #ifdef LINMINORIGINAL
1884: #else
1885: }
1.126 brouard 1886: #endif
1.191 brouard 1887: #ifdef DEBUGLINMIN
1888: printf("linmin end ");
1.202 brouard 1889: fprintf(ficlog,"linmin end ");
1.191 brouard 1890: #endif
1.126 brouard 1891: for (j=1;j<=n;j++) {
1.203 brouard 1892: #ifdef LINMINORIGINAL
1893: xi[j] *= xmin;
1894: #else
1895: #ifdef DEBUGLINMIN
1896: if(xxs <1.0)
1897: printf(" before xi[%d]=%12.8f", j,xi[j]);
1898: #endif
1899: 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) */
1900: #ifdef DEBUGLINMIN
1901: if(xxs <1.0)
1902: 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 );
1903: #endif
1904: #endif
1.187 brouard 1905: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1906: }
1.191 brouard 1907: #ifdef DEBUGLINMIN
1.203 brouard 1908: printf("\n");
1.191 brouard 1909: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 1910: 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 1911: for (j=1;j<=n;j++) {
1.202 brouard 1912: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1913: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1914: if(j % ncovmodel == 0){
1.191 brouard 1915: printf("\n");
1.202 brouard 1916: fprintf(ficlog,"\n");
1917: }
1.191 brouard 1918: }
1.203 brouard 1919: #else
1.191 brouard 1920: #endif
1.126 brouard 1921: free_vector(xicom,1,n);
1922: free_vector(pcom,1,n);
1923: }
1924:
1925:
1926: /*************** powell ************************/
1.162 brouard 1927: /*
1928: Minimization of a function func of n variables. Input consists of an initial starting point
1929: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1930: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1931: such that failure to decrease by more than this amount on one iteration signals doneness. On
1932: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1933: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1934: */
1.224 brouard 1935: #ifdef LINMINORIGINAL
1936: #else
1937: int *flatdir; /* Function is vanishing in that direction */
1.225 brouard 1938: int flat=0, flatd=0; /* Function is vanishing in that direction */
1.224 brouard 1939: #endif
1.126 brouard 1940: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1941: double (*func)(double []))
1942: {
1.224 brouard 1943: #ifdef LINMINORIGINAL
1944: void linmin(double p[], double xi[], int n, double *fret,
1.126 brouard 1945: double (*func)(double []));
1.224 brouard 1946: #else
1947: void linmin(double p[], double xi[], int n, double *fret,
1948: double (*func)(double []),int *flat);
1949: #endif
1.126 brouard 1950: int i,ibig,j;
1951: double del,t,*pt,*ptt,*xit;
1.181 brouard 1952: double directest;
1.126 brouard 1953: double fp,fptt;
1954: double *xits;
1955: int niterf, itmp;
1.224 brouard 1956: #ifdef LINMINORIGINAL
1957: #else
1958:
1959: flatdir=ivector(1,n);
1960: for (j=1;j<=n;j++) flatdir[j]=0;
1961: #endif
1.126 brouard 1962:
1963: pt=vector(1,n);
1964: ptt=vector(1,n);
1965: xit=vector(1,n);
1966: xits=vector(1,n);
1967: *fret=(*func)(p);
1968: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 1969: rcurr_time = time(NULL);
1.126 brouard 1970: for (*iter=1;;++(*iter)) {
1.187 brouard 1971: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1972: ibig=0;
1973: del=0.0;
1.157 brouard 1974: rlast_time=rcurr_time;
1975: /* (void) gettimeofday(&curr_time,&tzp); */
1976: rcurr_time = time(NULL);
1977: curr_time = *localtime(&rcurr_time);
1978: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1979: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1980: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1981: for (i=1;i<=n;i++) {
1.126 brouard 1982: printf(" %d %.12f",i, p[i]);
1983: fprintf(ficlog," %d %.12lf",i, p[i]);
1984: fprintf(ficrespow," %.12lf", p[i]);
1985: }
1986: printf("\n");
1987: fprintf(ficlog,"\n");
1988: fprintf(ficrespow,"\n");fflush(ficrespow);
1989: if(*iter <=3){
1.157 brouard 1990: tml = *localtime(&rcurr_time);
1991: strcpy(strcurr,asctime(&tml));
1992: rforecast_time=rcurr_time;
1.126 brouard 1993: itmp = strlen(strcurr);
1994: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.224 brouard 1995: strcurr[itmp-1]='\0';
1.162 brouard 1996: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1997: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1998: for(niterf=10;niterf<=30;niterf+=10){
1.224 brouard 1999: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
2000: forecast_time = *localtime(&rforecast_time);
2001: strcpy(strfor,asctime(&forecast_time));
2002: itmp = strlen(strfor);
2003: if(strfor[itmp-1]=='\n')
2004: strfor[itmp-1]='\0';
2005: 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);
2006: 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 2007: }
2008: }
1.187 brouard 2009: for (i=1;i<=n;i++) { /* For each direction i */
2010: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 2011: fptt=(*fret);
2012: #ifdef DEBUG
1.203 brouard 2013: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
2014: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 2015: #endif
1.203 brouard 2016: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 2017: fprintf(ficlog,"%d",i);fflush(ficlog);
1.224 brouard 2018: #ifdef LINMINORIGINAL
1.188 brouard 2019: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1.224 brouard 2020: #else
2021: linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
2022: flatdir[i]=flat; /* Function is vanishing in that direction i */
2023: #endif
2024: /* Outputs are fret(new point p) p is updated and xit rescaled */
1.188 brouard 2025: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1.224 brouard 2026: /* because that direction will be replaced unless the gain del is small */
2027: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
2028: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
2029: /* with the new direction. */
2030: del=fabs(fptt-(*fret));
2031: ibig=i;
1.126 brouard 2032: }
2033: #ifdef DEBUG
2034: printf("%d %.12e",i,(*fret));
2035: fprintf(ficlog,"%d %.12e",i,(*fret));
2036: for (j=1;j<=n;j++) {
1.224 brouard 2037: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
2038: printf(" x(%d)=%.12e",j,xit[j]);
2039: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1.126 brouard 2040: }
2041: for(j=1;j<=n;j++) {
1.225 brouard 2042: printf(" p(%d)=%.12e",j,p[j]);
2043: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 2044: }
2045: printf("\n");
2046: fprintf(ficlog,"\n");
2047: #endif
1.187 brouard 2048: } /* end loop on each direction i */
2049: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 2050: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 2051: /* New value of last point Pn is not computed, P(n-1) */
1.224 brouard 2052: for(j=1;j<=n;j++) {
1.225 brouard 2053: if(flatdir[j] >0){
2054: printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2055: fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2056: }
2057: /* printf("\n"); */
2058: /* fprintf(ficlog,"\n"); */
2059: }
1.182 brouard 2060: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 2061: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
2062: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
2063: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
2064: /* decreased of more than 3.84 */
2065: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
2066: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
2067: /* By adding 10 parameters more the gain should be 18.31 */
1.224 brouard 2068:
1.188 brouard 2069: /* Starting the program with initial values given by a former maximization will simply change */
2070: /* the scales of the directions and the directions, because the are reset to canonical directions */
2071: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
2072: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 2073: #ifdef DEBUG
2074: int k[2],l;
2075: k[0]=1;
2076: k[1]=-1;
2077: printf("Max: %.12e",(*func)(p));
2078: fprintf(ficlog,"Max: %.12e",(*func)(p));
2079: for (j=1;j<=n;j++) {
2080: printf(" %.12e",p[j]);
2081: fprintf(ficlog," %.12e",p[j]);
2082: }
2083: printf("\n");
2084: fprintf(ficlog,"\n");
2085: for(l=0;l<=1;l++) {
2086: for (j=1;j<=n;j++) {
2087: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
2088: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2089: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2090: }
2091: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2092: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2093: }
2094: #endif
2095:
1.224 brouard 2096: #ifdef LINMINORIGINAL
2097: #else
2098: free_ivector(flatdir,1,n);
2099: #endif
1.126 brouard 2100: free_vector(xit,1,n);
2101: free_vector(xits,1,n);
2102: free_vector(ptt,1,n);
2103: free_vector(pt,1,n);
2104: return;
1.192 brouard 2105: } /* enough precision */
1.126 brouard 2106: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 2107: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 2108: ptt[j]=2.0*p[j]-pt[j];
2109: xit[j]=p[j]-pt[j];
2110: pt[j]=p[j];
2111: }
1.181 brouard 2112: fptt=(*func)(ptt); /* f_3 */
1.224 brouard 2113: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
2114: if (*iter <=4) {
1.225 brouard 2115: #else
2116: #endif
1.224 brouard 2117: #ifdef POWELLNOF3INFF1TEST /* skips test F3 <F1 */
1.192 brouard 2118: #else
1.161 brouard 2119: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 2120: #endif
1.162 brouard 2121: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 2122: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 2123: /* Let f"(x2) be the 2nd derivative equal everywhere. */
2124: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
2125: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.224 brouard 2126: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
2127: /* also lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
2128: /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
1.161 brouard 2129: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.224 brouard 2130: /* Even if f3 <f1, directest can be negative and t >0 */
2131: /* mu² and del² are equal when f3=f1 */
2132: /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
2133: /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
2134: /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0 */
2135: /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0 */
1.183 brouard 2136: #ifdef NRCORIGINAL
2137: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
2138: #else
2139: 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 2140: t= t- del*SQR(fp-fptt);
1.183 brouard 2141: #endif
1.202 brouard 2142: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 2143: #ifdef DEBUG
1.181 brouard 2144: 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);
2145: 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 2146: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2147: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2148: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2149: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2150: 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);
2151: 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);
2152: #endif
1.183 brouard 2153: #ifdef POWELLORIGINAL
2154: if (t < 0.0) { /* Then we use it for new direction */
2155: #else
1.182 brouard 2156: if (directest*t < 0.0) { /* Contradiction between both tests */
1.224 brouard 2157: 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 2158: 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 2159: 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 2160: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
2161: }
1.181 brouard 2162: if (directest < 0.0) { /* Then we use it for new direction */
2163: #endif
1.191 brouard 2164: #ifdef DEBUGLINMIN
1.224 brouard 2165: printf("Before linmin in direction P%d-P0\n",n);
2166: for (j=1;j<=n;j++) {
2167: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2168: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2169: if(j % ncovmodel == 0){
2170: printf("\n");
2171: fprintf(ficlog,"\n");
2172: }
2173: }
2174: #endif
2175: #ifdef LINMINORIGINAL
2176: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
2177: #else
2178: linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
2179: flatdir[i]=flat; /* Function is vanishing in that direction i */
1.191 brouard 2180: #endif
1.224 brouard 2181:
1.191 brouard 2182: #ifdef DEBUGLINMIN
1.224 brouard 2183: for (j=1;j<=n;j++) {
2184: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2185: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2186: if(j % ncovmodel == 0){
2187: printf("\n");
2188: fprintf(ficlog,"\n");
2189: }
2190: }
2191: #endif
2192: for (j=1;j<=n;j++) {
2193: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
2194: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
2195: }
2196: #ifdef LINMINORIGINAL
2197: #else
1.225 brouard 2198: for (j=1, flatd=0;j<=n;j++) {
2199: if(flatdir[j]>0)
2200: flatd++;
2201: }
2202: if(flatd >0){
2203: printf("%d flat directions\n",flatd);
2204: fprintf(ficlog,"%d flat directions\n",flatd);
2205: for (j=1;j<=n;j++) {
2206: if(flatdir[j]>0){
2207: printf("%d ",j);
2208: fprintf(ficlog,"%d ",j);
2209: }
2210: }
2211: printf("\n");
2212: fprintf(ficlog,"\n");
2213: }
1.191 brouard 2214: #endif
1.224 brouard 2215: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2216: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2217:
1.126 brouard 2218: #ifdef DEBUG
1.224 brouard 2219: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2220: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2221: for(j=1;j<=n;j++){
2222: printf(" %lf",xit[j]);
2223: fprintf(ficlog," %lf",xit[j]);
2224: }
2225: printf("\n");
2226: fprintf(ficlog,"\n");
1.126 brouard 2227: #endif
1.192 brouard 2228: } /* end of t or directest negative */
1.224 brouard 2229: #ifdef POWELLNOF3INFF1TEST
1.192 brouard 2230: #else
1.162 brouard 2231: } /* end if (fptt < fp) */
1.192 brouard 2232: #endif
1.225 brouard 2233: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
1.224 brouard 2234: } /*NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done */
1.225 brouard 2235: #else
1.224 brouard 2236: #endif
1.192 brouard 2237: } /* loop iteration */
1.126 brouard 2238: }
2239:
2240: /**** Prevalence limit (stable or period prevalence) ****************/
2241:
1.203 brouard 2242: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
1.126 brouard 2243: {
1.218 brouard 2244: /* Computes the prevalence limit in each live state at age x and for covariate ij by left multiplying the unit
1.203 brouard 2245: matrix by transitions matrix until convergence is reached with precision ftolpl */
1.206 brouard 2246: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2247: /* Wx is row vector: population in state 1, population in state 2, population dead */
2248: /* or prevalence in state 1, prevalence in state 2, 0 */
2249: /* newm is the matrix after multiplications, its rows are identical at a factor */
2250: /* Initial matrix pimij */
2251: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2252: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2253: /* 0, 0 , 1} */
2254: /*
2255: * and after some iteration: */
2256: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2257: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2258: /* 0, 0 , 1} */
2259: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2260: /* {0.51571254859325999, 0.4842874514067399, */
2261: /* 0.51326036147820708, 0.48673963852179264} */
2262: /* If we start from prlim again, prlim tends to a constant matrix */
2263:
1.126 brouard 2264: int i, ii,j,k;
1.209 brouard 2265: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2266: /* double **matprod2(); */ /* test */
1.218 brouard 2267: double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126 brouard 2268: double **newm;
1.209 brouard 2269: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2270: int ncvloop=0;
1.169 brouard 2271:
1.209 brouard 2272: min=vector(1,nlstate);
2273: max=vector(1,nlstate);
2274: meandiff=vector(1,nlstate);
2275:
1.218 brouard 2276: /* Starting with matrix unity */
1.126 brouard 2277: for (ii=1;ii<=nlstate+ndeath;ii++)
2278: for (j=1;j<=nlstate+ndeath;j++){
2279: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2280: }
1.169 brouard 2281:
2282: cov[1]=1.;
2283:
2284: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2285: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2286: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2287: ncvloop++;
1.126 brouard 2288: newm=savm;
2289: /* Covariates have to be included here again */
1.138 brouard 2290: cov[2]=agefin;
1.187 brouard 2291: if(nagesqr==1)
2292: cov[3]= agefin*agefin;;
1.138 brouard 2293: for (k=1; k<=cptcovn;k++) {
1.200 brouard 2294: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.218 brouard 2295: /* Here comes the value of the covariate 'ij' */
1.200 brouard 2296: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
1.198 brouard 2297: /* 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 2298: }
1.186 brouard 2299: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2300: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2301: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
1.186 brouard 2302: for (k=1; k<=cptcovprod;k++) /* Useless */
1.200 brouard 2303: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2304: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.138 brouard 2305:
2306: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2307: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2308: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2309: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2310: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2311: /* age and covariate values of ij are in 'cov' */
1.142 brouard 2312: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2313:
1.126 brouard 2314: savm=oldm;
2315: oldm=newm;
1.209 brouard 2316:
2317: for(j=1; j<=nlstate; j++){
2318: max[j]=0.;
2319: min[j]=1.;
2320: }
2321: for(i=1;i<=nlstate;i++){
2322: sumnew=0;
2323: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2324: for(j=1; j<=nlstate; j++){
2325: prlim[i][j]= newm[i][j]/(1-sumnew);
2326: max[j]=FMAX(max[j],prlim[i][j]);
2327: min[j]=FMIN(min[j],prlim[i][j]);
2328: }
2329: }
2330:
1.126 brouard 2331: maxmax=0.;
1.209 brouard 2332: for(j=1; j<=nlstate; j++){
2333: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2334: maxmax=FMAX(maxmax,meandiff[j]);
2335: /* 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 2336: } /* j loop */
1.203 brouard 2337: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2338: /* 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 2339: if(maxmax < ftolpl){
1.209 brouard 2340: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2341: free_vector(min,1,nlstate);
2342: free_vector(max,1,nlstate);
2343: free_vector(meandiff,1,nlstate);
1.126 brouard 2344: return prlim;
2345: }
1.169 brouard 2346: } /* age loop */
1.208 brouard 2347: /* After some age loop it doesn't converge */
1.209 brouard 2348: 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 2349: 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 2350: /* 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); */
2351: free_vector(min,1,nlstate);
2352: free_vector(max,1,nlstate);
2353: free_vector(meandiff,1,nlstate);
1.208 brouard 2354:
1.169 brouard 2355: return prlim; /* should not reach here */
1.126 brouard 2356: }
2357:
1.217 brouard 2358:
2359: /**** Back Prevalence limit (stable or period prevalence) ****************/
2360:
1.218 brouard 2361: /* 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) */
2362: /* 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) */
2363: double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij)
1.217 brouard 2364: {
1.218 brouard 2365: /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit
1.217 brouard 2366: matrix by transitions matrix until convergence is reached with precision ftolpl */
2367: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2368: /* Wx is row vector: population in state 1, population in state 2, population dead */
2369: /* or prevalence in state 1, prevalence in state 2, 0 */
2370: /* newm is the matrix after multiplications, its rows are identical at a factor */
2371: /* Initial matrix pimij */
2372: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2373: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2374: /* 0, 0 , 1} */
2375: /*
2376: * and after some iteration: */
2377: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2378: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2379: /* 0, 0 , 1} */
2380: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2381: /* {0.51571254859325999, 0.4842874514067399, */
2382: /* 0.51326036147820708, 0.48673963852179264} */
2383: /* If we start from prlim again, prlim tends to a constant matrix */
2384:
2385: int i, ii,j,k;
2386: double *min, *max, *meandiff, maxmax,sumnew=0.;
2387: /* double **matprod2(); */ /* test */
2388: double **out, cov[NCOVMAX+1], **bmij();
2389: double **newm;
1.218 brouard 2390: double **dnewm, **doldm, **dsavm; /* for use */
2391: double **oldm, **savm; /* for use */
2392:
1.217 brouard 2393: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
2394: int ncvloop=0;
2395:
2396: min=vector(1,nlstate);
2397: max=vector(1,nlstate);
2398: meandiff=vector(1,nlstate);
2399:
1.218 brouard 2400: dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
2401: oldm=oldms; savm=savms;
2402:
2403: /* Starting with matrix unity */
2404: for (ii=1;ii<=nlstate+ndeath;ii++)
2405: for (j=1;j<=nlstate+ndeath;j++){
1.217 brouard 2406: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2407: }
2408:
2409: cov[1]=1.;
2410:
2411: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2412: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218 brouard 2413: /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
2414: for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217 brouard 2415: ncvloop++;
1.218 brouard 2416: newm=savm; /* oldm should be kept from previous iteration or unity at start */
2417: /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217 brouard 2418: /* Covariates have to be included here again */
2419: cov[2]=agefin;
2420: if(nagesqr==1)
2421: cov[3]= agefin*agefin;;
2422: for (k=1; k<=cptcovn;k++) {
2423: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
2424: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2425: /* 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])]); */
2426: }
2427: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2428: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2429: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
2430: for (k=1; k<=cptcovprod;k++) /* Useless */
2431: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2432: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2433:
2434: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2435: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2436: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
2437: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2438: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2439: /* ij should be linked to the correct index of cov */
2440: /* age and covariate values ij are in 'cov', but we need to pass
2441: * ij for the observed prevalence at age and status and covariate
2442: * number: prevacurrent[(int)agefin][ii][ij]
2443: */
2444: /* 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 *\/ */
2445: /* 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 *\/ */
2446: 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 2447: savm=oldm;
2448: oldm=newm;
2449: for(j=1; j<=nlstate; j++){
2450: max[j]=0.;
2451: min[j]=1.;
2452: }
2453: for(j=1; j<=nlstate; j++){
2454: for(i=1;i<=nlstate;i++){
1.218 brouard 2455: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
2456: bprlim[i][j]= newm[i][j];
2457: max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
2458: min[i]=FMIN(min[i],bprlim[i][j]);
1.217 brouard 2459: }
2460: }
1.218 brouard 2461:
1.217 brouard 2462: maxmax=0.;
2463: for(i=1; i<=nlstate; i++){
2464: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
2465: maxmax=FMAX(maxmax,meandiff[i]);
2466: /* 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); */
2467: } /* j loop */
2468: *ncvyear= -( (int)age- (int)agefin);
1.218 brouard 2469: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/
1.217 brouard 2470: if(maxmax < ftolpl){
1.220 brouard 2471: /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2472: free_vector(min,1,nlstate);
2473: free_vector(max,1,nlstate);
2474: free_vector(meandiff,1,nlstate);
2475: return bprlim;
2476: }
2477: } /* age loop */
2478: /* After some age loop it doesn't converge */
2479: 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\
2480: 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);
2481: /* 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); */
2482: free_vector(min,1,nlstate);
2483: free_vector(max,1,nlstate);
2484: free_vector(meandiff,1,nlstate);
2485:
2486: return bprlim; /* should not reach here */
2487: }
2488:
1.126 brouard 2489: /*************** transition probabilities ***************/
2490:
2491: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2492: {
1.138 brouard 2493: /* According to parameters values stored in x and the covariate's values stored in cov,
2494: computes the probability to be observed in state j being in state i by appying the
2495: model to the ncovmodel covariates (including constant and age).
2496: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2497: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2498: ncth covariate in the global vector x is given by the formula:
2499: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2500: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2501: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2502: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2503: Outputs ps[i][j] the probability to be observed in j being in j according to
2504: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2505: */
2506: double s1, lnpijopii;
1.126 brouard 2507: /*double t34;*/
1.164 brouard 2508: int i,j, nc, ii, jj;
1.126 brouard 2509:
1.223 brouard 2510: for(i=1; i<= nlstate; i++){
2511: for(j=1; j<i;j++){
2512: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2513: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2514: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2515: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2516: }
2517: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2518: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2519: }
2520: for(j=i+1; j<=nlstate+ndeath;j++){
2521: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2522: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2523: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2524: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2525: }
2526: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2527: }
2528: }
1.218 brouard 2529:
1.223 brouard 2530: for(i=1; i<= nlstate; i++){
2531: s1=0;
2532: for(j=1; j<i; j++){
2533: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2534: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2535: }
2536: for(j=i+1; j<=nlstate+ndeath; j++){
2537: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2538: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2539: }
2540: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2541: ps[i][i]=1./(s1+1.);
2542: /* Computing other pijs */
2543: for(j=1; j<i; j++)
2544: ps[i][j]= exp(ps[i][j])*ps[i][i];
2545: for(j=i+1; j<=nlstate+ndeath; j++)
2546: ps[i][j]= exp(ps[i][j])*ps[i][i];
2547: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2548: } /* end i */
1.218 brouard 2549:
1.223 brouard 2550: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2551: for(jj=1; jj<= nlstate+ndeath; jj++){
2552: ps[ii][jj]=0;
2553: ps[ii][ii]=1;
2554: }
2555: }
1.218 brouard 2556:
2557:
1.223 brouard 2558: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2559: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2560: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2561: /* } */
2562: /* printf("\n "); */
2563: /* } */
2564: /* printf("\n ");printf("%lf ",cov[2]);*/
2565: /*
2566: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1.218 brouard 2567: goto end;*/
1.223 brouard 2568: return ps;
1.126 brouard 2569: }
2570:
1.218 brouard 2571: /*************** backward transition probabilities ***************/
2572:
2573: /* 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 ) */
2574: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
2575: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij )
2576: {
1.222 brouard 2577: /* Computes the backward probability at age agefin and covariate ij
2578: * and returns in **ps as well as **bmij.
2579: */
1.218 brouard 2580: int i, ii, j,k;
1.222 brouard 2581:
2582: double **out, **pmij();
2583: double sumnew=0.;
1.218 brouard 2584: double agefin;
1.222 brouard 2585:
2586: double **dnewm, **dsavm, **doldm;
2587: double **bbmij;
2588:
1.218 brouard 2589: doldm=ddoldms; /* global pointers */
1.222 brouard 2590: dnewm=ddnewms;
2591: dsavm=ddsavms;
2592:
2593: agefin=cov[2];
2594: /* bmij *//* age is cov[2], ij is included in cov, but we need for
2595: the observed prevalence (with this covariate ij) */
2596: dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
2597: /* We do have the matrix Px in savm and we need pij */
2598: for (j=1;j<=nlstate+ndeath;j++){
2599: sumnew=0.; /* w1 p11 + w2 p21 only on live states */
2600: for (ii=1;ii<=nlstate;ii++){
2601: sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
2602: } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
2603: for (ii=1;ii<=nlstate+ndeath;ii++){
2604: if(sumnew >= 1.e-10){
2605: /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
2606: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
2607: /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
2608: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
2609: /* }else */
2610: doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
2611: }else{
2612: 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);
2613: }
2614: } /*End ii */
2615: } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
2616: /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
2617: bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
2618: /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
2619: /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
2620: /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
2621: /* left Product of this matrix by diag matrix of prevalences (savm) */
2622: for (j=1;j<=nlstate+ndeath;j++){
2623: for (ii=1;ii<=nlstate+ndeath;ii++){
2624: dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
2625: }
2626: } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
2627: ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
2628: /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
2629: /* end bmij */
2630: return ps;
1.218 brouard 2631: }
1.217 brouard 2632: /*************** transition probabilities ***************/
2633:
1.218 brouard 2634: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217 brouard 2635: {
2636: /* According to parameters values stored in x and the covariate's values stored in cov,
2637: computes the probability to be observed in state j being in state i by appying the
2638: model to the ncovmodel covariates (including constant and age).
2639: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2640: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2641: ncth covariate in the global vector x is given by the formula:
2642: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2643: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2644: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2645: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2646: Outputs ps[i][j] the probability to be observed in j being in j according to
2647: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2648: */
2649: double s1, lnpijopii;
2650: /*double t34;*/
2651: int i,j, nc, ii, jj;
2652:
1.218 brouard 2653: for(i=1; i<= nlstate; i++){
2654: for(j=1; j<i;j++){
2655: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2656: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2657: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2658: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2659: }
2660: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2661: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2662: }
2663: for(j=i+1; j<=nlstate+ndeath;j++){
2664: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2665: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2666: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2667: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2668: }
2669: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2670: }
2671: }
2672:
2673: for(i=1; i<= nlstate; i++){
2674: s1=0;
2675: for(j=1; j<i; j++){
2676: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2677: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2678: }
2679: for(j=i+1; j<=nlstate+ndeath; j++){
2680: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2681: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2682: }
2683: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2684: ps[i][i]=1./(s1+1.);
2685: /* Computing other pijs */
2686: for(j=1; j<i; j++)
2687: ps[i][j]= exp(ps[i][j])*ps[i][i];
2688: for(j=i+1; j<=nlstate+ndeath; j++)
2689: ps[i][j]= exp(ps[i][j])*ps[i][i];
2690: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2691: } /* end i */
2692:
2693: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2694: for(jj=1; jj<= nlstate+ndeath; jj++){
2695: ps[ii][jj]=0;
2696: ps[ii][ii]=1;
2697: }
2698: }
2699: /* Added for backcast */ /* Transposed matrix too */
2700: for(jj=1; jj<= nlstate+ndeath; jj++){
2701: s1=0.;
2702: for(ii=1; ii<= nlstate+ndeath; ii++){
2703: s1+=ps[ii][jj];
2704: }
2705: for(ii=1; ii<= nlstate; ii++){
2706: ps[ii][jj]=ps[ii][jj]/s1;
2707: }
2708: }
2709: /* Transposition */
2710: for(jj=1; jj<= nlstate+ndeath; jj++){
2711: for(ii=jj; ii<= nlstate+ndeath; ii++){
2712: s1=ps[ii][jj];
2713: ps[ii][jj]=ps[jj][ii];
2714: ps[jj][ii]=s1;
2715: }
2716: }
2717: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2718: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2719: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2720: /* } */
2721: /* printf("\n "); */
2722: /* } */
2723: /* printf("\n ");printf("%lf ",cov[2]);*/
2724: /*
2725: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2726: goto end;*/
2727: return ps;
1.217 brouard 2728: }
2729:
2730:
1.126 brouard 2731: /**************** Product of 2 matrices ******************/
2732:
1.145 brouard 2733: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2734: {
2735: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2736: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2737: /* in, b, out are matrice of pointers which should have been initialized
2738: before: only the contents of out is modified. The function returns
2739: a pointer to pointers identical to out */
1.145 brouard 2740: int i, j, k;
1.126 brouard 2741: for(i=nrl; i<= nrh; i++)
1.145 brouard 2742: for(k=ncolol; k<=ncoloh; k++){
2743: out[i][k]=0.;
2744: for(j=ncl; j<=nch; j++)
2745: out[i][k] +=in[i][j]*b[j][k];
2746: }
1.126 brouard 2747: return out;
2748: }
2749:
2750:
2751: /************* Higher Matrix Product ***************/
2752:
2753: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2754: {
1.218 brouard 2755: /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
1.126 brouard 2756: 'nhstepm*hstepm*stepm' months (i.e. until
2757: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2758: nhstepm*hstepm matrices.
2759: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2760: (typically every 2 years instead of every month which is too big
2761: for the memory).
2762: Model is determined by parameters x and covariates have to be
2763: included manually here.
2764:
2765: */
2766:
2767: int i, j, d, h, k;
1.131 brouard 2768: double **out, cov[NCOVMAX+1];
1.126 brouard 2769: double **newm;
1.187 brouard 2770: double agexact;
1.214 brouard 2771: double agebegin, ageend;
1.126 brouard 2772:
2773: /* Hstepm could be zero and should return the unit matrix */
2774: for (i=1;i<=nlstate+ndeath;i++)
2775: for (j=1;j<=nlstate+ndeath;j++){
2776: oldm[i][j]=(i==j ? 1.0 : 0.0);
2777: po[i][j][0]=(i==j ? 1.0 : 0.0);
2778: }
2779: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2780: for(h=1; h <=nhstepm; h++){
2781: for(d=1; d <=hstepm; d++){
2782: newm=savm;
2783: /* Covariates have to be included here again */
2784: cov[1]=1.;
1.214 brouard 2785: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 2786: cov[2]=agexact;
2787: if(nagesqr==1)
1.227 brouard 2788: cov[3]= agexact*agexact;
1.131 brouard 2789: for (k=1; k<=cptcovn;k++)
1.227 brouard 2790: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2791: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.186 brouard 2792: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1.227 brouard 2793: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2794: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2795: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.145 brouard 2796: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.227 brouard 2797: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2798: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2799:
2800:
1.126 brouard 2801: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2802: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 2803: /* right multiplication of oldm by the current matrix */
1.126 brouard 2804: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2805: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 brouard 2806: /* if((int)age == 70){ */
2807: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
2808: /* for(i=1; i<=nlstate+ndeath; i++) { */
2809: /* printf("%d pmmij ",i); */
2810: /* for(j=1;j<=nlstate+ndeath;j++) { */
2811: /* printf("%f ",pmmij[i][j]); */
2812: /* } */
2813: /* printf(" oldm "); */
2814: /* for(j=1;j<=nlstate+ndeath;j++) { */
2815: /* printf("%f ",oldm[i][j]); */
2816: /* } */
2817: /* printf("\n"); */
2818: /* } */
2819: /* } */
1.126 brouard 2820: savm=oldm;
2821: oldm=newm;
2822: }
2823: for(i=1; i<=nlstate+ndeath; i++)
2824: for(j=1;j<=nlstate+ndeath;j++) {
1.218 brouard 2825: po[i][j][h]=newm[i][j];
2826: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2827: }
1.128 brouard 2828: /*printf("h=%d ",h);*/
1.126 brouard 2829: } /* end h */
1.218 brouard 2830: /* printf("\n H=%d \n",h); */
1.126 brouard 2831: return po;
2832: }
2833:
1.217 brouard 2834: /************* Higher Back Matrix Product ***************/
1.218 brouard 2835: /* 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 2836: double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )
1.217 brouard 2837: {
1.218 brouard 2838: /* Computes the transition matrix starting at age 'age' over
1.217 brouard 2839: 'nhstepm*hstepm*stepm' months (i.e. until
1.218 brouard 2840: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2841: nhstepm*hstepm matrices.
2842: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2843: (typically every 2 years instead of every month which is too big
1.217 brouard 2844: for the memory).
1.218 brouard 2845: Model is determined by parameters x and covariates have to be
2846: included manually here.
1.217 brouard 2847:
1.222 brouard 2848: */
1.217 brouard 2849:
2850: int i, j, d, h, k;
2851: double **out, cov[NCOVMAX+1];
2852: double **newm;
2853: double agexact;
2854: double agebegin, ageend;
1.222 brouard 2855: double **oldm, **savm;
1.217 brouard 2856:
1.222 brouard 2857: oldm=oldms;savm=savms;
1.217 brouard 2858: /* Hstepm could be zero and should return the unit matrix */
2859: for (i=1;i<=nlstate+ndeath;i++)
2860: for (j=1;j<=nlstate+ndeath;j++){
2861: oldm[i][j]=(i==j ? 1.0 : 0.0);
2862: po[i][j][0]=(i==j ? 1.0 : 0.0);
2863: }
2864: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2865: for(h=1; h <=nhstepm; h++){
2866: for(d=1; d <=hstepm; d++){
2867: newm=savm;
2868: /* Covariates have to be included here again */
2869: cov[1]=1.;
2870: agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
2871: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
2872: cov[2]=agexact;
2873: if(nagesqr==1)
1.222 brouard 2874: cov[3]= agexact*agexact;
1.218 brouard 2875: for (k=1; k<=cptcovn;k++)
1.222 brouard 2876: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2877: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.217 brouard 2878: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1.222 brouard 2879: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2880: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2881: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.217 brouard 2882: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.222 brouard 2883: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2884: /* 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 2885:
2886:
1.217 brouard 2887: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2888: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 2889: /* Careful transposed matrix */
1.222 brouard 2890: /* age is in cov[2] */
1.218 brouard 2891: /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
1.222 brouard 2892: /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
1.218 brouard 2893: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1.222 brouard 2894: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217 brouard 2895: /* if((int)age == 70){ */
2896: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
2897: /* for(i=1; i<=nlstate+ndeath; i++) { */
2898: /* printf("%d pmmij ",i); */
2899: /* for(j=1;j<=nlstate+ndeath;j++) { */
2900: /* printf("%f ",pmmij[i][j]); */
2901: /* } */
2902: /* printf(" oldm "); */
2903: /* for(j=1;j<=nlstate+ndeath;j++) { */
2904: /* printf("%f ",oldm[i][j]); */
2905: /* } */
2906: /* printf("\n"); */
2907: /* } */
2908: /* } */
2909: savm=oldm;
2910: oldm=newm;
2911: }
2912: for(i=1; i<=nlstate+ndeath; i++)
2913: for(j=1;j<=nlstate+ndeath;j++) {
1.222 brouard 2914: po[i][j][h]=newm[i][j];
2915: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.217 brouard 2916: }
2917: /*printf("h=%d ",h);*/
2918: } /* end h */
1.222 brouard 2919: /* printf("\n H=%d \n",h); */
1.217 brouard 2920: return po;
2921: }
2922:
2923:
1.162 brouard 2924: #ifdef NLOPT
2925: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2926: double fret;
2927: double *xt;
2928: int j;
2929: myfunc_data *d2 = (myfunc_data *) pd;
2930: /* xt = (p1-1); */
2931: xt=vector(1,n);
2932: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2933:
2934: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2935: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2936: printf("Function = %.12lf ",fret);
2937: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2938: printf("\n");
2939: free_vector(xt,1,n);
2940: return fret;
2941: }
2942: #endif
1.126 brouard 2943:
2944: /*************** log-likelihood *************/
2945: double func( double *x)
2946: {
1.226 brouard 2947: int i, ii, j, k, mi, d, kk;
2948: int ioffset=0;
2949: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
2950: double **out;
2951: double lli; /* Individual log likelihood */
2952: int s1, s2;
1.228 brouard 2953: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
1.226 brouard 2954: double bbh, survp;
2955: long ipmx;
2956: double agexact;
2957: /*extern weight */
2958: /* We are differentiating ll according to initial status */
2959: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2960: /*for(i=1;i<imx;i++)
2961: printf(" %d\n",s[4][i]);
2962: */
1.162 brouard 2963:
1.226 brouard 2964: ++countcallfunc;
1.162 brouard 2965:
1.226 brouard 2966: cov[1]=1.;
1.126 brouard 2967:
1.226 brouard 2968: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 2969: ioffset=0;
1.226 brouard 2970: if(mle==1){
2971: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2972: /* Computes the values of the ncovmodel covariates of the model
2973: depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
2974: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2975: to be observed in j being in i according to the model.
