Annotation of imach/src/imach.c, revision 1.217
1.217 ! brouard 1: /* $Id: imach.c,v 1.216 2015/12/18 17:32:11 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.217 ! brouard 4: Revision 1.216 2015/12/18 17:32:11 brouard
! 5: Summary: 0.98r4 Warning and status=-2
! 6:
! 7: Version 0.98r4 is now:
! 8: - displaying an error when status is -1, date of interview unknown and date of death known;
! 9: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
! 10: Older changes concerning s=-2, dating from 2005 have been supersed.
! 11:
1.216 brouard 12: Revision 1.215 2015/12/16 08:52:24 brouard
13: Summary: 0.98r4 working
14:
1.215 brouard 15: Revision 1.214 2015/12/16 06:57:54 brouard
16: Summary: temporary not working
17:
1.214 brouard 18: Revision 1.213 2015/12/11 18:22:17 brouard
19: Summary: 0.98r4
20:
1.213 brouard 21: Revision 1.212 2015/11/21 12:47:24 brouard
22: Summary: minor typo
23:
1.212 brouard 24: Revision 1.211 2015/11/21 12:41:11 brouard
25: Summary: 0.98r3 with some graph of projected cross-sectional
26:
27: Author: Nicolas Brouard
28:
1.211 brouard 29: Revision 1.210 2015/11/18 17:41:20 brouard
30: Summary: Start working on projected prevalences
31:
1.210 brouard 32: Revision 1.209 2015/11/17 22:12:03 brouard
33: Summary: Adding ftolpl parameter
34: Author: N Brouard
35:
36: We had difficulties to get smoothed confidence intervals. It was due
37: to the period prevalence which wasn't computed accurately. The inner
38: parameter ftolpl is now an outer parameter of the .imach parameter
39: file after estepm. If ftolpl is small 1.e-4 and estepm too,
40: computation are long.
41:
1.209 brouard 42: Revision 1.208 2015/11/17 14:31:57 brouard
43: Summary: temporary
44:
1.208 brouard 45: Revision 1.207 2015/10/27 17:36:57 brouard
46: *** empty log message ***
47:
1.207 brouard 48: Revision 1.206 2015/10/24 07:14:11 brouard
49: *** empty log message ***
50:
1.206 brouard 51: Revision 1.205 2015/10/23 15:50:53 brouard
52: Summary: 0.98r3 some clarification for graphs on likelihood contributions
53:
1.205 brouard 54: Revision 1.204 2015/10/01 16:20:26 brouard
55: Summary: Some new graphs of contribution to likelihood
56:
1.204 brouard 57: Revision 1.203 2015/09/30 17:45:14 brouard
58: Summary: looking at better estimation of the hessian
59:
60: Also a better criteria for convergence to the period prevalence And
61: therefore adding the number of years needed to converge. (The
62: prevalence in any alive state shold sum to one
63:
1.203 brouard 64: Revision 1.202 2015/09/22 19:45:16 brouard
65: Summary: Adding some overall graph on contribution to likelihood. Might change
66:
1.202 brouard 67: Revision 1.201 2015/09/15 17:34:58 brouard
68: Summary: 0.98r0
69:
70: - Some new graphs like suvival functions
71: - Some bugs fixed like model=1+age+V2.
72:
1.201 brouard 73: Revision 1.200 2015/09/09 16:53:55 brouard
74: Summary: Big bug thanks to Flavia
75:
76: Even model=1+age+V2. did not work anymore
77:
1.200 brouard 78: Revision 1.199 2015/09/07 14:09:23 brouard
79: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
80:
1.199 brouard 81: Revision 1.198 2015/09/03 07:14:39 brouard
82: Summary: 0.98q5 Flavia
83:
1.198 brouard 84: Revision 1.197 2015/09/01 18:24:39 brouard
85: *** empty log message ***
86:
1.197 brouard 87: Revision 1.196 2015/08/18 23:17:52 brouard
88: Summary: 0.98q5
89:
1.196 brouard 90: Revision 1.195 2015/08/18 16:28:39 brouard
91: Summary: Adding a hack for testing purpose
92:
93: After reading the title, ftol and model lines, if the comment line has
94: a q, starting with #q, the answer at the end of the run is quit. It
95: permits to run test files in batch with ctest. The former workaround was
96: $ echo q | imach foo.imach
97:
1.195 brouard 98: Revision 1.194 2015/08/18 13:32:00 brouard
99: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
100:
1.194 brouard 101: Revision 1.193 2015/08/04 07:17:42 brouard
102: Summary: 0.98q4
103:
1.193 brouard 104: Revision 1.192 2015/07/16 16:49:02 brouard
105: Summary: Fixing some outputs
106:
1.192 brouard 107: Revision 1.191 2015/07/14 10:00:33 brouard
108: Summary: Some fixes
109:
1.191 brouard 110: Revision 1.190 2015/05/05 08:51:13 brouard
111: Summary: Adding digits in output parameters (7 digits instead of 6)
112:
113: Fix 1+age+.
114:
1.190 brouard 115: Revision 1.189 2015/04/30 14:45:16 brouard
116: Summary: 0.98q2
117:
1.189 brouard 118: Revision 1.188 2015/04/30 08:27:53 brouard
119: *** empty log message ***
120:
1.188 brouard 121: Revision 1.187 2015/04/29 09:11:15 brouard
122: *** empty log message ***
123:
1.187 brouard 124: Revision 1.186 2015/04/23 12:01:52 brouard
125: Summary: V1*age is working now, version 0.98q1
126:
127: Some codes had been disabled in order to simplify and Vn*age was
128: working in the optimization phase, ie, giving correct MLE parameters,
129: but, as usual, outputs were not correct and program core dumped.
130:
1.186 brouard 131: Revision 1.185 2015/03/11 13:26:42 brouard
132: Summary: Inclusion of compile and links command line for Intel Compiler
133:
1.185 brouard 134: Revision 1.184 2015/03/11 11:52:39 brouard
135: Summary: Back from Windows 8. Intel Compiler
136:
1.184 brouard 137: Revision 1.183 2015/03/10 20:34:32 brouard
138: Summary: 0.98q0, trying with directest, mnbrak fixed
139:
140: We use directest instead of original Powell test; probably no
141: incidence on the results, but better justifications;
142: We fixed Numerical Recipes mnbrak routine which was wrong and gave
143: wrong results.
144:
1.183 brouard 145: Revision 1.182 2015/02/12 08:19:57 brouard
146: Summary: Trying to keep directest which seems simpler and more general
147: Author: Nicolas Brouard
148:
1.182 brouard 149: Revision 1.181 2015/02/11 23:22:24 brouard
150: Summary: Comments on Powell added
151:
152: Author:
153:
1.181 brouard 154: Revision 1.180 2015/02/11 17:33:45 brouard
155: Summary: Finishing move from main to function (hpijx and prevalence_limit)
156:
1.180 brouard 157: Revision 1.179 2015/01/04 09:57:06 brouard
158: Summary: back to OS/X
159:
1.179 brouard 160: Revision 1.178 2015/01/04 09:35:48 brouard
161: *** empty log message ***
162:
1.178 brouard 163: Revision 1.177 2015/01/03 18:40:56 brouard
164: Summary: Still testing ilc32 on OSX
165:
1.177 brouard 166: Revision 1.176 2015/01/03 16:45:04 brouard
167: *** empty log message ***
168:
1.176 brouard 169: Revision 1.175 2015/01/03 16:33:42 brouard
170: *** empty log message ***
171:
1.175 brouard 172: Revision 1.174 2015/01/03 16:15:49 brouard
173: Summary: Still in cross-compilation
174:
1.174 brouard 175: Revision 1.173 2015/01/03 12:06:26 brouard
176: Summary: trying to detect cross-compilation
177:
1.173 brouard 178: Revision 1.172 2014/12/27 12:07:47 brouard
179: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
180:
1.172 brouard 181: Revision 1.171 2014/12/23 13:26:59 brouard
182: Summary: Back from Visual C
183:
184: Still problem with utsname.h on Windows
185:
1.171 brouard 186: Revision 1.170 2014/12/23 11:17:12 brouard
187: Summary: Cleaning some \%% back to %%
188:
189: The escape was mandatory for a specific compiler (which one?), but too many warnings.
190:
1.170 brouard 191: Revision 1.169 2014/12/22 23:08:31 brouard
192: Summary: 0.98p
193:
194: Outputs some informations on compiler used, OS etc. Testing on different platforms.
195:
1.169 brouard 196: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 197: Summary: update
1.169 brouard 198:
1.168 brouard 199: Revision 1.167 2014/12/22 13:50:56 brouard
200: Summary: Testing uname and compiler version and if compiled 32 or 64
201:
202: Testing on Linux 64
203:
1.167 brouard 204: Revision 1.166 2014/12/22 11:40:47 brouard
205: *** empty log message ***
206:
1.166 brouard 207: Revision 1.165 2014/12/16 11:20:36 brouard
208: Summary: After compiling on Visual C
209:
210: * imach.c (Module): Merging 1.61 to 1.162
211:
1.165 brouard 212: Revision 1.164 2014/12/16 10:52:11 brouard
213: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
214:
215: * imach.c (Module): Merging 1.61 to 1.162
216:
1.164 brouard 217: Revision 1.163 2014/12/16 10:30:11 brouard
218: * imach.c (Module): Merging 1.61 to 1.162
219:
1.163 brouard 220: Revision 1.162 2014/09/25 11:43:39 brouard
221: Summary: temporary backup 0.99!
222:
1.162 brouard 223: Revision 1.1 2014/09/16 11:06:58 brouard
224: Summary: With some code (wrong) for nlopt
225:
226: Author:
227:
228: Revision 1.161 2014/09/15 20:41:41 brouard
229: Summary: Problem with macro SQR on Intel compiler
230:
1.161 brouard 231: Revision 1.160 2014/09/02 09:24:05 brouard
232: *** empty log message ***
233:
1.160 brouard 234: Revision 1.159 2014/09/01 10:34:10 brouard
235: Summary: WIN32
236: Author: Brouard
237:
1.159 brouard 238: Revision 1.158 2014/08/27 17:11:51 brouard
239: *** empty log message ***
240:
1.158 brouard 241: Revision 1.157 2014/08/27 16:26:55 brouard
242: Summary: Preparing windows Visual studio version
243: Author: Brouard
244:
245: In order to compile on Visual studio, time.h is now correct and time_t
246: and tm struct should be used. difftime should be used but sometimes I
247: just make the differences in raw time format (time(&now).
248: Trying to suppress #ifdef LINUX
249: Add xdg-open for __linux in order to open default browser.
250:
1.157 brouard 251: Revision 1.156 2014/08/25 20:10:10 brouard
252: *** empty log message ***
253:
1.156 brouard 254: Revision 1.155 2014/08/25 18:32:34 brouard
255: Summary: New compile, minor changes
256: Author: Brouard
257:
1.155 brouard 258: Revision 1.154 2014/06/20 17:32:08 brouard
259: Summary: Outputs now all graphs of convergence to period prevalence
260:
1.154 brouard 261: Revision 1.153 2014/06/20 16:45:46 brouard
262: Summary: If 3 live state, convergence to period prevalence on same graph
263: Author: Brouard
264:
1.153 brouard 265: Revision 1.152 2014/06/18 17:54:09 brouard
266: Summary: open browser, use gnuplot on same dir than imach if not found in the path
267:
1.152 brouard 268: Revision 1.151 2014/06/18 16:43:30 brouard
269: *** empty log message ***
270:
1.151 brouard 271: Revision 1.150 2014/06/18 16:42:35 brouard
272: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
273: Author: brouard
274:
1.150 brouard 275: Revision 1.149 2014/06/18 15:51:14 brouard
276: Summary: Some fixes in parameter files errors
277: Author: Nicolas Brouard
278:
1.149 brouard 279: Revision 1.148 2014/06/17 17:38:48 brouard
280: Summary: Nothing new
281: Author: Brouard
282:
283: Just a new packaging for OS/X version 0.98nS
284:
1.148 brouard 285: Revision 1.147 2014/06/16 10:33:11 brouard
286: *** empty log message ***
287:
1.147 brouard 288: Revision 1.146 2014/06/16 10:20:28 brouard
289: Summary: Merge
290: Author: Brouard
291:
292: Merge, before building revised version.
293:
1.146 brouard 294: Revision 1.145 2014/06/10 21:23:15 brouard
295: Summary: Debugging with valgrind
296: Author: Nicolas Brouard
297:
298: Lot of changes in order to output the results with some covariates
299: After the Edimburgh REVES conference 2014, it seems mandatory to
300: improve the code.
301: No more memory valgrind error but a lot has to be done in order to
302: continue the work of splitting the code into subroutines.
303: Also, decodemodel has been improved. Tricode is still not
304: optimal. nbcode should be improved. Documentation has been added in
305: the source code.
306:
1.144 brouard 307: Revision 1.143 2014/01/26 09:45:38 brouard
308: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
309:
310: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
311: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
312:
1.143 brouard 313: Revision 1.142 2014/01/26 03:57:36 brouard
314: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
315:
316: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
317:
1.142 brouard 318: Revision 1.141 2014/01/26 02:42:01 brouard
319: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
320:
1.141 brouard 321: Revision 1.140 2011/09/02 10:37:54 brouard
322: Summary: times.h is ok with mingw32 now.
323:
1.140 brouard 324: Revision 1.139 2010/06/14 07:50:17 brouard
325: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
326: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
327:
1.139 brouard 328: Revision 1.138 2010/04/30 18:19:40 brouard
329: *** empty log message ***
330:
1.138 brouard 331: Revision 1.137 2010/04/29 18:11:38 brouard
332: (Module): Checking covariates for more complex models
333: than V1+V2. A lot of change to be done. Unstable.
334:
1.137 brouard 335: Revision 1.136 2010/04/26 20:30:53 brouard
336: (Module): merging some libgsl code. Fixing computation
337: of likelione (using inter/intrapolation if mle = 0) in order to
338: get same likelihood as if mle=1.
339: Some cleaning of code and comments added.
340:
1.136 brouard 341: Revision 1.135 2009/10/29 15:33:14 brouard
342: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
343:
1.135 brouard 344: Revision 1.134 2009/10/29 13:18:53 brouard
345: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
346:
1.134 brouard 347: Revision 1.133 2009/07/06 10:21:25 brouard
348: just nforces
349:
1.133 brouard 350: Revision 1.132 2009/07/06 08:22:05 brouard
351: Many tings
352:
1.132 brouard 353: Revision 1.131 2009/06/20 16:22:47 brouard
354: Some dimensions resccaled
355:
1.131 brouard 356: Revision 1.130 2009/05/26 06:44:34 brouard
357: (Module): Max Covariate is now set to 20 instead of 8. A
358: lot of cleaning with variables initialized to 0. Trying to make
359: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
360:
1.130 brouard 361: Revision 1.129 2007/08/31 13:49:27 lievre
362: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
363:
1.129 lievre 364: Revision 1.128 2006/06/30 13:02:05 brouard
365: (Module): Clarifications on computing e.j
366:
1.128 brouard 367: Revision 1.127 2006/04/28 18:11:50 brouard
368: (Module): Yes the sum of survivors was wrong since
369: imach-114 because nhstepm was no more computed in the age
370: loop. Now we define nhstepma in the age loop.
371: (Module): In order to speed up (in case of numerous covariates) we
372: compute health expectancies (without variances) in a first step
373: and then all the health expectancies with variances or standard
374: deviation (needs data from the Hessian matrices) which slows the
375: computation.
376: In the future we should be able to stop the program is only health
377: expectancies and graph are needed without standard deviations.
378:
1.127 brouard 379: Revision 1.126 2006/04/28 17:23:28 brouard
380: (Module): Yes the sum of survivors was wrong since
381: imach-114 because nhstepm was no more computed in the age
382: loop. Now we define nhstepma in the age loop.
383: Version 0.98h
384:
1.126 brouard 385: Revision 1.125 2006/04/04 15:20:31 lievre
386: Errors in calculation of health expectancies. Age was not initialized.
387: Forecasting file added.
388:
389: Revision 1.124 2006/03/22 17:13:53 lievre
390: Parameters are printed with %lf instead of %f (more numbers after the comma).
391: The log-likelihood is printed in the log file
392:
393: Revision 1.123 2006/03/20 10:52:43 brouard
394: * imach.c (Module): <title> changed, corresponds to .htm file
395: name. <head> headers where missing.
396:
397: * imach.c (Module): Weights can have a decimal point as for
398: English (a comma might work with a correct LC_NUMERIC environment,
399: otherwise the weight is truncated).
400: Modification of warning when the covariates values are not 0 or
401: 1.
402: Version 0.98g
403:
404: Revision 1.122 2006/03/20 09:45:41 brouard
405: (Module): Weights can have a decimal point as for
406: English (a comma might work with a correct LC_NUMERIC environment,
407: otherwise the weight is truncated).
408: Modification of warning when the covariates values are not 0 or
409: 1.
410: Version 0.98g
411:
412: Revision 1.121 2006/03/16 17:45:01 lievre
413: * imach.c (Module): Comments concerning covariates added
414:
415: * imach.c (Module): refinements in the computation of lli if
416: status=-2 in order to have more reliable computation if stepm is
417: not 1 month. Version 0.98f
418:
419: Revision 1.120 2006/03/16 15:10:38 lievre
420: (Module): refinements in the computation of lli if
421: status=-2 in order to have more reliable computation if stepm is
422: not 1 month. Version 0.98f
423:
424: Revision 1.119 2006/03/15 17:42:26 brouard
425: (Module): Bug if status = -2, the loglikelihood was
426: computed as likelihood omitting the logarithm. Version O.98e
427:
428: Revision 1.118 2006/03/14 18:20:07 brouard
429: (Module): varevsij Comments added explaining the second
430: table of variances if popbased=1 .
431: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
432: (Module): Function pstamp added
433: (Module): Version 0.98d
434:
435: Revision 1.117 2006/03/14 17:16:22 brouard
436: (Module): varevsij Comments added explaining the second
437: table of variances if popbased=1 .
438: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
439: (Module): Function pstamp added
440: (Module): Version 0.98d
441:
442: Revision 1.116 2006/03/06 10:29:27 brouard
443: (Module): Variance-covariance wrong links and
444: varian-covariance of ej. is needed (Saito).
445:
446: Revision 1.115 2006/02/27 12:17:45 brouard
447: (Module): One freematrix added in mlikeli! 0.98c
448:
449: Revision 1.114 2006/02/26 12:57:58 brouard
450: (Module): Some improvements in processing parameter
451: filename with strsep.
452:
453: Revision 1.113 2006/02/24 14:20:24 brouard
454: (Module): Memory leaks checks with valgrind and:
455: datafile was not closed, some imatrix were not freed and on matrix
456: allocation too.
457:
458: Revision 1.112 2006/01/30 09:55:26 brouard
459: (Module): Back to gnuplot.exe instead of wgnuplot.exe
460:
461: Revision 1.111 2006/01/25 20:38:18 brouard
462: (Module): Lots of cleaning and bugs added (Gompertz)
463: (Module): Comments can be added in data file. Missing date values
464: can be a simple dot '.'.
465:
466: Revision 1.110 2006/01/25 00:51:50 brouard
467: (Module): Lots of cleaning and bugs added (Gompertz)
468:
469: Revision 1.109 2006/01/24 19:37:15 brouard
470: (Module): Comments (lines starting with a #) are allowed in data.
471:
472: Revision 1.108 2006/01/19 18:05:42 lievre
473: Gnuplot problem appeared...
474: To be fixed
475:
476: Revision 1.107 2006/01/19 16:20:37 brouard
477: Test existence of gnuplot in imach path
478:
479: Revision 1.106 2006/01/19 13:24:36 brouard
480: Some cleaning and links added in html output
481:
482: Revision 1.105 2006/01/05 20:23:19 lievre
483: *** empty log message ***
484:
485: Revision 1.104 2005/09/30 16:11:43 lievre
486: (Module): sump fixed, loop imx fixed, and simplifications.
487: (Module): If the status is missing at the last wave but we know
488: that the person is alive, then we can code his/her status as -2
489: (instead of missing=-1 in earlier versions) and his/her
490: contributions to the likelihood is 1 - Prob of dying from last
491: health status (= 1-p13= p11+p12 in the easiest case of somebody in
492: the healthy state at last known wave). Version is 0.98
493:
494: Revision 1.103 2005/09/30 15:54:49 lievre
495: (Module): sump fixed, loop imx fixed, and simplifications.
496:
497: Revision 1.102 2004/09/15 17:31:30 brouard
498: Add the possibility to read data file including tab characters.
499:
500: Revision 1.101 2004/09/15 10:38:38 brouard
501: Fix on curr_time
502:
503: Revision 1.100 2004/07/12 18:29:06 brouard
504: Add version for Mac OS X. Just define UNIX in Makefile
505:
506: Revision 1.99 2004/06/05 08:57:40 brouard
507: *** empty log message ***
508:
509: Revision 1.98 2004/05/16 15:05:56 brouard
510: New version 0.97 . First attempt to estimate force of mortality
511: directly from the data i.e. without the need of knowing the health
512: state at each age, but using a Gompertz model: log u =a + b*age .
513: This is the basic analysis of mortality and should be done before any
514: other analysis, in order to test if the mortality estimated from the
515: cross-longitudinal survey is different from the mortality estimated
516: from other sources like vital statistic data.
517:
518: The same imach parameter file can be used but the option for mle should be -3.
519:
1.133 brouard 520: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 521: former routines in order to include the new code within the former code.
522:
523: The output is very simple: only an estimate of the intercept and of
524: the slope with 95% confident intervals.
525:
526: Current limitations:
527: A) Even if you enter covariates, i.e. with the
528: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
529: B) There is no computation of Life Expectancy nor Life Table.
530:
531: Revision 1.97 2004/02/20 13:25:42 lievre
532: Version 0.96d. Population forecasting command line is (temporarily)
533: suppressed.
534:
535: Revision 1.96 2003/07/15 15:38:55 brouard
536: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
537: rewritten within the same printf. Workaround: many printfs.
538:
539: Revision 1.95 2003/07/08 07:54:34 brouard
540: * imach.c (Repository):
541: (Repository): Using imachwizard code to output a more meaningful covariance
542: matrix (cov(a12,c31) instead of numbers.
543:
544: Revision 1.94 2003/06/27 13:00:02 brouard
545: Just cleaning
546:
547: Revision 1.93 2003/06/25 16:33:55 brouard
548: (Module): On windows (cygwin) function asctime_r doesn't
549: exist so I changed back to asctime which exists.
550: (Module): Version 0.96b
551:
552: Revision 1.92 2003/06/25 16:30:45 brouard
553: (Module): On windows (cygwin) function asctime_r doesn't
554: exist so I changed back to asctime which exists.
555:
556: Revision 1.91 2003/06/25 15:30:29 brouard
557: * imach.c (Repository): Duplicated warning errors corrected.
558: (Repository): Elapsed time after each iteration is now output. It
559: helps to forecast when convergence will be reached. Elapsed time
560: is stamped in powell. We created a new html file for the graphs
561: concerning matrix of covariance. It has extension -cov.htm.
562:
563: Revision 1.90 2003/06/24 12:34:15 brouard
564: (Module): Some bugs corrected for windows. Also, when
565: mle=-1 a template is output in file "or"mypar.txt with the design
566: of the covariance matrix to be input.
567:
568: Revision 1.89 2003/06/24 12:30:52 brouard
569: (Module): Some bugs corrected for windows. Also, when
570: mle=-1 a template is output in file "or"mypar.txt with the design
571: of the covariance matrix to be input.
572:
573: Revision 1.88 2003/06/23 17:54:56 brouard
574: * 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.
575:
576: Revision 1.87 2003/06/18 12:26:01 brouard
577: Version 0.96
578:
579: Revision 1.86 2003/06/17 20:04:08 brouard
580: (Module): Change position of html and gnuplot routines and added
581: routine fileappend.
582:
583: Revision 1.85 2003/06/17 13:12:43 brouard
584: * imach.c (Repository): Check when date of death was earlier that
585: current date of interview. It may happen when the death was just
586: prior to the death. In this case, dh was negative and likelihood
587: was wrong (infinity). We still send an "Error" but patch by
588: assuming that the date of death was just one stepm after the
589: interview.
590: (Repository): Because some people have very long ID (first column)
591: we changed int to long in num[] and we added a new lvector for
592: memory allocation. But we also truncated to 8 characters (left
593: truncation)
594: (Repository): No more line truncation errors.
595:
596: Revision 1.84 2003/06/13 21:44:43 brouard
597: * imach.c (Repository): Replace "freqsummary" at a correct
598: place. It differs from routine "prevalence" which may be called
599: many times. Probs is memory consuming and must be used with
600: parcimony.
601: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
602:
603: Revision 1.83 2003/06/10 13:39:11 lievre
604: *** empty log message ***
605:
606: Revision 1.82 2003/06/05 15:57:20 brouard
607: Add log in imach.c and fullversion number is now printed.
608:
609: */
610: /*
611: Interpolated Markov Chain
612:
613: Short summary of the programme:
614:
615: This program computes Healthy Life Expectancies from
616: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
617: first survey ("cross") where individuals from different ages are
618: interviewed on their health status or degree of disability (in the
619: case of a health survey which is our main interest) -2- at least a
620: second wave of interviews ("longitudinal") which measure each change
621: (if any) in individual health status. Health expectancies are
622: computed from the time spent in each health state according to a
623: model. More health states you consider, more time is necessary to reach the
624: Maximum Likelihood of the parameters involved in the model. The
625: simplest model is the multinomial logistic model where pij is the
626: probability to be observed in state j at the second wave
627: conditional to be observed in state i at the first wave. Therefore
628: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
629: 'age' is age and 'sex' is a covariate. If you want to have a more
630: complex model than "constant and age", you should modify the program
631: where the markup *Covariates have to be included here again* invites
632: you to do it. More covariates you add, slower the
633: convergence.
634:
635: The advantage of this computer programme, compared to a simple
636: multinomial logistic model, is clear when the delay between waves is not
637: identical for each individual. Also, if a individual missed an
638: intermediate interview, the information is lost, but taken into
639: account using an interpolation or extrapolation.
640:
641: hPijx is the probability to be observed in state i at age x+h
642: conditional to the observed state i at age x. The delay 'h' can be
643: split into an exact number (nh*stepm) of unobserved intermediate
644: states. This elementary transition (by month, quarter,
645: semester or year) is modelled as a multinomial logistic. The hPx
646: matrix is simply the matrix product of nh*stepm elementary matrices
647: and the contribution of each individual to the likelihood is simply
648: hPijx.
649:
650: Also this programme outputs the covariance matrix of the parameters but also
651: of the life expectancies. It also computes the period (stable) prevalence.
652:
1.133 brouard 653: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
654: Institut national d'études démographiques, Paris.
1.126 brouard 655: This software have been partly granted by Euro-REVES, a concerted action
656: from the European Union.
657: It is copyrighted identically to a GNU software product, ie programme and
658: software can be distributed freely for non commercial use. Latest version
659: can be accessed at http://euroreves.ined.fr/imach .
660:
661: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
662: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
663:
664: **********************************************************************/
665: /*
666: main
667: read parameterfile
668: read datafile
669: concatwav
670: freqsummary
671: if (mle >= 1)
672: mlikeli
673: print results files
674: if mle==1
675: computes hessian
676: read end of parameter file: agemin, agemax, bage, fage, estepm
677: begin-prev-date,...
678: open gnuplot file
679: open html file
1.145 brouard 680: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
681: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
682: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
683: freexexit2 possible for memory heap.
684:
685: h Pij x | pij_nom ficrestpij
686: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
687: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
688: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
689:
690: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
691: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
692: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
693: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
694: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
695:
1.126 brouard 696: forecasting if prevfcast==1 prevforecast call prevalence()
697: health expectancies
698: Variance-covariance of DFLE
699: prevalence()
700: movingaverage()
701: varevsij()
702: if popbased==1 varevsij(,popbased)
703: total life expectancies
704: Variance of period (stable) prevalence
705: end
706: */
707:
1.187 brouard 708: /* #define DEBUG */
709: /* #define DEBUGBRENT */
1.203 brouard 710: /* #define DEBUGLINMIN */
711: /* #define DEBUGHESS */
712: #define DEBUGHESSIJ
713: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan)*\/ */
1.165 brouard 714: #define POWELL /* Instead of NLOPT */
1.192 brouard 715: #define POWELLF1F3 /* Skip test */
1.186 brouard 716: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
717: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 718:
719: #include <math.h>
720: #include <stdio.h>
721: #include <stdlib.h>
722: #include <string.h>
1.159 brouard 723:
724: #ifdef _WIN32
725: #include <io.h>
1.172 brouard 726: #include <windows.h>
727: #include <tchar.h>
1.159 brouard 728: #else
1.126 brouard 729: #include <unistd.h>
1.159 brouard 730: #endif
1.126 brouard 731:
732: #include <limits.h>
733: #include <sys/types.h>
1.171 brouard 734:
735: #if defined(__GNUC__)
736: #include <sys/utsname.h> /* Doesn't work on Windows */
737: #endif
738:
1.126 brouard 739: #include <sys/stat.h>
740: #include <errno.h>
1.159 brouard 741: /* extern int errno; */
1.126 brouard 742:
1.157 brouard 743: /* #ifdef LINUX */
744: /* #include <time.h> */
745: /* #include "timeval.h" */
746: /* #else */
747: /* #include <sys/time.h> */
748: /* #endif */
749:
1.126 brouard 750: #include <time.h>
751:
1.136 brouard 752: #ifdef GSL
753: #include <gsl/gsl_errno.h>
754: #include <gsl/gsl_multimin.h>
755: #endif
756:
1.167 brouard 757:
1.162 brouard 758: #ifdef NLOPT
759: #include <nlopt.h>
760: typedef struct {
761: double (* function)(double [] );
762: } myfunc_data ;
763: #endif
764:
1.126 brouard 765: /* #include <libintl.h> */
766: /* #define _(String) gettext (String) */
767:
1.141 brouard 768: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 769:
770: #define GNUPLOTPROGRAM "gnuplot"
771: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
772: #define FILENAMELENGTH 132
773:
774: #define GLOCK_ERROR_NOPATH -1 /* empty path */
775: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
776:
1.144 brouard 777: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
778: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 779:
780: #define NINTERVMAX 8
1.144 brouard 781: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
782: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
783: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 784: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 785: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
786: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.126 brouard 787: #define MAXN 20000
1.144 brouard 788: #define YEARM 12. /**< Number of months per year */
1.126 brouard 789: #define AGESUP 130
790: #define AGEBASE 40
1.194 brouard 791: #define AGEOVERFLOW 1.e20
1.164 brouard 792: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 793: #ifdef _WIN32
794: #define DIRSEPARATOR '\\'
795: #define CHARSEPARATOR "\\"
796: #define ODIRSEPARATOR '/'
797: #else
1.126 brouard 798: #define DIRSEPARATOR '/'
799: #define CHARSEPARATOR "/"
800: #define ODIRSEPARATOR '\\'
801: #endif
802:
1.217 ! brouard 803: /* $Id: imach.c,v 1.216 2015/12/18 17:32:11 brouard Exp $ */
1.126 brouard 804: /* $State: Exp $ */
1.196 brouard 805: #include "version.h"
806: char version[]=__IMACH_VERSION__;
1.204 brouard 807: char copyright[]="October 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
1.217 ! brouard 808: char fullversion[]="$Revision: 1.216 $ $Date: 2015/12/18 17:32:11 $";
1.126 brouard 809: char strstart[80];
810: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 811: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 812: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 813: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
814: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
815: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
816: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
817: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
818: int cptcovprodnoage=0; /**< Number of covariate products without age */
819: int cptcoveff=0; /* Total number of covariates to vary for printing results */
820: int cptcov=0; /* Working variable */
1.126 brouard 821: int npar=NPARMAX;
822: int nlstate=2; /* Number of live states */
823: int ndeath=1; /* Number of dead states */
1.130 brouard 824: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 825: int popbased=0;
826:
827: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 828: int maxwav=0; /* Maxim number of waves */
829: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
830: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
831: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 832: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 833: int mle=1, weightopt=0;
1.126 brouard 834: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
835: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
836: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
837: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 838: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 839: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 840: double **matprod2(); /* test */
1.126 brouard 841: double **oldm, **newm, **savm; /* Working pointers to matrices */
842: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 843: /*FILE *fic ; */ /* Used in readdata only */
1.217 ! brouard 844: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 845: FILE *ficlog, *ficrespow;
1.130 brouard 846: int globpr=0; /* Global variable for printing or not */
1.126 brouard 847: double fretone; /* Only one call to likelihood */
1.130 brouard 848: long ipmx=0; /* Number of contributions */
1.126 brouard 849: double sw; /* Sum of weights */
850: char filerespow[FILENAMELENGTH];
851: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
852: FILE *ficresilk;
853: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
854: FILE *ficresprobmorprev;
855: FILE *fichtm, *fichtmcov; /* Html File */
856: FILE *ficreseij;
857: char filerese[FILENAMELENGTH];
858: FILE *ficresstdeij;
859: char fileresstde[FILENAMELENGTH];
860: FILE *ficrescveij;
861: char filerescve[FILENAMELENGTH];
862: FILE *ficresvij;
863: char fileresv[FILENAMELENGTH];
864: FILE *ficresvpl;
865: char fileresvpl[FILENAMELENGTH];
866: char title[MAXLINE];
1.217 ! brouard 867: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 868: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
869: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
870: char command[FILENAMELENGTH];
871: int outcmd=0;
872:
1.217 ! brouard 873: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 874: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 875: char filelog[FILENAMELENGTH]; /* Log file */
876: char filerest[FILENAMELENGTH];
877: char fileregp[FILENAMELENGTH];
878: char popfile[FILENAMELENGTH];
879:
880: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
881:
1.157 brouard 882: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
883: /* struct timezone tzp; */
884: /* extern int gettimeofday(); */
885: struct tm tml, *gmtime(), *localtime();
886:
887: extern time_t time();
888:
889: struct tm start_time, end_time, curr_time, last_time, forecast_time;
890: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
891: struct tm tm;
892:
1.126 brouard 893: char strcurr[80], strfor[80];
894:
895: char *endptr;
896: long lval;
897: double dval;
898:
899: #define NR_END 1
900: #define FREE_ARG char*
901: #define FTOL 1.0e-10
902:
903: #define NRANSI
904: #define ITMAX 200
905:
906: #define TOL 2.0e-4
907:
908: #define CGOLD 0.3819660
909: #define ZEPS 1.0e-10
910: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
911:
912: #define GOLD 1.618034
913: #define GLIMIT 100.0
914: #define TINY 1.0e-20
915:
916: static double maxarg1,maxarg2;
917: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
918: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
919:
920: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
921: #define rint(a) floor(a+0.5)
1.166 brouard 922: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 923: #define mytinydouble 1.0e-16
1.166 brouard 924: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
925: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
926: /* static double dsqrarg; */
927: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 928: static double sqrarg;
929: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
930: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
931: int agegomp= AGEGOMP;
932:
933: int imx;
934: int stepm=1;
935: /* Stepm, step in month: minimum step interpolation*/
936:
937: int estepm;
938: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
939:
940: int m,nb;
941: long *num;
1.197 brouard 942: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 943: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
944: covariate for which somebody answered excluding
945: undefined. Usually 2: 0 and 1. */
946: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
947: covariate for which somebody answered including
948: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 949: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
950: double **pmmij, ***probs;
951: double *ageexmed,*agecens;
952: double dateintmean=0;
953:
954: double *weight;
955: int **s; /* Status */
1.141 brouard 956: double *agedc;
1.145 brouard 957: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 958: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 959: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 960: double idx;
961: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.197 brouard 962: int *Tage;
1.145 brouard 963: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 964: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.141 brouard 965: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 966: double *lsurv, *lpop, *tpop;
967:
1.143 brouard 968: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
969: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 970:
971: /**************** split *************************/
972: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
973: {
974: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
975: the name of the file (name), its extension only (ext) and its first part of the name (finame)
976: */
977: char *ss; /* pointer */
1.186 brouard 978: int l1=0, l2=0; /* length counters */
1.126 brouard 979:
980: l1 = strlen(path ); /* length of path */
981: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
982: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
983: if ( ss == NULL ) { /* no directory, so determine current directory */
984: strcpy( name, path ); /* we got the fullname name because no directory */
985: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
986: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
987: /* get current working directory */
988: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 989: #ifdef WIN32
990: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
991: #else
992: if (getcwd(dirc, FILENAME_MAX) == NULL) {
993: #endif
1.126 brouard 994: return( GLOCK_ERROR_GETCWD );
995: }
996: /* got dirc from getcwd*/
997: printf(" DIRC = %s \n",dirc);
1.205 brouard 998: } else { /* strip directory from path */
1.126 brouard 999: ss++; /* after this, the filename */
1000: l2 = strlen( ss ); /* length of filename */
1001: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1002: strcpy( name, ss ); /* save file name */
1003: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1004: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1005: printf(" DIRC2 = %s \n",dirc);
1006: }
1007: /* We add a separator at the end of dirc if not exists */
1008: l1 = strlen( dirc ); /* length of directory */
1009: if( dirc[l1-1] != DIRSEPARATOR ){
1010: dirc[l1] = DIRSEPARATOR;
1011: dirc[l1+1] = 0;
1012: printf(" DIRC3 = %s \n",dirc);
1013: }
1014: ss = strrchr( name, '.' ); /* find last / */
1015: if (ss >0){
1016: ss++;
1017: strcpy(ext,ss); /* save extension */
1018: l1= strlen( name);
1019: l2= strlen(ss)+1;
1020: strncpy( finame, name, l1-l2);
1021: finame[l1-l2]= 0;
1022: }
1023:
1024: return( 0 ); /* we're done */
1025: }
1026:
1027:
1028: /******************************************/
1029:
1030: void replace_back_to_slash(char *s, char*t)
1031: {
1032: int i;
1033: int lg=0;
1034: i=0;
1035: lg=strlen(t);
1036: for(i=0; i<= lg; i++) {
1037: (s[i] = t[i]);
1038: if (t[i]== '\\') s[i]='/';
1039: }
1040: }
1041:
1.132 brouard 1042: char *trimbb(char *out, char *in)
1.137 brouard 1043: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1044: char *s;
1045: s=out;
1046: while (*in != '\0'){
1.137 brouard 1047: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1048: in++;
1049: }
1050: *out++ = *in++;
1051: }
1052: *out='\0';
1053: return s;
1054: }
1055:
1.187 brouard 1056: /* char *substrchaine(char *out, char *in, char *chain) */
1057: /* { */
1058: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1059: /* char *s, *t; */
1060: /* t=in;s=out; */
1061: /* while ((*in != *chain) && (*in != '\0')){ */
1062: /* *out++ = *in++; */
1063: /* } */
1064:
1065: /* /\* *in matches *chain *\/ */
1066: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1067: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1068: /* } */
1069: /* in--; chain--; */
1070: /* while ( (*in != '\0')){ */
1071: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1072: /* *out++ = *in++; */
1073: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1074: /* } */
1075: /* *out='\0'; */
1076: /* out=s; */
1077: /* return out; */
1078: /* } */
1079: char *substrchaine(char *out, char *in, char *chain)
1080: {
1081: /* Substract chain 'chain' from 'in', return and output 'out' */
1082: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1083:
1084: char *strloc;
1085:
1086: strcpy (out, in);
1087: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1088: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1089: if(strloc != NULL){
1090: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1091: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1092: /* strcpy (strloc, strloc +strlen(chain));*/
1093: }
1094: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1095: return out;
1096: }
1097:
1098:
1.145 brouard 1099: char *cutl(char *blocc, char *alocc, char *in, char occ)
1100: {
1.187 brouard 1101: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1102: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1103: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1104: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1105: */
1.160 brouard 1106: char *s, *t;
1.145 brouard 1107: t=in;s=in;
1108: while ((*in != occ) && (*in != '\0')){
1109: *alocc++ = *in++;
1110: }
1111: if( *in == occ){
1112: *(alocc)='\0';
1113: s=++in;
1114: }
1115:
1116: if (s == t) {/* occ not found */
1117: *(alocc-(in-s))='\0';
1118: in=s;
1119: }
1120: while ( *in != '\0'){
1121: *blocc++ = *in++;
1122: }
1123:
1124: *blocc='\0';
1125: return t;
1126: }
1.137 brouard 1127: char *cutv(char *blocc, char *alocc, char *in, char occ)
1128: {
1.187 brouard 1129: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1130: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1131: gives blocc="abcdef2ghi" and alocc="j".
1132: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1133: */
1134: char *s, *t;
1135: t=in;s=in;
1136: while (*in != '\0'){
1137: while( *in == occ){
1138: *blocc++ = *in++;
1139: s=in;
1140: }
1141: *blocc++ = *in++;
1142: }
1143: if (s == t) /* occ not found */
1144: *(blocc-(in-s))='\0';
1145: else
1146: *(blocc-(in-s)-1)='\0';
1147: in=s;
1148: while ( *in != '\0'){
1149: *alocc++ = *in++;
1150: }
1151:
1152: *alocc='\0';
1153: return s;
1154: }
1155:
1.126 brouard 1156: int nbocc(char *s, char occ)
1157: {
1158: int i,j=0;
1159: int lg=20;
1160: i=0;
1161: lg=strlen(s);
1162: for(i=0; i<= lg; i++) {
1163: if (s[i] == occ ) j++;
1164: }
1165: return j;
1166: }
1167:
1.137 brouard 1168: /* void cutv(char *u,char *v, char*t, char occ) */
1169: /* { */
1170: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1171: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1172: /* gives u="abcdef2ghi" and v="j" *\/ */
1173: /* int i,lg,j,p=0; */
1174: /* i=0; */
1175: /* lg=strlen(t); */
1176: /* for(j=0; j<=lg-1; j++) { */
1177: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1178: /* } */
1.126 brouard 1179:
1.137 brouard 1180: /* for(j=0; j<p; j++) { */
1181: /* (u[j] = t[j]); */
1182: /* } */
1183: /* u[p]='\0'; */
1.126 brouard 1184:
1.137 brouard 1185: /* for(j=0; j<= lg; j++) { */
1186: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1187: /* } */
1188: /* } */
1.126 brouard 1189:
1.160 brouard 1190: #ifdef _WIN32
1191: char * strsep(char **pp, const char *delim)
1192: {
1193: char *p, *q;
1194:
1195: if ((p = *pp) == NULL)
1196: return 0;
1197: if ((q = strpbrk (p, delim)) != NULL)
1198: {
1199: *pp = q + 1;
1200: *q = '\0';
1201: }
1202: else
1203: *pp = 0;
1204: return p;
1205: }
1206: #endif
1207:
1.126 brouard 1208: /********************** nrerror ********************/
1209:
1210: void nrerror(char error_text[])
1211: {
1212: fprintf(stderr,"ERREUR ...\n");
1213: fprintf(stderr,"%s\n",error_text);
1214: exit(EXIT_FAILURE);
1215: }
1216: /*********************** vector *******************/
1217: double *vector(int nl, int nh)
1218: {
1219: double *v;
1220: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1221: if (!v) nrerror("allocation failure in vector");
1222: return v-nl+NR_END;
1223: }
1224:
1225: /************************ free vector ******************/
1226: void free_vector(double*v, int nl, int nh)
1227: {
1228: free((FREE_ARG)(v+nl-NR_END));
1229: }
1230:
1231: /************************ivector *******************************/
1232: int *ivector(long nl,long nh)
1233: {
1234: int *v;
1235: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1236: if (!v) nrerror("allocation failure in ivector");
1237: return v-nl+NR_END;
1238: }
1239:
1240: /******************free ivector **************************/
1241: void free_ivector(int *v, long nl, long nh)
1242: {
1243: free((FREE_ARG)(v+nl-NR_END));
1244: }
1245:
1246: /************************lvector *******************************/
1247: long *lvector(long nl,long nh)
1248: {
1249: long *v;
1250: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1251: if (!v) nrerror("allocation failure in ivector");
1252: return v-nl+NR_END;
1253: }
1254:
1255: /******************free lvector **************************/
1256: void free_lvector(long *v, long nl, long nh)
1257: {
1258: free((FREE_ARG)(v+nl-NR_END));
1259: }
1260:
1261: /******************* imatrix *******************************/
1262: int **imatrix(long nrl, long nrh, long ncl, long nch)
1263: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1264: {
1265: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1266: int **m;
1267:
1268: /* allocate pointers to rows */
1269: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1270: if (!m) nrerror("allocation failure 1 in matrix()");
1271: m += NR_END;
1272: m -= nrl;
1273:
1274:
1275: /* allocate rows and set pointers to them */
1276: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1277: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1278: m[nrl] += NR_END;
1279: m[nrl] -= ncl;
1280:
1281: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1282:
1283: /* return pointer to array of pointers to rows */
1284: return m;
1285: }
1286:
1287: /****************** free_imatrix *************************/
1288: void free_imatrix(m,nrl,nrh,ncl,nch)
1289: int **m;
1290: long nch,ncl,nrh,nrl;
1291: /* free an int matrix allocated by imatrix() */
1292: {
1293: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1294: free((FREE_ARG) (m+nrl-NR_END));
1295: }
1296:
1297: /******************* matrix *******************************/
1298: double **matrix(long nrl, long nrh, long ncl, long nch)
1299: {
1300: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1301: double **m;
1302:
1303: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1304: if (!m) nrerror("allocation failure 1 in matrix()");
1305: m += NR_END;
1306: m -= nrl;
1307:
1308: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1309: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1310: m[nrl] += NR_END;
1311: m[nrl] -= ncl;
1312:
1313: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1314: return m;
1.145 brouard 1315: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1316: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1317: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1318: */
1319: }
1320:
1321: /*************************free matrix ************************/
1322: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1323: {
1324: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1325: free((FREE_ARG)(m+nrl-NR_END));
1326: }
1327:
1328: /******************* ma3x *******************************/
1329: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1330: {
1331: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1332: double ***m;
1333:
1334: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1335: if (!m) nrerror("allocation failure 1 in matrix()");
1336: m += NR_END;
1337: m -= nrl;
1338:
1339: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1340: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1341: m[nrl] += NR_END;
1342: m[nrl] -= ncl;
1343:
1344: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1345:
1346: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1347: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1348: m[nrl][ncl] += NR_END;
1349: m[nrl][ncl] -= nll;
1350: for (j=ncl+1; j<=nch; j++)
1351: m[nrl][j]=m[nrl][j-1]+nlay;
1352:
1353: for (i=nrl+1; i<=nrh; i++) {
1354: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1355: for (j=ncl+1; j<=nch; j++)
1356: m[i][j]=m[i][j-1]+nlay;
1357: }
1358: return m;
1359: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1360: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1361: */
1362: }
1363:
1364: /*************************free ma3x ************************/
1365: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1366: {
1367: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1368: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1369: free((FREE_ARG)(m+nrl-NR_END));
1370: }
1371:
1372: /*************** function subdirf ***********/
1373: char *subdirf(char fileres[])
1374: {
1375: /* Caution optionfilefiname is hidden */
1376: strcpy(tmpout,optionfilefiname);
1377: strcat(tmpout,"/"); /* Add to the right */
1378: strcat(tmpout,fileres);
1379: return tmpout;
1380: }
1381:
1382: /*************** function subdirf2 ***********/
1383: char *subdirf2(char fileres[], char *preop)
1384: {
1385:
1386: /* Caution optionfilefiname is hidden */
1387: strcpy(tmpout,optionfilefiname);
1388: strcat(tmpout,"/");
1389: strcat(tmpout,preop);
1390: strcat(tmpout,fileres);
1391: return tmpout;
1392: }
1393:
1394: /*************** function subdirf3 ***********/
1395: char *subdirf3(char fileres[], char *preop, char *preop2)
1396: {
1397:
1398: /* Caution optionfilefiname is hidden */
1399: strcpy(tmpout,optionfilefiname);
1400: strcat(tmpout,"/");
1401: strcat(tmpout,preop);
1402: strcat(tmpout,preop2);
1403: strcat(tmpout,fileres);
1404: return tmpout;
1405: }
1.213 brouard 1406:
1407: /*************** function subdirfext ***********/
1408: char *subdirfext(char fileres[], char *preop, char *postop)
1409: {
1410:
1411: strcpy(tmpout,preop);
1412: strcat(tmpout,fileres);
1413: strcat(tmpout,postop);
1414: return tmpout;
1415: }
1.126 brouard 1416:
1.213 brouard 1417: /*************** function subdirfext3 ***********/
1418: char *subdirfext3(char fileres[], char *preop, char *postop)
1419: {
1420:
1421: /* Caution optionfilefiname is hidden */
1422: strcpy(tmpout,optionfilefiname);
1423: strcat(tmpout,"/");
1424: strcat(tmpout,preop);
1425: strcat(tmpout,fileres);
1426: strcat(tmpout,postop);
1427: return tmpout;
1428: }
1429:
1.162 brouard 1430: char *asc_diff_time(long time_sec, char ascdiff[])
1431: {
1432: long sec_left, days, hours, minutes;
1433: days = (time_sec) / (60*60*24);
1434: sec_left = (time_sec) % (60*60*24);
1435: hours = (sec_left) / (60*60) ;
1436: sec_left = (sec_left) %(60*60);
1437: minutes = (sec_left) /60;
1438: sec_left = (sec_left) % (60);
1439: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1440: return ascdiff;
1441: }
1442:
1.126 brouard 1443: /***************** f1dim *************************/
1444: extern int ncom;
1445: extern double *pcom,*xicom;
1446: extern double (*nrfunc)(double []);
1447:
1448: double f1dim(double x)
1449: {
1450: int j;
1451: double f;
1452: double *xt;
1453:
1454: xt=vector(1,ncom);
1455: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1456: f=(*nrfunc)(xt);
1457: free_vector(xt,1,ncom);
1458: return f;
1459: }
1460:
1461: /*****************brent *************************/
1462: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1463: {
1464: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1465: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1466: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1467: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1468: * returned function value.
1469: */
1.126 brouard 1470: int iter;
1471: double a,b,d,etemp;
1.159 brouard 1472: double fu=0,fv,fw,fx;
1.164 brouard 1473: double ftemp=0.;
1.126 brouard 1474: double p,q,r,tol1,tol2,u,v,w,x,xm;
1475: double e=0.0;
1476:
1477: a=(ax < cx ? ax : cx);
1478: b=(ax > cx ? ax : cx);
1479: x=w=v=bx;
1480: fw=fv=fx=(*f)(x);
1481: for (iter=1;iter<=ITMAX;iter++) {
1482: xm=0.5*(a+b);
1483: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1484: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1485: printf(".");fflush(stdout);
1486: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1487: #ifdef DEBUGBRENT
1.126 brouard 1488: 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);
1489: 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);
1490: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1491: #endif
1492: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1493: *xmin=x;
1494: return fx;
1495: }
1496: ftemp=fu;
1497: if (fabs(e) > tol1) {
1498: r=(x-w)*(fx-fv);
1499: q=(x-v)*(fx-fw);
1500: p=(x-v)*q-(x-w)*r;
1501: q=2.0*(q-r);
1502: if (q > 0.0) p = -p;
1503: q=fabs(q);
1504: etemp=e;
1505: e=d;
1506: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1507: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1508: else {
1509: d=p/q;
1510: u=x+d;
1511: if (u-a < tol2 || b-u < tol2)
1512: d=SIGN(tol1,xm-x);
1513: }
1514: } else {
1515: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1516: }
1517: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1518: fu=(*f)(u);
1519: if (fu <= fx) {
1520: if (u >= x) a=x; else b=x;
1521: SHFT(v,w,x,u)
1.183 brouard 1522: SHFT(fv,fw,fx,fu)
1523: } else {
1524: if (u < x) a=u; else b=u;
1525: if (fu <= fw || w == x) {
1526: v=w;
1527: w=u;
1528: fv=fw;
1529: fw=fu;
1530: } else if (fu <= fv || v == x || v == w) {
1531: v=u;
1532: fv=fu;
1533: }
1534: }
1.126 brouard 1535: }
1536: nrerror("Too many iterations in brent");
1537: *xmin=x;
1538: return fx;
1539: }
1540:
1541: /****************** mnbrak ***********************/
1542:
1543: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1544: double (*func)(double))
1.183 brouard 1545: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1546: the downhill direction (defined by the function as evaluated at the initial points) and returns
1547: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1548: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1549: */
1.126 brouard 1550: double ulim,u,r,q, dum;
1551: double fu;
1.187 brouard 1552:
1553: double scale=10.;
1554: int iterscale=0;
1555:
1556: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1557: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1558:
1559:
1560: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1561: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1562: /* *bx = *ax - (*ax - *bx)/scale; */
1563: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1564: /* } */
1565:
1.126 brouard 1566: if (*fb > *fa) {
1567: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1568: SHFT(dum,*fb,*fa,dum)
1569: }
1.126 brouard 1570: *cx=(*bx)+GOLD*(*bx-*ax);
1571: *fc=(*func)(*cx);
1.183 brouard 1572: #ifdef DEBUG
1573: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1574: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1575: #endif
1576: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1577: r=(*bx-*ax)*(*fb-*fc);
1578: q=(*bx-*cx)*(*fb-*fa);
1579: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1580: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1581: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1582: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1583: fu=(*func)(u);
1.163 brouard 1584: #ifdef DEBUG
1585: /* f(x)=A(x-u)**2+f(u) */
1586: double A, fparabu;
1587: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1588: fparabu= *fa - A*(*ax-u)*(*ax-u);
1589: printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
1590: fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
1.183 brouard 1591: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1592: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1593: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1594: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1595: #endif
1.184 brouard 1596: #ifdef MNBRAKORIGINAL
1.183 brouard 1597: #else
1.191 brouard 1598: /* if (fu > *fc) { */
1599: /* #ifdef DEBUG */
1600: /* printf("mnbrak4 fu > fc \n"); */
1601: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1602: /* #endif */
1603: /* /\* 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 *\\/ *\/ */
1604: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1605: /* dum=u; /\* Shifting c and u *\/ */
1606: /* u = *cx; */
1607: /* *cx = dum; */
1608: /* dum = fu; */
1609: /* fu = *fc; */
1610: /* *fc =dum; */
1611: /* } else { /\* end *\/ */
1612: /* #ifdef DEBUG */
1613: /* printf("mnbrak3 fu < fc \n"); */
1614: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1615: /* #endif */
1616: /* dum=u; /\* Shifting c and u *\/ */
1617: /* u = *cx; */
1618: /* *cx = dum; */
1619: /* dum = fu; */
1620: /* fu = *fc; */
1621: /* *fc =dum; */
1622: /* } */
1.183 brouard 1623: #ifdef DEBUG
1.191 brouard 1624: printf("mnbrak34 fu < or >= fc \n");
1625: fprintf(ficlog, "mnbrak34 fu < fc\n");
1.183 brouard 1626: #endif
1.191 brouard 1627: dum=u; /* Shifting c and u */
1628: u = *cx;
1629: *cx = dum;
1630: dum = fu;
1631: fu = *fc;
1632: *fc =dum;
1.183 brouard 1633: #endif
1.162 brouard 1634: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1635: #ifdef DEBUG
1636: printf("mnbrak2 u after c but before ulim\n");
1637: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1638: #endif
1.126 brouard 1639: fu=(*func)(u);
1640: if (fu < *fc) {
1.183 brouard 1641: #ifdef DEBUG
1642: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1643: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1644: #endif
1.126 brouard 1645: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1646: SHFT(*fb,*fc,fu,(*func)(u))
1647: }
1.162 brouard 1648: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1649: #ifdef DEBUG
1650: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1651: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1652: #endif
1.126 brouard 1653: u=ulim;
1654: fu=(*func)(u);
1.183 brouard 1655: } else { /* u could be left to b (if r > q parabola has a maximum) */
1656: #ifdef DEBUG
1657: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1658: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1659: #endif
1.126 brouard 1660: u=(*cx)+GOLD*(*cx-*bx);
1661: fu=(*func)(u);
1.183 brouard 1662: } /* end tests */
1.126 brouard 1663: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1664: SHFT(*fa,*fb,*fc,fu)
1665: #ifdef DEBUG
1666: printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
1667: fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
1668: #endif
1669: } /* 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 1670: }
1671:
1672: /*************** linmin ************************/
1.162 brouard 1673: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1674: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1675: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1676: the value of func at the returned location p . This is actually all accomplished by calling the
1677: routines mnbrak and brent .*/
1.126 brouard 1678: int ncom;
1679: double *pcom,*xicom;
1680: double (*nrfunc)(double []);
1681:
1682: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1683: {
1684: double brent(double ax, double bx, double cx,
1685: double (*f)(double), double tol, double *xmin);
1686: double f1dim(double x);
1687: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1688: double *fc, double (*func)(double));
1689: int j;
1690: double xx,xmin,bx,ax;
1691: double fx,fb,fa;
1.187 brouard 1692:
1.203 brouard 1693: #ifdef LINMINORIGINAL
1694: #else
1695: double scale=10., axs, xxs; /* Scale added for infinity */
1696: #endif
1697:
1.126 brouard 1698: ncom=n;
1699: pcom=vector(1,n);
1700: xicom=vector(1,n);
1701: nrfunc=func;
1702: for (j=1;j<=n;j++) {
1703: pcom[j]=p[j];
1.202 brouard 1704: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1705: }
1.187 brouard 1706:
1.203 brouard 1707: #ifdef LINMINORIGINAL
1708: xx=1.;
1709: #else
1710: axs=0.0;
1711: xxs=1.;
1712: do{
1713: xx= xxs;
1714: #endif
1.187 brouard 1715: ax=0.;
1716: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1717: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1718: /* 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)) */
1719: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1720: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1721: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1722: /* 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 1723: #ifdef LINMINORIGINAL
1724: #else
1725: if (fx != fx){
1726: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1727: printf("|");
1728: fprintf(ficlog,"|");
1729: #ifdef DEBUGLINMIN
1730: 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);
1731: #endif
1732: }
1733: }while(fx != fx);
1734: #endif
1735:
1.191 brouard 1736: #ifdef DEBUGLINMIN
1737: 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 1738: 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 1739: #endif
1.187 brouard 1740: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1741: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1742: /* fmin = f(p[j] + xmin * xi[j]) */
1743: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1744: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1745: #ifdef DEBUG
1746: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1747: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1748: #endif
1.191 brouard 1749: #ifdef DEBUGLINMIN
1750: printf("linmin end ");
1.202 brouard 1751: fprintf(ficlog,"linmin end ");
1.191 brouard 1752: #endif
1.126 brouard 1753: for (j=1;j<=n;j++) {
1.203 brouard 1754: #ifdef LINMINORIGINAL
1755: xi[j] *= xmin;
1756: #else
1757: #ifdef DEBUGLINMIN
1758: if(xxs <1.0)
1759: printf(" before xi[%d]=%12.8f", j,xi[j]);
1760: #endif
1761: 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) */
1762: #ifdef DEBUGLINMIN
1763: if(xxs <1.0)
1764: 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 );
1765: #endif
1766: #endif
1.187 brouard 1767: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1768: }
1.191 brouard 1769: #ifdef DEBUGLINMIN
1.203 brouard 1770: printf("\n");
1.191 brouard 1771: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 1772: 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 1773: for (j=1;j<=n;j++) {
1.202 brouard 1774: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1775: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1776: if(j % ncovmodel == 0){
1.191 brouard 1777: printf("\n");