2976: */
2977: ioffset=2+nagesqr+cptcovage;
2978: /* for (k=1; k<=cptcovn;k++){ /\* Simple and product covariates without age* products *\/ */
2979: for (k=1; k<=ncoveff;k++){ /* Simple and product covariates without age* products */
2980: cov[++ioffset]=covar[Tvar[k]][i];
2981: }
2982: for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitatives and Fixed covariates */
1.228 brouard 2983: cov[++ioffset]=coqvar[Tvar[iqv]][i];
1.226 brouard 2984: }
2985:
2986: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
2987: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
2988: has been calculated etc */
2989: /* For an individual i, wav[i] gives the number of effective waves */
2990: /* We compute the contribution to Likelihood of each effective transition
2991: mw[mi][i] is real wave of the mi th effectve wave */
2992: /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
2993: s2=s[mw[mi+1][i]][i];
2994: And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
2995: But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
2996: meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
2997: */
2998: for(mi=1; mi<= wav[i]-1; mi++){
2999: for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
1.229 ! brouard 3000: /* cov[ioffset+itv]=cotvar[mw[mi][i]][Tvar[itv]][i]; /\* Not sure, Tvar V4+V3+V5 Tvaraff ? *\/ */
! 3001: cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i];
1.226 brouard 3002: }
3003: for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
3004: if(cotqvar[mw[mi][i]][iqtv][i] == -1){
3005: printf("i=%d, mi=%d, iqtv=%d, cotqvar[mw[mi][i]][iqtv][i]=%f",i,mi,iqtv,cotqvar[mw[mi][i]][iqtv][i]);
3006: }
1.229 ! brouard 3007: cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i];
! 3008: /* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i]; */
1.226 brouard 3009: }
3010: /* ioffset=2+nagesqr+cptcovn+nqv+ntv+nqtv; */
3011: for (ii=1;ii<=nlstate+ndeath;ii++)
3012: for (j=1;j<=nlstate+ndeath;j++){
3013: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3014: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3015: }
3016: for(d=0; d<dh[mi][i]; d++){
3017: newm=savm;
3018: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3019: cov[2]=agexact;
3020: if(nagesqr==1)
3021: cov[3]= agexact*agexact; /* Should be changed here */
3022: for (kk=1; kk<=cptcovage;kk++) {
3023: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
3024: }
3025: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3026: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3027: savm=oldm;
3028: oldm=newm;
3029: } /* end mult */
1.224 brouard 3030:
1.226 brouard 3031: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
3032: /* But now since version 0.9 we anticipate for bias at large stepm.
3033: * If stepm is larger than one month (smallest stepm) and if the exact delay
3034: * (in months) between two waves is not a multiple of stepm, we rounded to
3035: * the nearest (and in case of equal distance, to the lowest) interval but now
3036: * we keep into memory the bias bh[mi][i] and also the previous matrix product
3037: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
3038: * probability in order to take into account the bias as a fraction of the way
3039: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
3040: * -stepm/2 to stepm/2 .
3041: * For stepm=1 the results are the same as for previous versions of Imach.
3042: * For stepm > 1 the results are less biased than in previous versions.
3043: */
3044: s1=s[mw[mi][i]][i];
3045: s2=s[mw[mi+1][i]][i];
3046: bbh=(double)bh[mi][i]/(double)stepm;
3047: /* bias bh is positive if real duration
3048: * is higher than the multiple of stepm and negative otherwise.
3049: */
3050: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
3051: if( s2 > nlstate){
3052: /* i.e. if s2 is a death state and if the date of death is known
3053: then the contribution to the likelihood is the probability to
3054: die between last step unit time and current step unit time,
3055: which is also equal to probability to die before dh
3056: minus probability to die before dh-stepm .
3057: In version up to 0.92 likelihood was computed
3058: as if date of death was unknown. Death was treated as any other
3059: health state: the date of the interview describes the actual state
3060: and not the date of a change in health state. The former idea was
3061: to consider that at each interview the state was recorded
3062: (healthy, disable or death) and IMaCh was corrected; but when we
3063: introduced the exact date of death then we should have modified
3064: the contribution of an exact death to the likelihood. This new
3065: contribution is smaller and very dependent of the step unit
3066: stepm. It is no more the probability to die between last interview
3067: and month of death but the probability to survive from last
3068: interview up to one month before death multiplied by the
3069: probability to die within a month. Thanks to Chris
3070: Jackson for correcting this bug. Former versions increased
3071: mortality artificially. The bad side is that we add another loop
3072: which slows down the processing. The difference can be up to 10%
3073: lower mortality.
3074: */
3075: /* If, at the beginning of the maximization mostly, the
3076: cumulative probability or probability to be dead is
3077: constant (ie = 1) over time d, the difference is equal to
3078: 0. out[s1][3] = savm[s1][3]: probability, being at state
3079: s1 at precedent wave, to be dead a month before current
3080: wave is equal to probability, being at state s1 at
3081: precedent wave, to be dead at mont of the current
3082: wave. Then the observed probability (that this person died)
3083: is null according to current estimated parameter. In fact,
3084: it should be very low but not zero otherwise the log go to
3085: infinity.
3086: */
1.183 brouard 3087: /* #ifdef INFINITYORIGINAL */
3088: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3089: /* #else */
3090: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
3091: /* lli=log(mytinydouble); */
3092: /* else */
3093: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3094: /* #endif */
1.226 brouard 3095: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3096:
1.226 brouard 3097: } else if ( s2==-1 ) { /* alive */
3098: for (j=1,survp=0. ; j<=nlstate; j++)
3099: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3100: /*survp += out[s1][j]; */
3101: lli= log(survp);
3102: }
3103: else if (s2==-4) {
3104: for (j=3,survp=0. ; j<=nlstate; j++)
3105: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3106: lli= log(survp);
3107: }
3108: else if (s2==-5) {
3109: for (j=1,survp=0. ; j<=2; j++)
3110: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3111: lli= log(survp);
3112: }
3113: else{
3114: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3115: /* 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 */
3116: }
3117: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
3118: /*if(lli ==000.0)*/
3119: /*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); */
3120: ipmx +=1;
3121: sw += weight[i];
3122: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3123: /* if (lli < log(mytinydouble)){ */
3124: /* 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); */
3125: /* 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]); */
3126: /* } */
3127: } /* end of wave */
3128: } /* end of individual */
3129: } else if(mle==2){
3130: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3131: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3132: for(mi=1; mi<= wav[i]-1; mi++){
3133: for (ii=1;ii<=nlstate+ndeath;ii++)
3134: for (j=1;j<=nlstate+ndeath;j++){
3135: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3136: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3137: }
3138: for(d=0; d<=dh[mi][i]; d++){
3139: newm=savm;
3140: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3141: cov[2]=agexact;
3142: if(nagesqr==1)
3143: cov[3]= agexact*agexact;
3144: for (kk=1; kk<=cptcovage;kk++) {
3145: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3146: }
3147: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3148: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3149: savm=oldm;
3150: oldm=newm;
3151: } /* end mult */
3152:
3153: s1=s[mw[mi][i]][i];
3154: s2=s[mw[mi+1][i]][i];
3155: bbh=(double)bh[mi][i]/(double)stepm;
3156: 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 */
3157: ipmx +=1;
3158: sw += weight[i];
3159: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3160: } /* end of wave */
3161: } /* end of individual */
3162: } else if(mle==3){ /* exponential inter-extrapolation */
3163: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3164: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3165: for(mi=1; mi<= wav[i]-1; mi++){
3166: for (ii=1;ii<=nlstate+ndeath;ii++)
3167: for (j=1;j<=nlstate+ndeath;j++){
3168: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3169: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3170: }
3171: for(d=0; d<dh[mi][i]; d++){
3172: newm=savm;
3173: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3174: cov[2]=agexact;
3175: if(nagesqr==1)
3176: cov[3]= agexact*agexact;
3177: for (kk=1; kk<=cptcovage;kk++) {
3178: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3179: }
3180: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3181: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3182: savm=oldm;
3183: oldm=newm;
3184: } /* end mult */
3185:
3186: s1=s[mw[mi][i]][i];
3187: s2=s[mw[mi+1][i]][i];
3188: bbh=(double)bh[mi][i]/(double)stepm;
3189: 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 */
3190: ipmx +=1;
3191: sw += weight[i];
3192: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3193: } /* end of wave */
3194: } /* end of individual */
3195: }else if (mle==4){ /* ml=4 no inter-extrapolation */
3196: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3197: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3198: for(mi=1; mi<= wav[i]-1; mi++){
3199: for (ii=1;ii<=nlstate+ndeath;ii++)
3200: for (j=1;j<=nlstate+ndeath;j++){
3201: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3202: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3203: }
3204: for(d=0; d<dh[mi][i]; d++){
3205: newm=savm;
3206: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3207: cov[2]=agexact;
3208: if(nagesqr==1)
3209: cov[3]= agexact*agexact;
3210: for (kk=1; kk<=cptcovage;kk++) {
3211: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3212: }
1.126 brouard 3213:
1.226 brouard 3214: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3215: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3216: savm=oldm;
3217: oldm=newm;
3218: } /* end mult */
3219:
3220: s1=s[mw[mi][i]][i];
3221: s2=s[mw[mi+1][i]][i];
3222: if( s2 > nlstate){
3223: lli=log(out[s1][s2] - savm[s1][s2]);
3224: } else if ( s2==-1 ) { /* alive */
3225: for (j=1,survp=0. ; j<=nlstate; j++)
3226: survp += out[s1][j];
3227: lli= log(survp);
3228: }else{
3229: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3230: }
3231: ipmx +=1;
3232: sw += weight[i];
3233: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.126 brouard 3234: /* printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
1.226 brouard 3235: } /* end of wave */
3236: } /* end of individual */
3237: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
3238: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3239: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3240: for(mi=1; mi<= wav[i]-1; mi++){
3241: for (ii=1;ii<=nlstate+ndeath;ii++)
3242: for (j=1;j<=nlstate+ndeath;j++){
3243: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3244: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3245: }
3246: for(d=0; d<dh[mi][i]; d++){
3247: newm=savm;
3248: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3249: cov[2]=agexact;
3250: if(nagesqr==1)
3251: cov[3]= agexact*agexact;
3252: for (kk=1; kk<=cptcovage;kk++) {
3253: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3254: }
1.126 brouard 3255:
1.226 brouard 3256: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3257: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3258: savm=oldm;
3259: oldm=newm;
3260: } /* end mult */
3261:
3262: s1=s[mw[mi][i]][i];
3263: s2=s[mw[mi+1][i]][i];
3264: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3265: ipmx +=1;
3266: sw += weight[i];
3267: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3268: /*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]);*/
3269: } /* end of wave */
3270: } /* end of individual */
3271: } /* End of if */
3272: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3273: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3274: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3275: return -l;
1.126 brouard 3276: }
3277:
3278: /*************** log-likelihood *************/
3279: double funcone( double *x)
3280: {
1.228 brouard 3281: /* Same as func but slower because of a lot of printf and if */
1.126 brouard 3282: int i, ii, j, k, mi, d, kk;
1.228 brouard 3283: int ioffset=0;
1.131 brouard 3284: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 3285: double **out;
3286: double lli; /* Individual log likelihood */
3287: double llt;
3288: int s1, s2;
1.228 brouard 3289: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
3290:
1.126 brouard 3291: double bbh, survp;
1.187 brouard 3292: double agexact;
1.214 brouard 3293: double agebegin, ageend;
1.126 brouard 3294: /*extern weight */
3295: /* We are differentiating ll according to initial status */
3296: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3297: /*for(i=1;i<imx;i++)
3298: printf(" %d\n",s[4][i]);
3299: */
3300: cov[1]=1.;
3301:
3302: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3303: ioffset=0;
3304: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.225 brouard 3305: ioffset=2+nagesqr+cptcovage;
1.224 brouard 3306: /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
1.226 brouard 3307: for (k=1; k<=ncoveff+nqfveff;k++){ /* Simple and product fixed covariates without age* products */
1.225 brouard 3308: cov[++ioffset]=covar[Tvar[k]][i];
3309: }
1.226 brouard 3310: for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitative fixed covariates */
3311: cov[++ioffset]=coqvar[Tvar[iqv]][i];
1.225 brouard 3312: }
3313:
1.226 brouard 3314: for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */
1.225 brouard 3315: for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
1.228 brouard 3316: /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3317: /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
3318: k=ioffset-2-nagesqr-cptcovage+itv; /* position in simple model */
3319: cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i];
1.229 ! brouard 3320: /* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */
1.225 brouard 3321: }
3322: for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
1.228 brouard 3323: iv=TmodelInvQind[iqtv]; /* Counting the # varying covariate from 1 to ntveff */
1.229 ! brouard 3324: /* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); */
1.228 brouard 3325: cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i];
1.225 brouard 3326: }
1.126 brouard 3327: for (ii=1;ii<=nlstate+ndeath;ii++)
1.225 brouard 3328: for (j=1;j<=nlstate+ndeath;j++){
3329: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3330: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3331: }
1.214 brouard 3332:
3333: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
3334: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
3335: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
1.225 brouard 3336: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3337: and mw[mi+1][i]. dh depends on stepm.*/
3338: newm=savm;
3339: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3340: cov[2]=agexact;
3341: if(nagesqr==1)
3342: cov[3]= agexact*agexact;
3343: for (kk=1; kk<=cptcovage;kk++) {
3344: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3345: }
3346: /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
3347: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
3348: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3349: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3350: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
3351: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
3352: savm=oldm;
3353: oldm=newm;
1.126 brouard 3354: } /* end mult */
3355:
3356: s1=s[mw[mi][i]][i];
3357: s2=s[mw[mi+1][i]][i];
1.217 brouard 3358: /* if(s2==-1){ */
3359: /* printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */
3360: /* /\* exit(1); *\/ */
3361: /* } */
1.126 brouard 3362: bbh=(double)bh[mi][i]/(double)stepm;
3363: /* bias is positive if real duration
3364: * is higher than the multiple of stepm and negative otherwise.
3365: */
3366: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1.225 brouard 3367: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3368: } else if ( s2==-1 ) { /* alive */
1.225 brouard 3369: for (j=1,survp=0. ; j<=nlstate; j++)
3370: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3371: lli= log(survp);
1.126 brouard 3372: }else if (mle==1){
1.225 brouard 3373: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1.126 brouard 3374: } else if(mle==2){
1.225 brouard 3375: 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 3376: } else if(mle==3){ /* exponential inter-extrapolation */
1.225 brouard 3377: 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 3378: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1.225 brouard 3379: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 3380: } else{ /* mle=0 back to 1 */
1.225 brouard 3381: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3382: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 3383: } /* End of if */
3384: ipmx +=1;
3385: sw += weight[i];
3386: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 3387: /*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 3388: if(globpr){
1.225 brouard 3389: fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
1.126 brouard 3390: %11.6f %11.6f %11.6f ", \
1.225 brouard 3391: num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
3392: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
3393: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
3394: llt +=ll[k]*gipmx/gsw;
3395: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
3396: }
3397: fprintf(ficresilk," %10.6f\n", -llt);
1.126 brouard 3398: }
3399: } /* end of wave */
3400: } /* end of individual */
3401: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3402: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3403: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3404: if(globpr==0){ /* First time we count the contributions and weights */
3405: gipmx=ipmx;
3406: gsw=sw;
3407: }
3408: return -l;
3409: }
3410:
3411:
3412: /*************** function likelione ***********/
3413: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
3414: {
3415: /* This routine should help understanding what is done with
3416: the selection of individuals/waves and
3417: to check the exact contribution to the likelihood.
3418: Plotting could be done.
3419: */
3420: int k;
3421:
3422: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 3423: strcpy(fileresilk,"ILK_");
1.202 brouard 3424: strcat(fileresilk,fileresu);
1.126 brouard 3425: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
3426: printf("Problem with resultfile: %s\n", fileresilk);
3427: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
3428: }
1.214 brouard 3429: 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");
3430: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 3431: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
3432: for(k=1; k<=nlstate; k++)
3433: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
3434: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
3435: }
3436:
3437: *fretone=(*funcone)(p);
3438: if(*globpri !=0){
3439: fclose(ficresilk);
1.205 brouard 3440: if (mle ==0)
3441: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
3442: else if(mle >=1)
3443: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
3444: 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 3445:
1.208 brouard 3446:
3447: for (k=1; k<= nlstate ; k++) {
1.211 brouard 3448: 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 3449: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
3450: }
1.207 brouard 3451: 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 3452: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3453: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 3454: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3455: fflush(fichtm);
1.205 brouard 3456: }
1.126 brouard 3457: return;
3458: }
3459:
3460:
3461: /*********** Maximum Likelihood Estimation ***************/
3462:
3463: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
3464: {
1.165 brouard 3465: int i,j, iter=0;
1.126 brouard 3466: double **xi;
3467: double fret;
3468: double fretone; /* Only one call to likelihood */
3469: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 3470:
3471: #ifdef NLOPT
3472: int creturn;
3473: nlopt_opt opt;
3474: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
3475: double *lb;
3476: double minf; /* the minimum objective value, upon return */
3477: double * p1; /* Shifted parameters from 0 instead of 1 */
3478: myfunc_data dinst, *d = &dinst;
3479: #endif
3480:
3481:
1.126 brouard 3482: xi=matrix(1,npar,1,npar);
3483: for (i=1;i<=npar;i++)
3484: for (j=1;j<=npar;j++)
3485: xi[i][j]=(i==j ? 1.0 : 0.0);
3486: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 3487: strcpy(filerespow,"POW_");
1.126 brouard 3488: strcat(filerespow,fileres);
3489: if((ficrespow=fopen(filerespow,"w"))==NULL) {
3490: printf("Problem with resultfile: %s\n", filerespow);
3491: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
3492: }
3493: fprintf(ficrespow,"# Powell\n# iter -2*LL");
3494: for (i=1;i<=nlstate;i++)
3495: for(j=1;j<=nlstate+ndeath;j++)
3496: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
3497: fprintf(ficrespow,"\n");
1.162 brouard 3498: #ifdef POWELL
1.126 brouard 3499: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 3500: #endif
1.126 brouard 3501:
1.162 brouard 3502: #ifdef NLOPT
3503: #ifdef NEWUOA
3504: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
3505: #else
3506: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
3507: #endif
3508: lb=vector(0,npar-1);
3509: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
3510: nlopt_set_lower_bounds(opt, lb);
3511: nlopt_set_initial_step1(opt, 0.1);
3512:
3513: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
3514: d->function = func;
3515: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
3516: nlopt_set_min_objective(opt, myfunc, d);
3517: nlopt_set_xtol_rel(opt, ftol);
3518: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
3519: printf("nlopt failed! %d\n",creturn);
3520: }
3521: else {
3522: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
3523: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
3524: iter=1; /* not equal */
3525: }
3526: nlopt_destroy(opt);
3527: #endif
1.126 brouard 3528: free_matrix(xi,1,npar,1,npar);
3529: fclose(ficrespow);
1.203 brouard 3530: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
3531: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 3532: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 3533:
3534: }
3535:
3536: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 3537: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 3538: {
3539: double **a,**y,*x,pd;
1.203 brouard 3540: /* double **hess; */
1.164 brouard 3541: int i, j;
1.126 brouard 3542: int *indx;
3543:
3544: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 3545: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 3546: void lubksb(double **a, int npar, int *indx, double b[]) ;
3547: void ludcmp(double **a, int npar, int *indx, double *d) ;
3548: double gompertz(double p[]);
1.203 brouard 3549: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 3550:
3551: printf("\nCalculation of the hessian matrix. Wait...\n");
3552: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
3553: for (i=1;i<=npar;i++){
1.203 brouard 3554: printf("%d-",i);fflush(stdout);
3555: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 3556:
3557: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
3558:
3559: /* printf(" %f ",p[i]);
3560: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
3561: }
3562:
3563: for (i=1;i<=npar;i++) {
3564: for (j=1;j<=npar;j++) {
3565: if (j>i) {
1.203 brouard 3566: printf(".%d-%d",i,j);fflush(stdout);
3567: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
3568: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 3569:
3570: hess[j][i]=hess[i][j];
3571: /*printf(" %lf ",hess[i][j]);*/
3572: }
3573: }
3574: }
3575: printf("\n");
3576: fprintf(ficlog,"\n");
3577:
3578: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
3579: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
3580:
3581: a=matrix(1,npar,1,npar);
3582: y=matrix(1,npar,1,npar);
3583: x=vector(1,npar);
3584: indx=ivector(1,npar);
3585: for (i=1;i<=npar;i++)
3586: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
3587: ludcmp(a,npar,indx,&pd);
3588:
3589: for (j=1;j<=npar;j++) {
3590: for (i=1;i<=npar;i++) x[i]=0;
3591: x[j]=1;
3592: lubksb(a,npar,indx,x);
3593: for (i=1;i<=npar;i++){
3594: matcov[i][j]=x[i];
3595: }
3596: }
3597:
3598: printf("\n#Hessian matrix#\n");
3599: fprintf(ficlog,"\n#Hessian matrix#\n");
3600: for (i=1;i<=npar;i++) {
3601: for (j=1;j<=npar;j++) {
1.203 brouard 3602: printf("%.6e ",hess[i][j]);
3603: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 3604: }
3605: printf("\n");
3606: fprintf(ficlog,"\n");
3607: }
3608:
1.203 brouard 3609: /* printf("\n#Covariance matrix#\n"); */
3610: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
3611: /* for (i=1;i<=npar;i++) { */
3612: /* for (j=1;j<=npar;j++) { */
3613: /* printf("%.6e ",matcov[i][j]); */
3614: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
3615: /* } */
3616: /* printf("\n"); */
3617: /* fprintf(ficlog,"\n"); */
3618: /* } */
3619:
1.126 brouard 3620: /* Recompute Inverse */
1.203 brouard 3621: /* for (i=1;i<=npar;i++) */
3622: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
3623: /* ludcmp(a,npar,indx,&pd); */
3624:
3625: /* printf("\n#Hessian matrix recomputed#\n"); */
3626:
3627: /* for (j=1;j<=npar;j++) { */
3628: /* for (i=1;i<=npar;i++) x[i]=0; */
3629: /* x[j]=1; */
3630: /* lubksb(a,npar,indx,x); */
3631: /* for (i=1;i<=npar;i++){ */
3632: /* y[i][j]=x[i]; */
3633: /* printf("%.3e ",y[i][j]); */
3634: /* fprintf(ficlog,"%.3e ",y[i][j]); */
3635: /* } */
3636: /* printf("\n"); */
3637: /* fprintf(ficlog,"\n"); */
3638: /* } */
3639:
3640: /* Verifying the inverse matrix */
3641: #ifdef DEBUGHESS
3642: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 3643:
1.203 brouard 3644: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
3645: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 3646:
3647: for (j=1;j<=npar;j++) {
3648: for (i=1;i<=npar;i++){
1.203 brouard 3649: printf("%.2f ",y[i][j]);
3650: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 3651: }
3652: printf("\n");
3653: fprintf(ficlog,"\n");
3654: }
1.203 brouard 3655: #endif
1.126 brouard 3656:
3657: free_matrix(a,1,npar,1,npar);
3658: free_matrix(y,1,npar,1,npar);
3659: free_vector(x,1,npar);
3660: free_ivector(indx,1,npar);
1.203 brouard 3661: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 3662:
3663:
3664: }
3665:
3666: /*************** hessian matrix ****************/
3667: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 3668: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 3669: int i;
3670: int l=1, lmax=20;
1.203 brouard 3671: double k1,k2, res, fx;
1.132 brouard 3672: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 3673: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
3674: int k=0,kmax=10;
3675: double l1;
3676:
3677: fx=func(x);
3678: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 3679: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 3680: l1=pow(10,l);
3681: delts=delt;
3682: for(k=1 ; k <kmax; k=k+1){
3683: delt = delta*(l1*k);
3684: p2[theta]=x[theta] +delt;
1.145 brouard 3685: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 3686: p2[theta]=x[theta]-delt;
3687: k2=func(p2)-fx;
3688: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 3689: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 3690:
1.203 brouard 3691: #ifdef DEBUGHESSII
1.126 brouard 3692: 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);
3693: 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);
3694: #endif
3695: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
3696: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
3697: k=kmax;
3698: }
3699: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 3700: k=kmax; l=lmax*10;
1.126 brouard 3701: }
3702: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
3703: delts=delt;
3704: }
1.203 brouard 3705: } /* End loop k */
1.126 brouard 3706: }
3707: delti[theta]=delts;
3708: return res;
3709:
3710: }
3711:
1.203 brouard 3712: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 3713: {
3714: int i;
1.164 brouard 3715: int l=1, lmax=20;
1.126 brouard 3716: double k1,k2,k3,k4,res,fx;
1.132 brouard 3717: double p2[MAXPARM+1];
1.203 brouard 3718: int k, kmax=1;
3719: double v1, v2, cv12, lc1, lc2;
1.208 brouard 3720:
3721: int firstime=0;
1.203 brouard 3722:
1.126 brouard 3723: fx=func(x);
1.203 brouard 3724: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 3725: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 3726: p2[thetai]=x[thetai]+delti[thetai]*k;
3727: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3728: k1=func(p2)-fx;
3729:
1.203 brouard 3730: p2[thetai]=x[thetai]+delti[thetai]*k;
3731: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3732: k2=func(p2)-fx;
3733:
1.203 brouard 3734: p2[thetai]=x[thetai]-delti[thetai]*k;
3735: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3736: k3=func(p2)-fx;
3737:
1.203 brouard 3738: p2[thetai]=x[thetai]-delti[thetai]*k;
3739: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3740: k4=func(p2)-fx;
1.203 brouard 3741: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
3742: if(k1*k2*k3*k4 <0.){
1.208 brouard 3743: firstime=1;
1.203 brouard 3744: kmax=kmax+10;
1.208 brouard 3745: }
3746: if(kmax >=10 || firstime ==1){
1.218 brouard 3747: 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);
3748: 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 3749: printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
3750: fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
3751: }
3752: #ifdef DEBUGHESSIJ
3753: v1=hess[thetai][thetai];
3754: v2=hess[thetaj][thetaj];
3755: cv12=res;
3756: /* Computing eigen value of Hessian matrix */
3757: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3758: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3759: if ((lc2 <0) || (lc1 <0) ){
3760: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3761: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3762: 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);
3763: 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);
3764: }
1.126 brouard 3765: #endif
3766: }
3767: return res;
3768: }
3769:
1.203 brouard 3770: /* Not done yet: Was supposed to fix if not exactly at the maximum */
3771: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
3772: /* { */
3773: /* int i; */
3774: /* int l=1, lmax=20; */
3775: /* double k1,k2,k3,k4,res,fx; */
3776: /* double p2[MAXPARM+1]; */
3777: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
3778: /* int k=0,kmax=10; */
3779: /* double l1; */
3780:
3781: /* fx=func(x); */
3782: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
3783: /* l1=pow(10,l); */
3784: /* delts=delt; */
3785: /* for(k=1 ; k <kmax; k=k+1){ */
3786: /* delt = delti*(l1*k); */
3787: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
3788: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3789: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3790: /* k1=func(p2)-fx; */
3791:
3792: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3793: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3794: /* k2=func(p2)-fx; */
3795:
3796: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3797: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3798: /* k3=func(p2)-fx; */
3799:
3800: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3801: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3802: /* k4=func(p2)-fx; */
3803: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
3804: /* #ifdef DEBUGHESSIJ */
3805: /* 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); */
3806: /* 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); */
3807: /* #endif */
3808: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
3809: /* k=kmax; */
3810: /* } */
3811: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
3812: /* k=kmax; l=lmax*10; */
3813: /* } */
3814: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
3815: /* delts=delt; */
3816: /* } */
3817: /* } /\* End loop k *\/ */
3818: /* } */
3819: /* delti[theta]=delts; */
3820: /* return res; */
3821: /* } */
3822:
3823:
1.126 brouard 3824: /************** Inverse of matrix **************/
3825: void ludcmp(double **a, int n, int *indx, double *d)
3826: {
3827: int i,imax,j,k;
3828: double big,dum,sum,temp;
3829: double *vv;
3830:
3831: vv=vector(1,n);
3832: *d=1.0;
3833: for (i=1;i<=n;i++) {
3834: big=0.0;
3835: for (j=1;j<=n;j++)
3836: if ((temp=fabs(a[i][j])) > big) big=temp;
3837: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
3838: vv[i]=1.0/big;
3839: }
3840: for (j=1;j<=n;j++) {
3841: for (i=1;i<j;i++) {
3842: sum=a[i][j];
3843: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
3844: a[i][j]=sum;
3845: }
3846: big=0.0;
3847: for (i=j;i<=n;i++) {
3848: sum=a[i][j];
3849: for (k=1;k<j;k++)
3850: sum -= a[i][k]*a[k][j];
3851: a[i][j]=sum;
3852: if ( (dum=vv[i]*fabs(sum)) >= big) {
3853: big=dum;
3854: imax=i;
3855: }
3856: }
3857: if (j != imax) {
3858: for (k=1;k<=n;k++) {
3859: dum=a[imax][k];
3860: a[imax][k]=a[j][k];
3861: a[j][k]=dum;
3862: }
3863: *d = -(*d);
3864: vv[imax]=vv[j];
3865: }
3866: indx[j]=imax;
3867: if (a[j][j] == 0.0) a[j][j]=TINY;
3868: if (j != n) {
3869: dum=1.0/(a[j][j]);
3870: for (i=j+1;i<=n;i++) a[i][j] *= dum;
3871: }
3872: }
3873: free_vector(vv,1,n); /* Doesn't work */
3874: ;
3875: }
3876:
3877: void lubksb(double **a, int n, int *indx, double b[])
3878: {
3879: int i,ii=0,ip,j;
3880: double sum;
3881:
3882: for (i=1;i<=n;i++) {
3883: ip=indx[i];
3884: sum=b[ip];
3885: b[ip]=b[i];
3886: if (ii)
3887: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
3888: else if (sum) ii=i;
3889: b[i]=sum;
3890: }
3891: for (i=n;i>=1;i--) {
3892: sum=b[i];
3893: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
3894: b[i]=sum/a[i][i];
3895: }
3896: }
3897:
3898: void pstamp(FILE *fichier)
3899: {
1.196 brouard 3900: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 3901: }
3902:
3903: /************ Frequencies ********************/
1.226 brouard 3904: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
3905: int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
3906: int firstpass, int lastpass, int stepm, int weightopt, char model[])
3907: { /* Some frequencies */
3908:
1.227 brouard 3909: int i, m, jk, j1, bool, z1,j, k, iv;
1.226 brouard 3910: int iind=0, iage=0;
3911: int mi; /* Effective wave */
3912: int first;
3913: double ***freq; /* Frequencies */
3914: double *meanq;
3915: double **meanqt;
3916: double *pp, **prop, *posprop, *pospropt;
3917: double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
3918: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
3919: double agebegin, ageend;
3920:
3921: pp=vector(1,nlstate);
3922: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
3923: posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
3924: pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
3925: /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
3926: meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
3927: meanqt=matrix(1,lastpass,1,nqtveff);
3928: strcpy(fileresp,"P_");
3929: strcat(fileresp,fileresu);
3930: /*strcat(fileresphtm,fileresu);*/
3931: if((ficresp=fopen(fileresp,"w"))==NULL) {
3932: printf("Problem with prevalence resultfile: %s\n", fileresp);
3933: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
3934: exit(0);
3935: }
1.214 brouard 3936:
1.226 brouard 3937: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
3938: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
3939: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3940: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3941: fflush(ficlog);
3942: exit(70);
3943: }
3944: else{
3945: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.214 brouard 3946: <hr size=\"2\" color=\"#EC5E5E\"> \n\
3947: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 3948: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
3949: }
3950: 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 3951:
1.226 brouard 3952: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
3953: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
3954: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
3955: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
3956: fflush(ficlog);
3957: exit(70);
3958: }
3959: else{
3960: 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 3961: <hr size=\"2\" color=\"#EC5E5E\"> \n\
3962: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 3963: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
3964: }
3965: 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 3966:
1.226 brouard 3967: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
3968: j1=0;
1.126 brouard 3969:
1.227 brouard 3970: /* j=ncoveff; /\* Only fixed dummy covariates *\/ */
3971: j=cptcoveff; /* Only dummy covariates of the model */
1.226 brouard 3972: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.220 brouard 3973:
1.226 brouard 3974: first=1;
1.220 brouard 3975:
1.226 brouard 3976: /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
3977: reference=low_education V1=0,V2=0
3978: med_educ V1=1 V2=0,
3979: high_educ V1=0 V2=1
3980: Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
3981: */
1.126 brouard 3982:
1.227 brouard 3983: for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives V4=0, V3=0 for example, fixed or varying covariates */
1.226 brouard 3984: posproptt=0.;
3985: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
3986: scanf("%d", i);*/
3987: for (i=-5; i<=nlstate+ndeath; i++)
3988: for (jk=-5; jk<=nlstate+ndeath; jk++)
3989: for(m=iagemin; m <= iagemax+3; m++)
3990: freq[i][jk][m]=0;
3991:
3992: for (i=1; i<=nlstate; i++) {
3993: for(m=iagemin; m <= iagemax+3; m++)
3994: prop[i][m]=0;
3995: posprop[i]=0;
3996: pospropt[i]=0;
3997: }
1.227 brouard 3998: /* for (z1=1; z1<= nqfveff; z1++) { */
3999: /* meanq[z1]+=0.; */
4000: /* for(m=1;m<=lastpass;m++){ */
4001: /* meanqt[m][z1]=0.; */
4002: /* } */
4003: /* } */
1.220 brouard 4004:
1.226 brouard 4005: dateintsum=0;
4006: k2cpt=0;
1.227 brouard 4007: /* For that combination of covariate j1, we count and print the frequencies in one pass */
1.226 brouard 4008: for (iind=1; iind<=imx; iind++) { /* For each individual iind */
4009: bool=1;
1.227 brouard 4010: if(anyvaryingduminmodel==0){ /* If All fixed covariates */
4011: if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
4012: /* for (z1=1; z1<= nqfveff; z1++) { */
4013: /* meanq[z1]+=coqvar[Tvar[z1]][iind]; /\* Computes mean of quantitative with selected filter *\/ */
4014: /* } */
4015: for (z1=1; z1<=cptcoveff; z1++) {
4016: /* if(Tvaraff[z1] ==-20){ */
4017: /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
4018: /* }else if(Tvaraff[z1] ==-10){ */
4019: /* /\* sumnew+=coqvar[z1][iind]; *\/ */
4020: /* }else */
4021: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
4022: /* Tests if this individual iind responded to j1 (V4=1 V3=0) */
4023: bool=0;
4024: /* 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",
4025: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
4026: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
4027: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
4028: } /* Onlyf fixed */
4029: } /* end z1 */
4030: } /* cptcovn > 0 */
4031: } /* end any */
4032: if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */
1.226 brouard 4033: /* for(m=firstpass; m<=lastpass; m++){ */
1.227 brouard 4034: for(mi=1; mi<wav[iind];mi++){ /* For that wave */
1.226 brouard 4035: m=mw[mi][iind];
1.227 brouard 4036: if(anyvaryingduminmodel==1){ /* Some are varying covariates */
4037: for (z1=1; z1<=cptcoveff; z1++) {
4038: if( Fixed[Tmodelind[z1]]==1){
4039: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4040: if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
4041: bool=0;
4042: }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
4043: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4044: bool=0;
4045: }
4046: }
4047: }
4048: }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */
4049: /* bool =0 we keep that guy which corresponds to the combination of dummy values */
4050: if(bool==1){
4051: /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
4052: and mw[mi+1][iind]. dh depends on stepm. */
4053: agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
4054: ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
4055: if(m >=firstpass && m <=lastpass){
4056: k2=anint[m][iind]+(mint[m][iind]/12.);
4057: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
4058: if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
4059: if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
4060: if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
4061: prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4062: if (m<lastpass) {
4063: /* if(s[m][iind]==4 && s[m+1][iind]==4) */
4064: /* 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]); */
4065: if(s[m][iind]==-1)
4066: 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.));
4067: freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4068: /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
4069: 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 */
4070: }
4071: } /* end if between passes */
4072: if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
4073: dateintsum=dateintsum+k2;
4074: k2cpt++;
4075: /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
1.226 brouard 4076: }
1.227 brouard 4077: } /* end bool 2 */
1.226 brouard 4078: } /* end m */
4079: } /* end bool */
4080: } /* end iind = 1 to imx */
4081: /* prop[s][age] is feeded for any initial and valid live state as well as
4082: freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
4083:
4084:
4085: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
4086: pstamp(ficresp);
1.227 brouard 4087: /* if (ncoveff>0) { */
4088: if (cptcoveff>0) {
1.226 brouard 4089: fprintf(ficresp, "\n#********** Variable ");
4090: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
4091: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
1.227 brouard 4092: for (z1=1; z1<=cptcoveff; z1++){
1.226 brouard 4093: fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4094: fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4095: fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4096: }
4097: fprintf(ficresp, "**********\n#");
4098: fprintf(ficresphtm, "**********</h3>\n");
4099: fprintf(ficresphtmfr, "**********</h3>\n");
4100: fprintf(ficlog, "\n#********** Variable ");
1.227 brouard 4101: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.226 brouard 4102: fprintf(ficlog, "**********\n");
4103: }
4104: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
4105: for(i=1; i<=nlstate;i++) {
4106: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
4107: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
4108: }
4109: fprintf(ficresp, "\n");
4110: fprintf(ficresphtm, "\n");
4111:
4112: /* Header of frequency table by age */
4113: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
4114: fprintf(ficresphtmfr,"<th>Age</th> ");
4115: for(jk=-1; jk <=nlstate+ndeath; jk++){
4116: for(m=-1; m <=nlstate+ndeath; m++){
4117: if(jk!=0 && m!=0)
4118: fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
4119: }
4120: }
4121: fprintf(ficresphtmfr, "\n");
4122:
4123: /* For each age */
4124: for(iage=iagemin; iage <= iagemax+3; iage++){
4125: fprintf(ficresphtm,"<tr>");
4126: if(iage==iagemax+1){
4127: fprintf(ficlog,"1");
4128: fprintf(ficresphtmfr,"<tr><th>0</th> ");
4129: }else if(iage==iagemax+2){
4130: fprintf(ficlog,"0");
4131: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
4132: }else if(iage==iagemax+3){
4133: fprintf(ficlog,"Total");
4134: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
4135: }else{
4136: if(first==1){
4137: first=0;
4138: printf("See log file for details...\n");
4139: }
4140: fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
4141: fprintf(ficlog,"Age %d", iage);
4142: }
4143: for(jk=1; jk <=nlstate ; jk++){
4144: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
4145: pp[jk] += freq[jk][m][iage];
4146: }
4147: for(jk=1; jk <=nlstate ; jk++){
4148: for(m=-1, pos=0; m <=0 ; m++)
4149: pos += freq[jk][m][iage];
4150: if(pp[jk]>=1.e-10){
4151: if(first==1){
4152: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
4153: }
4154: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
4155: }else{
4156: if(first==1)
4157: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
4158: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
4159: }
4160: }
4161:
4162: for(jk=1; jk <=nlstate ; jk++){
4163: /* posprop[jk]=0; */
4164: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
4165: pp[jk] += freq[jk][m][iage];
4166: } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
4167:
4168: for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
4169: pos += pp[jk]; /* pos is the total number of transitions until this age */
4170: posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
4171: from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4172: pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
4173: from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4174: }
4175: for(jk=1; jk <=nlstate ; jk++){
4176: if(pos>=1.e-5){
4177: if(first==1)
4178: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
4179: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
4180: }else{
4181: if(first==1)
4182: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
4183: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
4184: }
4185: if( iage <= iagemax){
4186: if(pos>=1.e-5){
4187: fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
4188: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
4189: /*probs[iage][jk][j1]= pp[jk]/pos;*/
4190: /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
4191: }
4192: else{
4193: fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
4194: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
4195: }
4196: }
4197: pospropt[jk] +=posprop[jk];
4198: } /* end loop jk */
4199: /* pospropt=0.; */
4200: for(jk=-1; jk <=nlstate+ndeath; jk++){
4201: for(m=-1; m <=nlstate+ndeath; m++){
4202: if(freq[jk][m][iage] !=0 ) { /* minimizing output */
4203: if(first==1){
4204: printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
4205: }
4206: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
4207: }
4208: if(jk!=0 && m!=0)
4209: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
4210: }
4211: } /* end loop jk */
4212: posproptt=0.;
4213: for(jk=1; jk <=nlstate; jk++){
4214: posproptt += pospropt[jk];
4215: }
4216: fprintf(ficresphtmfr,"</tr>\n ");
4217: if(iage <= iagemax){
4218: fprintf(ficresp,"\n");
4219: fprintf(ficresphtm,"</tr>\n");
4220: }
4221: if(first==1)
4222: printf("Others in log...\n");
4223: fprintf(ficlog,"\n");
4224: } /* end loop age iage */
4225: fprintf(ficresphtm,"<tr><th>Tot</th>");
4226: for(jk=1; jk <=nlstate ; jk++){
4227: if(posproptt < 1.e-5){
4228: fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);
4229: }else{
4230: fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);
4231: }
4232: }
4233: fprintf(ficresphtm,"</tr>\n");
4234: fprintf(ficresphtm,"</table>\n");
4235: fprintf(ficresphtmfr,"</table>\n");
4236: if(posproptt < 1.e-5){
4237: fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4238: fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4239: fprintf(ficres,"\n This combination (%d) is not valid and no result will be produced\n\n",j1);
4240: invalidvarcomb[j1]=1;
4241: }else{
4242: fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
4243: invalidvarcomb[j1]=0;
4244: }
4245: fprintf(ficresphtmfr,"</table>\n");
4246: } /* end selected combination of covariate j1 */
4247: dateintmean=dateintsum/k2cpt;
1.220 brouard 4248:
1.226 brouard 4249: fclose(ficresp);
4250: fclose(ficresphtm);
4251: fclose(ficresphtmfr);
4252: free_vector(meanq,1,nqfveff);
4253: free_matrix(meanqt,1,lastpass,1,nqtveff);
4254: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
4255: free_vector(pospropt,1,nlstate);
4256: free_vector(posprop,1,nlstate);
4257: free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
4258: free_vector(pp,1,nlstate);
4259: /* End of freqsummary */
4260: }
1.126 brouard 4261:
4262: /************ Prevalence ********************/
1.227 brouard 4263: 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)
4264: {
4265: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
4266: in each health status at the date of interview (if between dateprev1 and dateprev2).