1.202 brouard 1778: fprintf(ficlog,"\n");
1779: }
1.191 brouard 1780: }
1.203 brouard 1781: #else
1.191 brouard 1782: #endif
1.126 brouard 1783: free_vector(xicom,1,n);
1784: free_vector(pcom,1,n);
1785: }
1786:
1787:
1788: /*************** powell ************************/
1.162 brouard 1789: /*
1790: Minimization of a function func of n variables. Input consists of an initial starting point
1791: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1792: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1793: such that failure to decrease by more than this amount on one iteration signals doneness. On
1794: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1795: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1796: */
1.126 brouard 1797: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1798: double (*func)(double []))
1799: {
1800: void linmin(double p[], double xi[], int n, double *fret,
1801: double (*func)(double []));
1802: int i,ibig,j;
1803: double del,t,*pt,*ptt,*xit;
1.181 brouard 1804: double directest;
1.126 brouard 1805: double fp,fptt;
1806: double *xits;
1807: int niterf, itmp;
1808:
1809: pt=vector(1,n);
1810: ptt=vector(1,n);
1811: xit=vector(1,n);
1812: xits=vector(1,n);
1813: *fret=(*func)(p);
1814: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 1815: rcurr_time = time(NULL);
1.126 brouard 1816: for (*iter=1;;++(*iter)) {
1.187 brouard 1817: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1818: ibig=0;
1819: del=0.0;
1.157 brouard 1820: rlast_time=rcurr_time;
1821: /* (void) gettimeofday(&curr_time,&tzp); */
1822: rcurr_time = time(NULL);
1823: curr_time = *localtime(&rcurr_time);
1824: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1825: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1826: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1827: for (i=1;i<=n;i++) {
1.126 brouard 1828: printf(" %d %.12f",i, p[i]);
1829: fprintf(ficlog," %d %.12lf",i, p[i]);
1830: fprintf(ficrespow," %.12lf", p[i]);
1831: }
1832: printf("\n");
1833: fprintf(ficlog,"\n");
1834: fprintf(ficrespow,"\n");fflush(ficrespow);
1835: if(*iter <=3){
1.157 brouard 1836: tml = *localtime(&rcurr_time);
1837: strcpy(strcurr,asctime(&tml));
1838: rforecast_time=rcurr_time;
1.126 brouard 1839: itmp = strlen(strcurr);
1840: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1841: strcurr[itmp-1]='\0';
1.162 brouard 1842: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1843: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1844: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1845: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1846: forecast_time = *localtime(&rforecast_time);
1847: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1848: itmp = strlen(strfor);
1849: if(strfor[itmp-1]=='\n')
1850: strfor[itmp-1]='\0';
1.157 brouard 1851: 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);
1852: 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 1853: }
1854: }
1.187 brouard 1855: for (i=1;i<=n;i++) { /* For each direction i */
1856: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1857: fptt=(*fret);
1858: #ifdef DEBUG
1.203 brouard 1859: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1860: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1861: #endif
1.203 brouard 1862: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1863: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 brouard 1864: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1865: /* Outputs are fret(new point p) p is updated and xit rescaled */
1866: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1867: /* because that direction will be replaced unless the gain del is small */
1868: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1869: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1870: /* with the new direction. */
1.126 brouard 1871: del=fabs(fptt-(*fret));
1872: ibig=i;
1873: }
1874: #ifdef DEBUG
1875: printf("%d %.12e",i,(*fret));
1876: fprintf(ficlog,"%d %.12e",i,(*fret));
1877: for (j=1;j<=n;j++) {
1878: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1879: printf(" x(%d)=%.12e",j,xit[j]);
1880: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1881: }
1882: for(j=1;j<=n;j++) {
1.162 brouard 1883: printf(" p(%d)=%.12e",j,p[j]);
1884: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1885: }
1886: printf("\n");
1887: fprintf(ficlog,"\n");
1888: #endif
1.187 brouard 1889: } /* end loop on each direction i */
1890: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1891: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1892: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1893: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1894: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1895: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1896: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1897: /* decreased of more than 3.84 */
1898: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1899: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1900: /* By adding 10 parameters more the gain should be 18.31 */
1901:
1902: /* Starting the program with initial values given by a former maximization will simply change */
1903: /* the scales of the directions and the directions, because the are reset to canonical directions */
1904: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1905: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1906: #ifdef DEBUG
1907: int k[2],l;
1908: k[0]=1;
1909: k[1]=-1;
1910: printf("Max: %.12e",(*func)(p));
1911: fprintf(ficlog,"Max: %.12e",(*func)(p));
1912: for (j=1;j<=n;j++) {
1913: printf(" %.12e",p[j]);
1914: fprintf(ficlog," %.12e",p[j]);
1915: }
1916: printf("\n");
1917: fprintf(ficlog,"\n");
1918: for(l=0;l<=1;l++) {
1919: for (j=1;j<=n;j++) {
1920: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1921: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1922: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1923: }
1924: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1925: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1926: }
1927: #endif
1928:
1929:
1930: free_vector(xit,1,n);
1931: free_vector(xits,1,n);
1932: free_vector(ptt,1,n);
1933: free_vector(pt,1,n);
1934: return;
1.192 brouard 1935: } /* enough precision */
1.126 brouard 1936: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1937: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1938: ptt[j]=2.0*p[j]-pt[j];
1939: xit[j]=p[j]-pt[j];
1940: pt[j]=p[j];
1941: }
1.181 brouard 1942: fptt=(*func)(ptt); /* f_3 */
1.192 brouard 1943: #ifdef POWELLF1F3
1944: #else
1.161 brouard 1945: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 1946: #endif
1.162 brouard 1947: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1948: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1949: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1950: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1951: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1952: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1953: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1954: #ifdef NRCORIGINAL
1955: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1956: #else
1957: 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 1958: t= t- del*SQR(fp-fptt);
1.183 brouard 1959: #endif
1.202 brouard 1960: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 1961: #ifdef DEBUG
1.181 brouard 1962: 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);
1963: 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 1964: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1965: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1966: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1967: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1968: 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);
1969: 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);
1970: #endif
1.183 brouard 1971: #ifdef POWELLORIGINAL
1972: if (t < 0.0) { /* Then we use it for new direction */
1973: #else
1.182 brouard 1974: if (directest*t < 0.0) { /* Contradiction between both tests */
1.202 brouard 1975: 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 1976: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1.202 brouard 1977: fprintf(ficlog,"directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1.192 brouard 1978: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1979: }
1.181 brouard 1980: if (directest < 0.0) { /* Then we use it for new direction */
1981: #endif
1.191 brouard 1982: #ifdef DEBUGLINMIN
1983: printf("Before linmin in direction P%d-P0\n",n);
1984: for (j=1;j<=n;j++) {
1.202 brouard 1985: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1986: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1987: if(j % ncovmodel == 0){
1.191 brouard 1988: printf("\n");
1.202 brouard 1989: fprintf(ficlog,"\n");
1990: }
1.191 brouard 1991: }
1992: #endif
1.187 brouard 1993: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.191 brouard 1994: #ifdef DEBUGLINMIN
1995: for (j=1;j<=n;j++) {
1996: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1.202 brouard 1997: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1998: if(j % ncovmodel == 0){
1.191 brouard 1999: printf("\n");
1.202 brouard 2000: fprintf(ficlog,"\n");
2001: }
1.191 brouard 2002: }
2003: #endif
1.126 brouard 2004: for (j=1;j<=n;j++) {
1.181 brouard 2005: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
2006: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 2007: }
1.181 brouard 2008: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2009: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 2010:
1.126 brouard 2011: #ifdef DEBUG
1.164 brouard 2012: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2013: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 2014: for(j=1;j<=n;j++){
2015: printf(" %.12e",xit[j]);
2016: fprintf(ficlog," %.12e",xit[j]);
2017: }
2018: printf("\n");
2019: fprintf(ficlog,"\n");
2020: #endif
1.192 brouard 2021: } /* end of t or directest negative */
2022: #ifdef POWELLF1F3
2023: #else
1.162 brouard 2024: } /* end if (fptt < fp) */
1.192 brouard 2025: #endif
2026: } /* loop iteration */
1.126 brouard 2027: }
2028:
2029: /**** Prevalence limit (stable or period prevalence) ****************/
2030:
1.203 brouard 2031: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
1.126 brouard 2032: {
2033: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1.203 brouard 2034: matrix by transitions matrix until convergence is reached with precision ftolpl */
1.206 brouard 2035: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2036: /* Wx is row vector: population in state 1, population in state 2, population dead */
2037: /* or prevalence in state 1, prevalence in state 2, 0 */
2038: /* newm is the matrix after multiplications, its rows are identical at a factor */
2039: /* Initial matrix pimij */
2040: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2041: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2042: /* 0, 0 , 1} */
2043: /*
2044: * and after some iteration: */
2045: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2046: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2047: /* 0, 0 , 1} */
2048: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2049: /* {0.51571254859325999, 0.4842874514067399, */
2050: /* 0.51326036147820708, 0.48673963852179264} */
2051: /* If we start from prlim again, prlim tends to a constant matrix */
2052:
1.126 brouard 2053: int i, ii,j,k;
1.209 brouard 2054: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2055: /* double **matprod2(); */ /* test */
1.131 brouard 2056: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 2057: double **newm;
1.209 brouard 2058: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2059: int ncvloop=0;
1.169 brouard 2060:
1.209 brouard 2061: min=vector(1,nlstate);
2062: max=vector(1,nlstate);
2063: meandiff=vector(1,nlstate);
2064:
1.126 brouard 2065: for (ii=1;ii<=nlstate+ndeath;ii++)
2066: for (j=1;j<=nlstate+ndeath;j++){
2067: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2068: }
1.169 brouard 2069:
2070: cov[1]=1.;
2071:
2072: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2073: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2074: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2075: ncvloop++;
1.126 brouard 2076: newm=savm;
2077: /* Covariates have to be included here again */
1.138 brouard 2078: cov[2]=agefin;
1.187 brouard 2079: if(nagesqr==1)
2080: cov[3]= agefin*agefin;;
1.138 brouard 2081: for (k=1; k<=cptcovn;k++) {
1.200 brouard 2082: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
2083: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
1.198 brouard 2084: /* 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 2085: }
1.186 brouard 2086: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2087: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2088: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
1.186 brouard 2089: for (k=1; k<=cptcovprod;k++) /* Useless */
1.200 brouard 2090: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2091: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.138 brouard 2092:
2093: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2094: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2095: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2096: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2097: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 2098: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2099:
1.126 brouard 2100: savm=oldm;
2101: oldm=newm;
1.209 brouard 2102:
2103: for(j=1; j<=nlstate; j++){
2104: max[j]=0.;
2105: min[j]=1.;
2106: }
2107: for(i=1;i<=nlstate;i++){
2108: sumnew=0;
2109: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2110: for(j=1; j<=nlstate; j++){
2111: prlim[i][j]= newm[i][j]/(1-sumnew);
2112: max[j]=FMAX(max[j],prlim[i][j]);
2113: min[j]=FMIN(min[j],prlim[i][j]);
2114: }
2115: }
2116:
1.126 brouard 2117: maxmax=0.;
1.209 brouard 2118: for(j=1; j<=nlstate; j++){
2119: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2120: maxmax=FMAX(maxmax,meandiff[j]);
2121: /* 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 2122: } /* j loop */
1.203 brouard 2123: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2124: /* 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 2125: if(maxmax < ftolpl){
1.209 brouard 2126: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2127: free_vector(min,1,nlstate);
2128: free_vector(max,1,nlstate);
2129: free_vector(meandiff,1,nlstate);
1.126 brouard 2130: return prlim;
2131: }
1.169 brouard 2132: } /* age loop */
1.208 brouard 2133: /* After some age loop it doesn't converge */
1.209 brouard 2134: 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 2135: 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 2136: /* 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); */
2137: free_vector(min,1,nlstate);
2138: free_vector(max,1,nlstate);
2139: free_vector(meandiff,1,nlstate);
1.208 brouard 2140:
1.169 brouard 2141: return prlim; /* should not reach here */
1.126 brouard 2142: }
2143:
1.217 ! brouard 2144:
! 2145: /**** Back Prevalence limit (stable or period prevalence) ****************/
! 2146:
! 2147: double **bprevalim(double **bprlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
! 2148: {
! 2149: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
! 2150: matrix by transitions matrix until convergence is reached with precision ftolpl */
! 2151: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
! 2152: /* Wx is row vector: population in state 1, population in state 2, population dead */
! 2153: /* or prevalence in state 1, prevalence in state 2, 0 */
! 2154: /* newm is the matrix after multiplications, its rows are identical at a factor */
! 2155: /* Initial matrix pimij */
! 2156: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
! 2157: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
! 2158: /* 0, 0 , 1} */
! 2159: /*
! 2160: * and after some iteration: */
! 2161: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
! 2162: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
! 2163: /* 0, 0 , 1} */
! 2164: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
! 2165: /* {0.51571254859325999, 0.4842874514067399, */
! 2166: /* 0.51326036147820708, 0.48673963852179264} */
! 2167: /* If we start from prlim again, prlim tends to a constant matrix */
! 2168:
! 2169: int i, ii,j,k;
! 2170: double *min, *max, *meandiff, maxmax,sumnew=0.;
! 2171: /* double **matprod2(); */ /* test */
! 2172: double **out, cov[NCOVMAX+1], **bmij();
! 2173: double **newm;
! 2174: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
! 2175: int ncvloop=0;
! 2176:
! 2177: min=vector(1,nlstate);
! 2178: max=vector(1,nlstate);
! 2179: meandiff=vector(1,nlstate);
! 2180:
! 2181: for (ii=1;ii<=nlstate+ndeath;ii++)
! 2182: for (j=1;j<=nlstate+ndeath;j++){
! 2183: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 2184: }
! 2185:
! 2186: cov[1]=1.;
! 2187:
! 2188: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
! 2189: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
! 2190: for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){
! 2191: ncvloop++;
! 2192: newm=savm;
! 2193: /* Covariates have to be included here again */
! 2194: cov[2]=agefin;
! 2195: if(nagesqr==1)
! 2196: cov[3]= agefin*agefin;;
! 2197: for (k=1; k<=cptcovn;k++) {
! 2198: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
! 2199: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
! 2200: /* 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])]); */
! 2201: }
! 2202: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
! 2203: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
! 2204: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
! 2205: for (k=1; k<=cptcovprod;k++) /* Useless */
! 2206: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
! 2207: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
! 2208:
! 2209: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
! 2210: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
! 2211: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
! 2212: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
! 2213: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
! 2214: out=matprod2(newm, oldm ,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate)); /* Bug Valgrind */
! 2215:
! 2216: savm=oldm;
! 2217: oldm=newm;
! 2218:
! 2219: for(j=1; j<=nlstate; j++){
! 2220: max[j]=0.;
! 2221: min[j]=1.;
! 2222: }
! 2223: /* sumnew=0; */
! 2224: /* for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; */
! 2225: for(j=1; j<=nlstate; j++){
! 2226: for(i=1;i<=nlstate;i++){
! 2227: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
! 2228: bprlim[i][j]= newm[i][j];
! 2229: max[i]=FMAX(max[i],bprlim[i][j]);
! 2230: min[i]=FMIN(min[i],bprlim[i][j]);
! 2231: }
! 2232: }
! 2233:
! 2234: maxmax=0.;
! 2235: for(i=1; i<=nlstate; i++){
! 2236: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
! 2237: maxmax=FMAX(maxmax,meandiff[i]);
! 2238: /* 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); */
! 2239: } /* j loop */
! 2240: *ncvyear= -( (int)age- (int)agefin);
! 2241: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
! 2242: if(maxmax < ftolpl){
! 2243: printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);
! 2244: free_vector(min,1,nlstate);
! 2245: free_vector(max,1,nlstate);
! 2246: free_vector(meandiff,1,nlstate);
! 2247: return bprlim;
! 2248: }
! 2249: } /* age loop */
! 2250: /* After some age loop it doesn't converge */
! 2251: 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\
! 2252: 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);
! 2253: /* 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); */
! 2254: free_vector(min,1,nlstate);
! 2255: free_vector(max,1,nlstate);
! 2256: free_vector(meandiff,1,nlstate);
! 2257:
! 2258: return bprlim; /* should not reach here */
! 2259: }
! 2260:
1.126 brouard 2261: /*************** transition probabilities ***************/
2262:
2263: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2264: {
1.138 brouard 2265: /* According to parameters values stored in x and the covariate's values stored in cov,
2266: computes the probability to be observed in state j being in state i by appying the
2267: model to the ncovmodel covariates (including constant and age).
2268: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2269: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2270: ncth covariate in the global vector x is given by the formula:
2271: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2272: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2273: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2274: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2275: Outputs ps[i][j] the probability to be observed in j being in j according to
2276: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2277: */
2278: double s1, lnpijopii;
1.126 brouard 2279: /*double t34;*/
1.164 brouard 2280: int i,j, nc, ii, jj;
1.126 brouard 2281:
2282: for(i=1; i<= nlstate; i++){
2283: for(j=1; j<i;j++){
1.138 brouard 2284: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2285: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2286: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2287: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2288: }
1.138 brouard 2289: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2290: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2291: }
2292: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 2293: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2294: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2295: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2296: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 2297: }
1.138 brouard 2298: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 2299: }
2300: }
2301:
2302: for(i=1; i<= nlstate; i++){
2303: s1=0;
1.131 brouard 2304: for(j=1; j<i; j++){
1.138 brouard 2305: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2306: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2307: }
2308: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 2309: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2310: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2311: }
1.138 brouard 2312: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 2313: ps[i][i]=1./(s1+1.);
1.138 brouard 2314: /* Computing other pijs */
1.126 brouard 2315: for(j=1; j<i; j++)
2316: ps[i][j]= exp(ps[i][j])*ps[i][i];
2317: for(j=i+1; j<=nlstate+ndeath; j++)
2318: ps[i][j]= exp(ps[i][j])*ps[i][i];
2319: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2320: } /* end i */
2321:
2322: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2323: for(jj=1; jj<= nlstate+ndeath; jj++){
2324: ps[ii][jj]=0;
2325: ps[ii][ii]=1;
2326: }
2327: }
2328:
1.145 brouard 2329:
2330: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2331: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2332: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2333: /* } */
2334: /* printf("\n "); */
2335: /* } */
2336: /* printf("\n ");printf("%lf ",cov[2]);*/
2337: /*
1.126 brouard 2338: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2339: goto end;*/
2340: return ps;
2341: }
2342:
1.217 ! brouard 2343: /*************** transition probabilities ***************/
! 2344:
! 2345: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
! 2346: {
! 2347: /* According to parameters values stored in x and the covariate's values stored in cov,
! 2348: computes the probability to be observed in state j being in state i by appying the
! 2349: model to the ncovmodel covariates (including constant and age).
! 2350: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
! 2351: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
! 2352: ncth covariate in the global vector x is given by the formula:
! 2353: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
! 2354: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
! 2355: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
! 2356: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
! 2357: Outputs ps[i][j] the probability to be observed in j being in j according to
! 2358: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
! 2359: */
! 2360: double s1, lnpijopii;
! 2361: /*double t34;*/
! 2362: int i,j, nc, ii, jj;
! 2363:
! 2364: for(i=1; i<= nlstate; i++){
! 2365: for(j=1; j<i;j++){
! 2366: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
! 2367: /*lnpijopii += param[i][j][nc]*cov[nc];*/
! 2368: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
! 2369: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
! 2370: }
! 2371: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
! 2372: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
! 2373: }
! 2374: for(j=i+1; j<=nlstate+ndeath;j++){
! 2375: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
! 2376: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
! 2377: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
! 2378: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
! 2379: }
! 2380: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
! 2381: }
! 2382: }
! 2383:
! 2384: for(i=1; i<= nlstate; i++){
! 2385: s1=0;
! 2386: for(j=1; j<i; j++){
! 2387: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
! 2388: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
! 2389: }
! 2390: for(j=i+1; j<=nlstate+ndeath; j++){
! 2391: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
! 2392: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
! 2393: }
! 2394: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
! 2395: ps[i][i]=1./(s1+1.);
! 2396: /* Computing other pijs */
! 2397: for(j=1; j<i; j++)
! 2398: ps[i][j]= exp(ps[i][j])*ps[i][i];
! 2399: for(j=i+1; j<=nlstate+ndeath; j++)
! 2400: ps[i][j]= exp(ps[i][j])*ps[i][i];
! 2401: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
! 2402: } /* end i */
! 2403:
! 2404: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
! 2405: for(jj=1; jj<= nlstate+ndeath; jj++){
! 2406: ps[ii][jj]=0;
! 2407: ps[ii][ii]=1;
! 2408: }
! 2409: }
! 2410: /* Added for backcast */
! 2411: for(jj=1; jj<= nlstate; jj++){
! 2412: s1=0.;
! 2413: for(ii=1; ii<= nlstate; ii++){
! 2414: s1+=ps[ii][jj];
! 2415: }
! 2416: for(ii=1; ii<= nlstate; ii++){
! 2417: ps[ii][jj]=ps[ii][jj]/s1;
! 2418: }
! 2419: }
! 2420:
! 2421: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
! 2422: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
! 2423: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
! 2424: /* } */
! 2425: /* printf("\n "); */
! 2426: /* } */
! 2427: /* printf("\n ");printf("%lf ",cov[2]);*/
! 2428: /*
! 2429: for(i=1; i<= npar; i++) printf("%f ",x[i]);
! 2430: goto end;*/
! 2431: return ps;
! 2432: }
! 2433:
! 2434:
1.126 brouard 2435: /**************** Product of 2 matrices ******************/
2436:
1.145 brouard 2437: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2438: {
2439: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2440: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2441: /* in, b, out are matrice of pointers which should have been initialized
2442: before: only the contents of out is modified. The function returns
2443: a pointer to pointers identical to out */
1.145 brouard 2444: int i, j, k;
1.126 brouard 2445: for(i=nrl; i<= nrh; i++)
1.145 brouard 2446: for(k=ncolol; k<=ncoloh; k++){
2447: out[i][k]=0.;
2448: for(j=ncl; j<=nch; j++)
2449: out[i][k] +=in[i][j]*b[j][k];
2450: }
1.126 brouard 2451: return out;
2452: }
2453:
2454:
2455: /************* Higher Matrix Product ***************/
2456:
2457: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2458: {
2459: /* Computes the transition matrix starting at age 'age' over
2460: 'nhstepm*hstepm*stepm' months (i.e. until
2461: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2462: nhstepm*hstepm matrices.
2463: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2464: (typically every 2 years instead of every month which is too big
2465: for the memory).
2466: Model is determined by parameters x and covariates have to be
2467: included manually here.
2468:
2469: */
2470:
2471: int i, j, d, h, k;
1.131 brouard 2472: double **out, cov[NCOVMAX+1];
1.126 brouard 2473: double **newm;
1.187 brouard 2474: double agexact;
1.214 brouard 2475: double agebegin, ageend;
1.126 brouard 2476:
2477: /* Hstepm could be zero and should return the unit matrix */
2478: for (i=1;i<=nlstate+ndeath;i++)
2479: for (j=1;j<=nlstate+ndeath;j++){
2480: oldm[i][j]=(i==j ? 1.0 : 0.0);
2481: po[i][j][0]=(i==j ? 1.0 : 0.0);
2482: }
2483: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2484: for(h=1; h <=nhstepm; h++){
2485: for(d=1; d <=hstepm; d++){
2486: newm=savm;
2487: /* Covariates have to be included here again */
2488: cov[1]=1.;
1.214 brouard 2489: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 2490: cov[2]=agexact;
2491: if(nagesqr==1)
2492: cov[3]= agexact*agexact;
1.131 brouard 2493: for (k=1; k<=cptcovn;k++)
1.200 brouard 2494: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2495: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.186 brouard 2496: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
2497: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2498: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2499: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.145 brouard 2500: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.200 brouard 2501: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2502: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
1.126 brouard 2503:
2504:
2505: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2506: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2507: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2508: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 ! brouard 2509: /* if((int)age == 70){ */
! 2510: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
! 2511: /* for(i=1; i<=nlstate+ndeath; i++) { */
! 2512: /* printf("%d pmmij ",i); */
! 2513: /* for(j=1;j<=nlstate+ndeath;j++) { */
! 2514: /* printf("%f ",pmmij[i][j]); */
! 2515: /* } */
! 2516: /* printf(" oldm "); */
! 2517: /* for(j=1;j<=nlstate+ndeath;j++) { */
! 2518: /* printf("%f ",oldm[i][j]); */
! 2519: /* } */
! 2520: /* printf("\n"); */
! 2521: /* } */
! 2522: /* } */
1.126 brouard 2523: savm=oldm;
2524: oldm=newm;
2525: }
2526: for(i=1; i<=nlstate+ndeath; i++)
2527: for(j=1;j<=nlstate+ndeath;j++) {
2528: po[i][j][h]=newm[i][j];
1.128 brouard 2529: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2530: }
1.128 brouard 2531: /*printf("h=%d ",h);*/
1.126 brouard 2532: } /* end h */
1.128 brouard 2533: /* printf("\n H=%d \n",h); */
1.126 brouard 2534: return po;
2535: }
2536:
1.217 ! brouard 2537: /************* Higher Back Matrix Product ***************/
! 2538:
! 2539: double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
! 2540: {
! 2541: /* Computes the transition matrix starting at age 'age' over
! 2542: 'nhstepm*hstepm*stepm' months (i.e. until
! 2543: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
! 2544: nhstepm*hstepm matrices.
! 2545: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
! 2546: (typically every 2 years instead of every month which is too big
! 2547: for the memory).
! 2548: Model is determined by parameters x and covariates have to be
! 2549: included manually here.
! 2550:
! 2551: */
! 2552:
! 2553: int i, j, d, h, k;
! 2554: double **out, cov[NCOVMAX+1];
! 2555: double **newm;
! 2556: double agexact;
! 2557: double agebegin, ageend;
! 2558:
! 2559: /* Hstepm could be zero and should return the unit matrix */
! 2560: for (i=1;i<=nlstate+ndeath;i++)
! 2561: for (j=1;j<=nlstate+ndeath;j++){
! 2562: oldm[i][j]=(i==j ? 1.0 : 0.0);
! 2563: po[i][j][0]=(i==j ? 1.0 : 0.0);
! 2564: }
! 2565: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
! 2566: for(h=1; h <=nhstepm; h++){
! 2567: for(d=1; d <=hstepm; d++){
! 2568: newm=savm;
! 2569: /* Covariates have to be included here again */
! 2570: cov[1]=1.;
! 2571: agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
! 2572: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
! 2573: cov[2]=agexact;
! 2574: if(nagesqr==1)
! 2575: cov[3]= agexact*agexact;
! 2576: for (k=1; k<=cptcovn;k++)
! 2577: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
! 2578: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
! 2579: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
! 2580: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
! 2581: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
! 2582: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
! 2583: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
! 2584: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
! 2585: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
! 2586:
! 2587:
! 2588: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
! 2589: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
! 2590: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
! 2591: oldm);
! 2592: /* if((int)age == 70){ */
! 2593: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
! 2594: /* for(i=1; i<=nlstate+ndeath; i++) { */
! 2595: /* printf("%d pmmij ",i); */
! 2596: /* for(j=1;j<=nlstate+ndeath;j++) { */
! 2597: /* printf("%f ",pmmij[i][j]); */
! 2598: /* } */
! 2599: /* printf(" oldm "); */
! 2600: /* for(j=1;j<=nlstate+ndeath;j++) { */
! 2601: /* printf("%f ",oldm[i][j]); */
! 2602: /* } */
! 2603: /* printf("\n"); */
! 2604: /* } */
! 2605: /* } */
! 2606: savm=oldm;
! 2607: oldm=newm;
! 2608: }
! 2609: for(i=1; i<=nlstate+ndeath; i++)
! 2610: for(j=1;j<=nlstate+ndeath;j++) {
! 2611: po[i][j][h]=newm[i][j];
! 2612: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
! 2613: }
! 2614: /*printf("h=%d ",h);*/
! 2615: } /* end h */
! 2616: /* printf("\n H=%d \n",h); */
! 2617: return po;
! 2618: }
! 2619:
! 2620:
1.162 brouard 2621: #ifdef NLOPT
2622: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2623: double fret;
2624: double *xt;
2625: int j;
2626: myfunc_data *d2 = (myfunc_data *) pd;
2627: /* xt = (p1-1); */
2628: xt=vector(1,n);
2629: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2630:
2631: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2632: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2633: printf("Function = %.12lf ",fret);
2634: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2635: printf("\n");
2636: free_vector(xt,1,n);
2637: return fret;
2638: }
2639: #endif
1.126 brouard 2640:
2641: /*************** log-likelihood *************/
2642: double func( double *x)
2643: {
2644: int i, ii, j, k, mi, d, kk;
1.131 brouard 2645: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2646: double **out;
2647: double sw; /* Sum of weights */
2648: double lli; /* Individual log likelihood */
2649: int s1, s2;
2650: double bbh, survp;
2651: long ipmx;
1.187 brouard 2652: double agexact;
1.126 brouard 2653: /*extern weight */
2654: /* We are differentiating ll according to initial status */
2655: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2656: /*for(i=1;i<imx;i++)
2657: printf(" %d\n",s[4][i]);
2658: */
1.162 brouard 2659:
2660: ++countcallfunc;
2661:
1.126 brouard 2662: cov[1]=1.;
2663:
2664: for(k=1; k<=nlstate; k++) ll[k]=0.;
2665:
2666: if(mle==1){
2667: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2668: /* Computes the values of the ncovmodel covariates of the model
2669: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2670: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2671: to be observed in j being in i according to the model.
2672: */
1.145 brouard 2673: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 brouard 2674: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2675: }
1.137 brouard 2676: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2677: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2678: has been calculated etc */
1.126 brouard 2679: for(mi=1; mi<= wav[i]-1; mi++){
2680: for (ii=1;ii<=nlstate+ndeath;ii++)
2681: for (j=1;j<=nlstate+ndeath;j++){
2682: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2683: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2684: }
2685: for(d=0; d<dh[mi][i]; d++){
2686: newm=savm;
1.187 brouard 2687: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2688: cov[2]=agexact;
2689: if(nagesqr==1)
2690: cov[3]= agexact*agexact;
1.126 brouard 2691: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2692: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2693: }
2694: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2695: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2696: savm=oldm;
2697: oldm=newm;
2698: } /* end mult */
2699:
2700: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2701: /* But now since version 0.9 we anticipate for bias at large stepm.
2702: * If stepm is larger than one month (smallest stepm) and if the exact delay
2703: * (in months) between two waves is not a multiple of stepm, we rounded to
2704: * the nearest (and in case of equal distance, to the lowest) interval but now
2705: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2706: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2707: * probability in order to take into account the bias as a fraction of the way
2708: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2709: * -stepm/2 to stepm/2 .
2710: * For stepm=1 the results are the same as for previous versions of Imach.
2711: * For stepm > 1 the results are less biased than in previous versions.
2712: */
2713: s1=s[mw[mi][i]][i];
2714: s2=s[mw[mi+1][i]][i];
2715: bbh=(double)bh[mi][i]/(double)stepm;
2716: /* bias bh is positive if real duration
2717: * is higher than the multiple of stepm and negative otherwise.
2718: */
2719: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2720: if( s2 > nlstate){
2721: /* i.e. if s2 is a death state and if the date of death is known
2722: then the contribution to the likelihood is the probability to
2723: die between last step unit time and current step unit time,
2724: which is also equal to probability to die before dh
2725: minus probability to die before dh-stepm .
2726: In version up to 0.92 likelihood was computed
2727: as if date of death was unknown. Death was treated as any other
2728: health state: the date of the interview describes the actual state
2729: and not the date of a change in health state. The former idea was
2730: to consider that at each interview the state was recorded
2731: (healthy, disable or death) and IMaCh was corrected; but when we
2732: introduced the exact date of death then we should have modified
2733: the contribution of an exact death to the likelihood. This new
2734: contribution is smaller and very dependent of the step unit
2735: stepm. It is no more the probability to die between last interview
2736: and month of death but the probability to survive from last
2737: interview up to one month before death multiplied by the
2738: probability to die within a month. Thanks to Chris
2739: Jackson for correcting this bug. Former versions increased
2740: mortality artificially. The bad side is that we add another loop
2741: which slows down the processing. The difference can be up to 10%
2742: lower mortality.
2743: */
1.183 brouard 2744: /* If, at the beginning of the maximization mostly, the
2745: cumulative probability or probability to be dead is
2746: constant (ie = 1) over time d, the difference is equal to
2747: 0. out[s1][3] = savm[s1][3]: probability, being at state
2748: s1 at precedent wave, to be dead a month before current
2749: wave is equal to probability, being at state s1 at
2750: precedent wave, to be dead at mont of the current
2751: wave. Then the observed probability (that this person died)
2752: is null according to current estimated parameter. In fact,
2753: it should be very low but not zero otherwise the log go to
2754: infinity.
2755: */
2756: /* #ifdef INFINITYORIGINAL */
2757: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2758: /* #else */
2759: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2760: /* lli=log(mytinydouble); */
2761: /* else */
2762: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2763: /* #endif */
1.216 brouard 2764: lli=log(out[s1][s2] - savm[s1][s2]);
2765:
2766: } else if ( s2==-1 ) { /* alive */
1.126 brouard 2767: for (j=1,survp=0. ; j<=nlstate; j++)
2768: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2769: /*survp += out[s1][j]; */
2770: lli= log(survp);
2771: }
2772: else if (s2==-4) {
2773: for (j=3,survp=0. ; j<=nlstate; j++)
2774: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2775: lli= log(survp);
2776: }
2777: else if (s2==-5) {
2778: for (j=1,survp=0. ; j<=2; j++)
2779: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2780: lli= log(survp);
2781: }
2782: else{
2783: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2784: /* 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 */
2785: }
2786: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2787: /*if(lli ==000.0)*/
2788: /*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); */
2789: ipmx +=1;
2790: sw += weight[i];
2791: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2792: /* if (lli < log(mytinydouble)){ */
2793: /* 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); */
2794: /* 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]); */
2795: /* } */
1.126 brouard 2796: } /* end of wave */
2797: } /* end of individual */
2798: } else if(mle==2){
2799: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2800: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2801: for(mi=1; mi<= wav[i]-1; mi++){
2802: for (ii=1;ii<=nlstate+ndeath;ii++)
2803: for (j=1;j<=nlstate+ndeath;j++){
2804: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2805: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2806: }
2807: for(d=0; d<=dh[mi][i]; d++){
2808: newm=savm;
1.187 brouard 2809: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2810: cov[2]=agexact;
2811: if(nagesqr==1)
2812: cov[3]= agexact*agexact;
1.126 brouard 2813: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2814: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2815: }
2816: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2817: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2818: savm=oldm;
2819: oldm=newm;
2820: } /* end mult */
2821:
2822: s1=s[mw[mi][i]][i];
2823: s2=s[mw[mi+1][i]][i];
2824: bbh=(double)bh[mi][i]/(double)stepm;
2825: 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 */
2826: ipmx +=1;
2827: sw += weight[i];
2828: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2829: } /* end of wave */
2830: } /* end of individual */
2831: } else if(mle==3){ /* exponential inter-extrapolation */
2832: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2833: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2834: for(mi=1; mi<= wav[i]-1; mi++){
2835: for (ii=1;ii<=nlstate+ndeath;ii++)
2836: for (j=1;j<=nlstate+ndeath;j++){
2837: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2838: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2839: }
2840: for(d=0; d<dh[mi][i]; d++){
2841: newm=savm;
1.187 brouard 2842: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2843: cov[2]=agexact;
2844: if(nagesqr==1)
2845: cov[3]= agexact*agexact;
1.126 brouard 2846: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2847: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2848: }
2849: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2850: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2851: savm=oldm;
2852: oldm=newm;
2853: } /* end mult */
2854:
2855: s1=s[mw[mi][i]][i];
2856: s2=s[mw[mi+1][i]][i];
2857: bbh=(double)bh[mi][i]/(double)stepm;
2858: 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 */
2859: ipmx +=1;
2860: sw += weight[i];
2861: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2862: } /* end of wave */
2863: } /* end of individual */
2864: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2865: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2866: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2867: for(mi=1; mi<= wav[i]-1; mi++){
2868: for (ii=1;ii<=nlstate+ndeath;ii++)
2869: for (j=1;j<=nlstate+ndeath;j++){
2870: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2871: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2872: }
2873: for(d=0; d<dh[mi][i]; d++){
2874: newm=savm;
1.187 brouard 2875: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2876: cov[2]=agexact;
2877: if(nagesqr==1)
2878: cov[3]= agexact*agexact;
1.126 brouard 2879: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2880: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2881: }
2882:
2883: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2884: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2885: savm=oldm;
2886: oldm=newm;
2887: } /* end mult */
2888:
2889: s1=s[mw[mi][i]][i];
2890: s2=s[mw[mi+1][i]][i];
2891: if( s2 > nlstate){
2892: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 2893: } else if ( s2==-1 ) { /* alive */
2894: for (j=1,survp=0. ; j<=nlstate; j++)
2895: survp += out[s1][j];
2896: lli= log(survp);
1.126 brouard 2897: }else{
2898: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2899: }
2900: ipmx +=1;
2901: sw += weight[i];
2902: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2903: /* 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]); */
2904: } /* end of wave */
2905: } /* end of individual */
2906: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2907: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2908: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2909: for(mi=1; mi<= wav[i]-1; mi++){
2910: for (ii=1;ii<=nlstate+ndeath;ii++)
2911: for (j=1;j<=nlstate+ndeath;j++){
2912: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2913: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2914: }
2915: for(d=0; d<dh[mi][i]; d++){
2916: newm=savm;
1.187 brouard 2917: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2918: cov[2]=agexact;
2919: if(nagesqr==1)
2920: cov[3]= agexact*agexact;
1.126 brouard 2921: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2922: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2923: }
2924:
2925: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2926: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2927: savm=oldm;
2928: oldm=newm;
2929: } /* end mult */
2930:
2931: s1=s[mw[mi][i]][i];
2932: s2=s[mw[mi+1][i]][i];
2933: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2934: ipmx +=1;
2935: sw += weight[i];
2936: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2937: /*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]);*/
2938: } /* end of wave */
2939: } /* end of individual */
2940: } /* End of if */
2941: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2942: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2943: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2944: return -l;
2945: }
2946:
2947: /*************** log-likelihood *************/
2948: double funcone( double *x)
2949: {
2950: /* Same as likeli but slower because of a lot of printf and if */
2951: int i, ii, j, k, mi, d, kk;
1.131 brouard 2952: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2953: double **out;
2954: double lli; /* Individual log likelihood */
2955: double llt;
2956: int s1, s2;
2957: double bbh, survp;
1.187 brouard 2958: double agexact;
1.214 brouard 2959: double agebegin, ageend;
1.126 brouard 2960: /*extern weight */
2961: /* We are differentiating ll according to initial status */
2962: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2963: /*for(i=1;i<imx;i++)
2964: printf(" %d\n",s[4][i]);
2965: */
2966: cov[1]=1.;
2967:
2968: for(k=1; k<=nlstate; k++) ll[k]=0.;
2969:
2970: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2971: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2972: for(mi=1; mi<= wav[i]-1; mi++){
2973: for (ii=1;ii<=nlstate+ndeath;ii++)
2974: for (j=1;j<=nlstate+ndeath;j++){
2975: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2976: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2977: }
1.214 brouard 2978:
2979: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
2980: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
2981: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
2982: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2983: and mw[mi+1][i]. dh depends on stepm.*/
1.126 brouard 2984: newm=savm;
1.187 brouard 2985: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2986: cov[2]=agexact;
2987: if(nagesqr==1)
2988: cov[3]= agexact*agexact;
1.126 brouard 2989: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2990: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2991: }
1.187 brouard 2992:
1.145 brouard 2993: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2994: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2995: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2996: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2997: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2998: savm=oldm;
2999: oldm=newm;
3000: } /* end mult */
3001:
3002: s1=s[mw[mi][i]][i];
3003: s2=s[mw[mi+1][i]][i];
1.217 ! brouard 3004: /* if(s2==-1){ */
! 3005: /* printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */
! 3006: /* /\* exit(1); *\/ */
! 3007: /* } */
1.126 brouard 3008: bbh=(double)bh[mi][i]/(double)stepm;
3009: /* bias is positive if real duration
3010: * is higher than the multiple of stepm and negative otherwise.
3011: */
3012: if( s2 > nlstate && (mle <5) ){ /* Jackson */
3013: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3014: } else if ( s2==-1 ) { /* alive */
1.126 brouard 3015: for (j=1,survp=0. ; j<=nlstate; j++)
3016: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3017: lli= log(survp);
3018: }else if (mle==1){
3019: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3020: } else if(mle==2){
3021: 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 */
3022: } else if(mle==3){ /* exponential inter-extrapolation */
3023: 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 */
3024: } else if (mle==4){ /* mle=4 no inter-extrapolation */
3025: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 3026: } else{ /* mle=0 back to 1 */
3027: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3028: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 3029: } /* End of if */
3030: ipmx +=1;
3031: sw += weight[i];
3032: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 3033: /*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 3034: if(globpr){
1.214 brouard 3035: fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\
1.126 brouard 3036: %11.6f %11.6f %11.6f ", \
1.214 brouard 3037: num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
1.126 brouard 3038: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
3039: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
3040: llt +=ll[k]*gipmx/gsw;
3041: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
3042: }
3043: fprintf(ficresilk," %10.6f\n", -llt);
3044: }
3045: } /* end of wave */
3046: } /* end of individual */
3047: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3048: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3049: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3050: if(globpr==0){ /* First time we count the contributions and weights */
3051: gipmx=ipmx;
3052: gsw=sw;
3053: }
3054: return -l;
3055: }
3056:
3057:
3058: /*************** function likelione ***********/
3059: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
3060: {
3061: /* This routine should help understanding what is done with
3062: the selection of individuals/waves and
3063: to check the exact contribution to the likelihood.
3064: Plotting could be done.
3065: */
3066: int k;
3067:
3068: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 3069: strcpy(fileresilk,"ILK_");
1.202 brouard 3070: strcat(fileresilk,fileresu);
1.126 brouard 3071: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
3072: printf("Problem with resultfile: %s\n", fileresilk);
3073: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
3074: }
1.214 brouard 3075: 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");
3076: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 3077: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
3078: for(k=1; k<=nlstate; k++)
3079: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
3080: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
3081: }
3082:
3083: *fretone=(*funcone)(p);
3084: if(*globpri !=0){
3085: fclose(ficresilk);
1.205 brouard 3086: if (mle ==0)
3087: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
3088: else if(mle >=1)
3089: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
3090: 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 3091:
1.208 brouard 3092:
3093: for (k=1; k<= nlstate ; k++) {
1.211 brouard 3094: 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 3095: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
3096: }
1.207 brouard 3097: 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 3098: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3099: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 3100: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3101: fflush(fichtm);
1.205 brouard 3102: }
1.126 brouard 3103: return;
3104: }
3105:
3106:
3107: /*********** Maximum Likelihood Estimation ***************/
3108:
3109: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
3110: {
1.165 brouard 3111: int i,j, iter=0;
1.126 brouard 3112: double **xi;
3113: double fret;
3114: double fretone; /* Only one call to likelihood */
3115: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 3116:
3117: #ifdef NLOPT
3118: int creturn;
3119: nlopt_opt opt;
3120: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
3121: double *lb;
3122: double minf; /* the minimum objective value, upon return */
3123: double * p1; /* Shifted parameters from 0 instead of 1 */
3124: myfunc_data dinst, *d = &dinst;
3125: #endif
3126:
3127:
1.126 brouard 3128: xi=matrix(1,npar,1,npar);
3129: for (i=1;i<=npar;i++)
3130: for (j=1;j<=npar;j++)
3131: xi[i][j]=(i==j ? 1.0 : 0.0);
3132: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 3133: strcpy(filerespow,"POW_");
1.126 brouard 3134: strcat(filerespow,fileres);
3135: if((ficrespow=fopen(filerespow,"w"))==NULL) {
3136: printf("Problem with resultfile: %s\n", filerespow);
3137: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
3138: }
3139: fprintf(ficrespow,"# Powell\n# iter -2*LL");
3140: for (i=1;i<=nlstate;i++)
3141: for(j=1;j<=nlstate+ndeath;j++)
3142: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
3143: fprintf(ficrespow,"\n");
1.162 brouard 3144: #ifdef POWELL
1.126 brouard 3145: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 3146: #endif
1.126 brouard 3147:
1.162 brouard 3148: #ifdef NLOPT
3149: #ifdef NEWUOA
3150: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
3151: #else
3152: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
3153: #endif
3154: lb=vector(0,npar-1);
3155: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
3156: nlopt_set_lower_bounds(opt, lb);
3157: nlopt_set_initial_step1(opt, 0.1);
3158:
3159: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
3160: d->function = func;
3161: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
3162: nlopt_set_min_objective(opt, myfunc, d);
3163: nlopt_set_xtol_rel(opt, ftol);
3164: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
3165: printf("nlopt failed! %d\n",creturn);
3166: }
3167: else {
3168: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
3169: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
3170: iter=1; /* not equal */
3171: }
3172: nlopt_destroy(opt);
3173: #endif
1.126 brouard 3174: free_matrix(xi,1,npar,1,npar);
3175: fclose(ficrespow);
1.203 brouard 3176: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
3177: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 3178: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 3179:
3180: }
3181:
3182: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 3183: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 3184: {
3185: double **a,**y,*x,pd;
1.203 brouard 3186: /* double **hess; */
1.164 brouard 3187: int i, j;
1.126 brouard 3188: int *indx;
3189:
3190: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 3191: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 3192: void lubksb(double **a, int npar, int *indx, double b[]) ;
3193: void ludcmp(double **a, int npar, int *indx, double *d) ;
3194: double gompertz(double p[]);
1.203 brouard 3195: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 3196:
3197: printf("\nCalculation of the hessian matrix. Wait...\n");
3198: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
3199: for (i=1;i<=npar;i++){
1.203 brouard 3200: printf("%d-",i);fflush(stdout);
3201: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 3202:
3203: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
3204:
3205: /* printf(" %f ",p[i]);
3206: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
3207: }
3208:
3209: for (i=1;i<=npar;i++) {
3210: for (j=1;j<=npar;j++) {
3211: if (j>i) {
1.203 brouard 3212: printf(".%d-%d",i,j);fflush(stdout);
3213: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
3214: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 3215:
3216: hess[j][i]=hess[i][j];
3217: /*printf(" %lf ",hess[i][j]);*/
3218: }
3219: }
3220: }
3221: printf("\n");
3222: fprintf(ficlog,"\n");
3223:
3224: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
3225: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
3226:
3227: a=matrix(1,npar,1,npar);
3228: y=matrix(1,npar,1,npar);
3229: x=vector(1,npar);
3230: indx=ivector(1,npar);
3231: for (i=1;i<=npar;i++)
3232: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
3233: ludcmp(a,npar,indx,&pd);
3234:
3235: for (j=1;j<=npar;j++) {
3236: for (i=1;i<=npar;i++) x[i]=0;
3237: x[j]=1;
3238: lubksb(a,npar,indx,x);
3239: for (i=1;i<=npar;i++){
3240: matcov[i][j]=x[i];
3241: }
3242: }
3243:
3244: printf("\n#Hessian matrix#\n");
3245: fprintf(ficlog,"\n#Hessian matrix#\n");
3246: for (i=1;i<=npar;i++) {
3247: for (j=1;j<=npar;j++) {
1.203 brouard 3248: printf("%.6e ",hess[i][j]);
3249: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 3250: }
3251: printf("\n");
3252: fprintf(ficlog,"\n");
3253: }
3254:
1.203 brouard 3255: /* printf("\n#Covariance matrix#\n"); */
3256: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
3257: /* for (i=1;i<=npar;i++) { */
3258: /* for (j=1;j<=npar;j++) { */
3259: /* printf("%.6e ",matcov[i][j]); */
3260: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
3261: /* } */
3262: /* printf("\n"); */
3263: /* fprintf(ficlog,"\n"); */
3264: /* } */
3265:
1.126 brouard 3266: /* Recompute Inverse */
1.203 brouard 3267: /* for (i=1;i<=npar;i++) */
3268: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
3269: /* ludcmp(a,npar,indx,&pd); */
3270:
3271: /* printf("\n#Hessian matrix recomputed#\n"); */
3272:
3273: /* for (j=1;j<=npar;j++) { */
3274: /* for (i=1;i<=npar;i++) x[i]=0; */
3275: /* x[j]=1; */
3276: /* lubksb(a,npar,indx,x); */
3277: /* for (i=1;i<=npar;i++){ */
3278: /* y[i][j]=x[i]; */
3279: /* printf("%.3e ",y[i][j]); */
3280: /* fprintf(ficlog,"%.3e ",y[i][j]); */
3281: /* } */
3282: /* printf("\n"); */
3283: /* fprintf(ficlog,"\n"); */
3284: /* } */
3285:
3286: /* Verifying the inverse matrix */
3287: #ifdef DEBUGHESS
3288: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 3289:
1.203 brouard 3290: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
3291: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 3292:
3293: for (j=1;j<=npar;j++) {
3294: for (i=1;i<=npar;i++){
1.203 brouard 3295: printf("%.2f ",y[i][j]);
3296: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 3297: }
3298: printf("\n");
3299: fprintf(ficlog,"\n");
3300: }
1.203 brouard 3301: #endif
1.126 brouard 3302:
3303: free_matrix(a,1,npar,1,npar);
3304: free_matrix(y,1,npar,1,npar);
3305: free_vector(x,1,npar);
3306: free_ivector(indx,1,npar);
1.203 brouard 3307: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 3308:
3309:
3310: }
3311:
3312: /*************** hessian matrix ****************/
3313: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 3314: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 3315: int i;
3316: int l=1, lmax=20;
1.203 brouard 3317: double k1,k2, res, fx;
1.132 brouard 3318: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 3319: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
3320: int k=0,kmax=10;
3321: double l1;
3322:
3323: fx=func(x);
3324: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 3325: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 3326: l1=pow(10,l);
3327: delts=delt;
3328: for(k=1 ; k <kmax; k=k+1){
3329: delt = delta*(l1*k);
3330: p2[theta]=x[theta] +delt;
1.145 brouard 3331: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 3332: p2[theta]=x[theta]-delt;
3333: k2=func(p2)-fx;
3334: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 3335: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 3336:
1.203 brouard 3337: #ifdef DEBUGHESSII
1.126 brouard 3338: 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);
3339: 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);
3340: #endif
3341: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
3342: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
3343: k=kmax;
3344: }
3345: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 3346: k=kmax; l=lmax*10;
1.126 brouard 3347: }
3348: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
3349: delts=delt;
3350: }
1.203 brouard 3351: } /* End loop k */
1.126 brouard 3352: }
3353: delti[theta]=delts;
3354: return res;
3355:
3356: }
3357:
1.203 brouard 3358: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 3359: {
3360: int i;
1.164 brouard 3361: int l=1, lmax=20;
1.126 brouard 3362: double k1,k2,k3,k4,res,fx;
1.132 brouard 3363: double p2[MAXPARM+1];
1.203 brouard 3364: int k, kmax=1;
3365: double v1, v2, cv12, lc1, lc2;
1.208 brouard 3366:
3367: int firstime=0;
1.203 brouard 3368:
1.126 brouard 3369: fx=func(x);
1.203 brouard 3370: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 3371: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 3372: p2[thetai]=x[thetai]+delti[thetai]*k;
3373: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3374: k1=func(p2)-fx;
3375:
1.203 brouard 3376: p2[thetai]=x[thetai]+delti[thetai]*k;
3377: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3378: k2=func(p2)-fx;
3379:
1.203 brouard 3380: p2[thetai]=x[thetai]-delti[thetai]*k;
3381: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3382: k3=func(p2)-fx;
3383:
1.203 brouard 3384: p2[thetai]=x[thetai]-delti[thetai]*k;
3385: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3386: k4=func(p2)-fx;
1.203 brouard 3387: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
3388: if(k1*k2*k3*k4 <0.){
1.208 brouard 3389: firstime=1;
1.203 brouard 3390: kmax=kmax+10;
1.208 brouard 3391: }
3392: if(kmax >=10 || firstime ==1){
1.203 brouard 3393: printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
3394: fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
3395: 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);
3396: 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);
3397: }
3398: #ifdef DEBUGHESSIJ
3399: v1=hess[thetai][thetai];
3400: v2=hess[thetaj][thetaj];
3401: cv12=res;
3402: /* Computing eigen value of Hessian matrix */
3403: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3404: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3405: if ((lc2 <0) || (lc1 <0) ){
3406: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3407: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3408: 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);
3409: 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);
3410: }
1.126 brouard 3411: #endif
3412: }
3413: return res;
3414: }
3415:
1.203 brouard 3416: /* Not done yet: Was supposed to fix if not exactly at the maximum */
3417: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
3418: /* { */
3419: /* int i; */
3420: /* int l=1, lmax=20; */
3421: /* double k1,k2,k3,k4,res,fx; */
3422: /* double p2[MAXPARM+1]; */
3423: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
3424: /* int k=0,kmax=10; */
3425: /* double l1; */
3426:
3427: /* fx=func(x); */
3428: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
3429: /* l1=pow(10,l); */
3430: /* delts=delt; */
3431: /* for(k=1 ; k <kmax; k=k+1){ */
3432: /* delt = delti*(l1*k); */
3433: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
3434: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3435: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3436: /* k1=func(p2)-fx; */
3437:
3438: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3439: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3440: /* k2=func(p2)-fx; */
3441:
3442: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3443: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3444: /* k3=func(p2)-fx; */
3445:
3446: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3447: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3448: /* k4=func(p2)-fx; */
3449: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
3450: /* #ifdef DEBUGHESSIJ */
3451: /* 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); */
3452: /* 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); */
3453: /* #endif */
3454: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
3455: /* k=kmax; */
3456: /* } */
3457: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
3458: /* k=kmax; l=lmax*10; */
3459: /* } */
3460: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
3461: /* delts=delt; */
3462: /* } */
3463: /* } /\* End loop k *\/ */
3464: /* } */
3465: /* delti[theta]=delts; */
3466: /* return res; */
3467: /* } */
3468:
3469:
1.126 brouard 3470: /************** Inverse of matrix **************/
3471: void ludcmp(double **a, int n, int *indx, double *d)
3472: {
3473: int i,imax,j,k;
3474: double big,dum,sum,temp;
3475: double *vv;
3476:
3477: vv=vector(1,n);
3478: *d=1.0;
3479: for (i=1;i<=n;i++) {
3480: big=0.0;
3481: for (j=1;j<=n;j++)
3482: if ((temp=fabs(a[i][j])) > big) big=temp;
3483: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
3484: vv[i]=1.0/big;
3485: }
3486: for (j=1;j<=n;j++) {
3487: for (i=1;i<j;i++) {
3488: sum=a[i][j];
3489: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
3490: a[i][j]=sum;
3491: }
3492: big=0.0;
3493: for (i=j;i<=n;i++) {
3494: sum=a[i][j];
3495: for (k=1;k<j;k++)
3496: sum -= a[i][k]*a[k][j];
3497: a[i][j]=sum;
3498: if ( (dum=vv[i]*fabs(sum)) >= big) {
3499: big=dum;
3500: imax=i;
3501: }
3502: }
3503: if (j != imax) {
3504: for (k=1;k<=n;k++) {
3505: dum=a[imax][k];
3506: a[imax][k]=a[j][k];
3507: a[j][k]=dum;
3508: }
3509: *d = -(*d);
3510: vv[imax]=vv[j];
3511: }
3512: indx[j]=imax;
3513: if (a[j][j] == 0.0) a[j][j]=TINY;
3514: if (j != n) {
3515: dum=1.0/(a[j][j]);
3516: for (i=j+1;i<=n;i++) a[i][j] *= dum;
3517: }
3518: }
3519: free_vector(vv,1,n); /* Doesn't work */
3520: ;
3521: }
3522:
3523: void lubksb(double **a, int n, int *indx, double b[])
3524: {
3525: int i,ii=0,ip,j;
3526: double sum;
3527:
3528: for (i=1;i<=n;i++) {
3529: ip=indx[i];
3530: sum=b[ip];
3531: b[ip]=b[i];
3532: if (ii)
3533: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
3534: else if (sum) ii=i;
3535: b[i]=sum;
3536: }
3537: for (i=n;i>=1;i--) {
3538: sum=b[i];
3539: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
3540: b[i]=sum/a[i][i];
3541: }
3542: }
3543:
3544: void pstamp(FILE *fichier)
3545: {
1.196 brouard 3546: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 3547: }
3548:
3549: /************ Frequencies ********************/
1.214 brouard 3550: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
3551: int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[],\
3552: int firstpass, int lastpass, int stepm, int weightopt, char model[])
1.126 brouard 3553: { /* Some frequencies */
3554:
1.164 brouard 3555: int i, m, jk, j1, bool, z1,j;
1.214 brouard 3556: int mi; /* Effective wave */
1.126 brouard 3557: int first;
3558: double ***freq; /* Frequencies */
3559: double *pp, **prop;
3560: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.214 brouard 3561: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
3562: double agebegin, ageend;
3563:
1.126 brouard 3564: pp=vector(1,nlstate);
3565: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.201 brouard 3566: strcpy(fileresp,"P_");
3567: strcat(fileresp,fileresu);
1.213 brouard 3568: /*strcat(fileresphtm,fileresu);*/
1.126 brouard 3569: if((ficresp=fopen(fileresp,"w"))==NULL) {
3570: printf("Problem with prevalence resultfile: %s\n", fileresp);
3571: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
3572: exit(0);
3573: }
1.214 brouard 3574:
1.213 brouard 3575: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
3576: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
3577: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3578: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3579: fflush(ficlog);
3580: exit(70);
3581: }
1.214 brouard 3582: else{
3583: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
3584: <hr size=\"2\" color=\"#EC5E5E\"> \n\
3585: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
3586: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
3587: }
3588: 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);
3589:
3590: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
3591: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
3592: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
3593: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
3594: fflush(ficlog);
3595: exit(70);
3596: }
3597: else{
3598: fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
3599: <hr size=\"2\" color=\"#EC5E5E\"> \n\
3600: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
3601: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
3602: }
3603: 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);
3604:
1.126 brouard 3605: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
3606: j1=0;
3607:
3608: j=cptcoveff;
3609: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3610:
3611: first=1;
3612:
1.214 brouard 3613: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ /* Loop on covariates combination */
1.126 brouard 3614: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
3615: scanf("%d", i);*/
3616: for (i=-5; i<=nlstate+ndeath; i++)
3617: for (jk=-5; jk<=nlstate+ndeath; jk++)
3618: for(m=iagemin; m <= iagemax+3; m++)
3619: freq[i][jk][m]=0;
1.143 brouard 3620:
3621: for (i=1; i<=nlstate; i++)
3622: for(m=iagemin; m <= iagemax+3; m++)
3623: prop[i][m]=0;
1.126 brouard 3624:
3625: dateintsum=0;
3626: k2cpt=0;
1.214 brouard 3627: for (i=1; i<=imx; i++) { /* For each individual i */
1.126 brouard 3628: bool=1;
1.210 brouard 3629: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
1.144 brouard 3630: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 3631: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
1.145 brouard 3632: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 3633: bool=0;
1.198 brouard 3634: /* 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",
3635: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
3636: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
3637: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
1.144 brouard 3638: }
1.210 brouard 3639: } /* cptcovn > 0 */
1.214 brouard 3640:
1.126 brouard 3641: if (bool==1){
1.214 brouard 3642: /* for(m=firstpass; m<=lastpass; m++){ */
3643: for(mi=1; mi<wav[i];mi++){
3644: m=mw[mi][i];
3645: /* dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective (mi) waves m=mw[mi][i]
3646: and mw[mi+1][i]. dh depends on stepm. */
3647: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
3648: ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /* Age at end of wave and transition */
3649: if(m >=firstpass && m <=lastpass){
3650: k2=anint[m][i]+(mint[m][i]/12.);
3651: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
3652: if(agev[m][i]==0) agev[m][i]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
3653: if(agev[m][i]==1) agev[m][i]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
3654: if (s[m][i]>0 && s[m][i]<=nlstate) /* If status at wave m is known and a live state */
3655: prop[s[m][i]][(int)agev[m][i]] += weight[i]; /* At age of beginning of transition, where status is known */
1.126 brouard 3656: if (m<lastpass) {
1.214 brouard 3657: /* if(s[m][i]==4 && s[m+1][i]==4) */
3658: /* printf(" num=%ld m=%d, i=%d s1=%d s2=%d agev at m=%d\n", num[i], m, i,s[m][i],s[m+1][i], (int)agev[m][i]); */
3659: if(s[m][i]==-1)
3660: printf(" num=%ld m=%d, i=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[i], m, i,s[m][i],s[m+1][i], (int)agev[m][i],agebegin, ageend, (int)((agebegin+ageend)/2.));
3661: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; /* At age of beginning of transition, where status is known */
3662: /* freq[s[m][i]][s[m+1][i]][(int)((agebegin+ageend)/2.)] += weight[i]; */
3663: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
1.126 brouard 3664: }
1.214 brouard 3665: }
3666: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3)) && (anint[m][i]!=9999) && (mint[m][i]!=99)) {
3667: dateintsum=dateintsum+k2;
3668: k2cpt++;
3669: /* printf("i=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",i, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
3670: }
3671: /*}*/
1.210 brouard 3672: } /* end m */
3673: } /* end bool */
3674: } /* end i = 1 to imx */
1.126 brouard 3675:
3676: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
3677: pstamp(ficresp);
3678: if (cptcovn>0) {
3679: fprintf(ficresp, "\n#********** Variable ");
1.214 brouard 3680: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
3681: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
1.213 brouard 3682: for (z1=1; z1<=cptcoveff; z1++){
3683: fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
3684: fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.214 brouard 3685: fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.213 brouard 3686: }
3687: fprintf(ficresp, "**********\n#");
1.214 brouard 3688: fprintf(ficresphtm, "**********</h3>\n");
3689: fprintf(ficresphtmfr, "**********</h3>\n");
1.143 brouard 3690: fprintf(ficlog, "\n#********** Variable ");
1.198 brouard 3691: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.214 brouard 3692: fprintf(ficlog, "**********\n");
1.126 brouard 3693: }
1.214 brouard 3694: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
1.213 brouard 3695: for(i=1; i<=nlstate;i++) {
1.126 brouard 3696: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1.213 brouard 3697: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
3698: }
1.126 brouard 3699: fprintf(ficresp, "\n");
1.213 brouard 3700: fprintf(ficresphtm, "\n");
1.126 brouard 3701:
1.214 brouard 3702: /* Header of frequency table by age */
3703: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
3704: fprintf(ficresphtmfr,"<th>Age</th> ");
3705: for(jk=-1; jk <=nlstate+ndeath; jk++){
3706: for(m=-1; m <=nlstate+ndeath; m++){
3707: if(jk!=0 && m!=0)
3708: fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
3709: }
3710: }
3711: fprintf(ficresphtmfr, "\n");
3712:
3713: /* For each age */
1.126 brouard 3714: for(i=iagemin; i <= iagemax+3; i++){
1.213 brouard 3715: fprintf(ficresphtm,"<tr>");
1.214 brouard 3716: if(i==iagemax+1){
3717: fprintf(ficlog,"1");
3718: fprintf(ficresphtmfr,"<tr><th>0</th> ");
3719: }else if(i==iagemax+2){
3720: fprintf(ficlog,"0");
3721: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
3722: }else if(i==iagemax+3){
1.126 brouard 3723: fprintf(ficlog,"Total");
1.214 brouard 3724: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
1.126 brouard 3725: }else{
3726: if(first==1){
3727: first=0;
3728: printf("See log file for details...\n");
3729: }
1.214 brouard 3730: fprintf(ficresphtmfr,"<tr><th>%d</th> ",i);
1.126 brouard 3731: fprintf(ficlog,"Age %d", i);
3732: }
3733: for(jk=1; jk <=nlstate ; jk++){
3734: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
3735: pp[jk] += freq[jk][m][i];
3736: }
3737: for(jk=1; jk <=nlstate ; jk++){
3738: for(m=-1, pos=0; m <=0 ; m++)
3739: pos += freq[jk][m][i];
3740: if(pp[jk]>=1.e-10){
3741: if(first==1){
1.132 brouard 3742: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 3743: }
3744: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3745: }else{
3746: if(first==1)
3747: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3748: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3749: }
3750: }
3751:
3752: for(jk=1; jk <=nlstate ; jk++){
3753: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
3754: pp[jk] += freq[jk][m][i];
3755: }
3756: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
3757: pos += pp[jk];
3758: posprop += prop[jk][i];
3759: }
3760: for(jk=1; jk <=nlstate ; jk++){
3761: if(pos>=1.e-5){
3762: if(first==1)
3763: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3764: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3765: }else{
3766: if(first==1)
3767: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3768: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3769: }
3770: if( i <= iagemax){
3771: if(pos>=1.e-5){
3772: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.213 brouard 3773: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.126 brouard 3774: /*probs[i][jk][j1]= pp[jk]/pos;*/
3775: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
3776: }
1.213 brouard 3777: else{
1.126 brouard 3778: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.213 brouard 3779: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",i, prop[jk][i],posprop);
3780: }
1.126 brouard 3781: }
3782: }
3783:
1.214 brouard 3784: for(jk=-1; jk <=nlstate+ndeath; jk++){
3785: for(m=-1; m <=nlstate+ndeath; m++){
3786: if(freq[jk][m][i] !=0 ) { /* minimizing output */
3787: if(first==1){
3788: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
3789: }
1.126 brouard 3790: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
3791: }
1.214 brouard 3792: if(jk!=0 && m!=0)
3793: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][i]);
3794: }
3795: }
3796: fprintf(ficresphtmfr,"</tr>\n ");
1.213 brouard 3797: if(i <= iagemax){
1.126 brouard 3798: fprintf(ficresp,"\n");
1.213 brouard 3799: fprintf(ficresphtm,"</tr>\n");
3800: }
1.126 brouard 3801: if(first==1)
3802: printf("Others in log...\n");
3803: fprintf(ficlog,"\n");
1.210 brouard 3804: } /* end loop i */
1.213 brouard 3805: fprintf(ficresphtm,"</table>\n");
1.214 brouard 3806: fprintf(ficresphtmfr,"</table>\n");
1.145 brouard 3807: /*}*/
1.210 brouard 3808: } /* end j1 */
1.126 brouard 3809: dateintmean=dateintsum/k2cpt;
3810:
3811: fclose(ficresp);
1.213 brouard 3812: fclose(ficresphtm);
1.214 brouard 3813: fclose(ficresphtmfr);
1.126 brouard 3814: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
3815: free_vector(pp,1,nlstate);
3816: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
3817: /* End of Freq */
3818: }
3819:
3820: /************ Prevalence ********************/
3821: 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)
3822: {
3823: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3824: in each health status at the date of interview (if between dateprev1 and dateprev2).