4267: We still use firstpass and lastpass as another selection.
4268: */
1.126 brouard 4269:
1.227 brouard 4270: int i, m, jk, j1, bool, z1,j, iv;
4271: int mi; /* Effective wave */
4272: int iage;
4273: double agebegin, ageend;
4274:
4275: double **prop;
4276: double posprop;
4277: double y2; /* in fractional years */
4278: int iagemin, iagemax;
4279: int first; /** to stop verbosity which is redirected to log file */
4280:
4281: iagemin= (int) agemin;
4282: iagemax= (int) agemax;
4283: /*pp=vector(1,nlstate);*/
4284: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
4285: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
4286: j1=0;
1.222 brouard 4287:
1.227 brouard 4288: /*j=cptcoveff;*/
4289: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.222 brouard 4290:
1.227 brouard 4291: first=1;
4292: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
4293: for (i=1; i<=nlstate; i++)
4294: for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
4295: prop[i][iage]=0.0;
4296: printf("Prevalence combination of varying and fixed dummies %d\n",j1);
4297: /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
4298: fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
4299:
4300: for (i=1; i<=imx; i++) { /* Each individual */
4301: bool=1;
4302: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
4303: for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
4304: m=mw[mi][i];
4305: /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
4306: /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
4307: for (z1=1; z1<=cptcoveff; z1++){
4308: if( Fixed[Tmodelind[z1]]==1){
4309: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4310: if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
4311: bool=0;
4312: }else if( Fixed[Tmodelind[z1]]== 0) /* fixed */
4313: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4314: bool=0;
4315: }
4316: }
4317: if(bool==1){ /* Otherwise we skip that wave/person */
4318: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
4319: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
4320: if(m >=firstpass && m <=lastpass){
4321: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
4322: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
4323: if(agev[m][i]==0) agev[m][i]=iagemax+1;
4324: if(agev[m][i]==1) agev[m][i]=iagemax+2;
4325: if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
4326: 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);
4327: exit(1);
4328: }
4329: if (s[m][i]>0 && s[m][i]<=nlstate) {
4330: /*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]]);*/
4331: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
4332: prop[s[m][i]][iagemax+3] += weight[i];
4333: } /* end valid statuses */
4334: } /* end selection of dates */
4335: } /* end selection of waves */
4336: } /* end bool */
4337: } /* end wave */
4338: } /* end individual */
4339: for(i=iagemin; i <= iagemax+3; i++){
4340: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
4341: posprop += prop[jk][i];
4342: }
4343:
4344: for(jk=1; jk <=nlstate ; jk++){
4345: if( i <= iagemax){
4346: if(posprop>=1.e-5){
4347: probs[i][jk][j1]= prop[jk][i]/posprop;
4348: } else{
4349: if(first==1){
4350: first=0;
4351: printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,j1,probs[i][jk][j1]);
4352: }
4353: }
4354: }
4355: }/* end jk */
4356: }/* end i */
1.222 brouard 4357: /*} *//* end i1 */
1.227 brouard 4358: } /* end j1 */
1.222 brouard 4359:
1.227 brouard 4360: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
4361: /*free_vector(pp,1,nlstate);*/
4362: free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
4363: } /* End of prevalence */
1.126 brouard 4364:
4365: /************* Waves Concatenation ***************/
4366:
4367: 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)
4368: {
4369: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
4370: Death is a valid wave (if date is known).
4371: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
4372: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
4373: and mw[mi+1][i]. dh depends on stepm.
1.227 brouard 4374: */
1.126 brouard 4375:
1.224 brouard 4376: int i=0, mi=0, m=0, mli=0;
1.126 brouard 4377: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
4378: double sum=0., jmean=0.;*/
1.224 brouard 4379: int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
1.126 brouard 4380: int j, k=0,jk, ju, jl;
4381: double sum=0.;
4382: first=0;
1.214 brouard 4383: firstwo=0;
1.217 brouard 4384: firsthree=0;
1.218 brouard 4385: firstfour=0;
1.164 brouard 4386: jmin=100000;
1.126 brouard 4387: jmax=-1;
4388: jmean=0.;
1.224 brouard 4389:
4390: /* Treating live states */
1.214 brouard 4391: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.224 brouard 4392: mi=0; /* First valid wave */
1.227 brouard 4393: mli=0; /* Last valid wave */
1.126 brouard 4394: m=firstpass;
1.214 brouard 4395: while(s[m][i] <= nlstate){ /* a live state */
1.227 brouard 4396: 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 */
4397: mli=m-1;/* mw[++mi][i]=m-1; */
4398: }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 */
4399: mw[++mi][i]=m;
4400: mli=m;
1.224 brouard 4401: } /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
4402: if(m < lastpass){ /* m < lastpass, standard case */
1.227 brouard 4403: m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
1.216 brouard 4404: }
1.227 brouard 4405: else{ /* m >= lastpass, eventual special issue with warning */
1.224 brouard 4406: #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
1.227 brouard 4407: break;
1.224 brouard 4408: #else
1.227 brouard 4409: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
4410: if(firsthree == 0){
4411: 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);
4412: firsthree=1;
4413: }
4414: 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);
4415: mw[++mi][i]=m;
4416: mli=m;
4417: }
4418: if(s[m][i]==-2){ /* Vital status is really unknown */
4419: nbwarn++;
4420: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */
4421: 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);
4422: 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);
4423: }
4424: break;
4425: }
4426: break;
1.224 brouard 4427: #endif
1.227 brouard 4428: }/* End m >= lastpass */
1.126 brouard 4429: }/* end while */
1.224 brouard 4430:
1.227 brouard 4431: /* 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 4432: /* After last pass */
1.224 brouard 4433: /* Treating death states */
1.214 brouard 4434: if (s[m][i] > nlstate){ /* In a death state */
1.227 brouard 4435: /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
4436: /* } */
1.126 brouard 4437: mi++; /* Death is another wave */
4438: /* if(mi==0) never been interviewed correctly before death */
1.227 brouard 4439: /* Only death is a correct wave */
1.126 brouard 4440: mw[mi][i]=m;
1.224 brouard 4441: }
4442: #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
1.227 brouard 4443: 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 4444: /* m++; */
4445: /* mi++; */
4446: /* s[m][i]=nlstate+1; /\* We are setting the status to the last of non live state *\/ */
4447: /* mw[mi][i]=m; */
1.218 brouard 4448: if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
1.227 brouard 4449: 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 */
4450: nbwarn++;
4451: if(firstfiv==0){
4452: 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 );
4453: firstfiv=1;
4454: }else{
4455: 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 );
4456: }
4457: }else{ /* Death occured afer last wave potential bias */
4458: nberr++;
4459: if(firstwo==0){
4460: 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 );
4461: firstwo=1;
4462: }
4463: 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 );
4464: }
1.218 brouard 4465: }else{ /* end date of interview is known */
1.227 brouard 4466: /* death is known but not confirmed by death status at any wave */
4467: if(firstfour==0){
4468: 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 );
4469: firstfour=1;
4470: }
4471: 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 4472: }
1.224 brouard 4473: } /* end if date of death is known */
4474: #endif
4475: wav[i]=mi; /* mi should be the last effective wave (or mli) */
4476: /* wav[i]=mw[mi][i]; */
1.126 brouard 4477: if(mi==0){
4478: nbwarn++;
4479: if(first==0){
1.227 brouard 4480: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
4481: first=1;
1.126 brouard 4482: }
4483: if(first==1){
1.227 brouard 4484: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.126 brouard 4485: }
4486: } /* end mi==0 */
4487: } /* End individuals */
1.214 brouard 4488: /* wav and mw are no more changed */
1.223 brouard 4489:
1.214 brouard 4490:
1.126 brouard 4491: for(i=1; i<=imx; i++){
4492: for(mi=1; mi<wav[i];mi++){
4493: if (stepm <=0)
1.227 brouard 4494: dh[mi][i]=1;
1.126 brouard 4495: else{
1.227 brouard 4496: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
4497: if (agedc[i] < 2*AGESUP) {
4498: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
4499: if(j==0) j=1; /* Survives at least one month after exam */
4500: else if(j<0){
4501: nberr++;
4502: 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]);
4503: j=1; /* Temporary Dangerous patch */
4504: 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);
4505: 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]);
4506: 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);
4507: }
4508: k=k+1;
4509: if (j >= jmax){
4510: jmax=j;
4511: ijmax=i;
4512: }
4513: if (j <= jmin){
4514: jmin=j;
4515: ijmin=i;
4516: }
4517: sum=sum+j;
4518: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
4519: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
4520: }
4521: }
4522: else{
4523: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.126 brouard 4524: /* 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 4525:
1.227 brouard 4526: k=k+1;
4527: if (j >= jmax) {
4528: jmax=j;
4529: ijmax=i;
4530: }
4531: else if (j <= jmin){
4532: jmin=j;
4533: ijmin=i;
4534: }
4535: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
4536: /*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]);*/
4537: if(j<0){
4538: nberr++;
4539: 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]);
4540: 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]);
4541: }
4542: sum=sum+j;
4543: }
4544: jk= j/stepm;
4545: jl= j -jk*stepm;
4546: ju= j -(jk+1)*stepm;
4547: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
4548: if(jl==0){
4549: dh[mi][i]=jk;
4550: bh[mi][i]=0;
4551: }else{ /* We want a negative bias in order to only have interpolation ie
4552: * to avoid the price of an extra matrix product in likelihood */
4553: dh[mi][i]=jk+1;
4554: bh[mi][i]=ju;
4555: }
4556: }else{
4557: if(jl <= -ju){
4558: dh[mi][i]=jk;
4559: bh[mi][i]=jl; /* bias is positive if real duration
4560: * is higher than the multiple of stepm and negative otherwise.
4561: */
4562: }
4563: else{
4564: dh[mi][i]=jk+1;
4565: bh[mi][i]=ju;
4566: }
4567: if(dh[mi][i]==0){
4568: dh[mi][i]=1; /* At least one step */
4569: bh[mi][i]=ju; /* At least one step */
4570: /* 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);*/
4571: }
4572: } /* end if mle */
1.126 brouard 4573: }
4574: } /* end wave */
4575: }
4576: jmean=sum/k;
4577: 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 4578: fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
1.227 brouard 4579: }
1.126 brouard 4580:
4581: /*********** Tricode ****************************/
1.220 brouard 4582: void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 4583: {
1.144 brouard 4584: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
4585: /* 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 4586: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.224 brouard 4587: * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
4588: * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
1.144 brouard 4589: */
1.130 brouard 4590:
1.145 brouard 4591: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 4592: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 4593: int cptcode=0; /* Modality max of covariates j */
4594: int modmincovj=0; /* Modality min of covariates j */
4595:
4596:
1.220 brouard 4597: /* cptcoveff=0; */
1.224 brouard 4598: /* *cptcov=0; */
1.126 brouard 4599:
1.144 brouard 4600: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 4601:
1.224 brouard 4602: /* Loop on covariates without age and products and no quantitative variable */
4603: /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
1.227 brouard 4604: for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
4605: for (j=-1; (j < maxncov); j++) Ndum[j]=0;
4606: if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
4607: switch(Fixed[k]) {
4608: case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
4609: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the modality of this covariate Vj*/
4610: ij=(int)(covar[Tvar[k]][i]);
4611: /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
4612: * If product of Vn*Vm, still boolean *:
4613: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
4614: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
4615: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
4616: modality of the nth covariate of individual i. */
4617: if (ij > modmaxcovj)
4618: modmaxcovj=ij;
4619: else if (ij < modmincovj)
4620: modmincovj=ij;
4621: if ((ij < -1) && (ij > NCOVMAX)){
4622: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
4623: exit(1);
4624: }else
4625: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
4626: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
4627: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
4628: /* getting the maximum value of the modality of the covariate
4629: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
4630: female ies 1, then modmaxcovj=1.
4631: */
4632: } /* end for loop on individuals i */
4633: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
4634: fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
4635: cptcode=modmaxcovj;
4636: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
4637: /*for (i=0; i<=cptcode; i++) {*/
4638: for (j=modmincovj; j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
4639: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
4640: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
4641: if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
4642: if( j != -1){
4643: ncodemax[k]++; /* ncodemax[k]= Number of modalities of the k th
4644: covariate for which somebody answered excluding
4645: undefined. Usually 2: 0 and 1. */
4646: }
4647: ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
4648: covariate for which somebody answered including
4649: undefined. Usually 3: -1, 0 and 1. */
4650: }
4651: /* In fact ncodemax[k]=2 (dichotom. variables only) but it could be more for
4652: * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
4653: } /* Ndum[-1] number of undefined modalities */
4654:
4655: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
4656: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
4657: If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
4658: modmincovj=3; modmaxcovj = 7;
4659: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
4660: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
4661: defining two dummy variables: variables V1_1 and V1_2.
4662: nbcode[Tvar[j]][ij]=k;
4663: nbcode[Tvar[j]][1]=0;
4664: nbcode[Tvar[j]][2]=1;
4665: nbcode[Tvar[j]][3]=2;
4666: To be continued (not working yet).
4667: */
4668: ij=0; /* ij is similar to i but can jump over null modalities */
4669: 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*/
4670: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
4671: break;
4672: }
4673: ij++;
4674: nbcode[Tvar[k]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1*/
4675: cptcode = ij; /* New max modality for covar j */
4676: } /* end of loop on modality i=-1 to 1 or more */
4677: break;
4678: case 1: /* Testing on varying covariate, could be simple and
4679: * should look at waves or product of fixed *
4680: * varying. No time to test -1, assuming 0 and 1 only */
4681: ij=0;
4682: for(i=0; i<=1;i++){
4683: nbcode[Tvar[k]][++ij]=i;
4684: }
1.225 brouard 4685: break;
1.227 brouard 4686: default:
1.225 brouard 4687: break;
1.227 brouard 4688: } /* end switch */
4689: } /* end dummy test */
1.225 brouard 4690:
1.192 brouard 4691: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
4692: /* /\*recode from 0 *\/ */
4693: /* k is a modality. If we have model=V1+V1*sex */
4694: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
4695: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
4696: /* } */
4697: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
4698: /* if (ij > ncodemax[j]) { */
4699: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4700: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4701: /* break; */
4702: /* } */
4703: /* } /\* end of loop on modality k *\/ */
1.137 brouard 4704: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
4705:
1.225 brouard 4706: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.227 brouard 4707: /* Look at fixed dummy (single or product) covariates to check empty modalities */
1.187 brouard 4708: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.225 brouard 4709: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
1.227 brouard 4710: ij=Tvar[i]; /* Tvar 5,4,3,6,5,7,1,4 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V4*age */
4711: Ndum[ij]++; /* Count the # of 1, 2 etc: {1,1,1,2,2,1,1} because V1 once, V2 once, two V4 and V5 in above */
4712: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, {2, 1, 1, 1, 2, 1, 1, 0, 0} */
1.225 brouard 4713: } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
4714:
4715: ij=0;
1.227 brouard 4716: /* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
4717: for (k=1; k<= cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
1.225 brouard 4718: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.227 brouard 4719: /* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? *\/ */
4720: if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */
4721: /* If product not in single variable we don't print results */
1.225 brouard 4722: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
1.227 brouard 4723: ++ij;
4724: Tvaraff[ij]=Tvar[k]; /*For printing */
4725: Tmodelind[ij]=k;
1.228 brouard 4726: TmodelInvind[k]=Tvar[k]- ncovcol-nqv;
1.227 brouard 4727: if(Fixed[k]!=0)
4728: anyvaryingduminmodel=1;
4729: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
4730: /* Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
4731: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
4732: /* Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
4733: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
4734: /* Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
4735: }
1.225 brouard 4736: } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
4737: /* ij--; */
4738: /* cptcoveff=ij; /\*Number of total covariates*\/ */
4739: *cptcov=ij; /*Number of total real effective covariates: effective
4740: * because they can be excluded from the model and real
1.227 brouard 4741: * if in the model but excluded because missing values, but how to get k from ij?*/
4742: for(j=ij+1; j<= cptcovt; j++){
4743: Tvaraff[j]=0;
4744: Tmodelind[j]=0;
4745: }
1.228 brouard 4746: for(j=ntveff+1; j<= cptcovt; j++){
4747: TmodelInvind[j]=0;
4748: }
1.227 brouard 4749: /* To be sorted */
4750: ;
1.126 brouard 4751: }
4752:
1.145 brouard 4753:
1.126 brouard 4754: /*********** Health Expectancies ****************/
4755:
1.127 brouard 4756: 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 4757:
4758: {
4759: /* Health expectancies, no variances */
1.164 brouard 4760: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 4761: int nhstepma, nstepma; /* Decreasing with age */
4762: double age, agelim, hf;
4763: double ***p3mat;
4764: double eip;
4765:
4766: pstamp(ficreseij);
4767: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
4768: fprintf(ficreseij,"# Age");
4769: for(i=1; i<=nlstate;i++){
4770: for(j=1; j<=nlstate;j++){
4771: fprintf(ficreseij," e%1d%1d ",i,j);
4772: }
4773: fprintf(ficreseij," e%1d. ",i);
4774: }
4775: fprintf(ficreseij,"\n");
4776:
4777:
4778: if(estepm < stepm){
4779: printf ("Problem %d lower than %d\n",estepm, stepm);
4780: }
4781: else hstepm=estepm;
4782: /* We compute the life expectancy from trapezoids spaced every estepm months
4783: * This is mainly to measure the difference between two models: for example
4784: * if stepm=24 months pijx are given only every 2 years and by summing them
4785: * we are calculating an estimate of the Life Expectancy assuming a linear
4786: * progression in between and thus overestimating or underestimating according
4787: * to the curvature of the survival function. If, for the same date, we
4788: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4789: * to compare the new estimate of Life expectancy with the same linear
4790: * hypothesis. A more precise result, taking into account a more precise
4791: * curvature will be obtained if estepm is as small as stepm. */
4792:
4793: /* For example we decided to compute the life expectancy with the smallest unit */
4794: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4795: nhstepm is the number of hstepm from age to agelim
4796: nstepm is the number of stepm from age to agelin.
4797: Look at hpijx to understand the reason of that which relies in memory size
4798: and note for a fixed period like estepm months */
4799: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4800: survival function given by stepm (the optimization length). Unfortunately it
4801: means that if the survival funtion is printed only each two years of age and if
4802: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4803: results. So we changed our mind and took the option of the best precision.
4804: */
4805: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4806:
4807: agelim=AGESUP;
4808: /* If stepm=6 months */
4809: /* Computed by stepm unit matrices, product of hstepm matrices, stored
4810: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
4811:
4812: /* nhstepm age range expressed in number of stepm */
4813: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4814: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4815: /* if (stepm >= YEARM) hstepm=1;*/
4816: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4817: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4818:
4819: for (age=bage; age<=fage; age ++){
4820: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4821: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4822: /* if (stepm >= YEARM) hstepm=1;*/
4823: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
4824:
4825: /* If stepm=6 months */
4826: /* Computed by stepm unit matrices, product of hstepma matrices, stored
4827: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
4828:
4829: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
4830:
4831: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4832:
4833: printf("%d|",(int)age);fflush(stdout);
4834: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
4835:
4836: /* Computing expectancies */
4837: for(i=1; i<=nlstate;i++)
4838: for(j=1; j<=nlstate;j++)
4839: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
4840: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
4841:
4842: /* 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]);*/
4843:
4844: }
4845:
4846: fprintf(ficreseij,"%3.0f",age );
4847: for(i=1; i<=nlstate;i++){
4848: eip=0;
4849: for(j=1; j<=nlstate;j++){
4850: eip +=eij[i][j][(int)age];
4851: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
4852: }
4853: fprintf(ficreseij,"%9.4f", eip );
4854: }
4855: fprintf(ficreseij,"\n");
4856:
4857: }
4858: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4859: printf("\n");
4860: fprintf(ficlog,"\n");
4861:
4862: }
4863:
1.127 brouard 4864: 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 4865:
4866: {
4867: /* Covariances of health expectancies eij and of total life expectancies according
1.222 brouard 4868: to initial status i, ei. .
1.126 brouard 4869: */
4870: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
4871: int nhstepma, nstepma; /* Decreasing with age */
4872: double age, agelim, hf;
4873: double ***p3matp, ***p3matm, ***varhe;
4874: double **dnewm,**doldm;
4875: double *xp, *xm;
4876: double **gp, **gm;
4877: double ***gradg, ***trgradg;
4878: int theta;
4879:
4880: double eip, vip;
4881:
4882: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
4883: xp=vector(1,npar);
4884: xm=vector(1,npar);
4885: dnewm=matrix(1,nlstate*nlstate,1,npar);
4886: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
4887:
4888: pstamp(ficresstdeij);
4889: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
4890: fprintf(ficresstdeij,"# Age");
4891: for(i=1; i<=nlstate;i++){
4892: for(j=1; j<=nlstate;j++)
4893: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
4894: fprintf(ficresstdeij," e%1d. ",i);
4895: }
4896: fprintf(ficresstdeij,"\n");
4897:
4898: pstamp(ficrescveij);
4899: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
4900: fprintf(ficrescveij,"# Age");
4901: for(i=1; i<=nlstate;i++)
4902: for(j=1; j<=nlstate;j++){
4903: cptj= (j-1)*nlstate+i;
4904: for(i2=1; i2<=nlstate;i2++)
4905: for(j2=1; j2<=nlstate;j2++){
4906: cptj2= (j2-1)*nlstate+i2;
4907: if(cptj2 <= cptj)
4908: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
4909: }
4910: }
4911: fprintf(ficrescveij,"\n");
4912:
4913: if(estepm < stepm){
4914: printf ("Problem %d lower than %d\n",estepm, stepm);
4915: }
4916: else hstepm=estepm;
4917: /* We compute the life expectancy from trapezoids spaced every estepm months
4918: * This is mainly to measure the difference between two models: for example
4919: * if stepm=24 months pijx are given only every 2 years and by summing them
4920: * we are calculating an estimate of the Life Expectancy assuming a linear
4921: * progression in between and thus overestimating or underestimating according
4922: * to the curvature of the survival function. If, for the same date, we
4923: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4924: * to compare the new estimate of Life expectancy with the same linear
4925: * hypothesis. A more precise result, taking into account a more precise
4926: * curvature will be obtained if estepm is as small as stepm. */
4927:
4928: /* For example we decided to compute the life expectancy with the smallest unit */
4929: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4930: nhstepm is the number of hstepm from age to agelim
4931: nstepm is the number of stepm from age to agelin.
4932: Look at hpijx to understand the reason of that which relies in memory size
4933: and note for a fixed period like estepm months */
4934: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4935: survival function given by stepm (the optimization length). Unfortunately it
4936: means that if the survival funtion is printed only each two years of age and if
4937: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4938: results. So we changed our mind and took the option of the best precision.
4939: */
4940: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4941:
4942: /* If stepm=6 months */
4943: /* nhstepm age range expressed in number of stepm */
4944: agelim=AGESUP;
4945: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
4946: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4947: /* if (stepm >= YEARM) hstepm=1;*/
4948: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4949:
4950: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4951: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4952: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
4953: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
4954: gp=matrix(0,nhstepm,1,nlstate*nlstate);
4955: gm=matrix(0,nhstepm,1,nlstate*nlstate);
4956:
4957: for (age=bage; age<=fage; age ++){
4958: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4959: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4960: /* if (stepm >= YEARM) hstepm=1;*/
4961: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218 brouard 4962:
1.126 brouard 4963: /* If stepm=6 months */
4964: /* Computed by stepm unit matrices, product of hstepma matrices, stored
4965: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
4966:
4967: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.218 brouard 4968:
1.126 brouard 4969: /* Computing Variances of health expectancies */
4970: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
4971: decrease memory allocation */
4972: for(theta=1; theta <=npar; theta++){
4973: for(i=1; i<=npar; i++){
1.222 brouard 4974: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4975: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126 brouard 4976: }
4977: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
4978: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
1.218 brouard 4979:
1.126 brouard 4980: for(j=1; j<= nlstate; j++){
1.222 brouard 4981: for(i=1; i<=nlstate; i++){
4982: for(h=0; h<=nhstepm-1; h++){
4983: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
4984: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
4985: }
4986: }
1.126 brouard 4987: }
1.218 brouard 4988:
1.126 brouard 4989: for(ij=1; ij<= nlstate*nlstate; ij++)
1.222 brouard 4990: for(h=0; h<=nhstepm-1; h++){
4991: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
4992: }
1.126 brouard 4993: }/* End theta */
4994:
4995:
4996: for(h=0; h<=nhstepm-1; h++)
4997: for(j=1; j<=nlstate*nlstate;j++)
1.222 brouard 4998: for(theta=1; theta <=npar; theta++)
4999: trgradg[h][j][theta]=gradg[h][theta][j];
1.126 brouard 5000:
1.218 brouard 5001:
1.222 brouard 5002: for(ij=1;ij<=nlstate*nlstate;ij++)
1.126 brouard 5003: for(ji=1;ji<=nlstate*nlstate;ji++)
1.222 brouard 5004: varhe[ij][ji][(int)age] =0.;
1.218 brouard 5005:
1.222 brouard 5006: printf("%d|",(int)age);fflush(stdout);
5007: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5008: for(h=0;h<=nhstepm-1;h++){
1.126 brouard 5009: for(k=0;k<=nhstepm-1;k++){
1.222 brouard 5010: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
5011: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
5012: for(ij=1;ij<=nlstate*nlstate;ij++)
5013: for(ji=1;ji<=nlstate*nlstate;ji++)
5014: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126 brouard 5015: }
5016: }
1.218 brouard 5017:
1.126 brouard 5018: /* Computing expectancies */
5019: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
5020: for(i=1; i<=nlstate;i++)
5021: for(j=1; j<=nlstate;j++)
1.222 brouard 5022: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5023: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.218 brouard 5024:
1.222 brouard 5025: /* 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 5026:
1.222 brouard 5027: }
1.218 brouard 5028:
1.126 brouard 5029: fprintf(ficresstdeij,"%3.0f",age );
5030: for(i=1; i<=nlstate;i++){
5031: eip=0.;
5032: vip=0.;
5033: for(j=1; j<=nlstate;j++){
1.222 brouard 5034: eip += eij[i][j][(int)age];
5035: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
5036: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
5037: 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 5038: }
5039: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
5040: }
5041: fprintf(ficresstdeij,"\n");
1.218 brouard 5042:
1.126 brouard 5043: fprintf(ficrescveij,"%3.0f",age );
5044: for(i=1; i<=nlstate;i++)
5045: for(j=1; j<=nlstate;j++){
1.222 brouard 5046: cptj= (j-1)*nlstate+i;
5047: for(i2=1; i2<=nlstate;i2++)
5048: for(j2=1; j2<=nlstate;j2++){
5049: cptj2= (j2-1)*nlstate+i2;
5050: if(cptj2 <= cptj)
5051: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
5052: }
1.126 brouard 5053: }
5054: fprintf(ficrescveij,"\n");
1.218 brouard 5055:
1.126 brouard 5056: }
5057: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
5058: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
5059: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
5060: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
5061: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5062: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5063: printf("\n");
5064: fprintf(ficlog,"\n");
1.218 brouard 5065:
1.126 brouard 5066: free_vector(xm,1,npar);
5067: free_vector(xp,1,npar);
5068: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
5069: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
5070: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
5071: }
1.218 brouard 5072:
1.126 brouard 5073: /************ Variance ******************/
1.209 brouard 5074: 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 5075: {
5076: /* Variance of health expectancies */
5077: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
5078: /* double **newm;*/
5079: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
5080:
5081: /* int movingaverage(); */
5082: double **dnewm,**doldm;
5083: double **dnewmp,**doldmp;
5084: int i, j, nhstepm, hstepm, h, nstepm ;
5085: int k;
5086: double *xp;
5087: double **gp, **gm; /* for var eij */
5088: double ***gradg, ***trgradg; /*for var eij */
5089: double **gradgp, **trgradgp; /* for var p point j */
5090: double *gpp, *gmp; /* for var p point j */
5091: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
5092: double ***p3mat;
5093: double age,agelim, hf;
5094: /* double ***mobaverage; */
5095: int theta;
5096: char digit[4];
5097: char digitp[25];
5098:
5099: char fileresprobmorprev[FILENAMELENGTH];
5100:
5101: if(popbased==1){
5102: if(mobilav!=0)
5103: strcpy(digitp,"-POPULBASED-MOBILAV_");
5104: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
5105: }
5106: else
5107: strcpy(digitp,"-STABLBASED_");
1.126 brouard 5108:
1.218 brouard 5109: /* if (mobilav!=0) { */
5110: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5111: /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
5112: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
5113: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
5114: /* } */
5115: /* } */
5116:
5117: strcpy(fileresprobmorprev,"PRMORPREV-");
5118: sprintf(digit,"%-d",ij);
5119: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
5120: strcat(fileresprobmorprev,digit); /* Tvar to be done */
5121: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
5122: strcat(fileresprobmorprev,fileresu);
5123: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
5124: printf("Problem with resultfile: %s\n", fileresprobmorprev);
5125: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
5126: }
5127: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5128: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5129: pstamp(ficresprobmorprev);
5130: 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);
5131: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
5132: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
5133: fprintf(ficresprobmorprev," p.%-d SE",j);
5134: for(i=1; i<=nlstate;i++)
5135: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
5136: }
5137: fprintf(ficresprobmorprev,"\n");
5138:
5139: fprintf(ficgp,"\n# Routine varevsij");
5140: fprintf(ficgp,"\nunset title \n");
5141: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
5142: 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");
5143: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
5144: /* } */
5145: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5146: pstamp(ficresvij);
5147: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
5148: if(popbased==1)
5149: 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);
5150: else
5151: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
5152: fprintf(ficresvij,"# Age");
5153: for(i=1; i<=nlstate;i++)
5154: for(j=1; j<=nlstate;j++)
5155: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
5156: fprintf(ficresvij,"\n");
5157:
5158: xp=vector(1,npar);
5159: dnewm=matrix(1,nlstate,1,npar);
5160: doldm=matrix(1,nlstate,1,nlstate);
5161: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
5162: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5163:
5164: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
5165: gpp=vector(nlstate+1,nlstate+ndeath);
5166: gmp=vector(nlstate+1,nlstate+ndeath);
5167: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126 brouard 5168:
1.218 brouard 5169: if(estepm < stepm){
5170: printf ("Problem %d lower than %d\n",estepm, stepm);
5171: }
5172: else hstepm=estepm;
5173: /* For example we decided to compute the life expectancy with the smallest unit */
5174: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5175: nhstepm is the number of hstepm from age to agelim
5176: nstepm is the number of stepm from age to agelim.