3825: We still use firstpass and lastpass as another selection.
3826: */
3827:
1.164 brouard 3828: int i, m, jk, j1, bool, z1,j;
1.214 brouard 3829: int mi; /* Effective wave */
3830: int iage;
3831: double agebegin, ageend;
1.164 brouard 3832:
3833: double **prop;
3834: double posprop;
1.126 brouard 3835: double y2; /* in fractional years */
3836: int iagemin, iagemax;
1.145 brouard 3837: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 3838:
3839: iagemin= (int) agemin;
3840: iagemax= (int) agemax;
3841: /*pp=vector(1,nlstate);*/
3842: prop=matrix(1,nlstate,iagemin,iagemax+3);
3843: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3844: j1=0;
3845:
1.145 brouard 3846: /*j=cptcoveff;*/
1.126 brouard 3847: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3848:
1.145 brouard 3849: first=1;
3850: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
1.214 brouard 3851: for (i=1; i<=nlstate; i++)
3852: for(iage=iagemin; iage <= iagemax+3; iage++)
3853: prop[i][iage]=0.0;
3854:
3855: for (i=1; i<=imx; i++) { /* Each individual */
3856: bool=1;
3857: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
3858: for (z1=1; z1<=cptcoveff; z1++)
3859: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
3860: bool=0;
3861: }
3862: if (bool==1) {
3863: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
3864: for(mi=1; mi<wav[i];mi++){
3865: m=mw[mi][i];
3866: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
3867: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
3868: if(m >=firstpass && m <=lastpass){
1.126 brouard 3869: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3870: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3871: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3872: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3873: if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
1.214 brouard 3874: if (s[m][i]>0 && s[m][i]<=nlstate) {
1.126 brouard 3875: /*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]]);*/
1.214 brouard 3876: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
3877: prop[s[m][i]][iagemax+3] += weight[i];
3878: } /* end valid statuses */
3879: } /* end selection of dates */
1.126 brouard 3880: } /* end selection of waves */
1.214 brouard 3881: } /* end effective waves */
3882: } /* end bool */
3883: }
3884: for(i=iagemin; i <= iagemax+3; i++){
3885: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3886: posprop += prop[jk][i];
3887: }
3888:
3889: for(jk=1; jk <=nlstate ; jk++){
3890: if( i <= iagemax){
3891: if(posprop>=1.e-5){
3892: probs[i][jk][j1]= prop[jk][i]/posprop;
3893: } else{
3894: if(first==1){
3895: first=0;
3896: printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
1.145 brouard 3897: }
1.214 brouard 3898: }
3899: }
3900: }/* end jk */
3901: }/* end i */
1.145 brouard 3902: /*} *//* end i1 */
3903: } /* end j1 */
1.126 brouard 3904:
3905: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3906: /*free_vector(pp,1,nlstate);*/
3907: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3908: } /* End of prevalence */
3909:
3910: /************* Waves Concatenation ***************/
3911:
3912: 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)
3913: {
3914: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3915: Death is a valid wave (if date is known).
3916: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3917: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3918: and mw[mi+1][i]. dh depends on stepm.
3919: */
3920:
3921: int i, mi, m;
3922: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3923: double sum=0., jmean=0.;*/
1.217 ! brouard 3924: int first, firstwo, firsthree;
1.126 brouard 3925: int j, k=0,jk, ju, jl;
3926: double sum=0.;
3927: first=0;
1.214 brouard 3928: firstwo=0;
1.217 ! brouard 3929: firsthree=0;
1.164 brouard 3930: jmin=100000;
1.126 brouard 3931: jmax=-1;
3932: jmean=0.;
1.214 brouard 3933: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.126 brouard 3934: mi=0;
3935: m=firstpass;
1.214 brouard 3936: while(s[m][i] <= nlstate){ /* a live state */
1.216 brouard 3937: if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
1.126 brouard 3938: mw[++mi][i]=m;
1.216 brouard 3939: }
3940: if(m >=lastpass){
3941: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
1.217 ! brouard 3942: if(firsthree == 0){
! 3943: printf("Information! Unknown health status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
! 3944: 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.\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);
! 3945: firsthree=1;
! 3946: }else{
! 3947: 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.\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);
! 3948: }
1.216 brouard 3949: mw[++mi][i]=m;
3950: }
3951: if(s[m][i]==-2){ /* Vital status is really unknown */
3952: nbwarn++;
3953: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */
3954: 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);
3955: fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
3956: }
3957: break;
3958: }
1.126 brouard 3959: break;
1.216 brouard 3960: }
1.126 brouard 3961: else
3962: m++;
3963: }/* end while */
1.216 brouard 3964:
3965: /* After last pass */
1.214 brouard 3966: if (s[m][i] > nlstate){ /* In a death state */
1.126 brouard 3967: mi++; /* Death is another wave */
3968: /* if(mi==0) never been interviewed correctly before death */
3969: /* Only death is a correct wave */
3970: mw[mi][i]=m;
1.216 brouard 3971: }else if ((int) andc[i] != 9999) { /* Status is either death or negative. A death occured after lastpass, we can't take it into account because of potential bias */
3972: /* m++; */
3973: /* mi++; */
3974: /* s[m][i]=nlstate+1; /\* We are setting the status to the last of non live state *\/ */
3975: /* mw[mi][i]=m; */
3976: nberr++;
1.214 brouard 3977: if(firstwo==0){
1.216 brouard 3978: printf("Error! Death for individual %ld line=%d occurred %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
3979: fprintf(ficlog,"Error! Death for individual %ld line=%d occurred %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\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 );
1.214 brouard 3980: firstwo=1;
1.216 brouard 3981: }else if(firstwo==1){
3982: fprintf(ficlog,"Error! Death for individual %ld line=%d occurred %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\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 );
1.214 brouard 3983: }
1.126 brouard 3984: }
3985: wav[i]=mi;
3986: if(mi==0){
3987: nbwarn++;
3988: if(first==0){
3989: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3990: first=1;
3991: }
3992: if(first==1){
3993: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3994: }
3995: } /* end mi==0 */
3996: } /* End individuals */
1.214 brouard 3997: /* wav and mw are no more changed */
1.126 brouard 3998:
1.214 brouard 3999:
1.126 brouard 4000: for(i=1; i<=imx; i++){
4001: for(mi=1; mi<wav[i];mi++){
4002: if (stepm <=0)
4003: dh[mi][i]=1;
4004: else{
4005: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
4006: if (agedc[i] < 2*AGESUP) {
4007: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
4008: if(j==0) j=1; /* Survives at least one month after exam */
4009: else if(j<0){
4010: nberr++;
4011: 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]);
4012: j=1; /* Temporary Dangerous patch */
4013: 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);
4014: 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]);
4015: 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);
4016: }
4017: k=k+1;
4018: if (j >= jmax){
4019: jmax=j;
4020: ijmax=i;
4021: }
4022: if (j <= jmin){
4023: jmin=j;
4024: ijmin=i;
4025: }
4026: sum=sum+j;
4027: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
4028: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
4029: }
4030: }
4031: else{
4032: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
4033: /* 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]); */
4034:
4035: k=k+1;
4036: if (j >= jmax) {
4037: jmax=j;
4038: ijmax=i;
4039: }
4040: else if (j <= jmin){
4041: jmin=j;
4042: ijmin=i;
4043: }
4044: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
4045: /*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]);*/
4046: if(j<0){
4047: nberr++;
4048: 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]);
4049: 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]);
4050: }
4051: sum=sum+j;
4052: }
4053: jk= j/stepm;
4054: jl= j -jk*stepm;
4055: ju= j -(jk+1)*stepm;
4056: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
4057: if(jl==0){
4058: dh[mi][i]=jk;
4059: bh[mi][i]=0;
4060: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 4061: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 4062: dh[mi][i]=jk+1;
4063: bh[mi][i]=ju;
4064: }
4065: }else{
4066: if(jl <= -ju){
4067: dh[mi][i]=jk;
4068: bh[mi][i]=jl; /* bias is positive if real duration
4069: * is higher than the multiple of stepm and negative otherwise.
4070: */
4071: }
4072: else{
4073: dh[mi][i]=jk+1;
4074: bh[mi][i]=ju;
4075: }
4076: if(dh[mi][i]==0){
4077: dh[mi][i]=1; /* At least one step */
4078: bh[mi][i]=ju; /* At least one step */
4079: /* 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);*/
4080: }
4081: } /* end if mle */
4082: }
4083: } /* end wave */
4084: }
4085: jmean=sum/k;
4086: 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 4087: fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
1.126 brouard 4088: }
4089:
4090: /*********** Tricode ****************************/
1.145 brouard 4091: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 4092: {
1.144 brouard 4093: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
4094: /* 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 4095: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 4096: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 4097: * nbcode[Tvar[j]][1]=
1.144 brouard 4098: */
1.130 brouard 4099:
1.145 brouard 4100: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 4101: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 4102: int cptcode=0; /* Modality max of covariates j */
4103: int modmincovj=0; /* Modality min of covariates j */
4104:
4105:
1.126 brouard 4106: cptcoveff=0;
4107:
1.144 brouard 4108: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 4109:
1.145 brouard 4110: /* Loop on covariates without age and products */
1.186 brouard 4111: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
1.192 brouard 4112: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.186 brouard 4113: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.136 brouard 4114: modality of this covariate Vj*/
1.145 brouard 4115: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
4116: * If product of Vn*Vm, still boolean *:
4117: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
4118: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
4119: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 4120: modality of the nth covariate of individual i. */
1.145 brouard 4121: if (ij > modmaxcovj)
4122: modmaxcovj=ij;
4123: else if (ij < modmincovj)
4124: modmincovj=ij;
4125: if ((ij < -1) && (ij > NCOVMAX)){
4126: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
4127: exit(1);
4128: }else
1.136 brouard 4129: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 4130: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 4131: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 4132: /* getting the maximum value of the modality of the covariate
4133: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
4134: female is 1, then modmaxcovj=1.*/
1.192 brouard 4135: } /* end for loop on individuals i */
1.145 brouard 4136: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.192 brouard 4137: fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.145 brouard 4138: cptcode=modmaxcovj;
1.137 brouard 4139: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 4140: /*for (i=0; i<=cptcode; i++) {*/
1.192 brouard 4141: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
4142: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
4143: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
4144: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
4145: if( k != -1){
4146: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
4147: covariate for which somebody answered excluding
4148: undefined. Usually 2: 0 and 1. */
4149: }
4150: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
4151: covariate for which somebody answered including
4152: undefined. Usually 3: -1, 0 and 1. */
1.145 brouard 4153: }
4154: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
4155: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 4156: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 4157:
1.136 brouard 4158: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 4159: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
4160: If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
1.145 brouard 4161: modmincovj=3; modmaxcovj = 7;
1.186 brouard 4162: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
4163: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
4164: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 4165: nbcode[Tvar[j]][ij]=k;
4166: nbcode[Tvar[j]][1]=0;
4167: nbcode[Tvar[j]][2]=1;
4168: nbcode[Tvar[j]][3]=2;
1.197 brouard 4169: To be continued (not working yet).
1.145 brouard 4170: */
1.197 brouard 4171: ij=0; /* ij is similar to i but can jump over null modalities */
4172: 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*/
4173: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
1.192 brouard 4174: break;
4175: }
4176: ij++;
1.197 brouard 4177: nbcode[Tvar[j]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
1.192 brouard 4178: cptcode = ij; /* New max modality for covar j */
4179: } /* end of loop on modality i=-1 to 1 or more */
4180:
4181: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
4182: /* /\*recode from 0 *\/ */
4183: /* k is a modality. If we have model=V1+V1*sex */
4184: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
4185: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
4186: /* } */
4187: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
4188: /* if (ij > ncodemax[j]) { */
4189: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4190: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4191: /* break; */
4192: /* } */
4193: /* } /\* end of loop on modality k *\/ */
1.137 brouard 4194: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
4195:
1.145 brouard 4196: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 4197:
1.187 brouard 4198: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.145 brouard 4199: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
4200: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.187 brouard 4201: Ndum[ij]++; /* Might be supersed V1 + V1*age */
1.145 brouard 4202: }
1.126 brouard 4203:
1.192 brouard 4204: ij=0;
1.145 brouard 4205: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
4206: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 4207: if((Ndum[i]!=0) && (i<=ncovcol)){
1.192 brouard 4208: ij++;
1.145 brouard 4209: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
4210: Tvaraff[ij]=i; /*For printing (unclear) */
1.192 brouard 4211: }else{
4212: /* Tvaraff[ij]=0; */
4213: }
1.126 brouard 4214: }
1.192 brouard 4215: /* ij--; */
1.144 brouard 4216: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 4217:
1.126 brouard 4218: }
4219:
1.145 brouard 4220:
1.126 brouard 4221: /*********** Health Expectancies ****************/
4222:
1.127 brouard 4223: 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 4224:
4225: {
4226: /* Health expectancies, no variances */
1.164 brouard 4227: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 4228: int nhstepma, nstepma; /* Decreasing with age */
4229: double age, agelim, hf;
4230: double ***p3mat;
4231: double eip;
4232:
4233: pstamp(ficreseij);
4234: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
4235: fprintf(ficreseij,"# Age");
4236: for(i=1; i<=nlstate;i++){
4237: for(j=1; j<=nlstate;j++){
4238: fprintf(ficreseij," e%1d%1d ",i,j);
4239: }
4240: fprintf(ficreseij," e%1d. ",i);
4241: }
4242: fprintf(ficreseij,"\n");
4243:
4244:
4245: if(estepm < stepm){
4246: printf ("Problem %d lower than %d\n",estepm, stepm);
4247: }
4248: else hstepm=estepm;
4249: /* We compute the life expectancy from trapezoids spaced every estepm months
4250: * This is mainly to measure the difference between two models: for example
4251: * if stepm=24 months pijx are given only every 2 years and by summing them
4252: * we are calculating an estimate of the Life Expectancy assuming a linear
4253: * progression in between and thus overestimating or underestimating according
4254: * to the curvature of the survival function. If, for the same date, we
4255: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4256: * to compare the new estimate of Life expectancy with the same linear
4257: * hypothesis. A more precise result, taking into account a more precise
4258: * curvature will be obtained if estepm is as small as stepm. */
4259:
4260: /* For example we decided to compute the life expectancy with the smallest unit */
4261: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4262: nhstepm is the number of hstepm from age to agelim
4263: nstepm is the number of stepm from age to agelin.
4264: Look at hpijx to understand the reason of that which relies in memory size
4265: and note for a fixed period like estepm months */
4266: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4267: survival function given by stepm (the optimization length). Unfortunately it
4268: means that if the survival funtion is printed only each two years of age and if
4269: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4270: results. So we changed our mind and took the option of the best precision.
4271: */
4272: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4273:
4274: agelim=AGESUP;
4275: /* If stepm=6 months */
4276: /* Computed by stepm unit matrices, product of hstepm matrices, stored
4277: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
4278:
4279: /* nhstepm age range expressed in number of stepm */
4280: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4281: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4282: /* if (stepm >= YEARM) hstepm=1;*/
4283: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4284: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4285:
4286: for (age=bage; age<=fage; age ++){
4287: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4288: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4289: /* if (stepm >= YEARM) hstepm=1;*/
4290: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
4291:
4292: /* If stepm=6 months */
4293: /* Computed by stepm unit matrices, product of hstepma matrices, stored
4294: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
4295:
4296: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
4297:
4298: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4299:
4300: printf("%d|",(int)age);fflush(stdout);
4301: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
4302:
4303: /* Computing expectancies */
4304: for(i=1; i<=nlstate;i++)
4305: for(j=1; j<=nlstate;j++)
4306: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
4307: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
4308:
4309: /* 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]);*/
4310:
4311: }
4312:
4313: fprintf(ficreseij,"%3.0f",age );
4314: for(i=1; i<=nlstate;i++){
4315: eip=0;
4316: for(j=1; j<=nlstate;j++){
4317: eip +=eij[i][j][(int)age];
4318: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
4319: }
4320: fprintf(ficreseij,"%9.4f", eip );
4321: }
4322: fprintf(ficreseij,"\n");
4323:
4324: }
4325: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4326: printf("\n");
4327: fprintf(ficlog,"\n");
4328:
4329: }
4330:
1.127 brouard 4331: 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 4332:
4333: {
4334: /* Covariances of health expectancies eij and of total life expectancies according
4335: to initial status i, ei. .
4336: */
4337: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
4338: int nhstepma, nstepma; /* Decreasing with age */
4339: double age, agelim, hf;
4340: double ***p3matp, ***p3matm, ***varhe;
4341: double **dnewm,**doldm;
4342: double *xp, *xm;
4343: double **gp, **gm;
4344: double ***gradg, ***trgradg;
4345: int theta;
4346:
4347: double eip, vip;
4348:
4349: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
4350: xp=vector(1,npar);
4351: xm=vector(1,npar);
4352: dnewm=matrix(1,nlstate*nlstate,1,npar);
4353: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
4354:
4355: pstamp(ficresstdeij);
4356: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
4357: fprintf(ficresstdeij,"# Age");
4358: for(i=1; i<=nlstate;i++){
4359: for(j=1; j<=nlstate;j++)
4360: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
4361: fprintf(ficresstdeij," e%1d. ",i);
4362: }
4363: fprintf(ficresstdeij,"\n");
4364:
4365: pstamp(ficrescveij);
4366: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
4367: fprintf(ficrescveij,"# Age");
4368: for(i=1; i<=nlstate;i++)
4369: for(j=1; j<=nlstate;j++){
4370: cptj= (j-1)*nlstate+i;
4371: for(i2=1; i2<=nlstate;i2++)
4372: for(j2=1; j2<=nlstate;j2++){
4373: cptj2= (j2-1)*nlstate+i2;
4374: if(cptj2 <= cptj)
4375: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
4376: }
4377: }
4378: fprintf(ficrescveij,"\n");
4379:
4380: if(estepm < stepm){
4381: printf ("Problem %d lower than %d\n",estepm, stepm);
4382: }
4383: else hstepm=estepm;
4384: /* We compute the life expectancy from trapezoids spaced every estepm months
4385: * This is mainly to measure the difference between two models: for example
4386: * if stepm=24 months pijx are given only every 2 years and by summing them
4387: * we are calculating an estimate of the Life Expectancy assuming a linear
4388: * progression in between and thus overestimating or underestimating according
4389: * to the curvature of the survival function. If, for the same date, we
4390: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4391: * to compare the new estimate of Life expectancy with the same linear
4392: * hypothesis. A more precise result, taking into account a more precise
4393: * curvature will be obtained if estepm is as small as stepm. */
4394:
4395: /* For example we decided to compute the life expectancy with the smallest unit */
4396: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4397: nhstepm is the number of hstepm from age to agelim
4398: nstepm is the number of stepm from age to agelin.
4399: Look at hpijx to understand the reason of that which relies in memory size
4400: and note for a fixed period like estepm months */
4401: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4402: survival function given by stepm (the optimization length). Unfortunately it
4403: means that if the survival funtion is printed only each two years of age and if
4404: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4405: results. So we changed our mind and took the option of the best precision.
4406: */
4407: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4408:
4409: /* If stepm=6 months */
4410: /* nhstepm age range expressed in number of stepm */
4411: agelim=AGESUP;
4412: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
4413: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4414: /* if (stepm >= YEARM) hstepm=1;*/
4415: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4416:
4417: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4418: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4419: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
4420: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
4421: gp=matrix(0,nhstepm,1,nlstate*nlstate);
4422: gm=matrix(0,nhstepm,1,nlstate*nlstate);
4423:
4424: for (age=bage; age<=fage; age ++){
4425: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4426: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4427: /* if (stepm >= YEARM) hstepm=1;*/
4428: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
4429:
4430: /* If stepm=6 months */
4431: /* Computed by stepm unit matrices, product of hstepma matrices, stored
4432: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
4433:
4434: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4435:
4436: /* Computing Variances of health expectancies */
4437: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
4438: decrease memory allocation */
4439: for(theta=1; theta <=npar; theta++){
4440: for(i=1; i<=npar; i++){
4441: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4442: xm[i] = x[i] - (i==theta ?delti[theta]:0);
4443: }
4444: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
4445: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
4446:
4447: for(j=1; j<= nlstate; j++){
4448: for(i=1; i<=nlstate; i++){
4449: for(h=0; h<=nhstepm-1; h++){
4450: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
4451: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
4452: }
4453: }
4454: }
4455:
4456: for(ij=1; ij<= nlstate*nlstate; ij++)
4457: for(h=0; h<=nhstepm-1; h++){
4458: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
4459: }
4460: }/* End theta */
4461:
4462:
4463: for(h=0; h<=nhstepm-1; h++)
4464: for(j=1; j<=nlstate*nlstate;j++)
4465: for(theta=1; theta <=npar; theta++)
4466: trgradg[h][j][theta]=gradg[h][theta][j];
4467:
4468:
4469: for(ij=1;ij<=nlstate*nlstate;ij++)
4470: for(ji=1;ji<=nlstate*nlstate;ji++)
4471: varhe[ij][ji][(int)age] =0.;
4472:
4473: printf("%d|",(int)age);fflush(stdout);
4474: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
4475: for(h=0;h<=nhstepm-1;h++){
4476: for(k=0;k<=nhstepm-1;k++){
4477: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
4478: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
4479: for(ij=1;ij<=nlstate*nlstate;ij++)
4480: for(ji=1;ji<=nlstate*nlstate;ji++)
4481: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
4482: }
4483: }
4484:
4485: /* Computing expectancies */
4486: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
4487: for(i=1; i<=nlstate;i++)
4488: for(j=1; j<=nlstate;j++)
4489: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
4490: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
4491:
4492: /* 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]);*/
4493:
4494: }
4495:
4496: fprintf(ficresstdeij,"%3.0f",age );
4497: for(i=1; i<=nlstate;i++){
4498: eip=0.;
4499: vip=0.;
4500: for(j=1; j<=nlstate;j++){
4501: eip += eij[i][j][(int)age];
4502: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
4503: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
4504: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
4505: }
4506: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
4507: }
4508: fprintf(ficresstdeij,"\n");
4509:
4510: fprintf(ficrescveij,"%3.0f",age );
4511: for(i=1; i<=nlstate;i++)
4512: for(j=1; j<=nlstate;j++){
4513: cptj= (j-1)*nlstate+i;
4514: for(i2=1; i2<=nlstate;i2++)
4515: for(j2=1; j2<=nlstate;j2++){
4516: cptj2= (j2-1)*nlstate+i2;
4517: if(cptj2 <= cptj)
4518: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
4519: }
4520: }
4521: fprintf(ficrescveij,"\n");
4522:
4523: }
4524: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
4525: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
4526: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
4527: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
4528: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4529: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4530: printf("\n");
4531: fprintf(ficlog,"\n");
4532:
4533: free_vector(xm,1,npar);
4534: free_vector(xp,1,npar);
4535: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
4536: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
4537: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
4538: }
4539:
4540: /************ Variance ******************/
1.209 brouard 4541: 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[])
1.126 brouard 4542: {
4543: /* Variance of health expectancies */
4544: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
4545: /* double **newm;*/
1.169 brouard 4546: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
4547:
4548: int movingaverage();
1.126 brouard 4549: double **dnewm,**doldm;
4550: double **dnewmp,**doldmp;
4551: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 4552: int k;
1.126 brouard 4553: double *xp;
4554: double **gp, **gm; /* for var eij */
4555: double ***gradg, ***trgradg; /*for var eij */
4556: double **gradgp, **trgradgp; /* for var p point j */
4557: double *gpp, *gmp; /* for var p point j */
4558: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
4559: double ***p3mat;
4560: double age,agelim, hf;
4561: double ***mobaverage;
4562: int theta;
4563: char digit[4];
4564: char digitp[25];
4565:
4566: char fileresprobmorprev[FILENAMELENGTH];
4567:
4568: if(popbased==1){
4569: if(mobilav!=0)
1.201 brouard 4570: strcpy(digitp,"-POPULBASED-MOBILAV_");
4571: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
1.126 brouard 4572: }
4573: else
1.201 brouard 4574: strcpy(digitp,"-STABLBASED_");
1.126 brouard 4575:
4576: if (mobilav!=0) {
4577: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4578: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4579: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4580: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4581: }
4582: }
4583:
1.201 brouard 4584: strcpy(fileresprobmorprev,"PRMORPREV-");
1.126 brouard 4585: sprintf(digit,"%-d",ij);
4586: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
4587: strcat(fileresprobmorprev,digit); /* Tvar to be done */
4588: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
1.202 brouard 4589: strcat(fileresprobmorprev,fileresu);
1.126 brouard 4590: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
4591: printf("Problem with resultfile: %s\n", fileresprobmorprev);
4592: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
4593: }
4594: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4595: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4596: pstamp(ficresprobmorprev);
4597: 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);
4598: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
4599: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4600: fprintf(ficresprobmorprev," p.%-d SE",j);
4601: for(i=1; i<=nlstate;i++)
4602: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
4603: }
4604: fprintf(ficresprobmorprev,"\n");
1.208 brouard 4605:
1.126 brouard 4606: fprintf(ficgp,"\n# Routine varevsij");
1.200 brouard 4607: fprintf(ficgp,"\nunset title \n");
4608: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
1.126 brouard 4609: 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");
4610: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
4611: /* } */
4612: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4613: pstamp(ficresvij);
4614: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
4615: if(popbased==1)
1.128 brouard 4616: 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);
1.126 brouard 4617: else
4618: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
4619: fprintf(ficresvij,"# Age");
4620: for(i=1; i<=nlstate;i++)
4621: for(j=1; j<=nlstate;j++)
4622: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
4623: fprintf(ficresvij,"\n");
4624:
4625: xp=vector(1,npar);
4626: dnewm=matrix(1,nlstate,1,npar);
4627: doldm=matrix(1,nlstate,1,nlstate);
4628: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
4629: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4630:
4631: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
4632: gpp=vector(nlstate+1,nlstate+ndeath);
4633: gmp=vector(nlstate+1,nlstate+ndeath);
4634: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
4635:
4636: if(estepm < stepm){
4637: printf ("Problem %d lower than %d\n",estepm, stepm);
4638: }
4639: else hstepm=estepm;
4640: /* For example we decided to compute the life expectancy with the smallest unit */
4641: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4642: nhstepm is the number of hstepm from age to agelim
1.208 brouard 4643: nstepm is the number of stepm from age to agelim.
1.209 brouard 4644: Look at function hpijx to understand why because of memory size limitations,
1.208 brouard 4645: we decided (b) to get a life expectancy respecting the most precise curvature of the
1.126 brouard 4646: survival function given by stepm (the optimization length). Unfortunately it
4647: means that if the survival funtion is printed every two years of age and if
4648: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4649: results. So we changed our mind and took the option of the best precision.
4650: */
4651: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4652: agelim = AGESUP;
4653: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4654: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4655: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4656: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4657: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
4658: gp=matrix(0,nhstepm,1,nlstate);
4659: gm=matrix(0,nhstepm,1,nlstate);
4660:
4661:
4662: for(theta=1; theta <=npar; theta++){
4663: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
4664: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4665: }
1.209 brouard 4666:
4667: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.126 brouard 4668:
4669: if (popbased==1) {
4670: if(mobilav ==0){
4671: for(i=1; i<=nlstate;i++)
4672: prlim[i][i]=probs[(int)age][i][ij];
4673: }else{ /* mobilav */
4674: for(i=1; i<=nlstate;i++)
4675: prlim[i][i]=mobaverage[(int)age][i][ij];
4676: }
4677: }
4678:
1.209 brouard 4679: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); /* Returns p3mat[i][j][h] for h=1 to nhstepm */
1.126 brouard 4680: for(j=1; j<= nlstate; j++){
4681: for(h=0; h<=nhstepm; h++){
4682: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
4683: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
4684: }
4685: }
1.209 brouard 4686: /* Next for computing probability of death (h=1 means
1.126 brouard 4687: computed over hstepm matrices product = hstepm*stepm months)
4688: as a weighted average of prlim.
4689: */
4690: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4691: for(i=1,gpp[j]=0.; i<= nlstate; i++)
4692: gpp[j] += prlim[i][i]*p3mat[i][j][1];
4693: }
4694: /* end probability of death */
4695:
4696: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
4697: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 4698:
4699: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
1.126 brouard 4700:
4701: if (popbased==1) {
4702: if(mobilav ==0){
4703: for(i=1; i<=nlstate;i++)
4704: prlim[i][i]=probs[(int)age][i][ij];
4705: }else{ /* mobilav */
4706: for(i=1; i<=nlstate;i++)
4707: prlim[i][i]=mobaverage[(int)age][i][ij];
4708: }
4709: }
4710:
1.209 brouard 4711: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
4712:
1.128 brouard 4713: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 4714: for(h=0; h<=nhstepm; h++){
4715: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
4716: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
4717: }
4718: }
4719: /* This for computing probability of death (h=1 means
4720: computed over hstepm matrices product = hstepm*stepm months)
4721: as a weighted average of prlim.
4722: */
4723: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4724: for(i=1,gmp[j]=0.; i<= nlstate; i++)
4725: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4726: }
4727: /* end probability of death */
4728:
4729: for(j=1; j<= nlstate; j++) /* vareij */
4730: for(h=0; h<=nhstepm; h++){
4731: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
4732: }
4733:
4734: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
4735: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
4736: }
4737:
4738: } /* End theta */
4739:
4740: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
4741:
4742: for(h=0; h<=nhstepm; h++) /* veij */
4743: for(j=1; j<=nlstate;j++)
4744: for(theta=1; theta <=npar; theta++)
4745: trgradg[h][j][theta]=gradg[h][theta][j];
4746:
4747: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
4748: for(theta=1; theta <=npar; theta++)
4749: trgradgp[j][theta]=gradgp[theta][j];
4750:
4751:
4752: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4753: for(i=1;i<=nlstate;i++)
4754: for(j=1;j<=nlstate;j++)
4755: vareij[i][j][(int)age] =0.;
4756:
4757: for(h=0;h<=nhstepm;h++){
4758: for(k=0;k<=nhstepm;k++){
4759: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
4760: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
4761: for(i=1;i<=nlstate;i++)
4762: for(j=1;j<=nlstate;j++)
4763: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
4764: }
4765: }
4766:
4767: /* pptj */
4768: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
4769: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
4770: for(j=nlstate+1;j<=nlstate+ndeath;j++)
4771: for(i=nlstate+1;i<=nlstate+ndeath;i++)
4772: varppt[j][i]=doldmp[j][i];
4773: /* end ppptj */
4774: /* x centered again */
1.209 brouard 4775:
4776: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
1.126 brouard 4777:
4778: if (popbased==1) {
4779: if(mobilav ==0){
4780: for(i=1; i<=nlstate;i++)
4781: prlim[i][i]=probs[(int)age][i][ij];
4782: }else{ /* mobilav */
4783: for(i=1; i<=nlstate;i++)
4784: prlim[i][i]=mobaverage[(int)age][i][ij];
4785: }
4786: }
4787:
4788: /* This for computing probability of death (h=1 means
4789: computed over hstepm (estepm) matrices product = hstepm*stepm months)
4790: as a weighted average of prlim.
4791: */
1.209 brouard 4792: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
1.126 brouard 4793: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4794: for(i=1,gmp[j]=0.;i<= nlstate; i++)
4795: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4796: }
4797: /* end probability of death */
4798:
4799: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
4800: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4801: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
4802: for(i=1; i<=nlstate;i++){
4803: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
4804: }
4805: }
4806: fprintf(ficresprobmorprev,"\n");
4807:
4808: fprintf(ficresvij,"%.0f ",age );
4809: for(i=1; i<=nlstate;i++)
4810: for(j=1; j<=nlstate;j++){
4811: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
4812: }
4813: fprintf(ficresvij,"\n");
4814: free_matrix(gp,0,nhstepm,1,nlstate);
4815: free_matrix(gm,0,nhstepm,1,nlstate);
4816: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
4817: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
4818: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4819: } /* End age */
4820: free_vector(gpp,nlstate+1,nlstate+ndeath);
4821: free_vector(gmp,nlstate+1,nlstate+ndeath);
4822: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
4823: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.199 brouard 4824: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
4825: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
1.126 brouard 4826: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 4827: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.201 brouard 4828: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4829: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
4830: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
4831: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 4832: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 4833: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 4834: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 4835: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
1.201 brouard 4836: 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);
1.199 brouard 4837: /* 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 4838: */
1.199 brouard 4839: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
1.201 brouard 4840: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4841:
4842: free_vector(xp,1,npar);
4843: free_matrix(doldm,1,nlstate,1,nlstate);
4844: free_matrix(dnewm,1,nlstate,1,npar);
4845: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4846: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
4847: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4848: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4849: fclose(ficresprobmorprev);
4850: fflush(ficgp);
4851: fflush(fichtm);
4852: } /* end varevsij */
4853:
4854: /************ Variance of prevlim ******************/
1.209 brouard 4855: 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 4856: {
1.205 brouard 4857: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 4858: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 4859:
1.126 brouard 4860: double **dnewm,**doldm;
4861: int i, j, nhstepm, hstepm;
4862: double *xp;
4863: double *gp, *gm;
4864: double **gradg, **trgradg;
1.208 brouard 4865: double **mgm, **mgp;
1.126 brouard 4866: double age,agelim;
4867: int theta;
4868:
4869: pstamp(ficresvpl);
4870: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
4871: fprintf(ficresvpl,"# Age");
4872: for(i=1; i<=nlstate;i++)
4873: fprintf(ficresvpl," %1d-%1d",i,i);
4874: fprintf(ficresvpl,"\n");
4875:
4876: xp=vector(1,npar);
4877: dnewm=matrix(1,nlstate,1,npar);
4878: doldm=matrix(1,nlstate,1,nlstate);
4879:
4880: hstepm=1*YEARM; /* Every year of age */
4881: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
4882: agelim = AGESUP;
4883: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4884: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4885: if (stepm >= YEARM) hstepm=1;
4886: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4887: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 4888: mgp=matrix(1,npar,1,nlstate);
4889: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 4890: gp=vector(1,nlstate);
4891: gm=vector(1,nlstate);
4892:
4893: for(theta=1; theta <=npar; theta++){
4894: for(i=1; i<=npar; i++){ /* Computes gradient */
4895: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4896: }
1.209 brouard 4897: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
4898: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
4899: else
4900: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 4901: for(i=1;i<=nlstate;i++){
1.126 brouard 4902: gp[i] = prlim[i][i];
1.208 brouard 4903: mgp[theta][i] = prlim[i][i];
4904: }
1.126 brouard 4905: for(i=1; i<=npar; i++) /* Computes gradient */
4906: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 4907: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
4908: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
4909: else
4910: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 4911: for(i=1;i<=nlstate;i++){
1.126 brouard 4912: gm[i] = prlim[i][i];
1.208 brouard 4913: mgm[theta][i] = prlim[i][i];
4914: }
1.126 brouard 4915: for(i=1;i<=nlstate;i++)
4916: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 4917: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 4918: } /* End theta */
4919:
4920: trgradg =matrix(1,nlstate,1,npar);
4921:
4922: for(j=1; j<=nlstate;j++)
4923: for(theta=1; theta <=npar; theta++)
4924: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 4925: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
4926: /* printf("\nmgm mgp %d ",(int)age); */
4927: /* for(j=1; j<=nlstate;j++){ */
4928: /* printf(" %d ",j); */
4929: /* for(theta=1; theta <=npar; theta++) */
4930: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
4931: /* printf("\n "); */
4932: /* } */
4933: /* } */
4934: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
4935: /* printf("\n gradg %d ",(int)age); */
4936: /* for(j=1; j<=nlstate;j++){ */
4937: /* printf("%d ",j); */
4938: /* for(theta=1; theta <=npar; theta++) */
4939: /* printf("%d %lf ",theta,gradg[theta][j]); */
4940: /* printf("\n "); */
4941: /* } */
4942: /* } */
1.126 brouard 4943:
4944: for(i=1;i<=nlstate;i++)
4945: varpl[i][(int)age] =0.;
1.209 brouard 4946: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.205 brouard 4947: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4948: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4949: }else{
1.126 brouard 4950: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4951: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 4952: }
1.126 brouard 4953: for(i=1;i<=nlstate;i++)
4954: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4955:
4956: fprintf(ficresvpl,"%.0f ",age );
4957: for(i=1; i<=nlstate;i++)
4958: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4959: fprintf(ficresvpl,"\n");
4960: free_vector(gp,1,nlstate);
4961: free_vector(gm,1,nlstate);
1.208 brouard 4962: free_matrix(mgm,1,npar,1,nlstate);
4963: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 4964: free_matrix(gradg,1,npar,1,nlstate);
4965: free_matrix(trgradg,1,nlstate,1,npar);
4966: } /* End age */
4967:
4968: free_vector(xp,1,npar);
4969: free_matrix(doldm,1,nlstate,1,npar);
4970: free_matrix(dnewm,1,nlstate,1,nlstate);
4971:
4972: }
4973:
4974: /************ Variance of one-step probabilities ******************/
4975: 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[])
4976: {
1.164 brouard 4977: int i, j=0, k1, l1, tj;
1.126 brouard 4978: int k2, l2, j1, z1;
1.164 brouard 4979: int k=0, l;
1.145 brouard 4980: int first=1, first1, first2;
1.126 brouard 4981: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4982: double **dnewm,**doldm;
4983: double *xp;
4984: double *gp, *gm;
4985: double **gradg, **trgradg;
4986: double **mu;
1.164 brouard 4987: double age, cov[NCOVMAX+1];
1.126 brouard 4988: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4989: int theta;
4990: char fileresprob[FILENAMELENGTH];
4991: char fileresprobcov[FILENAMELENGTH];
4992: char fileresprobcor[FILENAMELENGTH];
4993: double ***varpij;
4994:
1.201 brouard 4995: strcpy(fileresprob,"PROB_");
1.126 brouard 4996: strcat(fileresprob,fileres);
4997: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4998: printf("Problem with resultfile: %s\n", fileresprob);
4999: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
5000: }
1.201 brouard 5001: strcpy(fileresprobcov,"PROBCOV_");
1.202 brouard 5002: strcat(fileresprobcov,fileresu);
1.126 brouard 5003: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
5004: printf("Problem with resultfile: %s\n", fileresprobcov);
5005: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
5006: }
1.201 brouard 5007: strcpy(fileresprobcor,"PROBCOR_");
1.202 brouard 5008: strcat(fileresprobcor,fileresu);
1.126 brouard 5009: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
5010: printf("Problem with resultfile: %s\n", fileresprobcor);
5011: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
5012: }
5013: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
5014: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
5015: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
5016: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
5017: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
5018: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
5019: pstamp(ficresprob);
5020: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
5021: fprintf(ficresprob,"# Age");
5022: pstamp(ficresprobcov);
5023: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
5024: fprintf(ficresprobcov,"# Age");
5025: pstamp(ficresprobcor);
5026: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
5027: fprintf(ficresprobcor,"# Age");
5028:
5029:
5030: for(i=1; i<=nlstate;i++)
5031: for(j=1; j<=(nlstate+ndeath);j++){
5032: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
5033: fprintf(ficresprobcov," p%1d-%1d ",i,j);
5034: fprintf(ficresprobcor," p%1d-%1d ",i,j);
5035: }
5036: /* fprintf(ficresprob,"\n");
5037: fprintf(ficresprobcov,"\n");
5038: fprintf(ficresprobcor,"\n");
5039: */
1.131 brouard 5040: xp=vector(1,npar);
1.126 brouard 5041: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
5042: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
5043: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
5044: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
5045: first=1;
5046: fprintf(ficgp,"\n# Routine varprob");
5047: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
5048: fprintf(fichtm,"\n");
5049:
1.200 brouard 5050: 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);
1.197 brouard 5051: 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);
5052: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 5053: and drawn. It helps understanding how is the covariance between two incidences.\
5054: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
5055: 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. \
5056: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
5057: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
5058: standard deviations wide on each axis. <br>\
5059: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
5060: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
5061: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
5062:
5063: cov[1]=1;
1.145 brouard 5064: /* tj=cptcoveff; */
5065: tj = (int) pow(2,cptcoveff);
1.126 brouard 5066: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
5067: j1=0;
1.145 brouard 5068: for(j1=1; j1<=tj;j1++){
5069: /*for(i1=1; i1<=ncodemax[t];i1++){ */
5070: /*j1++;*/
1.126 brouard 5071: if (cptcovn>0) {
5072: fprintf(ficresprob, "\n#********** Variable ");
1.198 brouard 5073: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 5074: fprintf(ficresprob, "**********\n#\n");
5075: fprintf(ficresprobcov, "\n#********** Variable ");
1.198 brouard 5076: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 5077: fprintf(ficresprobcov, "**********\n#\n");
5078:
5079: fprintf(ficgp, "\n#********** Variable ");
1.198 brouard 5080: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 5081: fprintf(ficgp, "**********\n#\n");
5082:
5083:
5084: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.198 brouard 5085: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 5086: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
5087:
5088: fprintf(ficresprobcor, "\n#********** Variable ");
1.198 brouard 5089: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 5090: fprintf(ficresprobcor, "**********\n#");
5091: }
5092:
1.145 brouard 5093: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
5094: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
5095: gp=vector(1,(nlstate)*(nlstate+ndeath));
5096: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 5097: for (age=bage; age<=fage; age ++){
5098: cov[2]=age;
1.187 brouard 5099: if(nagesqr==1)
5100: cov[3]= age*age;
1.126 brouard 5101: for (k=1; k<=cptcovn;k++) {
1.200 brouard 5102: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
5103: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
1.145 brouard 5104: * 1 1 1 1 1
5105: * 2 2 1 1 1
5106: * 3 1 2 1 1
5107: */
5108: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 5109: }
1.186 brouard 5110: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 5111: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
1.126 brouard 5112: for (k=1; k<=cptcovprod;k++)
1.200 brouard 5113: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.126 brouard 5114:
5115:
5116: for(theta=1; theta <=npar; theta++){
5117: for(i=1; i<=npar; i++)
5118: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
5119:
5120: pmij(pmmij,cov,ncovmodel,xp,nlstate);
5121:
5122: k=0;
5123: for(i=1; i<= (nlstate); i++){
5124: for(j=1; j<=(nlstate+ndeath);j++){
5125: k=k+1;
5126: gp[k]=pmmij[i][j];
5127: }
5128: }
5129:
5130: for(i=1; i<=npar; i++)
5131: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
5132:
5133: pmij(pmmij,cov,ncovmodel,xp,nlstate);
5134: k=0;
5135: for(i=1; i<=(nlstate); i++){
5136: for(j=1; j<=(nlstate+ndeath);j++){
5137: k=k+1;
5138: gm[k]=pmmij[i][j];
5139: }
5140: }
5141:
5142: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
5143: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
5144: }
5145:
5146: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
5147: for(theta=1; theta <=npar; theta++)
5148: trgradg[j][theta]=gradg[theta][j];
5149:
5150: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
5151: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
5152:
5153: pmij(pmmij,cov,ncovmodel,x,nlstate);
5154:
5155: k=0;
5156: for(i=1; i<=(nlstate); i++){
5157: for(j=1; j<=(nlstate+ndeath);j++){
5158: k=k+1;
5159: mu[k][(int) age]=pmmij[i][j];
5160: }
5161: }
5162: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
5163: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
5164: varpij[i][j][(int)age] = doldm[i][j];
5165:
5166: /*printf("\n%d ",(int)age);
5167: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
5168: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
5169: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
5170: }*/
5171:
5172: fprintf(ficresprob,"\n%d ",(int)age);
5173: fprintf(ficresprobcov,"\n%d ",(int)age);
5174: fprintf(ficresprobcor,"\n%d ",(int)age);
5175:
5176: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
5177: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
5178: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
5179: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
5180: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
5181: }
5182: i=0;
5183: for (k=1; k<=(nlstate);k++){
5184: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 5185: i++;
1.126 brouard 5186: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
5187: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
5188: for (j=1; j<=i;j++){
1.145 brouard 5189: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 5190: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
5191: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
5192: }
5193: }
5194: }/* end of loop for state */
5195: } /* end of loop for age */
1.145 brouard 5196: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
5197: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
5198: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
5199: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
5200:
1.126 brouard 5201: /* Confidence intervalle of pij */
5202: /*
1.131 brouard 5203: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 5204: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
5205: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
5206: 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);
5207: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
5208: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
5209: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
5210: */
5211:
5212: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 5213: first1=1;first2=2;
1.126 brouard 5214: for (k2=1; k2<=(nlstate);k2++){
5215: for (l2=1; l2<=(nlstate+ndeath);l2++){
5216: if(l2==k2) continue;
5217: j=(k2-1)*(nlstate+ndeath)+l2;
5218: for (k1=1; k1<=(nlstate);k1++){
5219: for (l1=1; l1<=(nlstate+ndeath);l1++){
5220: if(l1==k1) continue;
5221: i=(k1-1)*(nlstate+ndeath)+l1;
5222: if(i<=j) continue;
5223: for (age=bage; age<=fage; age ++){
5224: if ((int)age %5==0){
5225: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
5226: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
5227: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
5228: mu1=mu[i][(int) age]/stepm*YEARM ;
5229: mu2=mu[j][(int) age]/stepm*YEARM;
5230: c12=cv12/sqrt(v1*v2);
5231: /* Computing eigen value of matrix of covariance */
5232: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
5233: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 5234: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 5235: if(first2==1){
5236: first1=0;
5237: 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);
5238: }
5239: 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);
5240: /* lc1=fabs(lc1); */ /* If we want to have them positive */
5241: /* lc2=fabs(lc2); */
1.135 brouard 5242: }
5243:
1.126 brouard 5244: /* Eigen vectors */
5245: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
5246: /*v21=sqrt(1.-v11*v11); *//* error */
5247: v21=(lc1-v1)/cv12*v11;
5248: v12=-v21;
5249: v22=v11;
5250: tnalp=v21/v11;
5251: if(first1==1){
5252: first1=0;
5253: 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);
5254: }
5255: 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);
5256: /*printf(fignu*/
5257: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
5258: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
5259: if(first==1){
5260: first=0;
1.200 brouard 5261: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
1.126 brouard 5262: fprintf(ficgp,"\nset parametric;unset label");
5263: 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);
1.199 brouard 5264: fprintf(ficgp,"\nset ter svg size 640, 480");
1.126 brouard 5265: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.201 brouard 5266: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">\
5267: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
5268: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\
5269: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5270: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 5271: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.201 brouard 5272: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 5273: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
5274: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
5275: 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",\
5276: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
5277: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
5278: }else{
5279: first=0;
5280: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
5281: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
5282: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
5283: 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",\
5284: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
5285: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
5286: }/* if first */
5287: } /* age mod 5 */
5288: } /* end loop age */
1.201 brouard 5289: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 5290: first=1;
5291: } /*l12 */
5292: } /* k12 */
5293: } /*l1 */
5294: }/* k1 */
1.169 brouard 5295: /* } */ /* loop covariates */
1.126 brouard 5296: }
5297: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
5298: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
5299: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
5300: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
5301: free_vector(xp,1,npar);
5302: fclose(ficresprob);
5303: fclose(ficresprobcov);
5304: fclose(ficresprobcor);
5305: fflush(ficgp);
5306: fflush(fichtmcov);
5307: }
5308:
5309:
5310: /******************* Printing html file ***********/
1.201 brouard 5311: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 5312: int lastpass, int stepm, int weightopt, char model[],\
5313: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.217 ! brouard 5314: int popforecast, int prevfcast, int backcast, int estepm , \
1.213 brouard 5315: double jprev1, double mprev1,double anprev1, double dateprev1, \
5316: double jprev2, double mprev2,double anprev2, double dateprev2){
1.126 brouard 5317: int jj1, k1, i1, cpt;
5318:
5319: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
5320: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
5321: </ul>");
1.214 brouard 5322: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
5323: 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",
5324: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
5325: 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 5326: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
5327: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 5328: fprintf(fichtm,"\
5329: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 5330: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 5331: fprintf(fichtm,"\
1.217 ! brouard 5332: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
! 5333: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
! 5334: fprintf(fichtm,"\
1.126 brouard 5335: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5336: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 5337: fprintf(fichtm,"\
1.217 ! brouard 5338: - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
! 5339: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
! 5340: fprintf(fichtm,"\
1.211 brouard 5341: - (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 5342: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5343: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 5344: if(prevfcast==1){
5345: fprintf(fichtm,"\
5346: - Prevalence projections by age and states: \
1.201 brouard 5347: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 5348: }
1.126 brouard 5349:
5350: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
5351:
1.145 brouard 5352: m=pow(2,cptcoveff);
1.126 brouard 5353: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
5354:
5355: jj1=0;
5356: for(k1=1; k1<=m;k1++){
1.192 brouard 5357: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 5358: jj1++;
5359: if (cptcovn > 0) {
5360: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.192 brouard 5361: for (cpt=1; cpt<=cptcoveff;cpt++){
1.198 brouard 5362: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
5363: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
1.192 brouard 5364: }
1.126 brouard 5365: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
5366: }
1.201 brouard 5367: /* aij, bij */
1.211 brouard 5368: 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> \
5369: <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 5370: /* Pij */
1.211 brouard 5371: 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 5372: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 5373: /* Quasi-incidences */
1.211 brouard 5374: fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.201 brouard 5375: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\
1.211 brouard 5376: incidence (rates) are the limit when h tends to zero of the ratio of the probability <sub>h</sub>P<sub>ij</sub> \
5377: 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 5378: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
5379: /* Survival functions (period) in state j */
5380: for(cpt=1; cpt<=nlstate;cpt++){
5381: 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> \
5382: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
5383: }
5384: /* State specific survival functions (period) */
5385: for(cpt=1; cpt<=nlstate;cpt++){
1.208 brouard 5386: fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
1.201 brouard 5387: Or probability to survive in various states (1 to %d) being in state %d at different ages.\
5388: <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);
5389: }
5390: /* Period (stable) prevalence in each health state */
5391: for(cpt=1; cpt<=nlstate;cpt++){
1.217 ! brouard 5392: 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 5393: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
5394: }
1.217 ! brouard 5395: if(backcast==1){
! 5396: /* Period (stable) back prevalence in each health state */
! 5397: for(cpt=1; cpt<=nlstate;cpt++){
! 5398: 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> \
! 5399: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);
! 5400: }
! 5401: }
1.211 brouard 5402: if(prevfcast==1){
5403: /* Projection of prevalence up to period (stable) prevalence in each health state */
5404: for(cpt=1; cpt<=nlstate;cpt++){
1.214 brouard 5405: 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 5406: <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);
1.211 brouard 5407: }
5408: }
5409:
1.126 brouard 5410: for(cpt=1; cpt<=nlstate;cpt++) {
1.205 brouard 5411: 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 5412: <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
1.126 brouard 5413: }
1.192 brouard 5414: /* } /\* end i1 *\/ */
1.126 brouard 5415: }/* End k1 */
5416: fprintf(fichtm,"</ul>");
5417:
5418: fprintf(fichtm,"\
5419: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 5420: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 5421: - 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 5422: But because parameters are usually highly correlated (a higher incidence of disability \
5423: and a higher incidence of recovery can give very close observed transition) it might \
5424: be very useful to look not only at linear confidence intervals estimated from the \
5425: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
5426: (parameters) of the logistic regression, it might be more meaningful to visualize the \
5427: covariance matrix of the one-step probabilities. \
5428: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 5429:
1.193 brouard 5430: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5431: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
1.126 brouard 5432: fprintf(fichtm,"\
5433: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5434: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 5435:
5436: fprintf(fichtm,"\
5437: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5438: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
1.126 brouard 5439: fprintf(fichtm,"\
5440: - 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): \
5441: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5442: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.126 brouard 5443: fprintf(fichtm,"\
5444: - (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): \