5177: Look at function hpijx to understand why because of memory size limitations,
5178: we decided (b) to get a life expectancy respecting the most precise curvature of the
5179: survival function given by stepm (the optimization length). Unfortunately it
5180: means that if the survival funtion is printed every two years of age and if
5181: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5182: results. So we changed our mind and took the option of the best precision.
5183: */
5184: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5185: agelim = AGESUP;
5186: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5187: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5188: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5189: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5190: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
5191: gp=matrix(0,nhstepm,1,nlstate);
5192: gm=matrix(0,nhstepm,1,nlstate);
5193:
5194:
5195: for(theta=1; theta <=npar; theta++){
5196: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
5197: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5198: }
5199:
5200: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5201:
5202: if (popbased==1) {
5203: if(mobilav ==0){
5204: for(i=1; i<=nlstate;i++)
5205: prlim[i][i]=probs[(int)age][i][ij];
5206: }else{ /* mobilav */
5207: for(i=1; i<=nlstate;i++)
5208: prlim[i][i]=mobaverage[(int)age][i][ij];
5209: }
5210: }
5211:
5212: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); /* Returns p3mat[i][j][h] for h=1 to nhstepm */
5213: for(j=1; j<= nlstate; j++){
5214: for(h=0; h<=nhstepm; h++){
5215: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
5216: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
5217: }
5218: }
5219: /* Next for computing probability of death (h=1 means
5220: computed over hstepm matrices product = hstepm*stepm months)
5221: as a weighted average of prlim.
5222: */
5223: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5224: for(i=1,gpp[j]=0.; i<= nlstate; i++)
5225: gpp[j] += prlim[i][i]*p3mat[i][j][1];
5226: }
5227: /* end probability of death */
5228:
5229: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
5230: xp[i] = x[i] - (i==theta ?delti[theta]:0);
5231:
5232: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
5233:
5234: if (popbased==1) {
5235: if(mobilav ==0){
5236: for(i=1; i<=nlstate;i++)
5237: prlim[i][i]=probs[(int)age][i][ij];
5238: }else{ /* mobilav */
5239: for(i=1; i<=nlstate;i++)
5240: prlim[i][i]=mobaverage[(int)age][i][ij];
5241: }
5242: }
5243:
5244: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
5245:
5246: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
5247: for(h=0; h<=nhstepm; h++){
5248: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
5249: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
5250: }
5251: }
5252: /* This for computing probability of death (h=1 means
5253: computed over hstepm matrices product = hstepm*stepm months)
5254: as a weighted average of prlim.
5255: */
5256: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5257: for(i=1,gmp[j]=0.; i<= nlstate; i++)
5258: gmp[j] += prlim[i][i]*p3mat[i][j][1];
5259: }
5260: /* end probability of death */
5261:
5262: for(j=1; j<= nlstate; j++) /* vareij */
5263: for(h=0; h<=nhstepm; h++){
5264: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
5265: }
5266:
5267: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
5268: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
5269: }
5270:
5271: } /* End theta */
5272:
5273: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
5274:
5275: for(h=0; h<=nhstepm; h++) /* veij */
5276: for(j=1; j<=nlstate;j++)
5277: for(theta=1; theta <=npar; theta++)
5278: trgradg[h][j][theta]=gradg[h][theta][j];
5279:
5280: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
5281: for(theta=1; theta <=npar; theta++)
5282: trgradgp[j][theta]=gradgp[theta][j];
5283:
5284:
5285: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
5286: for(i=1;i<=nlstate;i++)
5287: for(j=1;j<=nlstate;j++)
5288: vareij[i][j][(int)age] =0.;
5289:
5290: for(h=0;h<=nhstepm;h++){
5291: for(k=0;k<=nhstepm;k++){
5292: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
5293: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
5294: for(i=1;i<=nlstate;i++)
5295: for(j=1;j<=nlstate;j++)
5296: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
5297: }
5298: }
5299:
5300: /* pptj */
5301: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
5302: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
5303: for(j=nlstate+1;j<=nlstate+ndeath;j++)
5304: for(i=nlstate+1;i<=nlstate+ndeath;i++)
5305: varppt[j][i]=doldmp[j][i];
5306: /* end ppptj */
5307: /* x centered again */
5308:
5309: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
5310:
5311: if (popbased==1) {
5312: if(mobilav ==0){
5313: for(i=1; i<=nlstate;i++)
5314: prlim[i][i]=probs[(int)age][i][ij];
5315: }else{ /* mobilav */
5316: for(i=1; i<=nlstate;i++)
5317: prlim[i][i]=mobaverage[(int)age][i][ij];
5318: }
5319: }
5320:
5321: /* This for computing probability of death (h=1 means
5322: computed over hstepm (estepm) matrices product = hstepm*stepm months)
5323: as a weighted average of prlim.
5324: */
5325: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
5326: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5327: for(i=1,gmp[j]=0.;i<= nlstate; i++)
5328: gmp[j] += prlim[i][i]*p3mat[i][j][1];
5329: }
5330: /* end probability of death */
5331:
5332: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
5333: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
5334: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
5335: for(i=1; i<=nlstate;i++){
5336: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
5337: }
5338: }
5339: fprintf(ficresprobmorprev,"\n");
5340:
5341: fprintf(ficresvij,"%.0f ",age );
5342: for(i=1; i<=nlstate;i++)
5343: for(j=1; j<=nlstate;j++){
5344: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
5345: }
5346: fprintf(ficresvij,"\n");
5347: free_matrix(gp,0,nhstepm,1,nlstate);
5348: free_matrix(gm,0,nhstepm,1,nlstate);
5349: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
5350: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
5351: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5352: } /* End age */
5353: free_vector(gpp,nlstate+1,nlstate+ndeath);
5354: free_vector(gmp,nlstate+1,nlstate+ndeath);
5355: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
5356: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
5357: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
5358: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
5359: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
5360: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
5361: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
5362: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
5363: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
5364: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
5365: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
5366: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
5367: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
5368: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
5369: 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);
5370: /* 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 5371: */
1.218 brouard 5372: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
5373: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 5374:
1.218 brouard 5375: free_vector(xp,1,npar);
5376: free_matrix(doldm,1,nlstate,1,nlstate);
5377: free_matrix(dnewm,1,nlstate,1,npar);
5378: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5379: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
5380: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5381: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5382: fclose(ficresprobmorprev);
5383: fflush(ficgp);
5384: fflush(fichtm);
5385: } /* end varevsij */
1.126 brouard 5386:
5387: /************ Variance of prevlim ******************/
1.209 brouard 5388: 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 5389: {
1.205 brouard 5390: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 5391: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 5392:
1.126 brouard 5393: double **dnewm,**doldm;
5394: int i, j, nhstepm, hstepm;
5395: double *xp;
5396: double *gp, *gm;
5397: double **gradg, **trgradg;
1.208 brouard 5398: double **mgm, **mgp;
1.126 brouard 5399: double age,agelim;
5400: int theta;
5401:
5402: pstamp(ficresvpl);
5403: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
5404: fprintf(ficresvpl,"# Age");
5405: for(i=1; i<=nlstate;i++)
5406: fprintf(ficresvpl," %1d-%1d",i,i);
5407: fprintf(ficresvpl,"\n");
5408:
5409: xp=vector(1,npar);
5410: dnewm=matrix(1,nlstate,1,npar);
5411: doldm=matrix(1,nlstate,1,nlstate);
5412:
5413: hstepm=1*YEARM; /* Every year of age */
5414: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
5415: agelim = AGESUP;
5416: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5417: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5418: if (stepm >= YEARM) hstepm=1;
5419: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5420: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 5421: mgp=matrix(1,npar,1,nlstate);
5422: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 5423: gp=vector(1,nlstate);
5424: gm=vector(1,nlstate);
5425:
5426: for(theta=1; theta <=npar; theta++){
5427: for(i=1; i<=npar; i++){ /* Computes gradient */
5428: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5429: }
1.209 brouard 5430: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
5431: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5432: else
5433: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 5434: for(i=1;i<=nlstate;i++){
1.126 brouard 5435: gp[i] = prlim[i][i];
1.208 brouard 5436: mgp[theta][i] = prlim[i][i];
5437: }
1.126 brouard 5438: for(i=1; i<=npar; i++) /* Computes gradient */
5439: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 5440: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
5441: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5442: else
5443: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 5444: for(i=1;i<=nlstate;i++){
1.126 brouard 5445: gm[i] = prlim[i][i];
1.208 brouard 5446: mgm[theta][i] = prlim[i][i];
5447: }
1.126 brouard 5448: for(i=1;i<=nlstate;i++)
5449: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 5450: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 5451: } /* End theta */
5452:
5453: trgradg =matrix(1,nlstate,1,npar);
5454:
5455: for(j=1; j<=nlstate;j++)
5456: for(theta=1; theta <=npar; theta++)
5457: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 5458: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5459: /* printf("\nmgm mgp %d ",(int)age); */
5460: /* for(j=1; j<=nlstate;j++){ */
5461: /* printf(" %d ",j); */
5462: /* for(theta=1; theta <=npar; theta++) */
5463: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
5464: /* printf("\n "); */
5465: /* } */
5466: /* } */
5467: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5468: /* printf("\n gradg %d ",(int)age); */
5469: /* for(j=1; j<=nlstate;j++){ */
5470: /* printf("%d ",j); */
5471: /* for(theta=1; theta <=npar; theta++) */
5472: /* printf("%d %lf ",theta,gradg[theta][j]); */
5473: /* printf("\n "); */
5474: /* } */
5475: /* } */
1.126 brouard 5476:
5477: for(i=1;i<=nlstate;i++)
5478: varpl[i][(int)age] =0.;
1.209 brouard 5479: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.205 brouard 5480: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5481: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
5482: }else{
1.126 brouard 5483: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5484: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 5485: }
1.126 brouard 5486: for(i=1;i<=nlstate;i++)
5487: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
5488:
5489: fprintf(ficresvpl,"%.0f ",age );
5490: for(i=1; i<=nlstate;i++)
5491: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
5492: fprintf(ficresvpl,"\n");
5493: free_vector(gp,1,nlstate);
5494: free_vector(gm,1,nlstate);
1.208 brouard 5495: free_matrix(mgm,1,npar,1,nlstate);
5496: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 5497: free_matrix(gradg,1,npar,1,nlstate);
5498: free_matrix(trgradg,1,nlstate,1,npar);
5499: } /* End age */
5500:
5501: free_vector(xp,1,npar);
5502: free_matrix(doldm,1,nlstate,1,npar);
5503: free_matrix(dnewm,1,nlstate,1,nlstate);
5504:
5505: }
5506:
5507: /************ Variance of one-step probabilities ******************/
5508: 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 5509: {
5510: int i, j=0, k1, l1, tj;
5511: int k2, l2, j1, z1;
5512: int k=0, l;
5513: int first=1, first1, first2;
5514: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
5515: double **dnewm,**doldm;
5516: double *xp;
5517: double *gp, *gm;
5518: double **gradg, **trgradg;
5519: double **mu;
5520: double age, cov[NCOVMAX+1];
5521: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
5522: int theta;
5523: char fileresprob[FILENAMELENGTH];
5524: char fileresprobcov[FILENAMELENGTH];
5525: char fileresprobcor[FILENAMELENGTH];
5526: double ***varpij;
5527:
5528: strcpy(fileresprob,"PROB_");
5529: strcat(fileresprob,fileres);
5530: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
5531: printf("Problem with resultfile: %s\n", fileresprob);
5532: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
5533: }
5534: strcpy(fileresprobcov,"PROBCOV_");
5535: strcat(fileresprobcov,fileresu);
5536: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
5537: printf("Problem with resultfile: %s\n", fileresprobcov);
5538: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
5539: }
5540: strcpy(fileresprobcor,"PROBCOR_");
5541: strcat(fileresprobcor,fileresu);
5542: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
5543: printf("Problem with resultfile: %s\n", fileresprobcor);
5544: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
5545: }
5546: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
5547: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
5548: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
5549: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
5550: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
5551: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
5552: pstamp(ficresprob);
5553: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
5554: fprintf(ficresprob,"# Age");
5555: pstamp(ficresprobcov);
5556: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
5557: fprintf(ficresprobcov,"# Age");
5558: pstamp(ficresprobcor);
5559: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
5560: fprintf(ficresprobcor,"# Age");
1.126 brouard 5561:
5562:
1.222 brouard 5563: for(i=1; i<=nlstate;i++)
5564: for(j=1; j<=(nlstate+ndeath);j++){
5565: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
5566: fprintf(ficresprobcov," p%1d-%1d ",i,j);
5567: fprintf(ficresprobcor," p%1d-%1d ",i,j);
5568: }
5569: /* fprintf(ficresprob,"\n");
5570: fprintf(ficresprobcov,"\n");
5571: fprintf(ficresprobcor,"\n");
5572: */
5573: xp=vector(1,npar);
5574: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
5575: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
5576: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
5577: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
5578: first=1;
5579: fprintf(ficgp,"\n# Routine varprob");
5580: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
5581: fprintf(fichtm,"\n");
5582:
5583: 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);
5584: 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);
5585: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 5586: and drawn. It helps understanding how is the covariance between two incidences.\
5587: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.222 brouard 5588: 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 5589: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
5590: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
5591: standard deviations wide on each axis. <br>\
5592: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
5593: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
5594: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
5595:
1.222 brouard 5596: cov[1]=1;
5597: /* tj=cptcoveff; */
1.225 brouard 5598: tj = (int) pow(2,cptcoveff);
1.222 brouard 5599: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
5600: j1=0;
1.224 brouard 5601: for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/
1.222 brouard 5602: if (cptcovn>0) {
5603: fprintf(ficresprob, "\n#********** Variable ");
1.225 brouard 5604: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5605: fprintf(ficresprob, "**********\n#\n");
5606: fprintf(ficresprobcov, "\n#********** Variable ");
1.225 brouard 5607: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5608: fprintf(ficresprobcov, "**********\n#\n");
1.220 brouard 5609:
1.222 brouard 5610: fprintf(ficgp, "\n#********** Variable ");
1.225 brouard 5611: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5612: fprintf(ficgp, "**********\n#\n");
1.220 brouard 5613:
5614:
1.222 brouard 5615: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.225 brouard 5616: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5617: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 5618:
1.222 brouard 5619: fprintf(ficresprobcor, "\n#********** Variable ");
1.225 brouard 5620: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5621: fprintf(ficresprobcor, "**********\n#");
5622: if(invalidvarcomb[j1]){
5623: fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
5624: fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
5625: continue;
5626: }
5627: }
5628: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
5629: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
5630: gp=vector(1,(nlstate)*(nlstate+ndeath));
5631: gm=vector(1,(nlstate)*(nlstate+ndeath));
5632: for (age=bage; age<=fage; age ++){
5633: cov[2]=age;
5634: if(nagesqr==1)
5635: cov[3]= age*age;
5636: for (k=1; k<=cptcovn;k++) {
5637: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
5638: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
5639: * 1 1 1 1 1
5640: * 2 2 1 1 1
5641: * 3 1 2 1 1
5642: */
5643: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
5644: }
5645: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5646: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
5647: for (k=1; k<=cptcovprod;k++)
5648: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.220 brouard 5649:
5650:
1.222 brouard 5651: for(theta=1; theta <=npar; theta++){
5652: for(i=1; i<=npar; i++)
5653: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.220 brouard 5654:
1.222 brouard 5655: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1.220 brouard 5656:
1.222 brouard 5657: k=0;
5658: for(i=1; i<= (nlstate); i++){
5659: for(j=1; j<=(nlstate+ndeath);j++){
5660: k=k+1;
5661: gp[k]=pmmij[i][j];
5662: }
5663: }
1.220 brouard 5664:
1.222 brouard 5665: for(i=1; i<=npar; i++)
5666: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.220 brouard 5667:
1.222 brouard 5668: pmij(pmmij,cov,ncovmodel,xp,nlstate);
5669: k=0;
5670: for(i=1; i<=(nlstate); i++){
5671: for(j=1; j<=(nlstate+ndeath);j++){
5672: k=k+1;
5673: gm[k]=pmmij[i][j];
5674: }
5675: }
1.220 brouard 5676:
1.222 brouard 5677: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
5678: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
5679: }
1.126 brouard 5680:
1.222 brouard 5681: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
5682: for(theta=1; theta <=npar; theta++)
5683: trgradg[j][theta]=gradg[theta][j];
1.220 brouard 5684:
1.222 brouard 5685: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
5686: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.220 brouard 5687:
1.222 brouard 5688: pmij(pmmij,cov,ncovmodel,x,nlstate);
1.220 brouard 5689:
1.222 brouard 5690: k=0;
5691: for(i=1; i<=(nlstate); i++){
5692: for(j=1; j<=(nlstate+ndeath);j++){
5693: k=k+1;
5694: mu[k][(int) age]=pmmij[i][j];
5695: }
5696: }
5697: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
5698: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
5699: varpij[i][j][(int)age] = doldm[i][j];
1.220 brouard 5700:
1.222 brouard 5701: /*printf("\n%d ",(int)age);
5702: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
5703: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
5704: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
5705: }*/
1.220 brouard 5706:
1.222 brouard 5707: fprintf(ficresprob,"\n%d ",(int)age);
5708: fprintf(ficresprobcov,"\n%d ",(int)age);
5709: fprintf(ficresprobcor,"\n%d ",(int)age);
1.220 brouard 5710:
1.222 brouard 5711: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
5712: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
5713: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
5714: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
5715: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
5716: }
5717: i=0;
5718: for (k=1; k<=(nlstate);k++){
5719: for (l=1; l<=(nlstate+ndeath);l++){
5720: i++;
5721: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
5722: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
5723: for (j=1; j<=i;j++){
5724: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
5725: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
5726: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
5727: }
5728: }
5729: }/* end of loop for state */
5730: } /* end of loop for age */
5731: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
5732: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
5733: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
5734: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
5735:
5736: /* Confidence intervalle of pij */
5737: /*
5738: fprintf(ficgp,"\nunset parametric;unset label");
5739: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
5740: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
5741: 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);
5742: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
5743: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
5744: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
5745: */
5746:
5747: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
5748: first1=1;first2=2;
5749: for (k2=1; k2<=(nlstate);k2++){
5750: for (l2=1; l2<=(nlstate+ndeath);l2++){
5751: if(l2==k2) continue;
5752: j=(k2-1)*(nlstate+ndeath)+l2;
5753: for (k1=1; k1<=(nlstate);k1++){
5754: for (l1=1; l1<=(nlstate+ndeath);l1++){
5755: if(l1==k1) continue;
5756: i=(k1-1)*(nlstate+ndeath)+l1;
5757: if(i<=j) continue;
5758: for (age=bage; age<=fage; age ++){
5759: if ((int)age %5==0){
5760: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
5761: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
5762: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
5763: mu1=mu[i][(int) age]/stepm*YEARM ;
5764: mu2=mu[j][(int) age]/stepm*YEARM;
5765: c12=cv12/sqrt(v1*v2);
5766: /* Computing eigen value of matrix of covariance */
5767: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
5768: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
5769: if ((lc2 <0) || (lc1 <0) ){
5770: if(first2==1){
5771: first1=0;
5772: 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);
5773: }
5774: 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);
5775: /* lc1=fabs(lc1); */ /* If we want to have them positive */
5776: /* lc2=fabs(lc2); */
5777: }
1.220 brouard 5778:
1.222 brouard 5779: /* Eigen vectors */
5780: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
5781: /*v21=sqrt(1.-v11*v11); *//* error */
5782: v21=(lc1-v1)/cv12*v11;
5783: v12=-v21;
5784: v22=v11;
5785: tnalp=v21/v11;
5786: if(first1==1){
5787: first1=0;
5788: 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);
5789: }
5790: 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);
5791: /*printf(fignu*/
5792: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
5793: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
5794: if(first==1){
5795: first=0;
5796: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
5797: fprintf(ficgp,"\nset parametric;unset label");
5798: 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);
5799: fprintf(ficgp,"\nset ter svg size 640, 480");
5800: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.220 brouard 5801: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
1.201 brouard 5802: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.222 brouard 5803: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
5804: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5805: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5806: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
5807: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5808: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
5809: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
5810: 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", \
5811: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
5812: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
5813: }else{
5814: first=0;
5815: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
5816: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
5817: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
5818: 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", \
5819: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
5820: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
5821: }/* if first */
5822: } /* age mod 5 */
5823: } /* end loop age */
5824: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5825: first=1;
5826: } /*l12 */
5827: } /* k12 */
5828: } /*l1 */
5829: }/* k1 */
5830: } /* loop on combination of covariates j1 */
5831: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
5832: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
5833: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
5834: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
5835: free_vector(xp,1,npar);
5836: fclose(ficresprob);
5837: fclose(ficresprobcov);
5838: fclose(ficresprobcor);
5839: fflush(ficgp);
5840: fflush(fichtmcov);
5841: }
1.126 brouard 5842:
5843:
5844: /******************* Printing html file ***********/
1.201 brouard 5845: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 5846: int lastpass, int stepm, int weightopt, char model[],\
5847: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.217 brouard 5848: int popforecast, int prevfcast, int backcast, int estepm , \
1.213 brouard 5849: double jprev1, double mprev1,double anprev1, double dateprev1, \
5850: double jprev2, double mprev2,double anprev2, double dateprev2){
1.126 brouard 5851: int jj1, k1, i1, cpt;
5852:
5853: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
5854: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
5855: </ul>");
1.214 brouard 5856: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
5857: 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",
5858: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
5859: 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 5860: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
5861: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 5862: fprintf(fichtm,"\
5863: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 5864: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 5865: fprintf(fichtm,"\
1.217 brouard 5866: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
5867: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
5868: fprintf(fichtm,"\
1.126 brouard 5869: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5870: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 5871: fprintf(fichtm,"\
1.217 brouard 5872: - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
5873: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
5874: fprintf(fichtm,"\
1.211 brouard 5875: - (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 5876: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5877: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 5878: if(prevfcast==1){
5879: fprintf(fichtm,"\
5880: - Prevalence projections by age and states: \
1.201 brouard 5881: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 5882: }
1.126 brouard 5883:
1.222 brouard 5884: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
1.126 brouard 5885:
1.225 brouard 5886: m=pow(2,cptcoveff);
1.222 brouard 5887: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 5888:
1.222 brouard 5889: jj1=0;
5890: for(k1=1; k1<=m;k1++){
1.220 brouard 5891:
1.222 brouard 5892: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
5893: jj1++;
5894: if (cptcovn > 0) {
5895: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 5896: for (cpt=1; cpt<=cptcoveff;cpt++){
1.222 brouard 5897: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
5898: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
5899: }
5900: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
5901: if(invalidvarcomb[k1]){
5902: fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
5903: printf("\nCombination (%d) ignored because no cases \n",k1);
5904: continue;
5905: }
5906: }
5907: /* aij, bij */
5908: 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 5909: <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 5910: /* Pij */
5911: 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 5912: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 5913: /* Quasi-incidences */
5914: 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 5915: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211 brouard 5916: incidence (rates) are the limit when h tends to zero of the ratio of the probability <sub>h</sub>P<sub>ij</sub> \
5917: 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 5918: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 5919: /* Survival functions (period) in state j */
5920: for(cpt=1; cpt<=nlstate;cpt++){
5921: 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 5922: <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 5923: }
5924: /* State specific survival functions (period) */
5925: for(cpt=1; cpt<=nlstate;cpt++){
5926: fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
1.220 brouard 5927: Or probability to survive in various states (1 to %d) being in state %d at different ages. \
1.201 brouard 5928: <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 5929: }
5930: /* Period (stable) prevalence in each health state */
5931: for(cpt=1; cpt<=nlstate;cpt++){
5932: 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 5933: <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 5934: }
5935: if(backcast==1){
5936: /* Period (stable) back prevalence in each health state */
5937: for(cpt=1; cpt<=nlstate;cpt++){
5938: 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 5939: <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 5940: }
1.217 brouard 5941: }
1.222 brouard 5942: if(prevfcast==1){
5943: /* Projection of prevalence up to period (stable) prevalence in each health state */
5944: for(cpt=1; cpt<=nlstate;cpt++){
5945: 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 5946: <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 5947: }
5948: }
1.220 brouard 5949:
1.222 brouard 5950: for(cpt=1; cpt<=nlstate;cpt++) {
5951: 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 5952: <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 5953: }
5954: /* } /\* end i1 *\/ */
5955: }/* End k1 */
5956: fprintf(fichtm,"</ul>");
1.126 brouard 5957:
1.222 brouard 5958: fprintf(fichtm,"\
1.126 brouard 5959: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 5960: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 5961: - 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 5962: But because parameters are usually highly correlated (a higher incidence of disability \
5963: and a higher incidence of recovery can give very close observed transition) it might \
5964: be very useful to look not only at linear confidence intervals estimated from the \
5965: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
5966: (parameters) of the logistic regression, it might be more meaningful to visualize the \
5967: covariance matrix of the one-step probabilities. \
5968: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 5969:
1.222 brouard 5970: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
5971: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
5972: fprintf(fichtm,"\
1.126 brouard 5973: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 5974: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 5975:
1.222 brouard 5976: fprintf(fichtm,"\
1.126 brouard 5977: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 5978: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
5979: fprintf(fichtm,"\
1.126 brouard 5980: - 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): \
5981: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5982: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.222 brouard 5983: fprintf(fichtm,"\
1.126 brouard 5984: - (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): \
5985: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5986: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.222 brouard 5987: fprintf(fichtm,"\
1.128 brouard 5988: - 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 5989: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
5990: fprintf(fichtm,"\
1.128 brouard 5991: - 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 5992: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
5993: fprintf(fichtm,"\
1.126 brouard 5994: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.222 brouard 5995: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 5996:
5997: /* if(popforecast==1) fprintf(fichtm,"\n */
5998: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
5999: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
6000: /* <br>",fileres,fileres,fileres,fileres); */
6001: /* else */
6002: /* 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 6003: fflush(fichtm);
6004: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.126 brouard 6005:
1.225 brouard 6006: m=pow(2,cptcoveff);
1.222 brouard 6007: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 6008:
1.222 brouard 6009: jj1=0;
6010: for(k1=1; k1<=m;k1++){
6011: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
6012: jj1++;
1.126 brouard 6013: if (cptcovn > 0) {
6014: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 6015: for (cpt=1; cpt<=cptcoveff;cpt++) /**< cptcoveff number of variables */
1.222 brouard 6016: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 6017: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 6018:
1.222 brouard 6019: if(invalidvarcomb[k1]){
6020: fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
6021: continue;
6022: }
1.126 brouard 6023: }
6024: for(cpt=1; cpt<=nlstate;cpt++) {
1.218 brouard 6025: fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
6026: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d.svg\"> %s_%d-%d.svg</a>\n <br>\
1.205 brouard 6027: <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 6028: }
6029: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 6030: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
6031: true period expectancies (those weighted with period prevalences are also\
6032: drawn in addition to the population based expectancies computed using\
1.218 brouard 6033: observed and cahotic prevalences: <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\
1.205 brouard 6034: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.222 brouard 6035: /* } /\* end i1 *\/ */
6036: }/* End k1 */
6037: fprintf(fichtm,"</ul>");
6038: fflush(fichtm);
1.126 brouard 6039: }
6040:
6041: /******************* Gnuplot file **************/
1.223 brouard 6042: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
1.126 brouard 6043:
6044: char dirfileres[132],optfileres[132];
1.223 brouard 6045: char gplotcondition[132];
1.164 brouard 6046: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.211 brouard 6047: int lv=0, vlv=0, kl=0;
1.130 brouard 6048: int ng=0;
1.201 brouard 6049: int vpopbased;
1.223 brouard 6050: int ioffset; /* variable offset for columns */
1.219 brouard 6051:
1.126 brouard 6052: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
6053: /* printf("Problem with file %s",optionfilegnuplot); */
6054: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
6055: /* } */
6056:
6057: /*#ifdef windows */
6058: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.223 brouard 6059: /*#endif */
1.225 brouard 6060: m=pow(2,cptcoveff);
1.126 brouard 6061:
1.202 brouard 6062: /* Contribution to likelihood */
6063: /* Plot the probability implied in the likelihood */
1.223 brouard 6064: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
6065: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
6066: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
6067: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 6068: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 6069: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
6070: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
1.223 brouard 6071: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
6072: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
6073: 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));
6074: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
6075: 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));
6076: for (i=1; i<= nlstate ; i ++) {
6077: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
6078: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
6079: 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);
6080: for (j=2; j<= nlstate+ndeath ; j ++) {
6081: 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);
6082: }
6083: fprintf(ficgp,";\nset out; unset ylabel;\n");
6084: }
6085: /* 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 */
6086: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
6087: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
6088: fprintf(ficgp,"\nset out;unset log\n");
6089: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
1.202 brouard 6090:
1.126 brouard 6091: strcpy(dirfileres,optionfilefiname);
6092: strcpy(optfileres,"vpl");
1.223 brouard 6093: /* 1eme*/
1.211 brouard 6094: for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
1.220 brouard 6095: for (k1=1; k1<= m ; k1 ++) { /* For each valid combination of covariate */
1.211 brouard 6096: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
6097: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
1.225 brouard 6098: for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
6099: lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
1.223 brouard 6100: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6101: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6102: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6103: vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
6104: /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
6105: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6106: }
6107: fprintf(ficgp,"\n#\n");
1.223 brouard 6108: if(invalidvarcomb[k1]){
6109: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6110: continue;
6111: }
1.211 brouard 6112:
1.223 brouard 6113: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
6114: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
6115: fprintf(ficgp,"set xlabel \"Age\" \n\
1.219 brouard 6116: set ylabel \"Probability\" \n \
6117: set ter svg size 640, 480\n \
1.201 brouard 6118: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.219 brouard 6119:
1.223 brouard 6120: for (i=1; i<= nlstate ; i ++) {
6121: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
6122: else fprintf(ficgp," %%*lf (%%*lf)");
6123: }
6124: 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);
6125: for (i=1; i<= nlstate ; i ++) {
6126: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
6127: else fprintf(ficgp," %%*lf (%%*lf)");
6128: }
6129: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
6130: for (i=1; i<= nlstate ; i ++) {
6131: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
6132: else fprintf(ficgp," %%*lf (%%*lf)");
6133: }
6134: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
6135: if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
6136: /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
6137: fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
1.225 brouard 6138: if(cptcoveff ==0){
1.223 brouard 6139: fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ", 2+(cpt-1), cpt );
6140: }else{
6141: kl=0;
1.225 brouard 6142: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
6143: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
1.223 brouard 6144: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6145: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6146: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6147: vlv= nbcode[Tvaraff[k]][lv];
6148: kl++;
6149: /* 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 *\/ */
6150: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
6151: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
6152: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
1.225 brouard 6153: if(k==cptcoveff){
1.227 brouard 6154: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
6155: 4+(cpt-1), cpt ); /* 4 or 6 ?*/
1.223 brouard 6156: }else{
6157: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
6158: kl++;
6159: }
6160: } /* end covariate */
6161: } /* end if no covariate */
6162: } /* end if backcast */
6163: fprintf(ficgp,"\nset out \n");
1.201 brouard 6164: } /* k1 */
6165: } /* cpt */
1.126 brouard 6166: /*2 eme*/
6167: for (k1=1; k1<= m ; k1 ++) {
1.220 brouard 6168:
1.223 brouard 6169: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
1.225 brouard 6170: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6171: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 6172: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6173: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6174: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6175: vlv= nbcode[Tvaraff[k]][lv];
6176: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6177: }
6178: fprintf(ficgp,"\n#\n");
6179: if(invalidvarcomb[k1]){
6180: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6181: continue;
6182: }
1.219 brouard 6183:
1.223 brouard 6184: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
6185: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6186: if(vpopbased==0)
6187: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
6188: else
6189: fprintf(ficgp,"\nreplot ");
6190: for (i=1; i<= nlstate+1 ; i ++) {
6191: k=2*i;
6192: 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);
6193: for (j=1; j<= nlstate+1 ; j ++) {
6194: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6195: else fprintf(ficgp," %%*lf (%%*lf)");
6196: }
6197: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
6198: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
6199: 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);
6200: for (j=1; j<= nlstate+1 ; j ++) {
6201: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6202: else fprintf(ficgp," %%*lf (%%*lf)");
6203: }
6204: fprintf(ficgp,"\" t\"\" w l lt 0,");
6205: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
6206: for (j=1; j<= nlstate+1 ; j ++) {
6207: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6208: else fprintf(ficgp," %%*lf (%%*lf)");
6209: }
6210: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