5445: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5446: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.126 brouard 5447: fprintf(fichtm,"\
1.128 brouard 5448: - 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",
1.201 brouard 5449: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
1.126 brouard 5450: fprintf(fichtm,"\
1.128 brouard 5451: - 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",
1.201 brouard 5452: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
1.126 brouard 5453: fprintf(fichtm,"\
5454: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.201 brouard 5455: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 5456:
5457: /* if(popforecast==1) fprintf(fichtm,"\n */
5458: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
5459: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
5460: /* <br>",fileres,fileres,fileres,fileres); */
5461: /* else */
5462: /* 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); */
5463: fflush(fichtm);
5464: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
5465:
1.145 brouard 5466: m=pow(2,cptcoveff);
1.126 brouard 5467: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
5468:
5469: jj1=0;
5470: for(k1=1; k1<=m;k1++){
1.192 brouard 5471: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 5472: jj1++;
5473: if (cptcovn > 0) {
5474: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
5475: for (cpt=1; cpt<=cptcoveff;cpt++)
1.198 brouard 5476: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 5477: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
5478: }
5479: for(cpt=1; cpt<=nlstate;cpt++) {
5480: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.205 brouard 5481: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d%d.svg\"> %s_%d-%d.svg <br>\
5482: <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 5483: }
5484: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 5485: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
5486: true period expectancies (those weighted with period prevalences are also\
5487: drawn in addition to the population based expectancies computed using\
1.205 brouard 5488: observed and cahotic prevalences: <a href=\"%s_%d.svg\">%s_%d.svg<br>\
5489: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.192 brouard 5490: /* } /\* end i1 *\/ */
1.126 brouard 5491: }/* End k1 */
5492: fprintf(fichtm,"</ul>");
5493: fflush(fichtm);
5494: }
5495:
5496: /******************* Gnuplot file **************/
1.211 brouard 5497: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, char pathc[], double p[]){
1.126 brouard 5498:
5499: char dirfileres[132],optfileres[132];
1.164 brouard 5500: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.211 brouard 5501: int lv=0, vlv=0, kl=0;
1.130 brouard 5502: int ng=0;
1.201 brouard 5503: int vpopbased;
1.126 brouard 5504: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
5505: /* printf("Problem with file %s",optionfilegnuplot); */
5506: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
5507: /* } */
5508:
5509: /*#ifdef windows */
5510: fprintf(ficgp,"cd \"%s\" \n",pathc);
5511: /*#endif */
5512: m=pow(2,cptcoveff);
5513:
1.202 brouard 5514: /* Contribution to likelihood */
5515: /* Plot the probability implied in the likelihood */
5516: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
5517: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
5518: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
1.205 brouard 5519: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 5520: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 5521: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
5522: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
5523: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
1.204 brouard 5524: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
1.214 brouard 5525: fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
1.204 brouard 5526: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
1.214 brouard 5527: fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
1.204 brouard 5528: for (i=1; i<= nlstate ; i ++) {
5529: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
1.205 brouard 5530: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
1.214 brouard 5531: fprintf(ficgp," u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
1.204 brouard 5532: for (j=2; j<= nlstate+ndeath ; j ++) {
1.214 brouard 5533: fprintf(ficgp,",\\\n \"\" u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
1.204 brouard 5534: }
5535: fprintf(ficgp,";\nset out; unset ylabel;\n");
5536: }
5537: /* 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 */
5538: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
5539: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
1.203 brouard 5540: fprintf(ficgp,"\nset out;unset log\n");
1.202 brouard 5541: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
5542:
1.126 brouard 5543: strcpy(dirfileres,optionfilefiname);
5544: strcpy(optfileres,"vpl");
5545: /* 1eme*/
1.211 brouard 5546: for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
5547: for (k1=1; k1<= m ; k1 ++) { /* For each combination of covariate */
5548: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
5549: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
5550: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5551: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5552: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5553: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5554: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5555: vlv= nbcode[Tvaraff[lv]][lv];
5556: fprintf(ficgp," V%d=%d ",k,vlv);
5557: }
5558: fprintf(ficgp,"\n#\n");
5559:
1.201 brouard 5560: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
5561: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
1.126 brouard 5562: fprintf(ficgp,"set xlabel \"Age\" \n\
5563: set ylabel \"Probability\" \n\
1.199 brouard 5564: set ter svg size 640, 480\n\
1.201 brouard 5565: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 5566:
5567: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 5568: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5569: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 5570: }
1.201 brouard 5571: 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);
1.126 brouard 5572: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 5573: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5574: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 5575: }
1.201 brouard 5576: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 5577: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 5578: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5579: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 5580: }
1.201 brouard 5581: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
5582: fprintf(ficgp,"\nset out \n");
5583: } /* k1 */
5584: } /* cpt */
1.126 brouard 5585: /*2 eme*/
5586: for (k1=1; k1<= m ; k1 ++) {
1.211 brouard 5587: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
5588: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5589: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5590: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5591: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5592: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5593: vlv= nbcode[Tvaraff[lv]][lv];
5594: fprintf(ficgp," V%d=%d ",k,vlv);
5595: }
5596: fprintf(ficgp,"\n#\n");
5597:
1.201 brouard 5598: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
5599: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
5600: if(vpopbased==0)
5601: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
5602: else
5603: fprintf(ficgp,"\nreplot ");
5604: for (i=1; i<= nlstate+1 ; i ++) {
5605: k=2*i;
5606: 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);
5607: for (j=1; j<= nlstate+1 ; j ++) {
5608: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5609: else fprintf(ficgp," %%*lf (%%*lf)");
5610: }
5611: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
5612: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
5613: 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);
5614: for (j=1; j<= nlstate+1 ; j ++) {
5615: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5616: else fprintf(ficgp," %%*lf (%%*lf)");
5617: }
5618: fprintf(ficgp,"\" t\"\" w l lt 0,");
5619: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
5620: for (j=1; j<= nlstate+1 ; j ++) {
5621: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5622: else fprintf(ficgp," %%*lf (%%*lf)");
5623: }
5624: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
5625: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
5626: } /* state */
5627: } /* vpopbased */
5628: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
5629: } /* k1 */
1.211 brouard 5630:
5631:
1.126 brouard 5632: /*3eme*/
5633: for (k1=1; k1<= m ; k1 ++) {
5634: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.211 brouard 5635: fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt);
5636: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5637: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5638: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5639: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5640: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5641: vlv= nbcode[Tvaraff[lv]][lv];
5642: fprintf(ficgp," V%d=%d ",k,vlv);
5643: }
5644: fprintf(ficgp,"\n#\n");
5645:
1.126 brouard 5646: /* k=2+nlstate*(2*cpt-2); */
5647: k=2+(nlstate+1)*(cpt-1);
1.201 brouard 5648: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
1.199 brouard 5649: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 5650: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.126 brouard 5651: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
5652: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
5653: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
5654: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
5655: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
5656: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
5657:
5658: */
5659: for (i=1; i< nlstate ; i ++) {
1.201 brouard 5660: 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);
1.126 brouard 5661: /* 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);*/
5662:
5663: }
1.201 brouard 5664: 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 5665: }
5666: }
5667:
1.201 brouard 5668: /* Survival functions (period) from state i in state j by initial state i */
5669: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
5670: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.211 brouard 5671: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
5672: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5673: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5674: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5675: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5676: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5677: vlv= nbcode[Tvaraff[lv]][lv];
5678: fprintf(ficgp," V%d=%d ",k,vlv);
5679: }
5680: fprintf(ficgp,"\n#\n");
5681:
1.201 brouard 5682: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
5683: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
5684: set ter svg size 640, 480\n\
5685: unset log y\n\
5686: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 5687: k=3;
1.201 brouard 5688: for (i=1; i<= nlstate ; i ++){
1.217 ! brouard 5689: if(i==1){
1.201 brouard 5690: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
1.217 ! brouard 5691: }else{
1.201 brouard 5692: fprintf(ficgp,", '' ");
1.217 ! brouard 5693: }
1.201 brouard 5694: l=(nlstate+ndeath)*(i-1)+1;
5695: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
5696: for (j=2; j<= nlstate+ndeath ; j ++)
5697: fprintf(ficgp,"+$%d",k+l+j-1);
5698: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
5699: } /* nlstate */
5700: fprintf(ficgp,"\nset out\n");
5701: } /* end cpt state*/
5702: } /* end covariate */
5703:
5704: /* Survival functions (period) from state i in state j by final state j */
1.202 brouard 5705: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.201 brouard 5706: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
5707: fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
1.211 brouard 5708: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5709: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5710: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5711: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5712: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5713: vlv= nbcode[Tvaraff[lv]][lv];
5714: fprintf(ficgp," V%d=%d ",k,vlv);
5715: }
5716: fprintf(ficgp,"\n#\n");
5717:
1.201 brouard 5718: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
5719: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
5720: set ter svg size 640, 480\n\
5721: unset log y\n\
5722: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 5723: k=3;
1.201 brouard 5724: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
5725: if(j==1)
5726: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5727: else
5728: fprintf(ficgp,", '' ");
5729: l=(nlstate+ndeath)*(cpt-1) +j;
5730: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
5731: /* for (i=2; i<= nlstate+ndeath ; i ++) */
5732: /* fprintf(ficgp,"+$%d",k+l+i-1); */
5733: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
5734: } /* nlstate */
5735: fprintf(ficgp,", '' ");
5736: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
5737: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
5738: l=(nlstate+ndeath)*(cpt-1) +j;
5739: if(j < nlstate)
5740: fprintf(ficgp,"$%d +",k+l);
5741: else
5742: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
5743: }
5744: fprintf(ficgp,"\nset out\n");
5745: } /* end cpt state*/
5746: } /* end covariate */
5747:
1.202 brouard 5748: /* CV preval stable (period) for each covariate */
1.211 brouard 5749: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.153 brouard 5750: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.211 brouard 5751: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
5752: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5753: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5754: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5755: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5756: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5757: vlv= nbcode[Tvaraff[lv]][lv];
5758: fprintf(ficgp," V%d=%d ",k,vlv);
5759: }
5760: fprintf(ficgp,"\n#\n");
5761:
1.201 brouard 5762: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 5763: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.199 brouard 5764: set ter svg size 640, 480\n\
1.126 brouard 5765: unset log y\n\
1.153 brouard 5766: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 5767: k=3; /* Offset */
1.153 brouard 5768: for (i=1; i<= nlstate ; i ++){
5769: if(i==1)
1.201 brouard 5770: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
1.153 brouard 5771: else
5772: fprintf(ficgp,", '' ");
1.154 brouard 5773: l=(nlstate+ndeath)*(i-1)+1;
5774: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.201 brouard 5775: for (j=2; j<= nlstate ; j ++)
5776: fprintf(ficgp,"+$%d",k+l+j-1);
1.153 brouard 5777: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
5778: } /* nlstate */
1.201 brouard 5779: fprintf(ficgp,"\nset out\n");
1.153 brouard 5780: } /* end cpt state*/
5781: } /* end covariate */
1.201 brouard 5782:
1.217 ! brouard 5783: /* CV back preval stable (period) for each covariate */
! 5784: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
! 5785: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
! 5786: fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
! 5787: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
! 5788: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
! 5789: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
! 5790: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
! 5791: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
! 5792: vlv= nbcode[Tvaraff[lv]][lv];
! 5793: fprintf(ficgp," V%d=%d ",k,vlv);
! 5794: }
! 5795: fprintf(ficgp,"\n#\n");
! 5796:
! 5797: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
! 5798: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
! 5799: set ter svg size 640, 480\n\
! 5800: unset log y\n\
! 5801: plot [%.f:%.f] ", ageminpar, agemaxpar);
! 5802: k=3; /* Offset */
! 5803: for (i=1; i<= nlstate ; i ++){
! 5804: if(i==1)
! 5805: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
! 5806: else
! 5807: fprintf(ficgp,", '' ");
! 5808: l=(nlstate+ndeath)*(i-1)+1;
! 5809: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /* a vérifier */
! 5810: for (j=2; j<= nlstate ; j ++)
! 5811: fprintf(ficgp,"+$%d",k+l+j-1);
! 5812: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
! 5813: } /* nlstate */
! 5814: fprintf(ficgp,"\nset out\n");
! 5815: } /* end cpt state*/
! 5816: } /* end covariate */
! 5817:
1.211 brouard 5818: if(prevfcast==1){
5819: /* Projection from cross-sectional to stable (period) for each covariate */
5820:
5821: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
5822: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
5823: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
5824: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
5825: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
5826: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5827: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5828: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5829: vlv= nbcode[Tvaraff[lv]][lv];
5830: fprintf(ficgp," V%d=%d ",k,vlv);
5831: }
5832: fprintf(ficgp,"\n#\n");
5833:
5834: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
5835: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
5836: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
5837: set ter svg size 640, 480\n\
5838: unset log y\n\
5839: plot [%.f:%.f] ", ageminpar, agemaxpar);
5840: for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
5841: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
5842: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
5843: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
5844: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
5845: if(i==1){
5846: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
5847: }else{
5848: fprintf(ficgp,",\\\n '' ");
5849: }
5850: if(cptcoveff ==0){ /* No covariate */
5851: fprintf(ficgp," u 2:("); /* Age is in 2 */
5852: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
5853: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
5854: if(i==nlstate+1)
5855: fprintf(ficgp," $%d/(1.-$%d)) t 'p.%d' with line ", \
5856: 2+(cpt-1)*(nlstate+1)+1+(i-1), 2+1+(i-1)+(nlstate+1)*nlstate,cpt );
5857: else
5858: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
5859: 2+(cpt-1)*(nlstate+1)+1+(i-1), 2+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
5860: }else{
5861: fprintf(ficgp,"u 6:(("); /* Age is in 6 */
5862: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
5863: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
5864: kl=0;
5865: for (k=1; k<=cptcoveff; k++){ /* For each covariate */
5866: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
5867: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5868: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5869: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5870: vlv= nbcode[Tvaraff[lv]][lv];
5871: kl++;
5872: /* 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 *\/ */
5873: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
5874: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
5875: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
5876: if(k==cptcoveff)
5877: if(i==nlstate+1)
5878: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv], \
5879: 6+(cpt-1)*(nlstate+1)+1+(i-1), 6+1+(i-1)+(nlstate+1)*nlstate,cpt );
5880: else
5881: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv], \
5882: 6+(cpt-1)*(nlstate+1)+1+(i-1), 6+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
5883: else{
5884: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv]);
5885: kl++;
5886: }
5887: } /* end covariate */
5888: } /* end if covariate */
5889: } /* nlstate */
5890: fprintf(ficgp,"\nset out\n");
5891: } /* end cpt state*/
5892: } /* end covariate */
5893: } /* End if prevfcast */
5894:
5895:
1.126 brouard 5896: /* proba elementaires */
1.187 brouard 5897: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 5898: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 5899: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 5900: for(k=1; k <=(nlstate+ndeath); k++){
5901: if (k != i) {
1.187 brouard 5902: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 5903: for(j=1; j <=ncovmodel; j++){
1.187 brouard 5904: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 5905: jk++;
5906: }
1.187 brouard 5907: fprintf(ficgp,"\n");
1.126 brouard 5908: }
5909: }
5910: }
1.187 brouard 5911: fprintf(ficgp,"##############\n#\n");
5912:
1.145 brouard 5913: /*goto avoid;*/
1.200 brouard 5914: fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
1.187 brouard 5915: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
5916: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
5917: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
5918: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
5919: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5920: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
5921: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5922: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
5923: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
5924: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5925: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
5926: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
5927: fprintf(ficgp,"#\n");
1.201 brouard 5928: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.187 brouard 5929: fprintf(ficgp,"# ng=%d\n",ng);
5930: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 5931: for(jk=1; jk <=m; jk++) {
1.187 brouard 5932: fprintf(ficgp,"# jk=%d\n",jk);
1.201 brouard 5933: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
5934: fprintf(ficgp,"\nset ter svg size 640, 480 ");
5935: if (ng==1){
5936: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
5937: fprintf(ficgp,"\nunset log y");
5938: }else if (ng==2){
5939: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
5940: fprintf(ficgp,"\nset log y");
5941: }else if (ng==3){
1.126 brouard 5942: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
1.201 brouard 5943: fprintf(ficgp,"\nset log y");
5944: }else
5945: fprintf(ficgp,"\nunset title ");
5946: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 5947: i=1;
5948: for(k2=1; k2<=nlstate; k2++) {
5949: k3=i;
5950: for(k=1; k<=(nlstate+ndeath); k++) {
5951: if (k != k2){
1.201 brouard 5952: switch( ng) {
5953: case 1:
1.187 brouard 5954: if(nagesqr==0)
1.201 brouard 5955: fprintf(ficgp," p%d+p%d*x",i,i+1);
1.187 brouard 5956: else /* nagesqr =1 */
1.201 brouard 5957: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
5958: break;
5959: case 2: /* ng=2 */
1.187 brouard 5960: if(nagesqr==0)
5961: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
5962: else /* nagesqr =1 */
1.201 brouard 5963: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
5964: break;
5965: case 3:
5966: if(nagesqr==0)
5967: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
5968: else /* nagesqr =1 */
5969: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
5970: break;
5971: }
1.141 brouard 5972: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 brouard 5973: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.197 brouard 5974: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
5975: if(ij <=cptcovage) { /* Bug valgrind */
5976: if((j-2)==Tage[ij]) { /* Bug valgrind */
1.200 brouard 5977: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
5978: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
1.197 brouard 5979: ij++;
5980: }
1.186 brouard 5981: }
5982: else
1.198 brouard 5983: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.126 brouard 5984: }
1.217 ! brouard 5985: }else{
! 5986: i=i-ncovmodel;
! 5987: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
! 5988: fprintf(ficgp," (1.");
! 5989: }
! 5990:
! 5991: if(ng != 1){
! 5992: fprintf(ficgp,")/(1");
1.126 brouard 5993:
1.217 ! brouard 5994: for(k1=1; k1 <=nlstate; k1++){
! 5995: if(nagesqr==0)
! 5996: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
! 5997: else /* nagesqr =1 */
! 5998: 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);
! 5999:
! 6000: ij=1;
! 6001: for(j=3; j <=ncovmodel-nagesqr; j++){
! 6002: if(ij <=cptcovage) { /* Bug valgrind */
! 6003: if((j-2)==Tage[ij]) { /* Bug valgrind */
! 6004: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
! 6005: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
! 6006: ij++;
1.197 brouard 6007: }
1.186 brouard 6008: }
1.217 ! brouard 6009: else
! 6010: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.126 brouard 6011: }
6012: fprintf(ficgp,")");
1.217 ! brouard 6013: }
! 6014: fprintf(ficgp,")");
! 6015: if(ng ==2)
! 6016: fprintf(ficgp," t \"p%d%d\" ", k2,k);
! 6017: else /* ng= 3 */
! 6018: fprintf(ficgp," t \"i%d%d\" ", k2,k);
! 6019: }else{ /* end ng <> 1 */
! 6020: if( k !=k2) /* logit p11 is hard to draw */
1.201 brouard 6021: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
1.126 brouard 6022: }
1.217 ! brouard 6023: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
! 6024: fprintf(ficgp,",");
! 6025: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
! 6026: fprintf(ficgp,",");
! 6027: i=i+ncovmodel;
1.126 brouard 6028: } /* end k */
6029: } /* end k2 */
1.201 brouard 6030: fprintf(ficgp,"\n set out\n");
1.126 brouard 6031: } /* end jk */
6032: } /* end ng */
1.164 brouard 6033: /* avoid: */
1.126 brouard 6034: fflush(ficgp);
6035: } /* end gnuplot */
6036:
6037:
6038: /*************** Moving average **************/
6039: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
6040:
6041: int i, cpt, cptcod;
6042: int modcovmax =1;
6043: int mobilavrange, mob;
6044: double age;
6045:
6046: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
6047: a covariate has 2 modalities */
6048: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
6049:
6050: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
6051: if(mobilav==1) mobilavrange=5; /* default */
6052: else mobilavrange=mobilav;
6053: for (age=bage; age<=fage; age++)
6054: for (i=1; i<=nlstate;i++)
6055: for (cptcod=1;cptcod<=modcovmax;cptcod++)
6056: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
6057: /* We keep the original values on the extreme ages bage, fage and for
6058: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
6059: we use a 5 terms etc. until the borders are no more concerned.
6060: */
6061: for (mob=3;mob <=mobilavrange;mob=mob+2){
6062: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
6063: for (i=1; i<=nlstate;i++){
6064: for (cptcod=1;cptcod<=modcovmax;cptcod++){
6065: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
6066: for (cpt=1;cpt<=(mob-1)/2;cpt++){
6067: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
6068: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
6069: }
6070: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
6071: }
6072: }
6073: }/* end age */
6074: }/* end mob */
6075: }else return -1;
6076: return 0;
6077: }/* End movingaverage */
6078:
6079:
6080: /************** Forecasting ******************/
1.169 brouard 6081: 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 6082: /* proj1, year, month, day of starting projection
6083: agemin, agemax range of age
6084: dateprev1 dateprev2 range of dates during which prevalence is computed
6085: anproj2 year of en of projection (same day and month as proj1).
6086: */
1.164 brouard 6087: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 6088: double agec; /* generic age */
6089: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
6090: double *popeffectif,*popcount;
6091: double ***p3mat;
6092: double ***mobaverage;
6093: char fileresf[FILENAMELENGTH];
6094:
6095: agelim=AGESUP;
1.211 brouard 6096: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
6097: in each health status at the date of interview (if between dateprev1 and dateprev2).
6098: We still use firstpass and lastpass as another selection.
6099: */
1.214 brouard 6100: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
6101: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 6102: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6103:
1.201 brouard 6104: strcpy(fileresf,"F_");
6105: strcat(fileresf,fileresu);
1.126 brouard 6106: if((ficresf=fopen(fileresf,"w"))==NULL) {
6107: printf("Problem with forecast resultfile: %s\n", fileresf);
6108: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
6109: }
1.215 brouard 6110: printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
6111: fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 6112:
6113: if (cptcoveff==0) ncodemax[cptcoveff]=1;
6114:
6115: if (mobilav!=0) {
6116: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6117: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
6118: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6119: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6120: }
6121: }
6122:
6123: stepsize=(int) (stepm+YEARM-1)/YEARM;
6124: if (stepm<=12) stepsize=1;
6125: if(estepm < stepm){
6126: printf ("Problem %d lower than %d\n",estepm, stepm);
6127: }
6128: else hstepm=estepm;
6129:
6130: hstepm=hstepm/stepm;
6131: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
6132: fractional in yp1 */
6133: anprojmean=yp;
6134: yp2=modf((yp1*12),&yp);
6135: mprojmean=yp;
6136: yp1=modf((yp2*30.5),&yp);
6137: jprojmean=yp;
6138: if(jprojmean==0) jprojmean=1;
6139: if(mprojmean==0) jprojmean=1;
6140:
6141: i1=cptcoveff;
6142: if (cptcovn < 1){i1=1;}
6143:
6144: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
6145:
6146: fprintf(ficresf,"#****** Routine prevforecast **\n");
6147:
6148: /* if (h==(int)(YEARM*yearp)){ */
6149: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
6150: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
6151: k=k+1;
1.211 brouard 6152: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
1.126 brouard 6153: for(j=1;j<=cptcoveff;j++) {
1.211 brouard 6154: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 6155: }
1.211 brouard 6156: fprintf(ficresf," yearproj age");
1.126 brouard 6157: for(j=1; j<=nlstate+ndeath;j++){
6158: for(i=1; i<=nlstate;i++)
6159: fprintf(ficresf," p%d%d",i,j);
6160: fprintf(ficresf," p.%d",j);
6161: }
1.217 ! brouard 6162: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.126 brouard 6163: fprintf(ficresf,"\n");
6164: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
6165: for (agec=fage; agec>=(ageminpar-1); agec--){
6166: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
6167: nhstepm = nhstepm/hstepm;
6168: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6169: oldm=oldms;savm=savms;
1.217 ! brouard 6170: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
1.126 brouard 6171:
6172: for (h=0; h<=nhstepm; h++){
6173: if (h*hstepm/YEARM*stepm ==yearp) {
6174: fprintf(ficresf,"\n");
6175: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6176: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 6177: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
6178: }
6179: for(j=1; j<=nlstate+ndeath;j++) {
6180: ppij=0.;
6181: for(i=1; i<=nlstate;i++) {
6182: if (mobilav==1)
6183: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
6184: else {
6185: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
6186: }
6187: if (h*hstepm/YEARM*stepm== yearp) {
6188: fprintf(ficresf," %.3f", p3mat[i][j][h]);
6189: }
6190: } /* end i */
6191: if (h*hstepm/YEARM*stepm==yearp) {
6192: fprintf(ficresf," %.3f", ppij);
6193: }
6194: }/* end j */
6195: } /* end h */
6196: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6197: } /* end agec */
6198: } /* end yearp */
6199: } /* end cptcod */
6200: } /* end cptcov */
6201:
6202: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6203:
6204: fclose(ficresf);
1.215 brouard 6205: printf("End of Computing forecasting \n");
6206: fprintf(ficlog,"End of Computing forecasting\n");
6207:
1.126 brouard 6208: }
6209:
1.217 ! brouard 6210: /************** Back Forecasting ******************/
! 6211: 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){
! 6212: /* back1, year, month, day of starting backection
! 6213: agemin, agemax range of age
! 6214: dateprev1 dateprev2 range of dates during which prevalence is computed
! 6215: anback2 year of en of backection (same day and month as back1).
! 6216: */
! 6217: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
! 6218: double agec; /* generic age */
! 6219: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
! 6220: double *popeffectif,*popcount;
! 6221: double ***p3mat;
! 6222: double ***mobaverage;
! 6223: char fileresfb[FILENAMELENGTH];
! 6224:
! 6225: agelim=AGESUP;
! 6226: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
! 6227: in each health status at the date of interview (if between dateprev1 and dateprev2).
! 6228: We still use firstpass and lastpass as another selection.