6211: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
6212: } /* state */
6213: } /* vpopbased */
6214: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
1.201 brouard 6215: } /* k1 */
1.219 brouard 6216:
6217:
1.126 brouard 6218: /*3eme*/
6219: for (k1=1; k1<= m ; k1 ++) {
1.220 brouard 6220:
1.126 brouard 6221: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.211 brouard 6222: fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt);
1.225 brouard 6223: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6224: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 6225: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6226: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6227: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6228: vlv= nbcode[Tvaraff[k]][lv];
6229: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6230: }
6231: fprintf(ficgp,"\n#\n");
1.223 brouard 6232: if(invalidvarcomb[k1]){
6233: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6234: continue;
6235: }
1.219 brouard 6236:
1.126 brouard 6237: /* k=2+nlstate*(2*cpt-2); */
6238: k=2+(nlstate+1)*(cpt-1);
1.201 brouard 6239: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
1.199 brouard 6240: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 6241: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.126 brouard 6242: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
1.223 brouard 6243: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
6244: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
6245: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
6246: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
6247: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
1.219 brouard 6248:
1.126 brouard 6249: */
6250: for (i=1; i< nlstate ; i ++) {
1.223 brouard 6251: 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);
6252: /* 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 6253:
1.126 brouard 6254: }
1.201 brouard 6255: 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 6256: }
6257: }
6258:
1.223 brouard 6259: /* 4eme */
1.201 brouard 6260: /* Survival functions (period) from state i in state j by initial state i */
6261: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
1.220 brouard 6262:
1.201 brouard 6263: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.211 brouard 6264: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
1.225 brouard 6265: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6266: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 6267: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6268: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6269: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6270: vlv= nbcode[Tvaraff[k]][lv];
6271: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6272: }
6273: fprintf(ficgp,"\n#\n");
1.223 brouard 6274: if(invalidvarcomb[k1]){
6275: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6276: continue;
6277: }
1.220 brouard 6278:
1.201 brouard 6279: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
6280: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
1.220 brouard 6281: set ter svg size 640, 480\n \
6282: unset log y\n \
1.201 brouard 6283: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6284: k=3;
1.201 brouard 6285: for (i=1; i<= nlstate ; i ++){
1.223 brouard 6286: if(i==1){
6287: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6288: }else{
6289: fprintf(ficgp,", '' ");
6290: }
6291: l=(nlstate+ndeath)*(i-1)+1;
6292: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
6293: for (j=2; j<= nlstate+ndeath ; j ++)
6294: fprintf(ficgp,"+$%d",k+l+j-1);
6295: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
1.201 brouard 6296: } /* nlstate */
6297: fprintf(ficgp,"\nset out\n");
6298: } /* end cpt state*/
6299: } /* end covariate */
1.220 brouard 6300:
6301: /* 5eme */
1.201 brouard 6302: /* Survival functions (period) from state i in state j by final state j */
1.202 brouard 6303: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.201 brouard 6304: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
1.223 brouard 6305:
1.201 brouard 6306: fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
1.225 brouard 6307: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 brouard 6308: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6309: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6310: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6311: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6312: vlv= nbcode[Tvaraff[k]][lv];
6313: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6314: }
6315: fprintf(ficgp,"\n#\n");
1.223 brouard 6316: if(invalidvarcomb[k1]){
1.227 brouard 6317: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6318: continue;
1.223 brouard 6319: }
1.227 brouard 6320:
1.201 brouard 6321: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
6322: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
1.227 brouard 6323: set ter svg size 640, 480\n \
6324: unset log y\n \
1.201 brouard 6325: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6326: k=3;
1.201 brouard 6327: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
1.227 brouard 6328: if(j==1)
6329: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6330: else
6331: fprintf(ficgp,", '' ");
6332: l=(nlstate+ndeath)*(cpt-1) +j;
6333: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
6334: /* for (i=2; i<= nlstate+ndeath ; i ++) */
6335: /* fprintf(ficgp,"+$%d",k+l+i-1); */
6336: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
1.201 brouard 6337: } /* nlstate */
6338: fprintf(ficgp,", '' ");
6339: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
6340: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
1.227 brouard 6341: l=(nlstate+ndeath)*(cpt-1) +j;
6342: if(j < nlstate)
6343: fprintf(ficgp,"$%d +",k+l);
6344: else
6345: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
1.201 brouard 6346: }
6347: fprintf(ficgp,"\nset out\n");
6348: } /* end cpt state*/
6349: } /* end covariate */
1.227 brouard 6350:
1.220 brouard 6351: /* 6eme */
1.202 brouard 6352: /* CV preval stable (period) for each covariate */
1.211 brouard 6353: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.153 brouard 6354: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.227 brouard 6355:
1.211 brouard 6356: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
1.225 brouard 6357: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 brouard 6358: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6359: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6360: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6361: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6362: vlv= nbcode[Tvaraff[k]][lv];
6363: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6364: }
6365: fprintf(ficgp,"\n#\n");
1.223 brouard 6366: if(invalidvarcomb[k1]){
1.227 brouard 6367: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6368: continue;
1.223 brouard 6369: }
1.227 brouard 6370:
1.201 brouard 6371: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 6372: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.227 brouard 6373: set ter svg size 640, 480\n \
6374: unset log y\n \
1.153 brouard 6375: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6376: k=3; /* Offset */
1.153 brouard 6377: for (i=1; i<= nlstate ; i ++){
1.227 brouard 6378: if(i==1)
6379: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6380: else
6381: fprintf(ficgp,", '' ");
6382: l=(nlstate+ndeath)*(i-1)+1;
6383: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
6384: for (j=2; j<= nlstate ; j ++)
6385: fprintf(ficgp,"+$%d",k+l+j-1);
6386: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153 brouard 6387: } /* nlstate */
1.201 brouard 6388: fprintf(ficgp,"\nset out\n");
1.153 brouard 6389: } /* end cpt state*/
6390: } /* end covariate */
1.227 brouard 6391:
6392:
1.220 brouard 6393: /* 7eme */
1.218 brouard 6394: if(backcast == 1){
1.217 brouard 6395: /* CV back preval stable (period) for each covariate */
1.218 brouard 6396: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
6397: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.227 brouard 6398: fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
6399: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6400: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6401: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6402: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
1.223 brouard 6403: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.227 brouard 6404: vlv= nbcode[Tvaraff[k]][lv];
6405: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6406: }
6407: fprintf(ficgp,"\n#\n");
6408: if(invalidvarcomb[k1]){
6409: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6410: continue;
6411: }
6412:
6413: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
6414: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
6415: set ter svg size 640, 480\n \
6416: unset log y\n \
1.218 brouard 6417: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 6418: k=3; /* Offset */
6419: for (i=1; i<= nlstate ; i ++){
6420: if(i==1)
6421: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
6422: else
6423: fprintf(ficgp,", '' ");
6424: /* l=(nlstate+ndeath)*(i-1)+1; */
6425: l=(nlstate+ndeath)*(cpt-1)+1;
6426: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
6427: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
6428: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
6429: /* for (j=2; j<= nlstate ; j ++) */
6430: /* fprintf(ficgp,"+$%d",k+l+j-1); */
6431: /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
6432: fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
6433: } /* nlstate */
6434: fprintf(ficgp,"\nset out\n");
1.218 brouard 6435: } /* end cpt state*/
6436: } /* end covariate */
6437: } /* End if backcast */
6438:
1.223 brouard 6439: /* 8eme */
1.218 brouard 6440: if(prevfcast==1){
6441: /* Projection from cross-sectional to stable (period) for each covariate */
6442:
6443: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.211 brouard 6444: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.227 brouard 6445: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
6446: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
6447: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
6448: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6449: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6450: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6451: vlv= nbcode[Tvaraff[k]][lv];
6452: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6453: }
6454: fprintf(ficgp,"\n#\n");
6455: if(invalidvarcomb[k1]){
6456: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6457: continue;
6458: }
6459:
6460: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
6461: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
6462: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
6463: set ter svg size 640, 480\n \
6464: unset log y\n \
1.219 brouard 6465: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 6466: for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
6467: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6468: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6469: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6470: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6471: if(i==1){
6472: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
6473: }else{
6474: fprintf(ficgp,",\\\n '' ");
6475: }
6476: if(cptcoveff ==0){ /* No covariate */
6477: ioffset=2; /* Age is in 2 */
6478: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
6479: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
6480: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
6481: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
6482: fprintf(ficgp," u %d:(", ioffset);
6483: if(i==nlstate+1)
6484: fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ", \
6485: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
6486: else
6487: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
6488: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
6489: }else{ /* more than 2 covariates */
6490: if(cptcoveff ==1){
6491: ioffset=4; /* Age is in 4 */
6492: }else{
6493: ioffset=6; /* Age is in 6 */
6494: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6495: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6496: }
6497: fprintf(ficgp," u %d:(",ioffset);
6498: kl=0;
6499: strcpy(gplotcondition,"(");
6500: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
6501: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
6502: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6503: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6504: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6505: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
6506: kl++;
6507: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
6508: kl++;
6509: if(k <cptcoveff && cptcoveff>1)
6510: sprintf(gplotcondition+strlen(gplotcondition)," && ");
6511: }
6512: strcpy(gplotcondition+strlen(gplotcondition),")");
6513: /* 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 *\/ */
6514: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
6515: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
6516: /* '' 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*/
6517: if(i==nlstate+1){
6518: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
6519: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
6520: }else{
6521: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
6522: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
6523: }
6524: } /* end if covariate */
6525: } /* nlstate */
6526: fprintf(ficgp,"\nset out\n");
1.223 brouard 6527: } /* end cpt state*/
6528: } /* end covariate */
6529: } /* End if prevfcast */
1.227 brouard 6530:
6531:
1.223 brouard 6532: /* proba elementaires */
6533: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 6534: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 6535: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 6536: for(k=1; k <=(nlstate+ndeath); k++){
6537: if (k != i) {
1.227 brouard 6538: fprintf(ficgp,"# current state %d\n",k);
6539: for(j=1; j <=ncovmodel; j++){
6540: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
6541: jk++;
6542: }
6543: fprintf(ficgp,"\n");
1.126 brouard 6544: }
6545: }
1.223 brouard 6546: }
1.187 brouard 6547: fprintf(ficgp,"##############\n#\n");
1.227 brouard 6548:
1.145 brouard 6549: /*goto avoid;*/
1.200 brouard 6550: fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
1.187 brouard 6551: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
6552: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
6553: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
6554: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
6555: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6556: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
6557: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6558: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
6559: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
6560: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6561: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
6562: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
6563: fprintf(ficgp,"#\n");
1.223 brouard 6564: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
6565: fprintf(ficgp,"# ng=%d\n",ng);
1.225 brouard 6566: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.223 brouard 6567: for(jk=1; jk <=m; jk++) {
6568: fprintf(ficgp,"# jk=%d\n",jk);
6569: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
6570: fprintf(ficgp,"\nset ter svg size 640, 480 ");
6571: if (ng==1){
6572: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
6573: fprintf(ficgp,"\nunset log y");
6574: }else if (ng==2){
6575: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
6576: fprintf(ficgp,"\nset log y");
6577: }else if (ng==3){
6578: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
6579: fprintf(ficgp,"\nset log y");
6580: }else
6581: fprintf(ficgp,"\nunset title ");
6582: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
6583: i=1;
6584: for(k2=1; k2<=nlstate; k2++) {
6585: k3=i;
6586: for(k=1; k<=(nlstate+ndeath); k++) {
6587: if (k != k2){
6588: switch( ng) {
6589: case 1:
6590: if(nagesqr==0)
6591: fprintf(ficgp," p%d+p%d*x",i,i+1);
6592: else /* nagesqr =1 */
6593: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
6594: break;
6595: case 2: /* ng=2 */
6596: if(nagesqr==0)
6597: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
6598: else /* nagesqr =1 */
6599: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
6600: break;
6601: case 3:
6602: if(nagesqr==0)
6603: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
6604: else /* nagesqr =1 */
6605: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
6606: break;
6607: }
6608: ij=1;/* To be checked else nbcode[0][0] wrong */
6609: for(j=3; j <=ncovmodel-nagesqr; j++) {
6610: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
6611: if(ij <=cptcovage) { /* Bug valgrind */
6612: if((j-2)==Tage[ij]) { /* Bug valgrind */
6613: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
6614: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
6615: ij++;
6616: }
6617: }
6618: else
1.227 brouard 6619: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); /* Valgrind bug nbcode */
1.223 brouard 6620: }
6621: }else{
6622: i=i-ncovmodel;
6623: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
6624: fprintf(ficgp," (1.");
6625: }
1.227 brouard 6626:
1.223 brouard 6627: if(ng != 1){
6628: fprintf(ficgp,")/(1");
1.227 brouard 6629:
1.223 brouard 6630: for(k1=1; k1 <=nlstate; k1++){
6631: if(nagesqr==0)
6632: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
6633: else /* nagesqr =1 */
6634: 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 6635:
1.223 brouard 6636: ij=1;
6637: for(j=3; j <=ncovmodel-nagesqr; j++){
6638: if(ij <=cptcovage) { /* Bug valgrind */
6639: if((j-2)==Tage[ij]) { /* Bug valgrind */
6640: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
6641: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
6642: ij++;
6643: }
6644: }
6645: else
1.225 brouard 6646: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);/* Valgrind bug nbcode */
1.223 brouard 6647: }
6648: fprintf(ficgp,")");
6649: }
6650: fprintf(ficgp,")");
6651: if(ng ==2)
6652: fprintf(ficgp," t \"p%d%d\" ", k2,k);
6653: else /* ng= 3 */
6654: fprintf(ficgp," t \"i%d%d\" ", k2,k);
6655: }else{ /* end ng <> 1 */
6656: if( k !=k2) /* logit p11 is hard to draw */
6657: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
6658: }
6659: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
6660: fprintf(ficgp,",");
6661: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
6662: fprintf(ficgp,",");
6663: i=i+ncovmodel;
6664: } /* end k */
6665: } /* end k2 */
6666: fprintf(ficgp,"\n set out\n");
6667: } /* end jk */
6668: } /* end ng */
6669: /* avoid: */
6670: fflush(ficgp);
1.126 brouard 6671: } /* end gnuplot */
6672:
6673:
6674: /*************** Moving average **************/
1.219 brouard 6675: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.222 brouard 6676: int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
1.218 brouard 6677:
1.222 brouard 6678: int i, cpt, cptcod;
6679: int modcovmax =1;
6680: int mobilavrange, mob;
6681: int iage=0;
6682:
6683: double sum=0.;
6684: double age;
6685: double *sumnewp, *sumnewm;
6686: double *agemingood, *agemaxgood; /* Currently identical for all covariates */
6687:
6688:
1.225 brouard 6689: /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose */
1.222 brouard 6690: /* a covariate has 2 modalities, should be equal to ncovcombmax *\/ */
6691:
6692: sumnewp = vector(1,ncovcombmax);
6693: sumnewm = vector(1,ncovcombmax);
6694: agemingood = vector(1,ncovcombmax);
6695: agemaxgood = vector(1,ncovcombmax);
6696:
6697: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
6698: sumnewm[cptcod]=0.;
6699: sumnewp[cptcod]=0.;
6700: agemingood[cptcod]=0;
6701: agemaxgood[cptcod]=0;
6702: }
6703: if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
6704:
6705: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
6706: if(mobilav==1) mobilavrange=5; /* default */
6707: else mobilavrange=mobilav;
6708: for (age=bage; age<=fage; age++)
6709: for (i=1; i<=nlstate;i++)
6710: for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
6711: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
6712: /* We keep the original values on the extreme ages bage, fage and for
6713: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
6714: we use a 5 terms etc. until the borders are no more concerned.
6715: */
6716: for (mob=3;mob <=mobilavrange;mob=mob+2){
6717: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
6718: for (i=1; i<=nlstate;i++){
6719: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
6720: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
6721: for (cpt=1;cpt<=(mob-1)/2;cpt++){
6722: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
6723: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
6724: }
6725: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
6726: }
6727: }
6728: }/* end age */
6729: }/* end mob */
6730: }else
6731: return -1;
6732: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
6733: /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
6734: if(invalidvarcomb[cptcod]){
6735: printf("\nCombination (%d) ignored because no cases \n",cptcod);
6736: continue;
6737: }
1.219 brouard 6738:
1.222 brouard 6739: agemingood[cptcod]=fage-(mob-1)/2;
6740: for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
6741: sumnewm[cptcod]=0.;
6742: for (i=1; i<=nlstate;i++){
6743: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6744: }
6745: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
6746: agemingood[cptcod]=age;
6747: }else{ /* bad */
6748: for (i=1; i<=nlstate;i++){
6749: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6750: } /* i */
6751: } /* end bad */
6752: }/* age */
6753: sum=0.;
6754: for (i=1; i<=nlstate;i++){
6755: sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6756: }
6757: if(fabs(sum - 1.) > 1.e-3) { /* bad */
6758: 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);
6759: /* for (i=1; i<=nlstate;i++){ */
6760: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
6761: /* } /\* i *\/ */
6762: } /* end bad */
6763: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
6764: /* From youngest, finding the oldest wrong */
6765: agemaxgood[cptcod]=bage+(mob-1)/2;
6766: for (age=bage+(mob-1)/2; age<=fage; age++){
6767: sumnewm[cptcod]=0.;
6768: for (i=1; i<=nlstate;i++){
6769: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6770: }
6771: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
6772: agemaxgood[cptcod]=age;
6773: }else{ /* bad */
6774: for (i=1; i<=nlstate;i++){
6775: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6776: } /* i */
6777: } /* end bad */
6778: }/* age */
6779: sum=0.;
6780: for (i=1; i<=nlstate;i++){
6781: sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6782: }
6783: if(fabs(sum - 1.) > 1.e-3) { /* bad */
6784: 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);
6785: /* for (i=1; i<=nlstate;i++){ */
6786: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
6787: /* } /\* i *\/ */
6788: } /* end bad */
6789:
6790: for (age=bage; age<=fage; age++){
6791: printf("%d %d ", cptcod, (int)age);
6792: sumnewp[cptcod]=0.;
6793: sumnewm[cptcod]=0.;
6794: for (i=1; i<=nlstate;i++){
6795: sumnewp[cptcod]+=probs[(int)age][i][cptcod];
6796: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6797: /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
6798: }
6799: /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
6800: }
6801: /* printf("\n"); */
6802: /* } */
6803: /* brutal averaging */
6804: for (i=1; i<=nlstate;i++){
6805: for (age=1; age<=bage; age++){
6806: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6807: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
6808: }
6809: for (age=fage; age<=AGESUP; age++){
6810: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6811: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
6812: }
6813: } /* end i status */
6814: for (i=nlstate+1; i<=nlstate+ndeath;i++){
6815: for (age=1; age<=AGESUP; age++){
6816: /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
6817: mobaverage[(int)age][i][cptcod]=0.;
6818: }
6819: }
6820: }/* end cptcod */
6821: free_vector(sumnewm,1, ncovcombmax);
6822: free_vector(sumnewp,1, ncovcombmax);
6823: free_vector(agemaxgood,1, ncovcombmax);
6824: free_vector(agemingood,1, ncovcombmax);
6825: return 0;
6826: }/* End movingaverage */
1.218 brouard 6827:
1.126 brouard 6828:
6829: /************** Forecasting ******************/
1.225 brouard 6830: void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
1.126 brouard 6831: /* proj1, year, month, day of starting projection
6832: agemin, agemax range of age
6833: dateprev1 dateprev2 range of dates during which prevalence is computed
6834: anproj2 year of en of projection (same day and month as proj1).
6835: */
1.164 brouard 6836: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 6837: double agec; /* generic age */
6838: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
6839: double *popeffectif,*popcount;
6840: double ***p3mat;
1.218 brouard 6841: /* double ***mobaverage; */
1.126 brouard 6842: char fileresf[FILENAMELENGTH];
6843:
6844: agelim=AGESUP;
1.211 brouard 6845: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
6846: in each health status at the date of interview (if between dateprev1 and dateprev2).
6847: We still use firstpass and lastpass as another selection.
6848: */
1.214 brouard 6849: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
6850: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 6851:
1.201 brouard 6852: strcpy(fileresf,"F_");
6853: strcat(fileresf,fileresu);
1.126 brouard 6854: if((ficresf=fopen(fileresf,"w"))==NULL) {
6855: printf("Problem with forecast resultfile: %s\n", fileresf);
6856: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
6857: }
1.215 brouard 6858: printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
6859: fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 6860:
1.225 brouard 6861: if (cptcoveff==0) ncodemax[cptcoveff]=1;
1.126 brouard 6862:
6863:
6864: stepsize=(int) (stepm+YEARM-1)/YEARM;
6865: if (stepm<=12) stepsize=1;
6866: if(estepm < stepm){
6867: printf ("Problem %d lower than %d\n",estepm, stepm);
6868: }
6869: else hstepm=estepm;
6870:
6871: hstepm=hstepm/stepm;
6872: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
6873: fractional in yp1 */
6874: anprojmean=yp;
6875: yp2=modf((yp1*12),&yp);
6876: mprojmean=yp;
6877: yp1=modf((yp2*30.5),&yp);
6878: jprojmean=yp;
6879: if(jprojmean==0) jprojmean=1;
6880: if(mprojmean==0) jprojmean=1;
6881:
1.227 brouard 6882: i1=pow(2,cptcoveff);
1.126 brouard 6883: if (cptcovn < 1){i1=1;}
6884:
6885: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
6886:
6887: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.227 brouard 6888:
1.126 brouard 6889: /* if (h==(int)(YEARM*yearp)){ */
1.227 brouard 6890: for(k=1;k<=i1;k++){
6891: if(invalidvarcomb[k]){
6892: printf("\nCombination (%d) projection ignored because no cases \n",k);
6893: continue;
6894: }
6895: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
6896: for(j=1;j<=cptcoveff;j++) {
6897: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6898: }
6899: fprintf(ficresf," yearproj age");
6900: for(j=1; j<=nlstate+ndeath;j++){
6901: for(i=1; i<=nlstate;i++)
6902: fprintf(ficresf," p%d%d",i,j);
6903: fprintf(ficresf," wp.%d",j);
6904: }
6905: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
6906: fprintf(ficresf,"\n");
6907: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
6908: for (agec=fage; agec>=(ageminpar-1); agec--){
6909: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
6910: nhstepm = nhstepm/hstepm;
6911: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6912: oldm=oldms;savm=savms;
6913: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
6914:
6915: for (h=0; h<=nhstepm; h++){
6916: if (h*hstepm/YEARM*stepm ==yearp) {
6917: fprintf(ficresf,"\n");
6918: for(j=1;j<=cptcoveff;j++)
6919: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6920: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
6921: }
6922: for(j=1; j<=nlstate+ndeath;j++) {
6923: ppij=0.;
6924: for(i=1; i<=nlstate;i++) {
6925: if (mobilav==1)
6926: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];
6927: else {
6928: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
6929: }
6930: if (h*hstepm/YEARM*stepm== yearp) {
6931: fprintf(ficresf," %.3f", p3mat[i][j][h]);
6932: }
6933: } /* end i */
6934: if (h*hstepm/YEARM*stepm==yearp) {
6935: fprintf(ficresf," %.3f", ppij);
6936: }
6937: }/* end j */
6938: } /* end h */
6939: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6940: } /* end agec */
6941: } /* end yearp */
6942: } /* end k */
1.219 brouard 6943:
1.126 brouard 6944: fclose(ficresf);
1.215 brouard 6945: printf("End of Computing forecasting \n");
6946: fprintf(ficlog,"End of Computing forecasting\n");
6947:
1.126 brouard 6948: }
6949:
1.218 brouard 6950: /* /\************** Back Forecasting ******************\/ */
1.225 brouard 6951: /* void prevbackforecast(char fileres[], double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ */
1.218 brouard 6952: /* /\* back1, year, month, day of starting backection */
6953: /* agemin, agemax range of age */
6954: /* dateprev1 dateprev2 range of dates during which prevalence is computed */
6955: /* anback2 year of en of backection (same day and month as back1). */
6956: /* *\/ */
6957: /* int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */
6958: /* double agec; /\* generic age *\/ */
6959: /* double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */
6960: /* double *popeffectif,*popcount; */
6961: /* double ***p3mat; */
6962: /* /\* double ***mobaverage; *\/ */
6963: /* char fileresfb[FILENAMELENGTH]; */
6964:
6965: /* agelim=AGESUP; */
6966: /* /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */
6967: /* in each health status at the date of interview (if between dateprev1 and dateprev2). */
6968: /* We still use firstpass and lastpass as another selection. */
6969: /* *\/ */
6970: /* /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */
6971: /* /\* firstpass, lastpass, stepm, weightopt, model); *\/ */
6972: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
6973:
6974: /* strcpy(fileresfb,"FB_"); */
6975: /* strcat(fileresfb,fileresu); */
6976: /* if((ficresfb=fopen(fileresfb,"w"))==NULL) { */
6977: /* printf("Problem with back forecast resultfile: %s\n", fileresfb); */
6978: /* fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */
6979: /* } */
6980: /* printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
6981: /* fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
6982:
1.225 brouard 6983: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.218 brouard 6984:
6985: /* /\* if (mobilav!=0) { *\/ */
6986: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
6987: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
6988: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
6989: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
6990: /* /\* } *\/ */
6991: /* /\* } *\/ */
6992:
6993: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
6994: /* if (stepm<=12) stepsize=1; */
6995: /* if(estepm < stepm){ */
6996: /* printf ("Problem %d lower than %d\n",estepm, stepm); */
6997: /* } */
6998: /* else hstepm=estepm; */
6999:
7000: /* hstepm=hstepm/stepm; */
7001: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
7002: /* fractional in yp1 *\/ */
7003: /* anprojmean=yp; */
7004: /* yp2=modf((yp1*12),&yp); */
7005: /* mprojmean=yp; */
7006: /* yp1=modf((yp2*30.5),&yp); */
7007: /* jprojmean=yp; */
7008: /* if(jprojmean==0) jprojmean=1; */
7009: /* if(mprojmean==0) jprojmean=1; */
7010:
1.225 brouard 7011: /* i1=cptcoveff; */
1.218 brouard 7012: /* if (cptcovn < 1){i1=1;} */
1.217 brouard 7013:
1.218 brouard 7014: /* fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); */
1.217 brouard 7015:
1.218 brouard 7016: /* fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */
7017:
7018: /* /\* if (h==(int)(YEARM*yearp)){ *\/ */
7019: /* for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
1.225 brouard 7020: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
1.218 brouard 7021: /* k=k+1; */
7022: /* fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
1.225 brouard 7023: /* for(j=1;j<=cptcoveff;j++) { */
1.218 brouard 7024: /* fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
7025: /* } */
7026: /* fprintf(ficresfb," yearbproj age"); */
7027: /* for(j=1; j<=nlstate+ndeath;j++){ */
7028: /* for(i=1; i<=nlstate;i++) */
7029: /* fprintf(ficresfb," p%d%d",i,j); */
7030: /* fprintf(ficresfb," p.%d",j); */
7031: /* } */
7032: /* for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) { */
7033: /* /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { *\/ */
7034: /* fprintf(ficresfb,"\n"); */
7035: /* fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
7036: /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
7037: /* nhstepm=(int) rint((agelim-agec)*YEARM/stepm); */
7038: /* nhstepm = nhstepm/hstepm; */
7039: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7040: /* oldm=oldms;savm=savms; */
7041: /* hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k); */
7042: /* for (h=0; h<=nhstepm; h++){ */
7043: /* if (h*hstepm/YEARM*stepm ==yearp) { */
7044: /* fprintf(ficresfb,"\n"); */
1.225 brouard 7045: /* for(j=1;j<=cptcoveff;j++) */
1.218 brouard 7046: /* fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
7047: /* fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */
7048: /* } */
7049: /* for(j=1; j<=nlstate+ndeath;j++) { */
7050: /* ppij=0.; */
7051: /* for(i=1; i<=nlstate;i++) { */
7052: /* if (mobilav==1) */
7053: /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */
7054: /* else { */
7055: /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */
7056: /* } */
7057: /* if (h*hstepm/YEARM*stepm== yearp) { */
7058: /* fprintf(ficresfb," %.3f", p3mat[i][j][h]); */
7059: /* } */
7060: /* } /\* end i *\/ */
7061: /* if (h*hstepm/YEARM*stepm==yearp) { */
7062: /* fprintf(ficresfb," %.3f", ppij); */
7063: /* } */
7064: /* }/\* end j *\/ */
7065: /* } /\* end h *\/ */
7066: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7067: /* } /\* end agec *\/ */
7068: /* } /\* end yearp *\/ */
7069: /* } /\* end cptcod *\/ */
7070: /* } /\* end cptcov *\/ */
7071:
7072: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
7073:
7074: /* fclose(ficresfb); */
7075: /* printf("End of Computing Back forecasting \n"); */
7076: /* fprintf(ficlog,"End of Computing Back forecasting\n"); */
1.217 brouard 7077:
1.218 brouard 7078: /* } */
1.217 brouard 7079:
1.126 brouard 7080: /************** Forecasting *****not tested NB*************/
1.227 brouard 7081: /* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */
1.126 brouard 7082:
1.227 brouard 7083: /* int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
7084: /* int *popage; */
7085: /* double calagedatem, agelim, kk1, kk2; */
7086: /* double *popeffectif,*popcount; */
7087: /* double ***p3mat,***tabpop,***tabpopprev; */
7088: /* /\* double ***mobaverage; *\/ */
7089: /* char filerespop[FILENAMELENGTH]; */
1.126 brouard 7090:
1.227 brouard 7091: /* tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7092: /* tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7093: /* agelim=AGESUP; */
7094: /* calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
1.126 brouard 7095:
1.227 brouard 7096: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
1.126 brouard 7097:
7098:
1.227 brouard 7099: /* strcpy(filerespop,"POP_"); */
7100: /* strcat(filerespop,fileresu); */
7101: /* if((ficrespop=fopen(filerespop,"w"))==NULL) { */
7102: /* printf("Problem with forecast resultfile: %s\n", filerespop); */
7103: /* fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
7104: /* } */
7105: /* printf("Computing forecasting: result on file '%s' \n", filerespop); */
7106: /* fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
1.126 brouard 7107:
1.227 brouard 7108: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.126 brouard 7109:
1.227 brouard 7110: /* /\* if (mobilav!=0) { *\/ */
7111: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
7112: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
7113: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
7114: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
7115: /* /\* } *\/ */
7116: /* /\* } *\/ */
1.126 brouard 7117:
1.227 brouard 7118: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
7119: /* if (stepm<=12) stepsize=1; */
1.126 brouard 7120:
1.227 brouard 7121: /* agelim=AGESUP; */
1.126 brouard 7122:
1.227 brouard 7123: /* hstepm=1; */
7124: /* hstepm=hstepm/stepm; */
1.218 brouard 7125:
1.227 brouard 7126: /* if (popforecast==1) { */
7127: /* if((ficpop=fopen(popfile,"r"))==NULL) { */
7128: /* printf("Problem with population file : %s\n",popfile);exit(0); */
7129: /* fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
7130: /* } */
7131: /* popage=ivector(0,AGESUP); */
7132: /* popeffectif=vector(0,AGESUP); */
7133: /* popcount=vector(0,AGESUP); */
1.126 brouard 7134:
1.227 brouard 7135: /* i=1; */
7136: /* while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
1.218 brouard 7137:
1.227 brouard 7138: /* imx=i; */
7139: /* for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
7140: /* } */
1.218 brouard 7141:
1.227 brouard 7142: /* for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
7143: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
7144: /* k=k+1; */
7145: /* fprintf(ficrespop,"\n#******"); */
7146: /* for(j=1;j<=cptcoveff;j++) { */
7147: /* fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
7148: /* } */
7149: /* fprintf(ficrespop,"******\n"); */
7150: /* fprintf(ficrespop,"# Age"); */
7151: /* for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
7152: /* if (popforecast==1) fprintf(ficrespop," [Population]"); */
1.126 brouard 7153:
1.227 brouard 7154: /* for (cpt=0; cpt<=0;cpt++) { */
7155: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
1.126 brouard 7156:
1.227 brouard 7157: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
7158: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
7159: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 7160:
1.227 brouard 7161: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7162: /* oldm=oldms;savm=savms; */
7163: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.218 brouard 7164:
1.227 brouard 7165: /* for (h=0; h<=nhstepm; h++){ */
7166: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
7167: /* fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
7168: /* } */
7169: /* for(j=1; j<=nlstate+ndeath;j++) { */
7170: /* kk1=0.;kk2=0; */
7171: /* for(i=1; i<=nlstate;i++) { */
7172: /* if (mobilav==1) */
7173: /* kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
7174: /* else { */
7175: /* kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
7176: /* } */
7177: /* } */
7178: /* if (h==(int)(calagedatem+12*cpt)){ */
7179: /* tabpop[(int)(agedeb)][j][cptcod]=kk1; */
7180: /* /\*fprintf(ficrespop," %.3f", kk1); */
7181: /* if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
7182: /* } */
7183: /* } */
7184: /* for(i=1; i<=nlstate;i++){ */
7185: /* kk1=0.; */
7186: /* for(j=1; j<=nlstate;j++){ */
7187: /* kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; */
7188: /* } */
7189: /* tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
7190: /* } */
1.218 brouard 7191:
1.227 brouard 7192: /* if (h==(int)(calagedatem+12*cpt)) */
7193: /* for(j=1; j<=nlstate;j++) */
7194: /* fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
7195: /* } */
7196: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7197: /* } */
7198: /* } */
1.218 brouard 7199:
1.227 brouard 7200: /* /\******\/ */
1.218 brouard 7201:
1.227 brouard 7202: /* for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { */
7203: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
7204: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
7205: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
7206: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 7207:
1.227 brouard 7208: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7209: /* oldm=oldms;savm=savms; */
7210: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
7211: /* for (h=0; h<=nhstepm; h++){ */
7212: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
7213: /* fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
7214: /* } */
7215: /* for(j=1; j<=nlstate+ndeath;j++) { */
7216: /* kk1=0.;kk2=0; */
7217: /* for(i=1; i<=nlstate;i++) { */
7218: /* kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; */
7219: /* } */
7220: /* if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); */
7221: /* } */
7222: /* } */
7223: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7224: /* } */
7225: /* } */
7226: /* } */
7227: /* } */
1.218 brouard 7228:
1.227 brouard 7229: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
1.218 brouard 7230:
1.227 brouard 7231: /* if (popforecast==1) { */
7232: /* free_ivector(popage,0,AGESUP); */
7233: /* free_vector(popeffectif,0,AGESUP); */
7234: /* free_vector(popcount,0,AGESUP); */
7235: /* } */
7236: /* free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7237: /* free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7238: /* fclose(ficrespop); */
7239: /* } /\* End of popforecast *\/ */
1.218 brouard 7240:
1.126 brouard 7241: int fileappend(FILE *fichier, char *optionfich)
7242: {
7243: if((fichier=fopen(optionfich,"a"))==NULL) {
7244: printf("Problem with file: %s\n", optionfich);
7245: fprintf(ficlog,"Problem with file: %s\n", optionfich);
7246: return (0);
7247: }
7248: fflush(fichier);
7249: return (1);
7250: }
7251:
7252:
7253: /**************** function prwizard **********************/
7254: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
7255: {
7256:
7257: /* Wizard to print covariance matrix template */
7258:
1.164 brouard 7259: char ca[32], cb[32];
7260: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 7261: int numlinepar;
7262:
7263: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7264: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7265: for(i=1; i <=nlstate; i++){
7266: jj=0;
7267: for(j=1; j <=nlstate+ndeath; j++){
7268: if(j==i) continue;
7269: jj++;
7270: /*ca[0]= k+'a'-1;ca[1]='\0';*/
7271: printf("%1d%1d",i,j);
7272: fprintf(ficparo,"%1d%1d",i,j);
7273: for(k=1; k<=ncovmodel;k++){
7274: /* printf(" %lf",param[i][j][k]); */
7275: /* fprintf(ficparo," %lf",param[i][j][k]); */
7276: printf(" 0.");
7277: fprintf(ficparo," 0.");
7278: }
7279: printf("\n");
7280: fprintf(ficparo,"\n");
7281: }
7282: }
7283: printf("# Scales (for hessian or gradient estimation)\n");
7284: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
7285: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
7286: for(i=1; i <=nlstate; i++){
7287: jj=0;
7288: for(j=1; j <=nlstate+ndeath; j++){
7289: if(j==i) continue;
7290: jj++;
7291: fprintf(ficparo,"%1d%1d",i,j);
7292: printf("%1d%1d",i,j);
7293: fflush(stdout);
7294: for(k=1; k<=ncovmodel;k++){
7295: /* printf(" %le",delti3[i][j][k]); */
7296: /* fprintf(ficparo," %le",delti3[i][j][k]); */
7297: printf(" 0.");
7298: fprintf(ficparo," 0.");
7299: }
7300: numlinepar++;
7301: printf("\n");
7302: fprintf(ficparo,"\n");
7303: }
7304: }
7305: printf("# Covariance matrix\n");
7306: /* # 121 Var(a12)\n\ */
7307: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7308: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7309: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7310: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7311: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7312: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7313: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7314: fflush(stdout);
7315: fprintf(ficparo,"# Covariance matrix\n");
7316: /* # 121 Var(a12)\n\ */
7317: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7318: /* # ...\n\ */
7319: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7320:
7321: for(itimes=1;itimes<=2;itimes++){
7322: jj=0;
7323: for(i=1; i <=nlstate; i++){
7324: for(j=1; j <=nlstate+ndeath; j++){
7325: if(j==i) continue;
7326: for(k=1; k<=ncovmodel;k++){
7327: jj++;
7328: ca[0]= k+'a'-1;ca[1]='\0';
7329: if(itimes==1){
7330: printf("#%1d%1d%d",i,j,k);
7331: fprintf(ficparo,"#%1d%1d%d",i,j,k);
7332: }else{
7333: printf("%1d%1d%d",i,j,k);
7334: fprintf(ficparo,"%1d%1d%d",i,j,k);
7335: /* printf(" %.5le",matcov[i][j]); */
7336: }
7337: ll=0;
7338: for(li=1;li <=nlstate; li++){
7339: for(lj=1;lj <=nlstate+ndeath; lj++){
7340: if(lj==li) continue;
7341: for(lk=1;lk<=ncovmodel;lk++){
7342: ll++;
7343: if(ll<=jj){
7344: cb[0]= lk +'a'-1;cb[1]='\0';
7345: if(ll<jj){
7346: if(itimes==1){
7347: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7348: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7349: }else{
7350: printf(" 0.");
7351: fprintf(ficparo," 0.");
7352: }
7353: }else{
7354: if(itimes==1){
7355: printf(" Var(%s%1d%1d)",ca,i,j);
7356: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
7357: }else{
7358: printf(" 0.");
7359: fprintf(ficparo," 0.");
7360: }
7361: }
7362: }
7363: } /* end lk */
7364: } /* end lj */
7365: } /* end li */
7366: printf("\n");
7367: fprintf(ficparo,"\n");
7368: numlinepar++;
7369: } /* end k*/
7370: } /*end j */
7371: } /* end i */
7372: } /* end itimes */
7373:
7374: } /* end of prwizard */
7375: /******************* Gompertz Likelihood ******************************/
7376: double gompertz(double x[])
7377: {
7378: double A,B,L=0.0,sump=0.,num=0.;
7379: int i,n=0; /* n is the size of the sample */
7380:
1.220 brouard 7381: for (i=1;i<=imx ; i++) {
1.126 brouard 7382: sump=sump+weight[i];
7383: /* sump=sump+1;*/
7384: num=num+1;
7385: }
7386:
7387:
7388: /* for (i=0; i<=imx; i++)
7389: 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]);*/
7390:
7391: for (i=1;i<=imx ; i++)
7392: {
7393: if (cens[i] == 1 && wav[i]>1)
7394: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
7395:
7396: if (cens[i] == 0 && wav[i]>1)
7397: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
7398: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
7399:
7400: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
7401: if (wav[i] > 1 ) { /* ??? */
7402: L=L+A*weight[i];
7403: /* 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]);*/
7404: }
7405: }
7406:
7407: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
7408:
7409: return -2*L*num/sump;
7410: }
7411:
1.136 brouard 7412: #ifdef GSL
7413: /******************* Gompertz_f Likelihood ******************************/
7414: double gompertz_f(const gsl_vector *v, void *params)
7415: {
7416: double A,B,LL=0.0,sump=0.,num=0.;
7417: double *x= (double *) v->data;
7418: int i,n=0; /* n is the size of the sample */
7419:
7420: for (i=0;i<=imx-1 ; i++) {
7421: sump=sump+weight[i];
7422: /* sump=sump+1;*/
7423: num=num+1;
7424: }
7425:
7426:
7427: /* for (i=0; i<=imx; i++)
7428: 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]);*/
7429: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
7430: for (i=1;i<=imx ; i++)
7431: {
7432: if (cens[i] == 1 && wav[i]>1)
7433: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
7434:
7435: if (cens[i] == 0 && wav[i]>1)
7436: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
7437: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
7438:
7439: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
7440: if (wav[i] > 1 ) { /* ??? */
7441: LL=LL+A*weight[i];
7442: /* 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]);*/
7443: }
7444: }
7445:
7446: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
7447: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
7448:
7449: return -2*LL*num/sump;
7450: }
7451: #endif
7452:
1.126 brouard 7453: /******************* Printing html file ***********/
1.201 brouard 7454: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 7455: int lastpass, int stepm, int weightopt, char model[],\
7456: int imx, double p[],double **matcov,double agemortsup){
7457: int i,k;
7458:
7459: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
7460: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
7461: for (i=1;i<=2;i++)
7462: 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 7463: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 7464: fprintf(fichtm,"</ul>");
7465:
7466: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
7467:
7468: 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>");
7469:
7470: for (k=agegomp;k<(agemortsup-2);k++)
7471: 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]);
7472:
7473:
7474: fflush(fichtm);
7475: }
7476:
7477: /******************* Gnuplot file **************/
1.201 brouard 7478: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 7479:
7480: char dirfileres[132],optfileres[132];
1.164 brouard 7481:
1.126 brouard 7482: int ng;
7483:
7484:
7485: /*#ifdef windows */
7486: fprintf(ficgp,"cd \"%s\" \n",pathc);
7487: /*#endif */
7488:
7489:
7490: strcpy(dirfileres,optionfilefiname);
7491: strcpy(optfileres,"vpl");
1.199 brouard 7492: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 7493: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 7494: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 7495: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 7496: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
7497:
7498: }
7499:
1.136 brouard 7500: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
7501: {
1.126 brouard 7502:
1.136 brouard 7503: /*-------- data file ----------*/
7504: FILE *fic;
7505: char dummy[]=" ";
1.223 brouard 7506: int i=0, j=0, n=0, iv=0;
7507: int lstra;
1.136 brouard 7508: int linei, month, year,iout;
7509: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 7510: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 7511: char *stratrunc;
1.223 brouard 7512:
1.126 brouard 7513:
7514:
1.136 brouard 7515: if((fic=fopen(datafile,"r"))==NULL) {
1.218 brouard 7516: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
7517: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136 brouard 7518: }
1.126 brouard 7519:
1.136 brouard 7520: i=1;
7521: linei=0;
7522: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
7523: linei=linei+1;
7524: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
7525: if(line[j] == '\t')
7526: line[j] = ' ';
7527: }
7528: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
7529: ;
7530: };
7531: line[j+1]=0; /* Trims blanks at end of line */
7532: if(line[0]=='#'){
7533: fprintf(ficlog,"Comment line\n%s\n",line);
7534: printf("Comment line\n%s\n",line);
7535: continue;
7536: }
7537: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 7538: strcpy(line, linetmp);
1.223 brouard 7539:
7540: /* Loops on waves */
7541: for (j=maxwav;j>=1;j--){
7542: for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */
1.225 brouard 7543: cutv(stra, strb, line, ' ');
7544: if(strb[0]=='.') { /* Missing value */
7545: lval=-1;
7546: cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
7547: if(isalpha(strb[1])) { /* .m or .d Really Missing value */
7548: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j);
7549: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);
7550: return 1;
7551: }
7552: }else{
7553: errno=0;
7554: /* what_kind_of_number(strb); */
7555: dval=strtod(strb,&endptr);
7556: /* if( strb[0]=='\0' || (*endptr != '\0')){ */
7557: /* if(strb != endptr && *endptr == '\0') */
7558: /* dval=dlval; */
7559: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
7560: if( strb[0]=='\0' || (*endptr != '\0')){
7561: 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);
7562: 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);
7563: return 1;
7564: }
7565: cotqvar[j][iv][i]=dval;
7566: }
7567: strcpy(line,stra);
1.223 brouard 7568: }/* end loop ntqv */
1.225 brouard 7569:
1.223 brouard 7570: for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */
1.225 brouard 7571: cutv(stra, strb, line, ' ');
7572: if(strb[0]=='.') { /* Missing value */
7573: lval=-1;
7574: }else{
7575: errno=0;
7576: lval=strtol(strb,&endptr,10);
7577: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
7578: if( strb[0]=='\0' || (*endptr != '\0')){
7579: 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);
7580: 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);
7581: return 1;
7582: }
7583: }
7584: if(lval <-1 || lval >1){
7585: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 7586: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7587: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 7588: For example, for multinomial values like 1, 2 and 3,\n \
7589: build V1=0 V2=0 for the reference value (1),\n \
7590: V1=1 V2=0 for (2) \n \
1.223 brouard 7591: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 7592: output of IMaCh is often meaningless.\n \
1.223 brouard 7593: Exiting.\n",lval,linei, i,line,j);
1.225 brouard 7594: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 7595: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7596: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 7597: For example, for multinomial values like 1, 2 and 3,\n \
7598: build V1=0 V2=0 for the reference value (1),\n \
7599: V1=1 V2=0 for (2) \n \
1.223 brouard 7600: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
7601: output of IMaCh is often meaningless.\n \
7602: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.225 brouard 7603: return 1;
7604: }
7605: cotvar[j][iv][i]=(double)(lval);
7606: strcpy(line,stra);
1.223 brouard 7607: }/* end loop ntv */
1.225 brouard 7608:
1.223 brouard 7609: /* Statuses at wave */
1.137 brouard 7610: cutv(stra, strb, line, ' ');
1.223 brouard 7611: if(strb[0]=='.') { /* Missing value */
1.225 brouard 7612: lval=-1;
1.136 brouard 7613: }else{
1.225 brouard 7614: errno=0;
7615: lval=strtol(strb,&endptr,10);
7616: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
7617: if( strb[0]=='\0' || (*endptr != '\0')){
7618: 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);
7619: 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);
7620: return 1;
7621: }
1.136 brouard 7622: }
1.225 brouard 7623:
1.136 brouard 7624: s[j][i]=lval;
1.225 brouard 7625:
1.223 brouard 7626: /* Date of Interview */
1.136 brouard 7627: strcpy(line,stra);
7628: cutv(stra, strb,line,' ');
1.169 brouard 7629: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7630: }
1.169 brouard 7631: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.225 brouard 7632: month=99;
7633: year=9999;
1.136 brouard 7634: }else{
1.225 brouard 7635: 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);
7636: 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);
7637: return 1;
1.136 brouard 7638: }
7639: anint[j][i]= (double) year;
7640: mint[j][i]= (double)month;
7641: strcpy(line,stra);
1.223 brouard 7642: } /* End loop on waves */
1.225 brouard 7643:
1.223 brouard 7644: /* Date of death */
1.136 brouard 7645: cutv(stra, strb,line,' ');
1.169 brouard 7646: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7647: }
1.169 brouard 7648: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 7649: month=99;
7650: year=9999;
7651: }else{
1.141 brouard 7652: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
1.225 brouard 7653: 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);
7654: return 1;
1.136 brouard 7655: }
7656: andc[i]=(double) year;
7657: moisdc[i]=(double) month;
7658: strcpy(line,stra);
7659:
1.223 brouard 7660: /* Date of birth */
1.136 brouard 7661: cutv(stra, strb,line,' ');
1.169 brouard 7662: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7663: }
1.169 brouard 7664: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 7665: month=99;
7666: year=9999;
7667: }else{
1.141 brouard 7668: 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);
7669: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.225 brouard 7670: return 1;
1.136 brouard 7671: }
7672: if (year==9999) {
1.141 brouard 7673: 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);
7674: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.225 brouard 7675: return 1;
7676:
1.136 brouard 7677: }
7678: annais[i]=(double)(year);
7679: moisnais[i]=(double)(month);
7680: strcpy(line,stra);
1.225 brouard 7681:
1.223 brouard 7682: /* Sample weight */
1.136 brouard 7683: cutv(stra, strb,line,' ');
7684: errno=0;
7685: dval=strtod(strb,&endptr);
7686: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 7687: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
7688: 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 7689: fflush(ficlog);
7690: return 1;
7691: }
7692: weight[i]=dval;
7693: strcpy(line,stra);
1.225 brouard 7694:
1.223 brouard 7695: for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */
7696: cutv(stra, strb, line, ' ');
7697: if(strb[0]=='.') { /* Missing value */
1.225 brouard 7698: lval=-1;
1.223 brouard 7699: }else{
1.225 brouard 7700: errno=0;
7701: /* what_kind_of_number(strb); */
7702: dval=strtod(strb,&endptr);
7703: /* if(strb != endptr && *endptr == '\0') */
7704: /* dval=dlval; */
7705: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
7706: if( strb[0]=='\0' || (*endptr != '\0')){
7707: 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);
7708: 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);
7709: return 1;
7710: }
7711: coqvar[iv][i]=dval;
1.226 brouard 7712: covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */
1.223 brouard 7713: }
7714: strcpy(line,stra);
7715: }/* end loop nqv */
1.136 brouard 7716:
1.223 brouard 7717: /* Covariate values */
1.136 brouard 7718: for (j=ncovcol;j>=1;j--){
7719: cutv(stra, strb,line,' ');
1.223 brouard 7720: if(strb[0]=='.') { /* Missing covariate value */
1.225 brouard 7721: lval=-1;
1.136 brouard 7722: }else{
1.225 brouard 7723: errno=0;
7724: lval=strtol(strb,&endptr,10);
7725: if( strb[0]=='\0' || (*endptr != '\0')){
7726: 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);
7727: 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);
7728: return 1;
7729: }
1.136 brouard 7730: }
7731: if(lval <-1 || lval >1){
1.225 brouard 7732: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 7733: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7734: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 7735: For example, for multinomial values like 1, 2 and 3,\n \
7736: build V1=0 V2=0 for the reference value (1),\n \
7737: V1=1 V2=0 for (2) \n \
1.136 brouard 7738: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 7739: output of IMaCh is often meaningless.\n \
1.136 brouard 7740: Exiting.\n",lval,linei, i,line,j);
1.225 brouard 7741: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 7742: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7743: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 7744: For example, for multinomial values like 1, 2 and 3,\n \
7745: build V1=0 V2=0 for the reference value (1),\n \
7746: V1=1 V2=0 for (2) \n \
1.136 brouard 7747: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 7748: output of IMaCh is often meaningless.\n \
1.136 brouard 7749: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.225 brouard 7750: return 1;
1.136 brouard 7751: }
7752: covar[j][i]=(double)(lval);
7753: strcpy(line,stra);
7754: }
7755: lstra=strlen(stra);
1.225 brouard 7756:
1.136 brouard 7757: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
7758: stratrunc = &(stra[lstra-9]);
7759: num[i]=atol(stratrunc);
7760: }
7761: else
7762: num[i]=atol(stra);
7763: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
7764: 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;}*/
7765:
7766: i=i+1;
7767: } /* End loop reading data */
1.225 brouard 7768:
1.136 brouard 7769: *imax=i-1; /* Number of individuals */
7770: fclose(fic);
1.225 brouard 7771:
1.136 brouard 7772: return (0);
1.164 brouard 7773: /* endread: */
1.225 brouard 7774: printf("Exiting readdata: ");
7775: fclose(fic);
7776: return (1);
1.223 brouard 7777: }
1.126 brouard 7778:
1.145 brouard 7779: void removespace(char *str) {
7780: char *p1 = str, *p2 = str;
7781: do
7782: while (*p2 == ' ')
7783: p2++;
1.169 brouard 7784: while (*p1++ == *p2++);
1.145 brouard 7785: }
7786:
1.224 brouard 7787: int decodemodel ( char model[], int lastobs)
7788: /**< This routine decode the model and returns:
7789: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
7790: * - nagesqr = 1 if age*age in the model, otherwise 0.
7791: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
7792: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
7793: * - cptcovage number of covariates with age*products =2
7794: * - cptcovs number of simple covariates
7795: * - 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
7796: * which is a new column after the 9 (ncovcol) variables.
7797: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
7798: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
7799: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
7800: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
7801: */
1.136 brouard 7802: {
1.145 brouard 7803: int i, j, k, ks;
1.227 brouard 7804: int j1, k1, k2, k3, k4;
1.136 brouard 7805: char modelsav[80];
1.145 brouard 7806: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 7807: char *strpt;
1.136 brouard 7808:
1.145 brouard 7809: /*removespace(model);*/
1.136 brouard 7810: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 7811: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 7812: if (strstr(model,"AGE") !=0){
1.192 brouard 7813: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
7814: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 7815: return 1;
7816: }
1.141 brouard 7817: if (strstr(model,"v") !=0){
7818: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
7819: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
7820: return 1;
7821: }
1.187 brouard 7822: strcpy(modelsav,model);
7823: if ((strpt=strstr(model,"age*age")) !=0){
7824: printf(" strpt=%s, model=%s\n",strpt, model);
7825: if(strpt != model){
1.225 brouard 7826: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 7827: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 7828: corresponding column of parameters.\n",model);
1.225 brouard 7829: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 7830: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 7831: corresponding column of parameters.\n",model); fflush(ficlog);
1.225 brouard 7832: return 1;
7833: }
1.187 brouard 7834: nagesqr=1;
7835: if (strstr(model,"+age*age") !=0)
1.225 brouard 7836: substrchaine(modelsav, model, "+age*age");
1.187 brouard 7837: else if (strstr(model,"age*age+") !=0)
1.225 brouard 7838: substrchaine(modelsav, model, "age*age+");
1.187 brouard 7839: else
1.225 brouard 7840: substrchaine(modelsav, model, "age*age");
1.187 brouard 7841: }else
7842: nagesqr=0;
7843: if (strlen(modelsav) >1){
7844: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
7845: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
1.224 brouard 7846: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2 */
1.187 brouard 7847: cptcovt= j+1; /* Number of total covariates in the model, not including
1.225 brouard 7848: * cst, age and age*age
7849: * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
7850: /* including age products which are counted in cptcovage.
7851: * but the covariates which are products must be treated
7852: * separately: ncovn=4- 2=2 (V1+V3). */
1.187 brouard 7853: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
7854: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.225 brouard 7855:
7856:
1.187 brouard 7857: /* Design
7858: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
7859: * < ncovcol=8 >
7860: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
7861: * k= 1 2 3 4 5 6 7 8
7862: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
7863: * covar[k,i], value of kth covariate if not including age for individual i:
1.224 brouard 7864: * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
7865: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
1.187 brouard 7866: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
7867: * Tage[++cptcovage]=k
7868: * if products, new covar are created after ncovcol with k1
7869: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
7870: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
7871: * 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
7872: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
7873: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
7874: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
7875: * < ncovcol=8 >
7876: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
7877: * k= 1 2 3 4 5 6 7 8 9 10 11 12
7878: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
7879: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
7880: * p Tprod[1]@2={ 6, 5}
7881: *p Tvard[1][1]@4= {7, 8, 5, 6}
7882: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
7883: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
7884: *How to reorganize?
7885: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
7886: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
7887: * {2, 1, 4, 8, 5, 6, 3, 7}
7888: * Struct []
7889: */
1.225 brouard 7890:
1.187 brouard 7891: /* This loop fills the array Tvar from the string 'model'.*/
7892: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
7893: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
7894: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
7895: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
7896: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
7897: /* k=1 Tvar[1]=2 (from V2) */
7898: /* k=5 Tvar[5] */
7899: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 7900: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 7901: /* } */
1.198 brouard 7902: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 7903: /*
7904: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
1.227 brouard 7905: for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
7906: Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
7907: }
1.187 brouard 7908: cptcovage=0;
7909: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
1.225 brouard 7910: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
7911: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
7912: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
7913: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
7914: /*scanf("%d",i);*/
7915: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
7916: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
7917: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
7918: /* covar is not filled and then is empty */
7919: cptcovprod--;
7920: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
7921: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
1.226 brouard 7922: Typevar[k]=1; /* 1 for age product */
1.225 brouard 7923: cptcovage++; /* Sums the number of covariates which include age as a product */
7924: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
7925: /*printf("stre=%s ", stre);*/
7926: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
7927: cptcovprod--;
7928: cutl(stre,strb,strc,'V');
7929: Tvar[k]=atoi(stre);
7930: Typevar[k]=1; /* 1 for age product */
7931: cptcovage++;
7932: Tage[cptcovage]=k;
7933: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
7934: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
7935: cptcovn++;
7936: cptcovprodnoage++;k1++;
7937: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
7938: Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
7939: because this model-covariate is a construction we invent a new column
7940: which is after existing variables ncovcol+nqv+ntv+nqtv + k1
7941: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
7942: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
7943: Typevar[k]=2; /* 2 for double fixed dummy covariates */
7944: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
7945: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
1.227 brouard 7946: Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
1.225 brouard 7947: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
7948: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
7949: k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
7950: /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
7951: /* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
7952: /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
7953: /* 1 2 3 4 5 | Tvar[5+1)=1, Tvar[7]=2 */
7954: for (i=1; i<=lastobs;i++){
7955: /* Computes the new covariate which is a product of
7956: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
7957: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
7958: }
7959: } /* End age is not in the model */
7960: } /* End if model includes a product */
7961: else { /* no more sum */
7962: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
7963: /* scanf("%d",i);*/
7964: cutl(strd,strc,strb,'V');
1.227 brouard 7965: ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
1.225 brouard 7966: cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
7967: Tvar[k]=atoi(strd);
7968: Typevar[k]=0; /* 0 for simple covariates */
7969: }
7970: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.223 brouard 7971: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
1.225 brouard 7972: scanf("%d",i);*/
1.187 brouard 7973: } /* end of loop + on total covariates */
7974: } /* end if strlen(modelsave == 0) age*age might exist */
7975: } /* end if strlen(model == 0) */
1.136 brouard 7976:
7977: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
7978: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
1.225 brouard 7979:
1.136 brouard 7980: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.225 brouard 7981: printf("cptcovprod=%d ", cptcovprod);
7982: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
7983: scanf("%d ",i);*/
7984:
7985:
7986: /* Decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
7987: of variable (dummy vs quantitative, fixed vs time varying) is behind */
1.226 brouard 7988: /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1 = 5 possible variables data: 2 fixed 3, varying
7989: model= V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
7990: k = 1 2 3 4 5 6 7 8 9
7991: Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5
7992: Typevar[k]= 0 0 0 2 1 0 2 1 1
1.227 brouard 7993: Fixed[k] 1 1 1 1 3 0 0 or 2 2 3
7994: Dummy[k] 1 0 0 0 3 1 1 2 3
7995: Tmodelind[combination of covar]=k;
1.225 brouard 7996: */
7997: /* Dispatching between quantitative and time varying covariates */
1.226 brouard 7998: /* If Tvar[k] >ncovcol it is a product */
1.225 brouard 7999: /* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p Vp=Vn*Vm for product */
1.226 brouard 8000: /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
1.227 brouard 8001: printf("Model=%s\n\
8002: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
8003: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
8004: Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
8005: fprintf(ficlog,"Model=%s\n\
8006: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
8007: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
8008: Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
8009:
1.225 brouard 8010: for(k=1, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
1.226 brouard 8011: if (Tvar[k] <=ncovcol && (Typevar[k]==0 || Typevar[k]==2)){ /* Simple or product fixed dummy covariatee */
1.227 brouard 8012: Fixed[k]= 0;
8013: Dummy[k]= 0;
1.225 brouard 8014: ncoveff++;
8015: }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){ /* Remind that product Vn*Vm are added in k*/
1.227 brouard 8016: Fixed[k]= 0;
8017: Dummy[k]= 1;
1.225 brouard 8018: nqfveff++; /* Only simple fixed quantitative variable */
8019: }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){
1.227 brouard 8020: Fixed[k]= 1;
8021: Dummy[k]= 0;
1.225 brouard 8022: ntveff++; /* Only simple time varying dummy variable */
1.228 brouard 8023: printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv);
8024: printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
1.227 brouard 8025: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){
8026: Fixed[k]= 1;
8027: Dummy[k]= 1;
1.228 brouard 8028: TmodelInvQind[++nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
8029: /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
8030: printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%d,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv);
8031: printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
1.227 brouard 8032: }else if (Typevar[k] == 1) { /* product with age */
8033: if (Tvar[k] <=ncovcol ){ /* Simple or product fixed dummy covariatee */
8034: Fixed[k]= 2;
8035: Dummy[k]= 2;
8036: /* ncoveff++; */
8037: }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
8038: Fixed[k]= 2;
8039: Dummy[k]= 3;
8040: /* nqfveff++; /\* Only simple fixed quantitative variable *\/ */
8041: }else if( Tvar[k] <=ncovcol+nqv+ntv ){
8042: Fixed[k]= 3;
8043: Dummy[k]= 2;
8044: /* ntveff++; /\* Only simple time varying dummy variable *\/ */
8045: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
8046: Fixed[k]= 3;
8047: Dummy[k]= 3;
8048: /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
8049: }
8050: }else if (Typevar[k] == 2) { /* product without age */
8051: k1=Tposprod[k];
8052: if(Tvard[k1][1] <=ncovcol){
8053: if(Tvard[k1][2] <=ncovcol){
8054: Fixed[k]= 1;
8055: Dummy[k]= 0;
8056: }else if(Tvard[k1][2] <=ncovcol+nqv){
8057: Fixed[k]= 0; /* or 2 ?*/
8058: Dummy[k]= 1;
8059: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
8060: Fixed[k]= 1;
8061: Dummy[k]= 0;
8062: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
8063: Fixed[k]= 1;
8064: Dummy[k]= 1;
8065: }
8066: }else if(Tvard[k1][1] <=ncovcol+nqv){
8067: if(Tvard[k1][2] <=ncovcol){
8068: Fixed[k]= 0; /* or 2 ?*/
8069: Dummy[k]= 1;
8070: }else if(Tvard[k1][2] <=ncovcol+nqv){
8071: Fixed[k]= 0; /* or 2 ?*/
8072: Dummy[k]= 1;
8073: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
8074: Fixed[k]= 1;
8075: Dummy[k]= 1;
8076: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
8077: Fixed[k]= 1;
8078: Dummy[k]= 1;
8079: }
8080: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
8081: if(Tvard[k1][2] <=ncovcol){
8082: Fixed[k]= 1;
8083: Dummy[k]= 1;
8084: }else if(Tvard[k1][2] <=ncovcol+nqv){
8085: Fixed[k]= 1;
8086: Dummy[k]= 1;
8087: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
8088: Fixed[k]= 1;
8089: Dummy[k]= 0;
8090: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
8091: Fixed[k]= 1;
8092: Dummy[k]= 1;
8093: }
8094: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
8095: if(Tvard[k1][2] <=ncovcol){
8096: Fixed[k]= 1;
8097: Dummy[k]= 1;
8098: }else if(Tvard[k1][2] <=ncovcol+nqv){
8099: Fixed[k]= 1;
8100: Dummy[k]= 1;
8101: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
8102: Fixed[k]= 1;
8103: Dummy[k]= 1;
8104: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
8105: Fixed[k]= 1;
8106: Dummy[k]= 1;
8107: }
8108: }else{
8109: printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
8110: fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
1.226 brouard 8111: } /* end k1 */
1.225 brouard 8112: }else{
1.226 brouard 8113: printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
8114: fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
1.225 brouard 8115: }
1.227 brouard 8116: printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
8117: fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
8118: }
8119: /* Searching for doublons in the model */
8120: for(k1=1; k1<= cptcovt;k1++){
8121: for(k2=1; k2 <k1;k2++){
8122: if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){
8123: if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
8124: if(Tvar[k1]==Tvar[k2]){
8125: printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
8126: fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
8127: return(1);
8128: }
8129: }else if (Typevar[k1] ==2){
8130: k3=Tposprod[k1];
8131: k4=Tposprod[k2];
8132: if( ((Tvard[k3][1]== Tvard[k4][1])&&(Tvard[k3][2]== Tvard[k4][2])) || ((Tvard[k3][1]== Tvard[k4][2])&&(Tvard[k3][2]== Tvard[k4][1])) ){
8133: printf("Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
8134: fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
8135: return(1);
8136: }
8137: }
8138: }
8139: }
1.225 brouard 8140: }
8141: printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
8142: fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
1.137 brouard 8143: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 8144: /*endread:*/
1.225 brouard 8145: printf("Exiting decodemodel: ");
8146: return (1);
1.136 brouard 8147: }
8148:
1.169 brouard 8149: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 8150: {
8151: int i, m;
1.218 brouard 8152: int firstone=0;
8153:
1.136 brouard 8154: for (i=1; i<=imx; i++) {
8155: for(m=2; (m<= maxwav); m++) {
8156: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
8157: anint[m][i]=9999;
1.216 brouard 8158: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
8159: s[m][i]=-1;
1.136 brouard 8160: }
8161: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 8162: *nberr = *nberr + 1;
1.218 brouard 8163: if(firstone == 0){
8164: firstone=1;
8165: 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);
8166: }
8167: 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 8168: s[m][i]=-1;
8169: }
8170: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 8171: (*nberr)++;
1.136 brouard 8172: 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]);
8173: 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]);
8174: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
8175: }
8176: }
8177: }
8178:
8179: for (i=1; i<=imx; i++) {
8180: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
8181: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 8182: 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 8183: if (s[m][i] >= nlstate+1) {
1.169 brouard 8184: if(agedc[i]>0){
8185: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 8186: agev[m][i]=agedc[i];
1.214 brouard 8187: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 8188: }else {
1.136 brouard 8189: if ((int)andc[i]!=9999){
8190: nbwarn++;
8191: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
8192: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
8193: agev[m][i]=-1;
8194: }
8195: }
1.169 brouard 8196: } /* agedc > 0 */
1.214 brouard 8197: } /* end if */
1.136 brouard 8198: else if(s[m][i] !=9){ /* Standard case, age in fractional
8199: years but with the precision of a month */
8200: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
8201: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
8202: agev[m][i]=1;
8203: else if(agev[m][i] < *agemin){
8204: *agemin=agev[m][i];
8205: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
8206: }
8207: else if(agev[m][i] >*agemax){
8208: *agemax=agev[m][i];
1.156 brouard 8209: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 8210: }
8211: /*agev[m][i]=anint[m][i]-annais[i];*/
8212: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 8213: } /* en if 9*/
1.136 brouard 8214: else { /* =9 */
1.214 brouard 8215: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 8216: agev[m][i]=1;
8217: s[m][i]=-1;
8218: }
8219: }
1.214 brouard 8220: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 8221: agev[m][i]=1;
1.214 brouard 8222: else{
8223: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
8224: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
8225: agev[m][i]=0;
8226: }
8227: } /* End for lastpass */
8228: }
1.136 brouard 8229:
8230: for (i=1; i<=imx; i++) {
8231: for(m=firstpass; (m<=lastpass); m++){
8232: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 8233: (*nberr)++;
1.136 brouard 8234: 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);
8235: 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);
8236: return 1;
8237: }
8238: }
8239: }
8240:
8241: /*for (i=1; i<=imx; i++){
8242: for (m=firstpass; (m<lastpass); m++){
8243: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
8244: }
8245:
8246: }*/
8247:
8248:
1.139 brouard 8249: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
8250: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 8251:
8252: return (0);
1.164 brouard 8253: /* endread:*/
1.136 brouard 8254: printf("Exiting calandcheckages: ");
8255: return (1);
8256: }
8257:
1.172 brouard 8258: #if defined(_MSC_VER)
8259: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
8260: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
8261: //#include "stdafx.h"
8262: //#include <stdio.h>
8263: //#include <tchar.h>
8264: //#include <windows.h>
8265: //#include <iostream>
8266: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
8267:
8268: LPFN_ISWOW64PROCESS fnIsWow64Process;
8269:
8270: BOOL IsWow64()
8271: {
8272: BOOL bIsWow64 = FALSE;
8273:
8274: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
8275: // (HANDLE, PBOOL);
8276:
8277: //LPFN_ISWOW64PROCESS fnIsWow64Process;
8278:
8279: HMODULE module = GetModuleHandle(_T("kernel32"));
8280: const char funcName[] = "IsWow64Process";
8281: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
8282: GetProcAddress(module, funcName);
8283:
8284: if (NULL != fnIsWow64Process)
8285: {
8286: if (!fnIsWow64Process(GetCurrentProcess(),
8287: &bIsWow64))
8288: //throw std::exception("Unknown error");
8289: printf("Unknown error\n");
8290: }
8291: return bIsWow64 != FALSE;
8292: }
8293: #endif
1.177 brouard 8294:
1.191 brouard 8295: void syscompilerinfo(int logged)
1.167 brouard 8296: {
8297: /* #include "syscompilerinfo.h"*/
1.185 brouard 8298: /* command line Intel compiler 32bit windows, XP compatible:*/
8299: /* /GS /W3 /Gy
8300: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
8301: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
8302: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 8303: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
8304: */
8305: /* 64 bits */
1.185 brouard 8306: /*
8307: /GS /W3 /Gy
8308: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
8309: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
8310: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
8311: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
8312: /* Optimization are useless and O3 is slower than O2 */
8313: /*
8314: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
8315: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
8316: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
8317: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
8318: */
1.186 brouard 8319: /* Link is */ /* /OUT:"visual studio
1.185 brouard 8320: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
8321: /PDB:"visual studio
8322: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
8323: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
8324: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
8325: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
8326: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
8327: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
8328: uiAccess='false'"
8329: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
8330: /NOLOGO /TLBID:1
8331: */
1.177 brouard 8332: #if defined __INTEL_COMPILER
1.178 brouard 8333: #if defined(__GNUC__)
8334: struct utsname sysInfo; /* For Intel on Linux and OS/X */
8335: #endif
1.177 brouard 8336: #elif defined(__GNUC__)
1.179 brouard 8337: #ifndef __APPLE__
1.174 brouard 8338: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 8339: #endif
1.177 brouard 8340: struct utsname sysInfo;
1.178 brouard 8341: int cross = CROSS;
8342: if (cross){
8343: printf("Cross-");
1.191 brouard 8344: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 8345: }
1.174 brouard 8346: #endif
8347:
1.171 brouard 8348: #include <stdint.h>
1.178 brouard 8349:
1.191 brouard 8350: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 8351: #if defined(__clang__)
1.191 brouard 8352: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 8353: #endif
8354: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 8355: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 8356: #endif
8357: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 8358: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 8359: #endif
8360: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 8361: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 8362: #endif
8363: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 8364: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 8365: #endif
8366: #if defined(_MSC_VER)
1.191 brouard 8367: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 8368: #endif
8369: #if defined(__PGI)
1.191 brouard 8370: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 8371: #endif
8372: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 8373: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 8374: #endif
1.191 brouard 8375: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 8376:
1.167 brouard 8377: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
8378: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
8379: // Windows (x64 and x86)
1.191 brouard 8380: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 8381: #elif __unix__ // all unices, not all compilers
8382: // Unix
1.191 brouard 8383: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 8384: #elif __linux__
8385: // linux
1.191 brouard 8386: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 8387: #elif __APPLE__
1.174 brouard 8388: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 8389: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 8390: #endif
8391:
8392: /* __MINGW32__ */
8393: /* __CYGWIN__ */
8394: /* __MINGW64__ */
8395: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
8396: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
8397: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
8398: /* _WIN64 // Defined for applications for Win64. */
8399: /* _M_X64 // Defined for compilations that target x64 processors. */
8400: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 8401:
1.167 brouard 8402: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 8403: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 8404: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 8405: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 8406: #else
1.191 brouard 8407: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 8408: #endif
8409:
1.169 brouard 8410: #if defined(__GNUC__)
8411: # if defined(__GNUC_PATCHLEVEL__)
8412: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
8413: + __GNUC_MINOR__ * 100 \
8414: + __GNUC_PATCHLEVEL__)
8415: # else
8416: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
8417: + __GNUC_MINOR__ * 100)
8418: # endif
1.174 brouard 8419: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 8420: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 8421:
8422: if (uname(&sysInfo) != -1) {
8423: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 8424: 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 8425: }
8426: else
8427: perror("uname() error");
1.179 brouard 8428: //#ifndef __INTEL_COMPILER
8429: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 8430: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 8431: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 8432: #endif
1.169 brouard 8433: #endif
1.172 brouard 8434:
8435: // void main()
8436: // {
1.169 brouard 8437: #if defined(_MSC_VER)
1.174 brouard 8438: if (IsWow64()){
1.191 brouard 8439: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
8440: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 8441: }
8442: else{
1.191 brouard 8443: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
8444: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 8445: }
1.172 brouard 8446: // printf("\nPress Enter to continue...");
8447: // getchar();
8448: // }
8449:
1.169 brouard 8450: #endif
8451:
1.167 brouard 8452:
1.219 brouard 8453: }
1.136 brouard 8454:
1.219 brouard 8455: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.180 brouard 8456: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
8457: int i, j, k, i1 ;
1.202 brouard 8458: /* double ftolpl = 1.e-10; */
1.180 brouard 8459: double age, agebase, agelim;
1.203 brouard 8460: double tot;
1.180 brouard 8461:
1.202 brouard 8462: strcpy(filerespl,"PL_");
8463: strcat(filerespl,fileresu);
8464: if((ficrespl=fopen(filerespl,"w"))==NULL) {
8465: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
8466: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
8467: }
1.227 brouard 8468: printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
8469: fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
1.202 brouard 8470: pstamp(ficrespl);
1.203 brouard 8471: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 8472: fprintf(ficrespl,"#Age ");
8473: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
8474: fprintf(ficrespl,"\n");
1.180 brouard 8475:
1.219 brouard 8476: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180 brouard 8477:
1.219 brouard 8478: agebase=ageminpar;
8479: agelim=agemaxpar;
1.180 brouard 8480:
1.227 brouard 8481: /* i1=pow(2,ncoveff); */
8482: i1=pow(2,cptcoveff); /* Number of dummy covariates */
1.219 brouard 8483: if (cptcovn < 1){i1=1;}
1.180 brouard 8484:
1.220 brouard 8485: for(k=1; k<=i1;k++){
8486: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
1.180 brouard 8487: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
1.219 brouard 8488: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.220 brouard 8489: /* k=k+1; */
1.219 brouard 8490: /* to clean */
8491: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
8492: fprintf(ficrespl,"#******");
8493: printf("#******");
8494: fprintf(ficlog,"#******");
1.227 brouard 8495: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
8496: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
1.219 brouard 8497: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8498: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8499: }
8500: fprintf(ficrespl,"******\n");
8501: printf("******\n");
8502: fprintf(ficlog,"******\n");
1.227 brouard 8503: if(invalidvarcomb[k]){
8504: printf("\nCombination (%d) ignored because no case \n",k);
8505: fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
8506: fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
1.220 brouard 8507: continue;
1.227 brouard 8508: }
1.219 brouard 8509:
8510: fprintf(ficrespl,"#Age ");
1.227 brouard 8511: for(j=1;j<=cptcoveff;j++) {
1.219 brouard 8512: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8513: }
8514: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
8515: fprintf(ficrespl,"Total Years_to_converge\n");
1.227 brouard 8516:
1.219 brouard 8517: for (age=agebase; age<=agelim; age++){
8518: /* for (age=agebase; age<=agebase; age++){ */
8519: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
8520: fprintf(ficrespl,"%.0f ",age );
1.227 brouard 8521: for(j=1;j<=cptcoveff;j++)
8522: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.219 brouard 8523: tot=0.;
8524: for(i=1; i<=nlstate;i++){
1.227 brouard 8525: tot += prlim[i][i];
8526: fprintf(ficrespl," %.5f", prlim[i][i]);
1.219 brouard 8527: }
8528: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
8529: } /* Age */
8530: /* was end of cptcod */
8531: } /* cptcov */
8532: return 0;
1.180 brouard 8533: }
8534:
1.218 brouard 8535: 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){
8536: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
8537:
8538: /* Computes the back prevalence limit for any combination of covariate values
8539: * at any age between ageminpar and agemaxpar
8540: */
1.217 brouard 8541: int i, j, k, i1 ;
8542: /* double ftolpl = 1.e-10; */
8543: double age, agebase, agelim;
8544: double tot;
1.218 brouard 8545: /* double ***mobaverage; */
8546: /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
1.217 brouard 8547:
8548: strcpy(fileresplb,"PLB_");
8549: strcat(fileresplb,fileresu);
8550: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
8551: printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
8552: fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
8553: }
8554: printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
8555: fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
8556: pstamp(ficresplb);
8557: fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
8558: fprintf(ficresplb,"#Age ");
8559: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
8560: fprintf(ficresplb,"\n");
8561:
1.218 brouard 8562:
8563: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
8564:
8565: agebase=ageminpar;
8566: agelim=agemaxpar;
8567:
8568:
1.227 brouard 8569: i1=pow(2,cptcoveff);
1.218 brouard 8570: if (cptcovn < 1){i1=1;}
1.227 brouard 8571:
8572: for(k=1; k<=i1;k++){
1.218 brouard 8573: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
8574: fprintf(ficresplb,"#******");
8575: printf("#******");
8576: fprintf(ficlog,"#******");
1.227 brouard 8577: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
1.218 brouard 8578: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8579: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8580: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8581: }
8582: fprintf(ficresplb,"******\n");
8583: printf("******\n");
8584: fprintf(ficlog,"******\n");
1.227 brouard 8585: if(invalidvarcomb[k]){
8586: printf("\nCombination (%d) ignored because no cases \n",k);
8587: fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
8588: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
8589: continue;
8590: }
1.218 brouard 8591:
8592: fprintf(ficresplb,"#Age ");
1.227 brouard 8593: for(j=1;j<=cptcoveff;j++) {
1.218 brouard 8594: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8595: }
8596: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
8597: fprintf(ficresplb,"Total Years_to_converge\n");
8598:
8599:
8600: for (age=agebase; age<=agelim; age++){
8601: /* for (age=agebase; age<=agebase; age++){ */
8602: if(mobilavproj > 0){
8603: /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
8604: /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.227 brouard 8605: bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);
1.218 brouard 8606: }else if (mobilavproj == 0){
1.227 brouard 8607: 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);
8608: 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);
8609: exit(1);
1.218 brouard 8610: }else{
1.227 brouard 8611: /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
8612: bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);
1.218 brouard 8613: }
8614: fprintf(ficresplb,"%.0f ",age );
1.227 brouard 8615: for(j=1;j<=cptcoveff;j++)
8616: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.218 brouard 8617: tot=0.;
8618: for(i=1; i<=nlstate;i++){
1.227 brouard 8619: tot += bprlim[i][i];
8620: fprintf(ficresplb," %.5f", bprlim[i][i]);
1.218 brouard 8621: }
8622: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
8623: } /* Age */
8624: /* was end of cptcod */
8625: } /* cptcov */
8626:
8627: /* hBijx(p, bage, fage); */
8628: /* fclose(ficrespijb); */
8629:
8630: return 0;
1.217 brouard 8631: }
1.218 brouard 8632:
1.180 brouard 8633: int hPijx(double *p, int bage, int fage){
8634: /*------------- h Pij x at various ages ------------*/
8635:
8636: int stepsize;
8637: int agelim;
8638: int hstepm;
8639: int nhstepm;
8640: int h, i, i1, j, k;
8641:
8642: double agedeb;
8643: double ***p3mat;
8644:
1.201 brouard 8645: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 8646: if((ficrespij=fopen(filerespij,"w"))==NULL) {
8647: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
8648: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
8649: }
8650: printf("Computing pij: result on file '%s' \n", filerespij);
8651: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
8652:
8653: stepsize=(int) (stepm+YEARM-1)/YEARM;
8654: /*if (stepm<=24) stepsize=2;*/
8655:
8656: agelim=AGESUP;
8657: hstepm=stepsize*YEARM; /* Every year of age */
8658: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.218 brouard 8659:
1.180 brouard 8660: /* hstepm=1; aff par mois*/
8661: pstamp(ficrespij);
8662: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.227 brouard 8663: i1= pow(2,cptcoveff);
1.218 brouard 8664: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
8665: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
8666: /* k=k+1; */
1.227 brouard 8667: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.183 brouard 8668: fprintf(ficrespij,"\n#****** ");
1.227 brouard 8669: for(j=1;j<=cptcoveff;j++)
1.198 brouard 8670: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.183 brouard 8671: fprintf(ficrespij,"******\n");
8672:
8673: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
8674: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
8675: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
8676:
8677: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 8678:
1.183 brouard 8679: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8680: oldm=oldms;savm=savms;
8681: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
8682: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
8683: for(i=1; i<=nlstate;i++)
8684: for(j=1; j<=nlstate+ndeath;j++)
8685: fprintf(ficrespij," %1d-%1d",i,j);
8686: fprintf(ficrespij,"\n");
8687: for (h=0; h<=nhstepm; h++){
8688: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
8689: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 8690: for(i=1; i<=nlstate;i++)
8691: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 8692: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 8693: fprintf(ficrespij,"\n");
8694: }
1.183 brouard 8695: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8696: fprintf(ficrespij,"\n");
8697: }
1.180 brouard 8698: /*}*/
8699: }
1.218 brouard 8700: return 0;
1.180 brouard 8701: }
1.218 brouard 8702:
8703: int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217 brouard 8704: /*------------- h Bij x at various ages ------------*/
8705:
8706: int stepsize;
1.218 brouard 8707: /* int agelim; */
8708: int ageminl;
1.217 brouard 8709: int hstepm;
8710: int nhstepm;
8711: int h, i, i1, j, k;
1.218 brouard 8712:
1.217 brouard 8713: double agedeb;
8714: double ***p3mat;
1.218 brouard 8715:
8716: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
8717: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
8718: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
8719: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
8720: }
8721: printf("Computing pij back: result on file '%s' \n", filerespijb);
8722: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
8723:
8724: stepsize=(int) (stepm+YEARM-1)/YEARM;
8725: /*if (stepm<=24) stepsize=2;*/
1.217 brouard 8726:
1.218 brouard 8727: /* agelim=AGESUP; */
8728: ageminl=30;
8729: hstepm=stepsize*YEARM; /* Every year of age */
8730: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
8731:
8732: /* hstepm=1; aff par mois*/
8733: pstamp(ficrespijb);
8734: fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");
1.227 brouard 8735: i1= pow(2,cptcoveff);
1.218 brouard 8736: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
8737: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
8738: /* k=k+1; */
1.227 brouard 8739: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.218 brouard 8740: fprintf(ficrespijb,"\n#****** ");
1.227 brouard 8741: for(j=1;j<=cptcoveff;j++)
1.218 brouard 8742: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8743: fprintf(ficrespijb,"******\n");
1.222 brouard 8744: if(invalidvarcomb[k]){
8745: fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
8746: continue;
8747: }
1.218 brouard 8748:
8749: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
8750: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
8751: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
8752: nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
8753: nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
8754:
8755: /* nhstepm=nhstepm*YEARM; aff par mois*/
8756:
8757: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8758: /* oldm=oldms;savm=savms; */
8759: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
8760: hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
8761: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
8762: fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
8763: for(i=1; i<=nlstate;i++)
8764: for(j=1; j<=nlstate+ndeath;j++)
8765: fprintf(ficrespijb," %1d-%1d",i,j);
8766: fprintf(ficrespijb,"\n");
8767: for (h=0; h<=nhstepm; h++){
8768: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
8769: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
8770: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
1.217 brouard 8771: for(i=1; i<=nlstate;i++)
8772: for(j=1; j<=nlstate+ndeath;j++)
1.218 brouard 8773: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
1.217 brouard 8774: fprintf(ficrespijb,"\n");
8775: }
1.218 brouard 8776: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8777: fprintf(ficrespijb,"\n");
1.217 brouard 8778: }
1.218 brouard 8779: /*}*/
8780: }
8781: return 0;
8782: } /* hBijx */
1.217 brouard 8783:
1.180 brouard 8784:
1.136 brouard 8785: /***********************************************/
8786: /**************** Main Program *****************/
8787: /***********************************************/
8788:
8789: int main(int argc, char *argv[])
8790: {
8791: #ifdef GSL
8792: const gsl_multimin_fminimizer_type *T;
8793: size_t iteri = 0, it;
8794: int rval = GSL_CONTINUE;
8795: int status = GSL_SUCCESS;
8796: double ssval;
8797: #endif
8798: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 8799: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.209 brouard 8800: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 8801: int jj, ll, li, lj, lk;
1.136 brouard 8802: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 8803: int num_filled;
1.136 brouard 8804: int itimes;
8805: int NDIM=2;
8806: int vpopbased=0;
8807:
1.164 brouard 8808: char ca[32], cb[32];
1.136 brouard 8809: /* FILE *fichtm; *//* Html File */
8810: /* FILE *ficgp;*/ /*Gnuplot File */
8811: struct stat info;
1.191 brouard 8812: double agedeb=0.;
1.194 brouard 8813:
8814: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219 brouard 8815: double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136 brouard 8816:
1.165 brouard 8817: double fret;
1.191 brouard 8818: double dum=0.; /* Dummy variable */
1.136 brouard 8819: double ***p3mat;
1.218 brouard 8820: /* double ***mobaverage; */
1.164 brouard 8821:
8822: char line[MAXLINE];
1.197 brouard 8823: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
8824:
8825: char model[MAXLINE], modeltemp[MAXLINE];
1.136 brouard 8826: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 8827: char *tok, *val; /* pathtot */
1.136 brouard 8828: int firstobs=1, lastobs=10;
1.195 brouard 8829: int c, h , cpt, c2;
1.191 brouard 8830: int jl=0;
8831: int i1, j1, jk, stepsize=0;
1.194 brouard 8832: int count=0;
8833:
1.164 brouard 8834: int *tab;
1.136 brouard 8835: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.217 brouard 8836: int backcast=0;
1.136 brouard 8837: int mobilav=0,popforecast=0;
1.191 brouard 8838: int hstepm=0, nhstepm=0;
1.136 brouard 8839: int agemortsup;
8840: float sumlpop=0.;
8841: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
8842: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
8843:
1.191 brouard 8844: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 8845: double ftolpl=FTOL;
8846: double **prlim;
1.217 brouard 8847: double **bprlim;
1.136 brouard 8848: double ***param; /* Matrix of parameters */
8849: double *p;
8850: double **matcov; /* Matrix of covariance */
1.203 brouard 8851: double **hess; /* Hessian matrix */
1.136 brouard 8852: double ***delti3; /* Scale */
8853: double *delti; /* Scale */
8854: double ***eij, ***vareij;
8855: double **varpl; /* Variances of prevalence limits by age */
8856: double *epj, vepp;
1.164 brouard 8857:
1.136 brouard 8858: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.217 brouard 8859: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;
8860:
1.136 brouard 8861: double **ximort;
1.145 brouard 8862: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 8863: int *dcwave;
8864:
1.164 brouard 8865: char z[1]="c";
1.136 brouard 8866:
8867: /*char *strt;*/
8868: char strtend[80];
1.126 brouard 8869:
1.164 brouard 8870:
1.126 brouard 8871: /* setlocale (LC_ALL, ""); */
8872: /* bindtextdomain (PACKAGE, LOCALEDIR); */
8873: /* textdomain (PACKAGE); */
8874: /* setlocale (LC_CTYPE, ""); */
8875: /* setlocale (LC_MESSAGES, ""); */
8876:
8877: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 8878: rstart_time = time(NULL);
8879: /* (void) gettimeofday(&start_time,&tzp);*/
8880: start_time = *localtime(&rstart_time);
1.126 brouard 8881: curr_time=start_time;
1.157 brouard 8882: /*tml = *localtime(&start_time.tm_sec);*/
8883: /* strcpy(strstart,asctime(&tml)); */
8884: strcpy(strstart,asctime(&start_time));
1.126 brouard 8885:
8886: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 8887: /* tp.tm_sec = tp.tm_sec +86400; */
8888: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 8889: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
8890: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
8891: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 8892: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 8893: /* strt=asctime(&tmg); */
8894: /* printf("Time(after) =%s",strstart); */
8895: /* (void) time (&time_value);
8896: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
8897: * tm = *localtime(&time_value);
8898: * strstart=asctime(&tm);
8899: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
8900: */
8901:
8902: nberr=0; /* Number of errors and warnings */
8903: nbwarn=0;
1.184 brouard 8904: #ifdef WIN32
8905: _getcwd(pathcd, size);
8906: #else
1.126 brouard 8907: getcwd(pathcd, size);
1.184 brouard 8908: #endif
1.191 brouard 8909: syscompilerinfo(0);
1.196 brouard 8910: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 8911: if(argc <=1){
8912: printf("\nEnter the parameter file name: ");
1.205 brouard 8913: if(!fgets(pathr,FILENAMELENGTH,stdin)){
8914: printf("ERROR Empty parameter file name\n");
8915: goto end;
8916: }
1.126 brouard 8917: i=strlen(pathr);
8918: if(pathr[i-1]=='\n')
8919: pathr[i-1]='\0';
1.156 brouard 8920: i=strlen(pathr);
1.205 brouard 8921: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 8922: pathr[i-1]='\0';
1.205 brouard 8923: }
8924: i=strlen(pathr);
8925: if( i==0 ){
8926: printf("ERROR Empty parameter file name\n");
8927: goto end;
8928: }
8929: for (tok = pathr; tok != NULL; ){
1.126 brouard 8930: printf("Pathr |%s|\n",pathr);
8931: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
8932: printf("val= |%s| pathr=%s\n",val,pathr);
8933: strcpy (pathtot, val);
8934: if(pathr[0] == '\0') break; /* Dirty */
8935: }
8936: }
8937: else{
8938: strcpy(pathtot,argv[1]);
8939: }
8940: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
8941: /*cygwin_split_path(pathtot,path,optionfile);
8942: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
8943: /* cutv(path,optionfile,pathtot,'\\');*/
8944:
8945: /* Split argv[0], imach program to get pathimach */
8946: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
8947: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
8948: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
8949: /* strcpy(pathimach,argv[0]); */
8950: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
8951: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
8952: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 8953: #ifdef WIN32
8954: _chdir(path); /* Can be a relative path */
8955: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
8956: #else
1.126 brouard 8957: chdir(path); /* Can be a relative path */
1.184 brouard 8958: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
8959: #endif
8960: printf("Current directory %s!\n",pathcd);
1.126 brouard 8961: strcpy(command,"mkdir ");
8962: strcat(command,optionfilefiname);
8963: if((outcmd=system(command)) != 0){
1.169 brouard 8964: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 8965: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
8966: /* fclose(ficlog); */
8967: /* exit(1); */
8968: }
8969: /* if((imk=mkdir(optionfilefiname))<0){ */
8970: /* perror("mkdir"); */
8971: /* } */
8972:
8973: /*-------- arguments in the command line --------*/
8974:
1.186 brouard 8975: /* Main Log file */
1.126 brouard 8976: strcat(filelog, optionfilefiname);
8977: strcat(filelog,".log"); /* */
8978: if((ficlog=fopen(filelog,"w"))==NULL) {
8979: printf("Problem with logfile %s\n",filelog);
8980: goto end;
8981: }
8982: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 8983: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 8984: fprintf(ficlog,"\nEnter the parameter file name: \n");
8985: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
8986: path=%s \n\
8987: optionfile=%s\n\
8988: optionfilext=%s\n\
1.156 brouard 8989: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 8990:
1.197 brouard 8991: syscompilerinfo(1);
1.167 brouard 8992:
1.126 brouard 8993: printf("Local time (at start):%s",strstart);
8994: fprintf(ficlog,"Local time (at start): %s",strstart);
8995: fflush(ficlog);
8996: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 8997: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 8998:
8999: /* */
9000: strcpy(fileres,"r");
9001: strcat(fileres, optionfilefiname);
1.201 brouard 9002: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 9003: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 9004: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 9005:
1.186 brouard 9006: /* Main ---------arguments file --------*/
1.126 brouard 9007:
9008: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 9009: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
9010: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 9011: fflush(ficlog);
1.149 brouard 9012: /* goto end; */
9013: exit(70);
1.126 brouard 9014: }
9015:
9016:
9017:
9018: strcpy(filereso,"o");
1.201 brouard 9019: strcat(filereso,fileresu);
1.126 brouard 9020: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
9021: printf("Problem with Output resultfile: %s\n", filereso);
9022: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
9023: fflush(ficlog);
9024: goto end;
9025: }
9026:
9027: /* Reads comments: lines beginning with '#' */
9028: numlinepar=0;
1.197 brouard 9029:
9030: /* First parameter line */
9031: while(fgets(line, MAXLINE, ficpar)) {
9032: /* If line starts with a # it is a comment */
9033: if (line[0] == '#') {
9034: numlinepar++;
9035: fputs(line,stdout);
9036: fputs(line,ficparo);
9037: fputs(line,ficlog);
9038: continue;
9039: }else
9040: break;
9041: }
9042: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
9043: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
9044: if (num_filled != 5) {
9045: printf("Should be 5 parameters\n");
9046: }
1.126 brouard 9047: numlinepar++;
1.197 brouard 9048: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
9049: }
9050: /* Second parameter line */
9051: while(fgets(line, MAXLINE, ficpar)) {
9052: /* If line starts with a # it is a comment */
9053: if (line[0] == '#') {
9054: numlinepar++;
9055: fputs(line,stdout);
9056: fputs(line,ficparo);
9057: fputs(line,ficlog);
9058: continue;
9059: }else
9060: break;
9061: }
1.223 brouard 9062: 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", \
9063: &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
9064: if (num_filled != 11) {
9065: 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 9066: printf("but line=%s\n",line);
1.197 brouard 9067: }
1.223 brouard 9068: 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 9069: }
1.203 brouard 9070: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 9071: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 9072: /* Third parameter line */
9073: while(fgets(line, MAXLINE, ficpar)) {
9074: /* If line starts with a # it is a comment */
9075: if (line[0] == '#') {
9076: numlinepar++;
9077: fputs(line,stdout);
9078: fputs(line,ficparo);
9079: fputs(line,ficlog);
9080: continue;
9081: }else
9082: break;
9083: }
1.201 brouard 9084: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
9085: if (num_filled == 0)
9086: model[0]='\0';
9087: else if (num_filled != 1){
1.197 brouard 9088: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
9089: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
9090: model[0]='\0';
9091: goto end;
9092: }
9093: else{
9094: if (model[0]=='+'){
9095: for(i=1; i<=strlen(model);i++)
9096: modeltemp[i-1]=model[i];
1.201 brouard 9097: strcpy(model,modeltemp);
1.197 brouard 9098: }
9099: }
1.199 brouard 9100: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 9101: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 9102: }
9103: /* 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); */
9104: /* numlinepar=numlinepar+3; /\* In general *\/ */
9105: /* 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 9106: 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);
9107: 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 9108: fflush(ficlog);
1.190 brouard 9109: /* if(model[0]=='#'|| model[0]== '\0'){ */
9110: if(model[0]=='#'){
1.187 brouard 9111: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
9112: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
9113: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
9114: if(mle != -1){
9115: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
9116: exit(1);
9117: }
9118: }
1.126 brouard 9119: while((c=getc(ficpar))=='#' && c!= EOF){
9120: ungetc(c,ficpar);
9121: fgets(line, MAXLINE, ficpar);
9122: numlinepar++;
1.195 brouard 9123: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
9124: z[0]=line[1];
9125: }
9126: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 9127: fputs(line, stdout);
9128: //puts(line);
1.126 brouard 9129: fputs(line,ficparo);
9130: fputs(line,ficlog);
9131: }
9132: ungetc(c,ficpar);
9133:
9134:
1.145 brouard 9135: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.225 brouard 9136: coqvar=matrix(1,nqv,1,n); /**< Fixed quantitative covariate */
9137: cotvar=ma3x(1,maxwav,1,ntv,1,n); /**< Time varying covariate */
9138: cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /**< Time varying quantitative covariate */
1.136 brouard 9139: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
9140: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
9141: v1+v2*age+v2*v3 makes cptcovn = 3
9142: */
9143: if (strlen(model)>1)
1.187 brouard 9144: 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 9145: else
1.187 brouard 9146: ncovmodel=2; /* Constant and age */
1.133 brouard 9147: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
9148: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 9149: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
9150: 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);
9151: 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);
9152: fflush(stdout);
9153: fclose (ficlog);
9154: goto end;
9155: }
1.126 brouard 9156: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
9157: delti=delti3[1][1];
9158: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
9159: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
9160: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 9161: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
9162: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 9163: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
9164: fclose (ficparo);
9165: fclose (ficlog);
9166: goto end;
9167: exit(0);
1.220 brouard 9168: } else if(mle==-5) { /* Main Wizard */
1.126 brouard 9169: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 9170: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
9171: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 9172: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
9173: matcov=matrix(1,npar,1,npar);
1.203 brouard 9174: hess=matrix(1,npar,1,npar);
1.220 brouard 9175: } else{ /* Begin of mle != -1 or -5 */
1.145 brouard 9176: /* Read guessed parameters */
1.126 brouard 9177: /* Reads comments: lines beginning with '#' */
9178: while((c=getc(ficpar))=='#' && c!= EOF){
9179: ungetc(c,ficpar);
9180: fgets(line, MAXLINE, ficpar);
9181: numlinepar++;
1.141 brouard 9182: fputs(line,stdout);
1.126 brouard 9183: fputs(line,ficparo);
9184: fputs(line,ficlog);
9185: }
9186: ungetc(c,ficpar);
9187:
9188: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
9189: for(i=1; i <=nlstate; i++){
1.220 brouard 9190: j=0;
1.126 brouard 9191: for(jj=1; jj <=nlstate+ndeath; jj++){
1.220 brouard 9192: if(jj==i) continue;
9193: j++;
9194: fscanf(ficpar,"%1d%1d",&i1,&j1);
9195: if ((i1 != i) || (j1 != jj)){
9196: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126 brouard 9197: It might be a problem of design; if ncovcol and the model are correct\n \
9198: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.220 brouard 9199: exit(1);
9200: }
9201: fprintf(ficparo,"%1d%1d",i1,j1);
9202: if(mle==1)
9203: printf("%1d%1d",i,jj);
9204: fprintf(ficlog,"%1d%1d",i,jj);
9205: for(k=1; k<=ncovmodel;k++){
9206: fscanf(ficpar," %lf",¶m[i][j][k]);
9207: if(mle==1){
9208: printf(" %lf",param[i][j][k]);
9209: fprintf(ficlog," %lf",param[i][j][k]);
9210: }
9211: else
9212: fprintf(ficlog," %lf",param[i][j][k]);
9213: fprintf(ficparo," %lf",param[i][j][k]);
9214: }
9215: fscanf(ficpar,"\n");
9216: numlinepar++;
9217: if(mle==1)
9218: printf("\n");
9219: fprintf(ficlog,"\n");
9220: fprintf(ficparo,"\n");
1.126 brouard 9221: }
9222: }
9223: fflush(ficlog);
9224:
1.145 brouard 9225: /* Reads scales values */
1.126 brouard 9226: p=param[1][1];
9227:
9228: /* Reads comments: lines beginning with '#' */
9229: while((c=getc(ficpar))=='#' && c!= EOF){
9230: ungetc(c,ficpar);
9231: fgets(line, MAXLINE, ficpar);
9232: numlinepar++;
1.141 brouard 9233: fputs(line,stdout);
1.126 brouard 9234: fputs(line,ficparo);
9235: fputs(line,ficlog);
9236: }
9237: ungetc(c,ficpar);
9238:
9239: for(i=1; i <=nlstate; i++){
9240: for(j=1; j <=nlstate+ndeath-1; j++){
1.220 brouard 9241: fscanf(ficpar,"%1d%1d",&i1,&j1);
9242: if ( (i1-i) * (j1-j) != 0){
9243: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
9244: exit(1);
9245: }
9246: printf("%1d%1d",i,j);
9247: fprintf(ficparo,"%1d%1d",i1,j1);
9248: fprintf(ficlog,"%1d%1d",i1,j1);
9249: for(k=1; k<=ncovmodel;k++){
9250: fscanf(ficpar,"%le",&delti3[i][j][k]);
9251: printf(" %le",delti3[i][j][k]);
9252: fprintf(ficparo," %le",delti3[i][j][k]);
9253: fprintf(ficlog," %le",delti3[i][j][k]);
9254: }
9255: fscanf(ficpar,"\n");
9256: numlinepar++;
9257: printf("\n");
9258: fprintf(ficparo,"\n");
9259: fprintf(ficlog,"\n");
1.126 brouard 9260: }
9261: }
9262: fflush(ficlog);
1.220 brouard 9263:
1.145 brouard 9264: /* Reads covariance matrix */
1.126 brouard 9265: delti=delti3[1][1];
1.220 brouard 9266:
9267:
1.126 brouard 9268: /* 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 9269:
1.126 brouard 9270: /* Reads comments: lines beginning with '#' */
9271: while((c=getc(ficpar))=='#' && c!= EOF){
9272: ungetc(c,ficpar);
9273: fgets(line, MAXLINE, ficpar);
9274: numlinepar++;
1.141 brouard 9275: fputs(line,stdout);
1.126 brouard 9276: fputs(line,ficparo);
9277: fputs(line,ficlog);
9278: }
9279: ungetc(c,ficpar);
1.220 brouard 9280:
1.126 brouard 9281: matcov=matrix(1,npar,1,npar);
1.203 brouard 9282: hess=matrix(1,npar,1,npar);
1.131 brouard 9283: for(i=1; i <=npar; i++)
9284: for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220 brouard 9285:
1.194 brouard 9286: /* Scans npar lines */
1.126 brouard 9287: for(i=1; i <=npar; i++){
1.226 brouard 9288: count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
1.194 brouard 9289: if(count != 3){
1.226 brouard 9290: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 9291: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
9292: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 9293: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 9294: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
9295: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 9296: exit(1);
1.220 brouard 9297: }else{
1.226 brouard 9298: if(mle==1)
9299: printf("%1d%1d%d",i1,j1,jk);
9300: }
9301: fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
9302: fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
1.126 brouard 9303: for(j=1; j <=i; j++){
1.226 brouard 9304: fscanf(ficpar," %le",&matcov[i][j]);
9305: if(mle==1){
9306: printf(" %.5le",matcov[i][j]);
9307: }
9308: fprintf(ficlog," %.5le",matcov[i][j]);
9309: fprintf(ficparo," %.5le",matcov[i][j]);
1.126 brouard 9310: }
9311: fscanf(ficpar,"\n");
9312: numlinepar++;
9313: if(mle==1)
1.220 brouard 9314: printf("\n");
1.126 brouard 9315: fprintf(ficlog,"\n");
9316: fprintf(ficparo,"\n");
9317: }
1.194 brouard 9318: /* End of read covariance matrix npar lines */
1.126 brouard 9319: for(i=1; i <=npar; i++)
9320: for(j=i+1;j<=npar;j++)
1.226 brouard 9321: matcov[i][j]=matcov[j][i];
1.126 brouard 9322:
9323: if(mle==1)
9324: printf("\n");
9325: fprintf(ficlog,"\n");
9326:
9327: fflush(ficlog);
9328:
9329: /*-------- Rewriting parameter file ----------*/
9330: strcpy(rfileres,"r"); /* "Rparameterfile */
9331: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
9332: strcat(rfileres,"."); /* */
9333: strcat(rfileres,optionfilext); /* Other files have txt extension */
9334: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 9335: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
9336: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 9337: }
9338: fprintf(ficres,"#%s\n",version);
9339: } /* End of mle != -3 */
1.218 brouard 9340:
1.186 brouard 9341: /* Main data
9342: */
1.126 brouard 9343: n= lastobs;
9344: num=lvector(1,n);
9345: moisnais=vector(1,n);
9346: annais=vector(1,n);
9347: moisdc=vector(1,n);
9348: andc=vector(1,n);
1.220 brouard 9349: weight=vector(1,n);
1.126 brouard 9350: agedc=vector(1,n);
9351: cod=ivector(1,n);
1.220 brouard 9352: for(i=1;i<=n;i++){
9353: num[i]=0;
9354: moisnais[i]=0;
9355: annais[i]=0;
9356: moisdc[i]=0;
9357: andc[i]=0;
9358: agedc[i]=0;
9359: cod[i]=0;
9360: weight[i]=1.0; /* Equal weights, 1 by default */
9361: }
1.126 brouard 9362: mint=matrix(1,maxwav,1,n);
9363: anint=matrix(1,maxwav,1,n);
1.131 brouard 9364: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 9365: tab=ivector(1,NCOVMAX);
1.144 brouard 9366: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 9367: 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 9368:
1.136 brouard 9369: /* Reads data from file datafile */
9370: if (readdata(datafile, firstobs, lastobs, &imx)==1)
9371: goto end;
9372:
9373: /* Calculation of the number of parameters from char model */
1.137 brouard 9374: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
9375: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
9376: k=3 V4 Tvar[k=3]= 4 (from V4)
9377: k=2 V1 Tvar[k=2]= 1 (from V1)
9378: k=1 Tvar[1]=2 (from V2)
9379: */
9380: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
1.226 brouard 9381: Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
9382: Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
9383: Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
1.137 brouard 9384: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
9385: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
9386: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
9387: */
9388: /* For model-covariate k tells which data-covariate to use but
9389: because this model-covariate is a construction we invent a new column
9390: ncovcol + k1
9391: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
9392: Tvar[3=V1*V4]=4+1 etc */
1.227 brouard 9393: Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
9394: Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
1.137 brouard 9395: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
9396: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
1.227 brouard 9397: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
1.137 brouard 9398: */
1.145 brouard 9399: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
9400: 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 9401: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
9402: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 9403: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 9404: 4 covariates (3 plus signs)
9405: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
9406: */
1.227 brouard 9407: Tmodelind=ivector(1,NCOVMAX);/** five the k model position of an
9408: * individual dummy, fixed or varying:
9409: * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
9410: * 3, 1, 0, 0, 0, 0, 0, 0},
9411: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.228 brouard 9412: TmodelInvind=ivector(1,NCOVMAX);
9413: TmodelInvQind=ivector(1,NCOVMAX);/** five the k model position of an
9414: * individual quantitative, fixed or varying:
9415: * Tmodelqind[1]=1,Tvaraff[1]@9={4,
9416: * 3, 1, 0, 0, 0, 0, 0, 0},
9417: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.186 brouard 9418: /* Main decodemodel */
9419:
1.187 brouard 9420:
1.223 brouard 9421: if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/
1.136 brouard 9422: goto end;
9423:
1.137 brouard 9424: if((double)(lastobs-imx)/(double)imx > 1.10){
9425: nbwarn++;
9426: 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);
9427: 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);
9428: }
1.136 brouard 9429: /* if(mle==1){*/
1.137 brouard 9430: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
9431: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 9432: }
9433:
9434: /*-calculation of age at interview from date of interview and age at death -*/
9435: agev=matrix(1,maxwav,1,imx);
9436:
9437: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
9438: goto end;
9439:
1.126 brouard 9440:
1.136 brouard 9441: agegomp=(int)agemin;
9442: free_vector(moisnais,1,n);
9443: free_vector(annais,1,n);
1.126 brouard 9444: /* free_matrix(mint,1,maxwav,1,n);
9445: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 9446: /* free_vector(moisdc,1,n); */
9447: /* free_vector(andc,1,n); */
1.145 brouard 9448: /* */
9449:
1.126 brouard 9450: wav=ivector(1,imx);
1.214 brouard 9451: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
9452: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
9453: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
9454: 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.*/
9455: bh=imatrix(1,lastpass-firstpass+2,1,imx);
9456: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 9457:
9458: /* Concatenates waves */
1.214 brouard 9459: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
9460: Death is a valid wave (if date is known).
9461: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
9462: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
9463: and mw[mi+1][i]. dh depends on stepm.
9464: */
9465:
1.126 brouard 9466: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 9467: /* */
9468:
1.215 brouard 9469: free_vector(moisdc,1,n);
9470: free_vector(andc,1,n);
9471:
1.126 brouard 9472: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
9473: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
9474: ncodemax[1]=1;
1.145 brouard 9475: Ndum =ivector(-1,NCOVMAX);
1.225 brouard 9476: cptcoveff=0;
1.220 brouard 9477: if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
9478: tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.227 brouard 9479: }
9480:
9481: ncovcombmax=pow(2,cptcoveff);
9482: invalidvarcomb=ivector(1, ncovcombmax);
9483: for(i=1;i<ncovcombmax;i++)
9484: invalidvarcomb[i]=0;
9485:
1.211 brouard 9486: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 9487: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 9488: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.227 brouard 9489:
1.200 brouard 9490: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 9491: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 9492: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 9493: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
9494: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
9495: * (currently 0 or 1) in the data.
9496: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
9497: * corresponding modality (h,j).
9498: */
9499:
1.145 brouard 9500: h=0;
9501: /*if (cptcovn > 0) */
1.126 brouard 9502: m=pow(2,cptcoveff);
9503:
1.144 brouard 9504: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 9505: * For k=4 covariates, h goes from 1 to m=2**k
9506: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
9507: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 9508: * h\k 1 2 3 4
1.143 brouard 9509: *______________________________
9510: * 1 i=1 1 i=1 1 i=1 1 i=1 1
9511: * 2 2 1 1 1
9512: * 3 i=2 1 2 1 1
9513: * 4 2 2 1 1
9514: * 5 i=3 1 i=2 1 2 1
9515: * 6 2 1 2 1
9516: * 7 i=4 1 2 2 1
9517: * 8 2 2 2 1
1.197 brouard 9518: * 9 i=5 1 i=3 1 i=2 1 2
9519: * 10 2 1 1 2
9520: * 11 i=6 1 2 1 2
9521: * 12 2 2 1 2
9522: * 13 i=7 1 i=4 1 2 2
9523: * 14 2 1 2 2
9524: * 15 i=8 1 2 2 2
9525: * 16 2 2 2 2
1.143 brouard 9526: */
1.212 brouard 9527: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 9528: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
9529: * and the value of each covariate?
9530: * V1=1, V2=1, V3=2, V4=1 ?
9531: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
9532: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
9533: * In order to get the real value in the data, we use nbcode
9534: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
9535: * We are keeping this crazy system in order to be able (in the future?)
9536: * to have more than 2 values (0 or 1) for a covariate.
9537: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
9538: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
9539: * bbbbbbbb
9540: * 76543210
9541: * h-1 00000101 (6-1=5)
1.219 brouard 9542: *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211 brouard 9543: * &
9544: * 1 00000001 (1)
1.219 brouard 9545: * 00000000 = 1 & ((h-1) >> (k-1))
9546: * +1= 00000001 =1
1.211 brouard 9547: *
9548: * h=14, k=3 => h'=h-1=13, k'=k-1=2
9549: * h' 1101 =2^3+2^2+0x2^1+2^0
9550: * >>k' 11
9551: * & 00000001
9552: * = 00000001
9553: * +1 = 00000010=2 = codtabm(14,3)
9554: * Reverse h=6 and m=16?
9555: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
9556: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
9557: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
9558: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
9559: * V3=decodtabm(14,3,2**4)=2
9560: * h'=13 1101 =2^3+2^2+0x2^1+2^0
9561: *(h-1) >> (j-1) 0011 =13 >> 2
9562: * &1 000000001
9563: * = 000000001
9564: * +1= 000000010 =2
9565: * 2211
9566: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
9567: * V3=2
1.220 brouard 9568: * codtabm and decodtabm are identical
1.211 brouard 9569: */
9570:
1.145 brouard 9571:
9572: free_ivector(Ndum,-1,NCOVMAX);
9573:
9574:
1.126 brouard 9575:
1.186 brouard 9576: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 9577: strcpy(optionfilegnuplot,optionfilefiname);
9578: if(mle==-3)
1.201 brouard 9579: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 9580: strcat(optionfilegnuplot,".gp");
9581:
9582: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
9583: printf("Problem with file %s",optionfilegnuplot);
9584: }
9585: else{
1.204 brouard 9586: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 9587: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 9588: //fprintf(ficgp,"set missing 'NaNq'\n");
9589: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 9590: }
9591: /* fclose(ficgp);*/
1.186 brouard 9592:
9593:
9594: /* Initialisation of --------- index.htm --------*/
1.126 brouard 9595:
9596: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
9597: if(mle==-3)
1.201 brouard 9598: strcat(optionfilehtm,"-MORT_");
1.126 brouard 9599: strcat(optionfilehtm,".htm");
9600: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 9601: printf("Problem with %s \n",optionfilehtm);
9602: exit(0);
1.126 brouard 9603: }
9604:
9605: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
9606: strcat(optionfilehtmcov,"-cov.htm");
9607: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
9608: printf("Problem with %s \n",optionfilehtmcov), exit(0);
9609: }
9610: else{
9611: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
9612: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 9613: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 9614: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
9615: }
9616:
1.213 brouard 9617: 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 9618: <hr size=\"2\" color=\"#EC5E5E\"> \n\
9619: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 9620: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 9621: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 9622: \n\
9623: <hr size=\"2\" color=\"#EC5E5E\">\
9624: <ul><li><h4>Parameter files</h4>\n\
9625: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
9626: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
9627: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
9628: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
9629: - Date and time at start: %s</ul>\n",\
9630: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
9631: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
9632: fileres,fileres,\
9633: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
9634: fflush(fichtm);
9635:
9636: strcpy(pathr,path);
9637: strcat(pathr,optionfilefiname);
1.184 brouard 9638: #ifdef WIN32
9639: _chdir(optionfilefiname); /* Move to directory named optionfile */
9640: #else
1.126 brouard 9641: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 9642: #endif
9643:
1.126 brouard 9644:
1.220 brouard 9645: /* Calculates basic frequencies. Computes observed prevalence at single age
9646: and for any valid combination of covariates
1.126 brouard 9647: and prints on file fileres'p'. */
1.227 brouard 9648: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
9649: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 9650:
9651: fprintf(fichtm,"\n");
9652: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
9653: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
9654: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
9655: imx,agemin,agemax,jmin,jmax,jmean);
9656: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.220 brouard 9657: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9658: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9659: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9660: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218 brouard 9661:
1.126 brouard 9662: /* For Powell, parameters are in a vector p[] starting at p[1]
9663: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
9664: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
9665:
9666: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 9667: /* For mortality only */
1.126 brouard 9668: if (mle==-3){
1.136 brouard 9669: ximort=matrix(1,NDIM,1,NDIM);
1.220 brouard 9670: for(i=1;i<=NDIM;i++)
9671: for(j=1;j<=NDIM;j++)
9672: ximort[i][j]=0.;
1.186 brouard 9673: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 9674: cens=ivector(1,n);
9675: ageexmed=vector(1,n);
9676: agecens=vector(1,n);
9677: dcwave=ivector(1,n);
1.223 brouard 9678:
1.126 brouard 9679: for (i=1; i<=imx; i++){
9680: dcwave[i]=-1;
9681: for (m=firstpass; m<=lastpass; m++)
1.226 brouard 9682: if (s[m][i]>nlstate) {
9683: dcwave[i]=m;
9684: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
9685: break;
9686: }
1.126 brouard 9687: }
1.226 brouard 9688:
1.126 brouard 9689: for (i=1; i<=imx; i++) {
9690: if (wav[i]>0){
1.226 brouard 9691: ageexmed[i]=agev[mw[1][i]][i];
9692: j=wav[i];
9693: agecens[i]=1.;
9694:
9695: if (ageexmed[i]> 1 && wav[i] > 0){
9696: agecens[i]=agev[mw[j][i]][i];
9697: cens[i]= 1;
9698: }else if (ageexmed[i]< 1)
9699: cens[i]= -1;
9700: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
9701: cens[i]=0 ;
1.126 brouard 9702: }
9703: else cens[i]=-1;
9704: }
9705:
9706: for (i=1;i<=NDIM;i++) {
9707: for (j=1;j<=NDIM;j++)
1.226 brouard 9708: ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126 brouard 9709: }
9710:
1.145 brouard 9711: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 9712: /*printf("%lf %lf", p[1], p[2]);*/
9713:
9714:
1.136 brouard 9715: #ifdef GSL
9716: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 9717: #else
1.126 brouard 9718: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 9719: #endif
1.201 brouard 9720: strcpy(filerespow,"POW-MORT_");
9721: strcat(filerespow,fileresu);
1.126 brouard 9722: if((ficrespow=fopen(filerespow,"w"))==NULL) {
9723: printf("Problem with resultfile: %s\n", filerespow);
9724: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
9725: }
1.136 brouard 9726: #ifdef GSL
9727: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 9728: #else
1.126 brouard 9729: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 9730: #endif
1.126 brouard 9731: /* for (i=1;i<=nlstate;i++)
9732: for(j=1;j<=nlstate+ndeath;j++)
9733: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
9734: */
9735: fprintf(ficrespow,"\n");
1.136 brouard 9736: #ifdef GSL
9737: /* gsl starts here */
9738: T = gsl_multimin_fminimizer_nmsimplex;
9739: gsl_multimin_fminimizer *sfm = NULL;
9740: gsl_vector *ss, *x;
9741: gsl_multimin_function minex_func;
9742:
9743: /* Initial vertex size vector */
9744: ss = gsl_vector_alloc (NDIM);
9745:
9746: if (ss == NULL){
9747: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
9748: }
9749: /* Set all step sizes to 1 */
9750: gsl_vector_set_all (ss, 0.001);
9751:
9752: /* Starting point */
1.126 brouard 9753:
1.136 brouard 9754: x = gsl_vector_alloc (NDIM);
9755:
9756: if (x == NULL){
9757: gsl_vector_free(ss);
9758: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
9759: }
9760:
9761: /* Initialize method and iterate */
9762: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 9763: /* gsl_vector_set(x, 0, 0.0268); */
9764: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 9765: gsl_vector_set(x, 0, p[1]);
9766: gsl_vector_set(x, 1, p[2]);
9767:
9768: minex_func.f = &gompertz_f;
9769: minex_func.n = NDIM;
9770: minex_func.params = (void *)&p; /* ??? */
9771:
9772: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
9773: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
9774:
9775: printf("Iterations beginning .....\n\n");
9776: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
9777:
9778: iteri=0;
9779: while (rval == GSL_CONTINUE){
9780: iteri++;
9781: status = gsl_multimin_fminimizer_iterate(sfm);
9782:
9783: if (status) printf("error: %s\n", gsl_strerror (status));
9784: fflush(0);
9785:
9786: if (status)
9787: break;
9788:
9789: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
9790: ssval = gsl_multimin_fminimizer_size (sfm);
9791:
9792: if (rval == GSL_SUCCESS)
9793: printf ("converged to a local maximum at\n");
9794:
9795: printf("%5d ", iteri);
9796: for (it = 0; it < NDIM; it++){
9797: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
9798: }
9799: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
9800: }
9801:
9802: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
9803:
9804: gsl_vector_free(x); /* initial values */
9805: gsl_vector_free(ss); /* inital step size */
9806: for (it=0; it<NDIM; it++){
9807: p[it+1]=gsl_vector_get(sfm->x,it);
9808: fprintf(ficrespow," %.12lf", p[it]);
9809: }
9810: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
9811: #endif
9812: #ifdef POWELL
9813: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
9814: #endif
1.126 brouard 9815: fclose(ficrespow);
9816:
1.203 brouard 9817: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 9818:
9819: for(i=1; i <=NDIM; i++)
9820: for(j=i+1;j<=NDIM;j++)
1.220 brouard 9821: matcov[i][j]=matcov[j][i];
1.126 brouard 9822:
9823: printf("\nCovariance matrix\n ");
1.203 brouard 9824: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 9825: for(i=1; i <=NDIM; i++) {
9826: for(j=1;j<=NDIM;j++){
1.220 brouard 9827: printf("%f ",matcov[i][j]);
9828: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 9829: }
1.203 brouard 9830: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 9831: }
9832:
9833: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 9834: for (i=1;i<=NDIM;i++) {
1.126 brouard 9835: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 9836: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
9837: }
1.126 brouard 9838: lsurv=vector(1,AGESUP);
9839: lpop=vector(1,AGESUP);
9840: tpop=vector(1,AGESUP);
9841: lsurv[agegomp]=100000;
9842:
9843: for (k=agegomp;k<=AGESUP;k++) {
9844: agemortsup=k;
9845: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
9846: }
9847:
9848: for (k=agegomp;k<agemortsup;k++)
9849: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
9850:
9851: for (k=agegomp;k<agemortsup;k++){
9852: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
9853: sumlpop=sumlpop+lpop[k];
9854: }
9855:
9856: tpop[agegomp]=sumlpop;
9857: for (k=agegomp;k<(agemortsup-3);k++){
9858: /* tpop[k+1]=2;*/
9859: tpop[k+1]=tpop[k]-lpop[k];
9860: }
9861:
9862:
9863: printf("\nAge lx qx dx Lx Tx e(x)\n");
9864: for (k=agegomp;k<(agemortsup-2);k++)
9865: 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]);
9866:
9867:
9868: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220 brouard 9869: ageminpar=50;
9870: agemaxpar=100;
1.194 brouard 9871: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
9872: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
9873: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9874: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
9875: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
9876: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9877: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 9878: }else{
9879: printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
9880: 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 9881: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220 brouard 9882: }
1.201 brouard 9883: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 9884: stepm, weightopt,\
9885: model,imx,p,matcov,agemortsup);
9886:
9887: free_vector(lsurv,1,AGESUP);
9888: free_vector(lpop,1,AGESUP);
9889: free_vector(tpop,1,AGESUP);
1.220 brouard 9890: free_matrix(ximort,1,NDIM,1,NDIM);
1.136 brouard 9891: free_ivector(cens,1,n);
9892: free_vector(agecens,1,n);
9893: free_ivector(dcwave,1,n);
1.220 brouard 9894: #ifdef GSL
1.136 brouard 9895: #endif
1.186 brouard 9896: } /* Endof if mle==-3 mortality only */
1.205 brouard 9897: /* Standard */
9898: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
9899: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
9900: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 9901: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 9902: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
9903: for (k=1; k<=npar;k++)
9904: printf(" %d %8.5f",k,p[k]);
9905: printf("\n");
1.205 brouard 9906: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
9907: /* mlikeli uses func not funcone */
9908: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
9909: }
9910: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
9911: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
9912: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
9913: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
9914: }
9915: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 9916: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
9917: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
9918: for (k=1; k<=npar;k++)
9919: printf(" %d %8.5f",k,p[k]);
9920: printf("\n");
9921:
9922: /*--------- results files --------------*/
1.224 brouard 9923: 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 9924:
9925:
9926: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9927: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9928: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9929: for(i=1,jk=1; i <=nlstate; i++){
9930: for(k=1; k <=(nlstate+ndeath); k++){
1.225 brouard 9931: if (k != i) {
9932: printf("%d%d ",i,k);
9933: fprintf(ficlog,"%d%d ",i,k);
9934: fprintf(ficres,"%1d%1d ",i,k);
9935: for(j=1; j <=ncovmodel; j++){
9936: printf("%12.7f ",p[jk]);
9937: fprintf(ficlog,"%12.7f ",p[jk]);
9938: fprintf(ficres,"%12.7f ",p[jk]);
9939: jk++;
9940: }
9941: printf("\n");
9942: fprintf(ficlog,"\n");
9943: fprintf(ficres,"\n");
9944: }
1.126 brouard 9945: }
9946: }
1.203 brouard 9947: if(mle != 0){
9948: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 9949: ftolhess=ftol; /* Usually correct */
1.203 brouard 9950: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
9951: 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");
9952: 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");
9953: for(i=1,jk=1; i <=nlstate; i++){
1.225 brouard 9954: for(k=1; k <=(nlstate+ndeath); k++){
9955: if (k != i) {
9956: printf("%d%d ",i,k);
9957: fprintf(ficlog,"%d%d ",i,k);
9958: for(j=1; j <=ncovmodel; j++){
9959: 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]));
9960: 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]));
9961: jk++;
9962: }
9963: printf("\n");
9964: fprintf(ficlog,"\n");
9965: }
9966: }
1.193 brouard 9967: }
1.203 brouard 9968: } /* end of hesscov and Wald tests */
1.225 brouard 9969:
1.203 brouard 9970: /* */
1.126 brouard 9971: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
9972: printf("# Scales (for hessian or gradient estimation)\n");
9973: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
9974: for(i=1,jk=1; i <=nlstate; i++){
9975: for(j=1; j <=nlstate+ndeath; j++){
1.225 brouard 9976: if (j!=i) {
9977: fprintf(ficres,"%1d%1d",i,j);
9978: printf("%1d%1d",i,j);
9979: fprintf(ficlog,"%1d%1d",i,j);
9980: for(k=1; k<=ncovmodel;k++){
9981: printf(" %.5e",delti[jk]);
9982: fprintf(ficlog," %.5e",delti[jk]);
9983: fprintf(ficres," %.5e",delti[jk]);
9984: jk++;
9985: }
9986: printf("\n");
9987: fprintf(ficlog,"\n");
9988: fprintf(ficres,"\n");
9989: }
1.126 brouard 9990: }
9991: }
9992:
9993: 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 9994: if(mle >= 1) /* To big for the screen */
1.126 brouard 9995: 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");
9996: 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");
9997: /* # 121 Var(a12)\n\ */
9998: /* # 122 Cov(b12,a12) Var(b12)\n\ */
9999: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
10000: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
10001: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
10002: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
10003: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
10004: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
10005:
10006:
10007: /* Just to have a covariance matrix which will be more understandable
10008: even is we still don't want to manage dictionary of variables
10009: */
10010: for(itimes=1;itimes<=2;itimes++){
10011: jj=0;
10012: for(i=1; i <=nlstate; i++){
1.225 brouard 10013: for(j=1; j <=nlstate+ndeath; j++){
10014: if(j==i) continue;
10015: for(k=1; k<=ncovmodel;k++){
10016: jj++;
10017: ca[0]= k+'a'-1;ca[1]='\0';
10018: if(itimes==1){
10019: if(mle>=1)
10020: printf("#%1d%1d%d",i,j,k);
10021: fprintf(ficlog,"#%1d%1d%d",i,j,k);
10022: fprintf(ficres,"#%1d%1d%d",i,j,k);
10023: }else{
10024: if(mle>=1)
10025: printf("%1d%1d%d",i,j,k);
10026: fprintf(ficlog,"%1d%1d%d",i,j,k);
10027: fprintf(ficres,"%1d%1d%d",i,j,k);
10028: }
10029: ll=0;
10030: for(li=1;li <=nlstate; li++){
10031: for(lj=1;lj <=nlstate+ndeath; lj++){
10032: if(lj==li) continue;
10033: for(lk=1;lk<=ncovmodel;lk++){
10034: ll++;
10035: if(ll<=jj){
10036: cb[0]= lk +'a'-1;cb[1]='\0';
10037: if(ll<jj){
10038: if(itimes==1){
10039: if(mle>=1)
10040: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
10041: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
10042: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
10043: }else{
10044: if(mle>=1)
10045: printf(" %.5e",matcov[jj][ll]);
10046: fprintf(ficlog," %.5e",matcov[jj][ll]);
10047: fprintf(ficres," %.5e",matcov[jj][ll]);
10048: }
10049: }else{
10050: if(itimes==1){
10051: if(mle>=1)
10052: printf(" Var(%s%1d%1d)",ca,i,j);
10053: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
10054: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
10055: }else{
10056: if(mle>=1)
10057: printf(" %.7e",matcov[jj][ll]);
10058: fprintf(ficlog," %.7e",matcov[jj][ll]);
10059: fprintf(ficres," %.7e",matcov[jj][ll]);
10060: }
10061: }
10062: }
10063: } /* end lk */
10064: } /* end lj */
10065: } /* end li */
10066: if(mle>=1)
10067: printf("\n");
10068: fprintf(ficlog,"\n");
10069: fprintf(ficres,"\n");
10070: numlinepar++;
10071: } /* end k*/
10072: } /*end j */
1.126 brouard 10073: } /* end i */
10074: } /* end itimes */
10075:
10076: fflush(ficlog);
10077: fflush(ficres);
1.225 brouard 10078: while(fgets(line, MAXLINE, ficpar)) {
10079: /* If line starts with a # it is a comment */
10080: if (line[0] == '#') {
10081: numlinepar++;
10082: fputs(line,stdout);
10083: fputs(line,ficparo);
10084: fputs(line,ficlog);
10085: continue;
10086: }else
10087: break;
10088: }
10089:
1.209 brouard 10090: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
10091: /* ungetc(c,ficpar); */
10092: /* fgets(line, MAXLINE, ficpar); */
10093: /* fputs(line,stdout); */
10094: /* fputs(line,ficparo); */
10095: /* } */
10096: /* ungetc(c,ficpar); */
1.126 brouard 10097:
10098: estepm=0;
1.209 brouard 10099: if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){
1.225 brouard 10100:
10101: if (num_filled != 6) {
10102: 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);
10103: 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);
10104: goto end;
10105: }
10106: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
10107: }
10108: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
10109: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
10110:
1.209 brouard 10111: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 10112: if (estepm==0 || estepm < stepm) estepm=stepm;
10113: if (fage <= 2) {
10114: bage = ageminpar;
10115: fage = agemaxpar;
10116: }
10117:
10118: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 10119: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
10120: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220 brouard 10121:
1.186 brouard 10122: /* Other stuffs, more or less useful */
1.126 brouard 10123: while((c=getc(ficpar))=='#' && c!= EOF){
10124: ungetc(c,ficpar);
10125: fgets(line, MAXLINE, ficpar);
1.141 brouard 10126: fputs(line,stdout);
1.126 brouard 10127: fputs(line,ficparo);
10128: }
10129: ungetc(c,ficpar);
10130:
10131: 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);
10132: 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);
10133: 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);
10134: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
10135: 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);
10136:
10137: while((c=getc(ficpar))=='#' && c!= EOF){
10138: ungetc(c,ficpar);
10139: fgets(line, MAXLINE, ficpar);
1.141 brouard 10140: fputs(line,stdout);
1.126 brouard 10141: fputs(line,ficparo);
10142: }
10143: ungetc(c,ficpar);
10144:
10145:
10146: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
10147: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
10148:
10149: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 10150: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 10151: fprintf(ficparo,"pop_based=%d\n",popbased);
10152: fprintf(ficres,"pop_based=%d\n",popbased);
10153:
10154: while((c=getc(ficpar))=='#' && c!= EOF){
10155: ungetc(c,ficpar);
10156: fgets(line, MAXLINE, ficpar);
1.141 brouard 10157: fputs(line,stdout);
1.126 brouard 10158: fputs(line,ficparo);
10159: }
10160: ungetc(c,ficpar);
10161:
10162: 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);
10163: 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);
10164: 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);
10165: 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);
10166: 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);
10167: /* day and month of proj2 are not used but only year anproj2.*/
10168:
1.217 brouard 10169: while((c=getc(ficpar))=='#' && c!= EOF){
10170: ungetc(c,ficpar);
10171: fgets(line, MAXLINE, ficpar);
10172: fputs(line,stdout);
10173: fputs(line,ficparo);
10174: }
10175: ungetc(c,ficpar);
10176:
10177: 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 10178: 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);
10179: 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);
10180: 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 10181: /* day and month of proj2 are not used but only year anproj2.*/
1.126 brouard 10182:
10183:
1.220 brouard 10184: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145 brouard 10185: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 10186:
10187: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 10188: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.220 brouard 10189: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 10190: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
10191: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 10192: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 10193: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
10194: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 10195: }else{
1.218 brouard 10196: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
1.220 brouard 10197: }
10198: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
1.225 brouard 10199: model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
10200: jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
1.220 brouard 10201:
1.225 brouard 10202: /*------------ free_vector -------------*/
10203: /* chdir(path); */
1.220 brouard 10204:
1.215 brouard 10205: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
10206: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
10207: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
10208: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.126 brouard 10209: free_lvector(num,1,n);
10210: free_vector(agedc,1,n);
10211: /*free_matrix(covar,0,NCOVMAX,1,n);*/
10212: /*free_matrix(covar,1,NCOVMAX,1,n);*/
10213: fclose(ficparo);
10214: fclose(ficres);
1.220 brouard 10215:
10216:
1.186 brouard 10217: /* Other results (useful)*/
1.220 brouard 10218:
10219:
1.126 brouard 10220: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 10221: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
10222: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 10223: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 10224: fclose(ficrespl);
10225:
10226: /*------------- h Pij x at various ages ------------*/
1.180 brouard 10227: /*#include "hpijx.h"*/
10228: hPijx(p, bage, fage);
1.145 brouard 10229: fclose(ficrespij);
1.227 brouard 10230:
1.220 brouard 10231: /* ncovcombmax= pow(2,cptcoveff); */
1.219 brouard 10232: /*-------------- Variance of one-step probabilities---*/
1.145 brouard 10233: k=1;
1.126 brouard 10234: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.227 brouard 10235:
1.219 brouard 10236: /* Prevalence for each covariates in probs[age][status][cov] */
1.218 brouard 10237: probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.126 brouard 10238: for(i=1;i<=AGESUP;i++)
1.219 brouard 10239: for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.225 brouard 10240: for(k=1;k<=ncovcombmax;k++)
10241: probs[i][j][k]=0.;
1.219 brouard 10242: prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
10243: if (mobilav!=0 ||mobilavproj !=0 ) {
10244: mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.227 brouard 10245: for(i=1;i<=AGESUP;i++)
10246: for(j=1;j<=nlstate;j++)
10247: for(k=1;k<=ncovcombmax;k++)
10248: mobaverages[i][j][k]=0.;
1.219 brouard 10249: mobaverage=mobaverages;
10250: if (mobilav!=0) {
1.227 brouard 10251: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
10252: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
10253: printf(" Error in movingaverage mobilav=%d\n",mobilav);
10254: }
1.219 brouard 10255: }
10256: /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
10257: /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
10258: else if (mobilavproj !=0) {
1.227 brouard 10259: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
10260: fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
10261: printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
10262: }
1.219 brouard 10263: }
10264: }/* end if moving average */
1.227 brouard 10265:
1.126 brouard 10266: /*---------- Forecasting ------------------*/
10267: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
10268: if(prevfcast==1){
10269: /* if(stepm ==1){*/
1.225 brouard 10270: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 10271: }
1.217 brouard 10272: if(backcast==1){
1.219 brouard 10273: ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
10274: ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
10275: ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
10276:
10277: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
10278:
10279: bprlim=matrix(1,nlstate,1,nlstate);
10280: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
10281: fclose(ficresplb);
10282:
1.222 brouard 10283: hBijx(p, bage, fage, mobaverage);
10284: fclose(ficrespijb);
1.219 brouard 10285: free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
10286:
10287: /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
1.225 brouard 10288: bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
1.219 brouard 10289: free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
10290: free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
10291: free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
10292: }
1.217 brouard 10293:
1.186 brouard 10294:
10295: /* ------ Other prevalence ratios------------ */
1.126 brouard 10296:
1.215 brouard 10297: free_ivector(wav,1,imx);
10298: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
10299: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
10300: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.218 brouard 10301:
10302:
1.127 brouard 10303: /*---------- Health expectancies, no variances ------------*/
1.218 brouard 10304:
1.201 brouard 10305: strcpy(filerese,"E_");
10306: strcat(filerese,fileresu);
1.126 brouard 10307: if((ficreseij=fopen(filerese,"w"))==NULL) {
10308: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
10309: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
10310: }
1.208 brouard 10311: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
10312: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.219 brouard 10313:
1.227 brouard 10314: for (k=1; k <= (int) pow(2,cptcoveff); k++){ /* For any combination of dummy covariates, fixed and varying */
1.219 brouard 10315: fprintf(ficreseij,"\n#****** ");
1.225 brouard 10316: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 10317: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.219 brouard 10318: }
10319: fprintf(ficreseij,"******\n");
10320:
10321: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
10322: oldm=oldms;savm=savms;
10323: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
1.127 brouard 10324:
1.219 brouard 10325: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127 brouard 10326: }
10327: fclose(ficreseij);
1.208 brouard 10328: printf("done evsij\n");fflush(stdout);
10329: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.218 brouard 10330:
1.227 brouard 10331: /*---------- State-specific expectancies and variances ------------*/
1.218 brouard 10332:
10333:
1.201 brouard 10334: strcpy(filerest,"T_");
10335: strcat(filerest,fileresu);
1.127 brouard 10336: if((ficrest=fopen(filerest,"w"))==NULL) {
10337: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
10338: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
10339: }
1.208 brouard 10340: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
10341: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.218 brouard 10342:
1.126 brouard 10343:
1.201 brouard 10344: strcpy(fileresstde,"STDE_");
10345: strcat(fileresstde,fileresu);
1.126 brouard 10346: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
1.227 brouard 10347: printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
10348: fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
1.126 brouard 10349: }
1.227 brouard 10350: printf(" Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
10351: fprintf(ficlog," Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 10352:
1.201 brouard 10353: strcpy(filerescve,"CVE_");
10354: strcat(filerescve,fileresu);
1.126 brouard 10355: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
1.227 brouard 10356: printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
10357: fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
1.126 brouard 10358: }
1.227 brouard 10359: printf(" Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
10360: fprintf(ficlog," Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 10361:
1.201 brouard 10362: strcpy(fileresv,"V_");
10363: strcat(fileresv,fileresu);
1.126 brouard 10364: if((ficresvij=fopen(fileresv,"w"))==NULL) {
10365: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
10366: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
10367: }
1.227 brouard 10368: printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
10369: fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 10370:
1.145 brouard 10371: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
10372: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
10373:
1.225 brouard 10374: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.227 brouard 10375: printf("\n#****** ");
1.208 brouard 10376: fprintf(ficrest,"\n#****** ");
1.227 brouard 10377: fprintf(ficlog,"\n#****** ");
10378: for(j=1;j<=cptcoveff;j++){
10379: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10380: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10381: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10382: }
1.208 brouard 10383: fprintf(ficrest,"******\n");
1.227 brouard 10384: fprintf(ficlog,"******\n");
10385: printf("******\n");
1.208 brouard 10386:
10387: fprintf(ficresstdeij,"\n#****** ");
10388: fprintf(ficrescveij,"\n#****** ");
1.225 brouard 10389: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 10390: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10391: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 10392: }
10393: fprintf(ficresstdeij,"******\n");
10394: fprintf(ficrescveij,"******\n");
10395:
10396: fprintf(ficresvij,"\n#****** ");
1.225 brouard 10397: for(j=1;j<=cptcoveff;j++)
1.227 brouard 10398: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 10399: fprintf(ficresvij,"******\n");
10400:
10401: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
10402: oldm=oldms;savm=savms;
1.227 brouard 10403: printf(" cvevsij combination#=%d, ",k);
10404: fprintf(ficlog, " cvevsij combination#=%d, ",k);
1.208 brouard 10405: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
10406: printf(" end cvevsij \n ");
10407: fprintf(ficlog, " end cvevsij \n ");
10408:
10409: /*
10410: */
10411: /* goto endfree; */
10412:
10413: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
10414: pstamp(ficrest);
10415:
10416:
10417: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.227 brouard 10418: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
10419: cptcod= 0; /* To be deleted */
10420: printf("varevsij vpopbased=%d \n",vpopbased);
10421: fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
10422: 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 */
10423: 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 ");
10424: if(vpopbased==1)
10425: 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);
10426: else
10427: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
10428: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
10429: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
10430: fprintf(ficrest,"\n");
10431: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
10432: epj=vector(1,nlstate+1);
10433: printf("Computing age specific period (stable) prevalences in each health state \n");
10434: fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
10435: for(age=bage; age <=fage ;age++){
10436: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
10437: if (vpopbased==1) {
10438: if(mobilav ==0){
10439: for(i=1; i<=nlstate;i++)
10440: prlim[i][i]=probs[(int)age][i][k];
10441: }else{ /* mobilav */
10442: for(i=1; i<=nlstate;i++)
10443: prlim[i][i]=mobaverage[(int)age][i][k];
10444: }
10445: }
1.219 brouard 10446:
1.227 brouard 10447: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
10448: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
10449: /* printf(" age %4.0f ",age); */
10450: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
10451: for(i=1, epj[j]=0.;i <=nlstate;i++) {
10452: epj[j] += prlim[i][i]*eij[i][j][(int)age];
10453: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
10454: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
10455: }
10456: epj[nlstate+1] +=epj[j];
10457: }
10458: /* printf(" age %4.0f \n",age); */
1.219 brouard 10459:
1.227 brouard 10460: for(i=1, vepp=0.;i <=nlstate;i++)
10461: for(j=1;j <=nlstate;j++)
10462: vepp += vareij[i][j][(int)age];
10463: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
10464: for(j=1;j <=nlstate;j++){
10465: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
10466: }
10467: fprintf(ficrest,"\n");
10468: }
1.208 brouard 10469: } /* End vpopbased */
10470: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
10471: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
10472: free_vector(epj,1,nlstate+1);
10473: printf("done \n");fflush(stdout);
10474: fprintf(ficlog,"done\n");fflush(ficlog);
10475:
1.145 brouard 10476: /*}*/
1.208 brouard 10477: } /* End k */
1.227 brouard 10478:
10479: printf("done State-specific expectancies\n");fflush(stdout);
10480: fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
10481:
1.126 brouard 10482: /*------- Variance of period (stable) prevalence------*/
1.227 brouard 10483:
1.201 brouard 10484: strcpy(fileresvpl,"VPL_");
10485: strcat(fileresvpl,fileresu);
1.126 brouard 10486: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
10487: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
10488: exit(0);
10489: }
1.208 brouard 10490: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
10491: fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.227 brouard 10492:
1.145 brouard 10493: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
10494: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
1.227 brouard 10495:
1.225 brouard 10496: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.227 brouard 10497: fprintf(ficresvpl,"\n#****** ");
10498: printf("\n#****** ");
10499: fprintf(ficlog,"\n#****** ");
10500: for(j=1;j<=cptcoveff;j++) {
10501: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10502: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10503: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10504: }
10505: fprintf(ficresvpl,"******\n");
10506: printf("******\n");
10507: fprintf(ficlog,"******\n");
10508:
10509: varpl=matrix(1,nlstate,(int) bage, (int) fage);
10510: oldm=oldms;savm=savms;
10511: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
10512: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 10513: /*}*/
1.126 brouard 10514: }
1.227 brouard 10515:
1.126 brouard 10516: fclose(ficresvpl);
1.208 brouard 10517: printf("done variance-covariance of period prevalence\n");fflush(stdout);
10518: fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
1.227 brouard 10519:
10520: free_vector(weight,1,n);
10521: free_imatrix(Tvard,1,NCOVMAX,1,2);
10522: free_imatrix(s,1,maxwav+1,1,n);
10523: free_matrix(anint,1,maxwav,1,n);
10524: free_matrix(mint,1,maxwav,1,n);
10525: free_ivector(cod,1,n);
10526: free_ivector(tab,1,NCOVMAX);
10527: fclose(ficresstdeij);
10528: fclose(ficrescveij);
10529: fclose(ficresvij);
10530: fclose(ficrest);
10531: fclose(ficpar);
10532:
10533:
1.126 brouard 10534: /*---------- End : free ----------------*/
1.219 brouard 10535: if (mobilav!=0 ||mobilavproj !=0)
10536: 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 10537: free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220 brouard 10538: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
10539: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126 brouard 10540: } /* mle==-3 arrives here for freeing */
1.227 brouard 10541: /* endfree:*/
10542: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
10543: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
10544: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
10545: free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
10546: free_ma3x(cotvar,1,maxwav,1,ntv,1,n);
10547: free_matrix(coqvar,1,maxwav,1,n);
10548: free_matrix(covar,0,NCOVMAX,1,n);
10549: free_matrix(matcov,1,npar,1,npar);
10550: free_matrix(hess,1,npar,1,npar);
10551: /*free_vector(delti,1,npar);*/
10552: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
10553: free_matrix(agev,1,maxwav,1,imx);
10554: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
10555:
10556: free_ivector(ncodemax,1,NCOVMAX);
10557: free_ivector(ncodemaxwundef,1,NCOVMAX);
10558: free_ivector(Dummy,-1,NCOVMAX);
10559: free_ivector(Fixed,-1,NCOVMAX);
10560: free_ivector(Typevar,-1,NCOVMAX);
10561: free_ivector(Tvar,1,NCOVMAX);
10562: free_ivector(Tposprod,1,NCOVMAX);
10563: free_ivector(Tprod,1,NCOVMAX);
10564: free_ivector(Tvaraff,1,NCOVMAX);
10565: free_ivector(invalidvarcomb,1,ncovcombmax);
10566: free_ivector(Tage,1,NCOVMAX);
10567: free_ivector(Tmodelind,1,NCOVMAX);
1.228 brouard 10568: free_ivector(TmodelInvind,1,NCOVMAX);
10569: free_ivector(TmodelInvQind,1,NCOVMAX);
1.227 brouard 10570:
10571: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
10572: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 10573: fflush(fichtm);
10574: fflush(ficgp);
10575:
1.227 brouard 10576:
1.126 brouard 10577: if((nberr >0) || (nbwarn>0)){
1.216 brouard 10578: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
10579: 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 10580: }else{
10581: printf("End of Imach\n");
10582: fprintf(ficlog,"End of Imach\n");
10583: }
10584: printf("See log file on %s\n",filelog);
10585: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 10586: /*(void) gettimeofday(&end_time,&tzp);*/
10587: rend_time = time(NULL);
10588: end_time = *localtime(&rend_time);
10589: /* tml = *localtime(&end_time.tm_sec); */
10590: strcpy(strtend,asctime(&end_time));
1.126 brouard 10591: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
10592: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 10593: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.227 brouard 10594:
1.157 brouard 10595: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
10596: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
10597: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 10598: /* printf("Total time was %d uSec.\n", total_usecs);*/
10599: /* if(fileappend(fichtm,optionfilehtm)){ */
10600: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
10601: fclose(fichtm);
10602: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
10603: fclose(fichtmcov);
10604: fclose(ficgp);
10605: fclose(ficlog);
10606: /*------ End -----------*/
1.227 brouard 10607:
10608:
10609: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 10610: #ifdef WIN32
1.227 brouard 10611: if (_chdir(pathcd) != 0)
10612: printf("Can't move to directory %s!\n",path);
10613: if(_getcwd(pathcd,MAXLINE) > 0)
1.184 brouard 10614: #else
1.227 brouard 10615: if(chdir(pathcd) != 0)
10616: printf("Can't move to directory %s!\n", path);
10617: if (getcwd(pathcd, MAXLINE) > 0)
1.184 brouard 10618: #endif
1.126 brouard 10619: printf("Current directory %s!\n",pathcd);
10620: /*strcat(plotcmd,CHARSEPARATOR);*/
10621: sprintf(plotcmd,"gnuplot");
1.157 brouard 10622: #ifdef _WIN32
1.126 brouard 10623: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
10624: #endif
10625: if(!stat(plotcmd,&info)){
1.158 brouard 10626: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 10627: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 10628: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 10629: }else
10630: strcpy(pplotcmd,plotcmd);
1.157 brouard 10631: #ifdef __unix
1.126 brouard 10632: strcpy(plotcmd,GNUPLOTPROGRAM);
10633: if(!stat(plotcmd,&info)){
1.158 brouard 10634: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 10635: }else
10636: strcpy(pplotcmd,plotcmd);
10637: #endif
10638: }else
10639: strcpy(pplotcmd,plotcmd);
10640:
10641: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 10642: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.227 brouard 10643:
1.126 brouard 10644: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 10645: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 10646: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 10647: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 10648: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 10649: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 10650: }
1.158 brouard 10651: printf(" Successful, please wait...");
1.126 brouard 10652: while (z[0] != 'q') {
10653: /* chdir(path); */
1.154 brouard 10654: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 10655: scanf("%s",z);
10656: /* if (z[0] == 'c') system("./imach"); */
10657: if (z[0] == 'e') {
1.158 brouard 10658: #ifdef __APPLE__
1.152 brouard 10659: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 10660: #elif __linux
10661: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 10662: #else
1.152 brouard 10663: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 10664: #endif
10665: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
10666: system(pplotcmd);
1.126 brouard 10667: }
10668: else if (z[0] == 'g') system(plotcmd);
10669: else if (z[0] == 'q') exit(0);
10670: }
1.227 brouard 10671: end:
1.126 brouard 10672: while (z[0] != 'q') {
1.195 brouard 10673: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 10674: scanf("%s",z);
10675: }
10676: }
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