! 6229: */
! 6230: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
! 6231: /* firstpass, lastpass, stepm, weightopt, model); */
! 6232: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
! 6233:
! 6234: strcpy(fileresfb,"FB_");
! 6235: strcat(fileresfb,fileresu);
! 6236: if((ficresfb=fopen(fileresfb,"w"))==NULL) {
! 6237: printf("Problem with back forecast resultfile: %s\n", fileresfb);
! 6238: fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
! 6239: }
! 6240: printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb);
! 6241: fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb);
! 6242:
! 6243: if (cptcoveff==0) ncodemax[cptcoveff]=1;
! 6244:
! 6245: if (mobilav!=0) {
! 6246: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 6247: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
! 6248: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
! 6249: printf(" Error in movingaverage mobilav=%d\n",mobilav);
! 6250: }
! 6251: }
! 6252:
! 6253: stepsize=(int) (stepm+YEARM-1)/YEARM;
! 6254: if (stepm<=12) stepsize=1;
! 6255: if(estepm < stepm){
! 6256: printf ("Problem %d lower than %d\n",estepm, stepm);
! 6257: }
! 6258: else hstepm=estepm;
! 6259:
! 6260: hstepm=hstepm/stepm;
! 6261: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
! 6262: fractional in yp1 */
! 6263: anprojmean=yp;
! 6264: yp2=modf((yp1*12),&yp);
! 6265: mprojmean=yp;
! 6266: yp1=modf((yp2*30.5),&yp);
! 6267: jprojmean=yp;
! 6268: if(jprojmean==0) jprojmean=1;
! 6269: if(mprojmean==0) jprojmean=1;
! 6270:
! 6271: i1=cptcoveff;
! 6272: if (cptcovn < 1){i1=1;}
! 6273:
! 6274: fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
! 6275:
! 6276: fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
! 6277:
! 6278: /* if (h==(int)(YEARM*yearp)){ */
! 6279: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
! 6280: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
! 6281: k=k+1;
! 6282: fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#");
! 6283: for(j=1;j<=cptcoveff;j++) {
! 6284: fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 6285: }
! 6286: fprintf(ficresfb," yearbproj age");
! 6287: for(j=1; j<=nlstate+ndeath;j++){
! 6288: for(i=1; i<=nlstate;i++)
! 6289: fprintf(ficresfb," p%d%d",i,j);
! 6290: fprintf(ficresfb," p.%d",j);
! 6291: }
! 6292: for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {
! 6293: /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { */
! 6294: fprintf(ficresfb,"\n");
! 6295: fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);
! 6296: for (agec=fage; agec>=(ageminpar-1); agec--){
! 6297: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
! 6298: nhstepm = nhstepm/hstepm;
! 6299: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 6300: oldm=oldms;savm=savms;
! 6301: hbxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
! 6302:
! 6303: for (h=0; h<=nhstepm; h++){
! 6304: if (h*hstepm/YEARM*stepm ==yearp) {
! 6305: fprintf(ficresfb,"\n");
! 6306: for(j=1;j<=cptcoveff;j++)
! 6307: fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 6308: fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm);
! 6309: }
! 6310: for(j=1; j<=nlstate+ndeath;j++) {
! 6311: ppij=0.;
! 6312: for(i=1; i<=nlstate;i++) {
! 6313: if (mobilav==1)
! 6314: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
! 6315: else {
! 6316: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
! 6317: }
! 6318: if (h*hstepm/YEARM*stepm== yearp) {
! 6319: fprintf(ficresfb," %.3f", p3mat[i][j][h]);
! 6320: }
! 6321: } /* end i */
! 6322: if (h*hstepm/YEARM*stepm==yearp) {
! 6323: fprintf(ficresfb," %.3f", ppij);
! 6324: }
! 6325: }/* end j */
! 6326: } /* end h */
! 6327: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 6328: } /* end agec */
! 6329: } /* end yearp */
! 6330: } /* end cptcod */
! 6331: } /* end cptcov */
! 6332:
! 6333: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 6334:
! 6335: fclose(ficresfb);
! 6336: printf("End of Computing Back forecasting \n");
! 6337: fprintf(ficlog,"End of Computing Back forecasting\n");
! 6338:
! 6339: }
! 6340:
1.126 brouard 6341: /************** Forecasting *****not tested NB*************/
1.169 brouard 6342: void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
1.126 brouard 6343:
6344: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
6345: int *popage;
6346: double calagedatem, agelim, kk1, kk2;
6347: double *popeffectif,*popcount;
6348: double ***p3mat,***tabpop,***tabpopprev;
6349: double ***mobaverage;
6350: char filerespop[FILENAMELENGTH];
6351:
6352: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6353: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6354: agelim=AGESUP;
6355: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
6356:
6357: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6358:
6359:
1.201 brouard 6360: strcpy(filerespop,"POP_");
6361: strcat(filerespop,fileresu);
1.126 brouard 6362: if((ficrespop=fopen(filerespop,"w"))==NULL) {
6363: printf("Problem with forecast resultfile: %s\n", filerespop);
6364: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
6365: }
6366: printf("Computing forecasting: result on file '%s' \n", filerespop);
6367: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
6368:
6369: if (cptcoveff==0) ncodemax[cptcoveff]=1;
6370:
6371: if (mobilav!=0) {
6372: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6373: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
6374: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6375: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6376: }
6377: }
6378:
6379: stepsize=(int) (stepm+YEARM-1)/YEARM;
6380: if (stepm<=12) stepsize=1;
6381:
6382: agelim=AGESUP;
6383:
6384: hstepm=1;
6385: hstepm=hstepm/stepm;
6386:
6387: if (popforecast==1) {
6388: if((ficpop=fopen(popfile,"r"))==NULL) {
6389: printf("Problem with population file : %s\n",popfile);exit(0);
6390: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
6391: }
6392: popage=ivector(0,AGESUP);
6393: popeffectif=vector(0,AGESUP);
6394: popcount=vector(0,AGESUP);
6395:
6396: i=1;
6397: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
6398:
6399: imx=i;
6400: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
6401: }
6402:
6403: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
6404: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
6405: k=k+1;
6406: fprintf(ficrespop,"\n#******");
6407: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 6408: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 6409: }
6410: fprintf(ficrespop,"******\n");
6411: fprintf(ficrespop,"# Age");
6412: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
6413: if (popforecast==1) fprintf(ficrespop," [Population]");
6414:
6415: for (cpt=0; cpt<=0;cpt++) {
6416: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
6417:
6418: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
6419: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
6420: nhstepm = nhstepm/hstepm;
6421:
6422: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6423: oldm=oldms;savm=savms;
6424: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6425:
6426: for (h=0; h<=nhstepm; h++){
6427: if (h==(int) (calagedatem+YEARM*cpt)) {
6428: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
6429: }
6430: for(j=1; j<=nlstate+ndeath;j++) {
6431: kk1=0.;kk2=0;
6432: for(i=1; i<=nlstate;i++) {
6433: if (mobilav==1)
6434: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
6435: else {
6436: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
6437: }
6438: }
6439: if (h==(int)(calagedatem+12*cpt)){
6440: tabpop[(int)(agedeb)][j][cptcod]=kk1;
6441: /*fprintf(ficrespop," %.3f", kk1);
6442: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
6443: }
6444: }
6445: for(i=1; i<=nlstate;i++){
6446: kk1=0.;
6447: for(j=1; j<=nlstate;j++){
6448: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
6449: }
6450: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
6451: }
6452:
6453: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
6454: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
6455: }
6456: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6457: }
6458: }
6459:
6460: /******/
6461:
6462: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
6463: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
6464: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
6465: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
6466: nhstepm = nhstepm/hstepm;
6467:
6468: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6469: oldm=oldms;savm=savms;
6470: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6471: for (h=0; h<=nhstepm; h++){
6472: if (h==(int) (calagedatem+YEARM*cpt)) {
6473: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
6474: }
6475: for(j=1; j<=nlstate+ndeath;j++) {
6476: kk1=0.;kk2=0;
6477: for(i=1; i<=nlstate;i++) {
6478: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
6479: }
6480: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
6481: }
6482: }
6483: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6484: }
6485: }
6486: }
6487: }
6488:
6489: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6490:
6491: if (popforecast==1) {
6492: free_ivector(popage,0,AGESUP);
6493: free_vector(popeffectif,0,AGESUP);
6494: free_vector(popcount,0,AGESUP);
6495: }
6496: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6497: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6498: fclose(ficrespop);
6499: } /* End of popforecast */
6500:
6501: int fileappend(FILE *fichier, char *optionfich)
6502: {
6503: if((fichier=fopen(optionfich,"a"))==NULL) {
6504: printf("Problem with file: %s\n", optionfich);
6505: fprintf(ficlog,"Problem with file: %s\n", optionfich);
6506: return (0);
6507: }
6508: fflush(fichier);
6509: return (1);
6510: }
6511:
6512:
6513: /**************** function prwizard **********************/
6514: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
6515: {
6516:
6517: /* Wizard to print covariance matrix template */
6518:
1.164 brouard 6519: char ca[32], cb[32];
6520: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 6521: int numlinepar;
6522:
6523: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6524: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6525: for(i=1; i <=nlstate; i++){
6526: jj=0;
6527: for(j=1; j <=nlstate+ndeath; j++){
6528: if(j==i) continue;
6529: jj++;
6530: /*ca[0]= k+'a'-1;ca[1]='\0';*/
6531: printf("%1d%1d",i,j);
6532: fprintf(ficparo,"%1d%1d",i,j);
6533: for(k=1; k<=ncovmodel;k++){
6534: /* printf(" %lf",param[i][j][k]); */
6535: /* fprintf(ficparo," %lf",param[i][j][k]); */
6536: printf(" 0.");
6537: fprintf(ficparo," 0.");
6538: }
6539: printf("\n");
6540: fprintf(ficparo,"\n");
6541: }
6542: }
6543: printf("# Scales (for hessian or gradient estimation)\n");
6544: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
6545: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
6546: for(i=1; i <=nlstate; i++){
6547: jj=0;
6548: for(j=1; j <=nlstate+ndeath; j++){
6549: if(j==i) continue;
6550: jj++;
6551: fprintf(ficparo,"%1d%1d",i,j);
6552: printf("%1d%1d",i,j);
6553: fflush(stdout);
6554: for(k=1; k<=ncovmodel;k++){
6555: /* printf(" %le",delti3[i][j][k]); */
6556: /* fprintf(ficparo," %le",delti3[i][j][k]); */
6557: printf(" 0.");
6558: fprintf(ficparo," 0.");
6559: }
6560: numlinepar++;
6561: printf("\n");
6562: fprintf(ficparo,"\n");
6563: }
6564: }
6565: printf("# Covariance matrix\n");
6566: /* # 121 Var(a12)\n\ */
6567: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6568: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6569: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6570: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6571: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6572: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6573: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6574: fflush(stdout);
6575: fprintf(ficparo,"# Covariance matrix\n");
6576: /* # 121 Var(a12)\n\ */
6577: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6578: /* # ...\n\ */
6579: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6580:
6581: for(itimes=1;itimes<=2;itimes++){
6582: jj=0;
6583: for(i=1; i <=nlstate; i++){
6584: for(j=1; j <=nlstate+ndeath; j++){
6585: if(j==i) continue;
6586: for(k=1; k<=ncovmodel;k++){
6587: jj++;
6588: ca[0]= k+'a'-1;ca[1]='\0';
6589: if(itimes==1){
6590: printf("#%1d%1d%d",i,j,k);
6591: fprintf(ficparo,"#%1d%1d%d",i,j,k);
6592: }else{
6593: printf("%1d%1d%d",i,j,k);
6594: fprintf(ficparo,"%1d%1d%d",i,j,k);
6595: /* printf(" %.5le",matcov[i][j]); */
6596: }
6597: ll=0;
6598: for(li=1;li <=nlstate; li++){
6599: for(lj=1;lj <=nlstate+ndeath; lj++){
6600: if(lj==li) continue;
6601: for(lk=1;lk<=ncovmodel;lk++){
6602: ll++;
6603: if(ll<=jj){
6604: cb[0]= lk +'a'-1;cb[1]='\0';
6605: if(ll<jj){
6606: if(itimes==1){
6607: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6608: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6609: }else{
6610: printf(" 0.");
6611: fprintf(ficparo," 0.");
6612: }
6613: }else{
6614: if(itimes==1){
6615: printf(" Var(%s%1d%1d)",ca,i,j);
6616: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
6617: }else{
6618: printf(" 0.");
6619: fprintf(ficparo," 0.");
6620: }
6621: }
6622: }
6623: } /* end lk */
6624: } /* end lj */
6625: } /* end li */
6626: printf("\n");
6627: fprintf(ficparo,"\n");
6628: numlinepar++;
6629: } /* end k*/
6630: } /*end j */
6631: } /* end i */
6632: } /* end itimes */
6633:
6634: } /* end of prwizard */
6635: /******************* Gompertz Likelihood ******************************/
6636: double gompertz(double x[])
6637: {
6638: double A,B,L=0.0,sump=0.,num=0.;
6639: int i,n=0; /* n is the size of the sample */
6640:
6641: for (i=0;i<=imx-1 ; i++) {
6642: sump=sump+weight[i];
6643: /* sump=sump+1;*/
6644: num=num+1;
6645: }
6646:
6647:
6648: /* for (i=0; i<=imx; i++)
6649: 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]);*/
6650:
6651: for (i=1;i<=imx ; i++)
6652: {
6653: if (cens[i] == 1 && wav[i]>1)
6654: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
6655:
6656: if (cens[i] == 0 && wav[i]>1)
6657: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
6658: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
6659:
6660: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
6661: if (wav[i] > 1 ) { /* ??? */
6662: L=L+A*weight[i];
6663: /* 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]);*/
6664: }
6665: }
6666:
6667: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
6668:
6669: return -2*L*num/sump;
6670: }
6671:
1.136 brouard 6672: #ifdef GSL
6673: /******************* Gompertz_f Likelihood ******************************/
6674: double gompertz_f(const gsl_vector *v, void *params)
6675: {
6676: double A,B,LL=0.0,sump=0.,num=0.;
6677: double *x= (double *) v->data;
6678: int i,n=0; /* n is the size of the sample */
6679:
6680: for (i=0;i<=imx-1 ; i++) {
6681: sump=sump+weight[i];
6682: /* sump=sump+1;*/
6683: num=num+1;
6684: }
6685:
6686:
6687: /* for (i=0; i<=imx; i++)
6688: 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]);*/
6689: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
6690: for (i=1;i<=imx ; i++)
6691: {
6692: if (cens[i] == 1 && wav[i]>1)
6693: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
6694:
6695: if (cens[i] == 0 && wav[i]>1)
6696: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
6697: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
6698:
6699: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
6700: if (wav[i] > 1 ) { /* ??? */
6701: LL=LL+A*weight[i];
6702: /* 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]);*/
6703: }
6704: }
6705:
6706: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
6707: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
6708:
6709: return -2*LL*num/sump;
6710: }
6711: #endif
6712:
1.126 brouard 6713: /******************* Printing html file ***********/
1.201 brouard 6714: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 6715: int lastpass, int stepm, int weightopt, char model[],\
6716: int imx, double p[],double **matcov,double agemortsup){
6717: int i,k;
6718:
6719: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
6720: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
6721: for (i=1;i<=2;i++)
6722: 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 6723: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 6724: fprintf(fichtm,"</ul>");
6725:
6726: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
6727:
6728: 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>");
6729:
6730: for (k=agegomp;k<(agemortsup-2);k++)
6731: 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]);
6732:
6733:
6734: fflush(fichtm);
6735: }
6736:
6737: /******************* Gnuplot file **************/
1.201 brouard 6738: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 6739:
6740: char dirfileres[132],optfileres[132];
1.164 brouard 6741:
1.126 brouard 6742: int ng;
6743:
6744:
6745: /*#ifdef windows */
6746: fprintf(ficgp,"cd \"%s\" \n",pathc);
6747: /*#endif */
6748:
6749:
6750: strcpy(dirfileres,optionfilefiname);
6751: strcpy(optfileres,"vpl");
1.199 brouard 6752: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 6753: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 6754: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 6755: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 6756: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
6757:
6758: }
6759:
1.136 brouard 6760: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
6761: {
1.126 brouard 6762:
1.136 brouard 6763: /*-------- data file ----------*/
6764: FILE *fic;
6765: char dummy[]=" ";
1.164 brouard 6766: int i=0, j=0, n=0;
1.136 brouard 6767: int linei, month, year,iout;
6768: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 6769: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 6770: char *stratrunc;
6771: int lstra;
1.126 brouard 6772:
6773:
1.136 brouard 6774: if((fic=fopen(datafile,"r"))==NULL) {
1.195 brouard 6775: printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
6776: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
1.136 brouard 6777: }
1.126 brouard 6778:
1.136 brouard 6779: i=1;
6780: linei=0;
6781: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
6782: linei=linei+1;
6783: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
6784: if(line[j] == '\t')
6785: line[j] = ' ';
6786: }
6787: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
6788: ;
6789: };
6790: line[j+1]=0; /* Trims blanks at end of line */
6791: if(line[0]=='#'){
6792: fprintf(ficlog,"Comment line\n%s\n",line);
6793: printf("Comment line\n%s\n",line);
6794: continue;
6795: }
6796: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 6797: strcpy(line, linetmp);
1.136 brouard 6798:
1.126 brouard 6799:
1.136 brouard 6800: for (j=maxwav;j>=1;j--){
1.137 brouard 6801: cutv(stra, strb, line, ' ');
1.136 brouard 6802: if(strb[0]=='.') { /* Missing status */
6803: lval=-1;
6804: }else{
6805: errno=0;
6806: lval=strtol(strb,&endptr,10);
6807: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
6808: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 6809: 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);
6810: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
1.136 brouard 6811: return 1;
6812: }
6813: }
6814: s[j][i]=lval;
6815:
6816: strcpy(line,stra);
6817: cutv(stra, strb,line,' ');
1.169 brouard 6818: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 6819: }
1.169 brouard 6820: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 6821: month=99;
6822: year=9999;
6823: }else{
1.141 brouard 6824: 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);
6825: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
1.136 brouard 6826: return 1;
6827: }
6828: anint[j][i]= (double) year;
6829: mint[j][i]= (double)month;
6830: strcpy(line,stra);
6831: } /* ENd Waves */
6832:
6833: cutv(stra, strb,line,' ');
1.169 brouard 6834: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 6835: }
1.169 brouard 6836: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 6837: month=99;
6838: year=9999;
6839: }else{
1.141 brouard 6840: 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);
6841: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.136 brouard 6842: return 1;
6843: }
6844: andc[i]=(double) year;
6845: moisdc[i]=(double) month;
6846: strcpy(line,stra);
6847:
6848: cutv(stra, strb,line,' ');
1.169 brouard 6849: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 6850: }
1.169 brouard 6851: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 6852: month=99;
6853: year=9999;
6854: }else{
1.141 brouard 6855: 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);
6856: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.136 brouard 6857: return 1;
6858: }
6859: if (year==9999) {
1.141 brouard 6860: 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);
6861: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.136 brouard 6862: return 1;
1.126 brouard 6863:
1.136 brouard 6864: }
6865: annais[i]=(double)(year);
6866: moisnais[i]=(double)(month);
6867: strcpy(line,stra);
6868:
6869: cutv(stra, strb,line,' ');
6870: errno=0;
6871: dval=strtod(strb,&endptr);
6872: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 6873: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
6874: 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 6875: fflush(ficlog);
6876: return 1;
6877: }
6878: weight[i]=dval;
6879: strcpy(line,stra);
6880:
6881: for (j=ncovcol;j>=1;j--){
6882: cutv(stra, strb,line,' ');
6883: if(strb[0]=='.') { /* Missing status */
6884: lval=-1;
6885: }else{
6886: errno=0;
6887: lval=strtol(strb,&endptr,10);
6888: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 6889: 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);
6890: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);fflush(ficlog);
1.136 brouard 6891: return 1;
6892: }
6893: }
6894: if(lval <-1 || lval >1){
1.141 brouard 6895: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 6896: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
6897: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
6898: For example, for multinomial values like 1, 2 and 3,\n \
6899: build V1=0 V2=0 for the reference value (1),\n \
6900: V1=1 V2=0 for (2) \n \
6901: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
6902: output of IMaCh is often meaningless.\n \
6903: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 6904: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 6905: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
6906: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
6907: For example, for multinomial values like 1, 2 and 3,\n \
6908: build V1=0 V2=0 for the reference value (1),\n \
6909: V1=1 V2=0 for (2) \n \
6910: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
6911: output of IMaCh is often meaningless.\n \
6912: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
6913: return 1;
6914: }
6915: covar[j][i]=(double)(lval);
6916: strcpy(line,stra);
6917: }
6918: lstra=strlen(stra);
6919:
6920: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
6921: stratrunc = &(stra[lstra-9]);
6922: num[i]=atol(stratrunc);
6923: }
6924: else
6925: num[i]=atol(stra);
6926: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
6927: 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;}*/
6928:
6929: i=i+1;
6930: } /* End loop reading data */
1.126 brouard 6931:
1.136 brouard 6932: *imax=i-1; /* Number of individuals */
6933: fclose(fic);
6934:
6935: return (0);
1.164 brouard 6936: /* endread: */
1.136 brouard 6937: printf("Exiting readdata: ");
6938: fclose(fic);
6939: return (1);
1.126 brouard 6940:
6941:
6942:
1.136 brouard 6943: }
1.145 brouard 6944: void removespace(char *str) {
6945: char *p1 = str, *p2 = str;
6946: do
6947: while (*p2 == ' ')
6948: p2++;
1.169 brouard 6949: while (*p1++ == *p2++);
1.145 brouard 6950: }
6951:
6952: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 6953: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
6954: * - nagesqr = 1 if age*age in the model, otherwise 0.
6955: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
6956: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 6957: * - cptcovage number of covariates with age*products =2
6958: * - cptcovs number of simple covariates
6959: * - 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
6960: * which is a new column after the 9 (ncovcol) variables.
6961: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
6962: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
6963: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
6964: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
6965: */
1.136 brouard 6966: {
1.145 brouard 6967: int i, j, k, ks;
1.164 brouard 6968: int j1, k1, k2;
1.136 brouard 6969: char modelsav[80];
1.145 brouard 6970: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 6971: char *strpt;
1.136 brouard 6972:
1.145 brouard 6973: /*removespace(model);*/
1.136 brouard 6974: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 6975: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 6976: if (strstr(model,"AGE") !=0){
1.192 brouard 6977: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
6978: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 6979: return 1;
6980: }
1.141 brouard 6981: if (strstr(model,"v") !=0){
6982: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
6983: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
6984: return 1;
6985: }
1.187 brouard 6986: strcpy(modelsav,model);
6987: if ((strpt=strstr(model,"age*age")) !=0){
6988: printf(" strpt=%s, model=%s\n",strpt, model);
6989: if(strpt != model){
6990: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 6991: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 6992: corresponding column of parameters.\n",model);
6993: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 6994: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 6995: corresponding column of parameters.\n",model); fflush(ficlog);
6996: return 1;
6997: }
6998:
6999: nagesqr=1;
7000: if (strstr(model,"+age*age") !=0)
7001: substrchaine(modelsav, model, "+age*age");
7002: else if (strstr(model,"age*age+") !=0)
7003: substrchaine(modelsav, model, "age*age+");
7004: else
7005: substrchaine(modelsav, model, "age*age");
7006: }else
7007: nagesqr=0;
7008: if (strlen(modelsav) >1){
7009: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
7010: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
7011: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
7012: cptcovt= j+1; /* Number of total covariates in the model, not including
7013: * cst, age and age*age
7014: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
7015: /* including age products which are counted in cptcovage.
7016: * but the covariates which are products must be treated
7017: * separately: ncovn=4- 2=2 (V1+V3). */
7018: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
7019: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
7020:
7021:
7022: /* Design
7023: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
7024: * < ncovcol=8 >
7025: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
7026: * k= 1 2 3 4 5 6 7 8
7027: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
7028: * covar[k,i], value of kth covariate if not including age for individual i:
7029: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
7030: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
7031: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
7032: * Tage[++cptcovage]=k
7033: * if products, new covar are created after ncovcol with k1
7034: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
7035: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
7036: * 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
7037: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
7038: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
7039: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
7040: * < ncovcol=8 >
7041: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
7042: * k= 1 2 3 4 5 6 7 8 9 10 11 12
7043: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
7044: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
7045: * p Tprod[1]@2={ 6, 5}
7046: *p Tvard[1][1]@4= {7, 8, 5, 6}
7047: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
7048: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
7049: *How to reorganize?
7050: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
7051: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
7052: * {2, 1, 4, 8, 5, 6, 3, 7}
7053: * Struct []
7054: */
1.145 brouard 7055:
1.187 brouard 7056: /* This loop fills the array Tvar from the string 'model'.*/
7057: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
7058: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
7059: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
7060: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
7061: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
7062: /* k=1 Tvar[1]=2 (from V2) */
7063: /* k=5 Tvar[5] */
7064: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 7065: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 7066: /* } */
1.198 brouard 7067: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 7068: /*
7069: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
7070: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 7071: Tvar[k]=0;
1.187 brouard 7072: cptcovage=0;
7073: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
7074: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
7075: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
7076: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
7077: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
7078: /*scanf("%d",i);*/
7079: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
7080: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
7081: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
7082: /* covar is not filled and then is empty */
7083: cptcovprod--;
7084: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
7085: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
7086: cptcovage++; /* Sums the number of covariates which include age as a product */
7087: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
7088: /*printf("stre=%s ", stre);*/
7089: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
7090: cptcovprod--;
7091: cutl(stre,strb,strc,'V');
7092: Tvar[k]=atoi(stre);
7093: cptcovage++;
7094: Tage[cptcovage]=k;
7095: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
7096: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
7097: cptcovn++;
7098: cptcovprodnoage++;k1++;
7099: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
7100: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
7101: because this model-covariate is a construction we invent a new column
7102: ncovcol + k1
7103: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
7104: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
7105: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
7106: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
7107: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
7108: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
7109: k2=k2+2;
7110: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
7111: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
7112: for (i=1; i<=lastobs;i++){
7113: /* Computes the new covariate which is a product of
7114: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
7115: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
7116: }
7117: } /* End age is not in the model */
7118: } /* End if model includes a product */
7119: else { /* no more sum */
7120: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
7121: /* scanf("%d",i);*/
7122: cutl(strd,strc,strb,'V');
7123: ks++; /**< Number of simple covariates */
1.145 brouard 7124: cptcovn++;
1.187 brouard 7125: Tvar[k]=atoi(strd);
7126: }
7127: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
7128: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
7129: scanf("%d",i);*/
7130: } /* end of loop + on total covariates */
7131: } /* end if strlen(modelsave == 0) age*age might exist */
7132: } /* end if strlen(model == 0) */
1.136 brouard 7133:
7134: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
7135: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
7136:
7137: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
7138: printf("cptcovprod=%d ", cptcovprod);
7139: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
7140:
7141: scanf("%d ",i);*/
7142:
7143:
1.137 brouard 7144: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 7145: /*endread:*/
1.136 brouard 7146: printf("Exiting decodemodel: ");
7147: return (1);
7148: }
7149:
1.169 brouard 7150: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 7151: {
7152: int i, m;
7153:
7154: for (i=1; i<=imx; i++) {
7155: for(m=2; (m<= maxwav); m++) {
7156: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
7157: anint[m][i]=9999;
1.216 brouard 7158: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
7159: s[m][i]=-1;
1.136 brouard 7160: }
7161: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 7162: *nberr = *nberr + 1;
7163: 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 are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
7164: 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 are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
1.136 brouard 7165: s[m][i]=-1;
7166: }
7167: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 7168: (*nberr)++;
1.136 brouard 7169: 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]);
7170: 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]);
7171: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
7172: }
7173: }
7174: }
7175:
7176: for (i=1; i<=imx; i++) {
7177: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
7178: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 7179: 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 7180: if (s[m][i] >= nlstate+1) {
1.169 brouard 7181: if(agedc[i]>0){
7182: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 7183: agev[m][i]=agedc[i];
1.214 brouard 7184: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 7185: }else {
1.136 brouard 7186: if ((int)andc[i]!=9999){
7187: nbwarn++;
7188: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
7189: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
7190: agev[m][i]=-1;
7191: }
7192: }
1.169 brouard 7193: } /* agedc > 0 */
1.214 brouard 7194: } /* end if */
1.136 brouard 7195: else if(s[m][i] !=9){ /* Standard case, age in fractional
7196: years but with the precision of a month */
7197: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
7198: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
7199: agev[m][i]=1;
7200: else if(agev[m][i] < *agemin){
7201: *agemin=agev[m][i];
7202: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
7203: }
7204: else if(agev[m][i] >*agemax){
7205: *agemax=agev[m][i];
1.156 brouard 7206: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 7207: }
7208: /*agev[m][i]=anint[m][i]-annais[i];*/
7209: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 7210: } /* en if 9*/
1.136 brouard 7211: else { /* =9 */
1.214 brouard 7212: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 7213: agev[m][i]=1;
7214: s[m][i]=-1;
7215: }
7216: }
1.214 brouard 7217: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 7218: agev[m][i]=1;
1.214 brouard 7219: else{
7220: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
7221: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
7222: agev[m][i]=0;
7223: }
7224: } /* End for lastpass */
7225: }
1.136 brouard 7226:
7227: for (i=1; i<=imx; i++) {
7228: for(m=firstpass; (m<=lastpass); m++){
7229: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 7230: (*nberr)++;
1.136 brouard 7231: 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);
7232: 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);
7233: return 1;
7234: }
7235: }
7236: }
7237:
7238: /*for (i=1; i<=imx; i++){
7239: for (m=firstpass; (m<lastpass); m++){
7240: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
7241: }
7242:
7243: }*/
7244:
7245:
1.139 brouard 7246: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
7247: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 7248:
7249: return (0);
1.164 brouard 7250: /* endread:*/
1.136 brouard 7251: printf("Exiting calandcheckages: ");
7252: return (1);
7253: }
7254:
1.172 brouard 7255: #if defined(_MSC_VER)
7256: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
7257: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
7258: //#include "stdafx.h"
7259: //#include <stdio.h>
7260: //#include <tchar.h>
7261: //#include <windows.h>
7262: //#include <iostream>
7263: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
7264:
7265: LPFN_ISWOW64PROCESS fnIsWow64Process;
7266:
7267: BOOL IsWow64()
7268: {
7269: BOOL bIsWow64 = FALSE;
7270:
7271: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
7272: // (HANDLE, PBOOL);
7273:
7274: //LPFN_ISWOW64PROCESS fnIsWow64Process;
7275:
7276: HMODULE module = GetModuleHandle(_T("kernel32"));
7277: const char funcName[] = "IsWow64Process";
7278: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
7279: GetProcAddress(module, funcName);
7280:
7281: if (NULL != fnIsWow64Process)
7282: {
7283: if (!fnIsWow64Process(GetCurrentProcess(),
7284: &bIsWow64))
7285: //throw std::exception("Unknown error");
7286: printf("Unknown error\n");
7287: }
7288: return bIsWow64 != FALSE;
7289: }
7290: #endif
1.177 brouard 7291:
1.191 brouard 7292: void syscompilerinfo(int logged)
1.167 brouard 7293: {
7294: /* #include "syscompilerinfo.h"*/
1.185 brouard 7295: /* command line Intel compiler 32bit windows, XP compatible:*/
7296: /* /GS /W3 /Gy
7297: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
7298: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
7299: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 7300: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
7301: */
7302: /* 64 bits */
1.185 brouard 7303: /*
7304: /GS /W3 /Gy
7305: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
7306: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
7307: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
7308: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
7309: /* Optimization are useless and O3 is slower than O2 */
7310: /*
7311: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
7312: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
7313: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
7314: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
7315: */
1.186 brouard 7316: /* Link is */ /* /OUT:"visual studio
1.185 brouard 7317: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
7318: /PDB:"visual studio
7319: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
7320: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
7321: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
7322: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
7323: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
7324: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
7325: uiAccess='false'"
7326: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
7327: /NOLOGO /TLBID:1
7328: */
1.177 brouard 7329: #if defined __INTEL_COMPILER
1.178 brouard 7330: #if defined(__GNUC__)
7331: struct utsname sysInfo; /* For Intel on Linux and OS/X */
7332: #endif
1.177 brouard 7333: #elif defined(__GNUC__)
1.179 brouard 7334: #ifndef __APPLE__
1.174 brouard 7335: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 7336: #endif
1.177 brouard 7337: struct utsname sysInfo;
1.178 brouard 7338: int cross = CROSS;
7339: if (cross){
7340: printf("Cross-");
1.191 brouard 7341: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 7342: }
1.174 brouard 7343: #endif
7344:
1.171 brouard 7345: #include <stdint.h>
1.178 brouard 7346:
1.191 brouard 7347: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 7348: #if defined(__clang__)
1.191 brouard 7349: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 7350: #endif
7351: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 7352: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 7353: #endif
7354: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 7355: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 7356: #endif
7357: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 7358: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 7359: #endif
7360: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 7361: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 7362: #endif
7363: #if defined(_MSC_VER)
1.191 brouard 7364: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 7365: #endif
7366: #if defined(__PGI)
1.191 brouard 7367: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 7368: #endif
7369: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 7370: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 7371: #endif
1.191 brouard 7372: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 7373:
1.167 brouard 7374: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
7375: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
7376: // Windows (x64 and x86)
1.191 brouard 7377: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 7378: #elif __unix__ // all unices, not all compilers
7379: // Unix
1.191 brouard 7380: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 7381: #elif __linux__
7382: // linux
1.191 brouard 7383: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 7384: #elif __APPLE__
1.174 brouard 7385: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 7386: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 7387: #endif
7388:
7389: /* __MINGW32__ */
7390: /* __CYGWIN__ */
7391: /* __MINGW64__ */
7392: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
7393: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
7394: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
7395: /* _WIN64 // Defined for applications for Win64. */
7396: /* _M_X64 // Defined for compilations that target x64 processors. */
7397: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 7398:
1.167 brouard 7399: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 7400: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 7401: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 7402: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 7403: #else
1.191 brouard 7404: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 7405: #endif
7406:
1.169 brouard 7407: #if defined(__GNUC__)
7408: # if defined(__GNUC_PATCHLEVEL__)
7409: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
7410: + __GNUC_MINOR__ * 100 \
7411: + __GNUC_PATCHLEVEL__)
7412: # else
7413: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
7414: + __GNUC_MINOR__ * 100)
7415: # endif
1.174 brouard 7416: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 7417: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 7418:
7419: if (uname(&sysInfo) != -1) {
7420: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 7421: 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 7422: }
7423: else
7424: perror("uname() error");
1.179 brouard 7425: //#ifndef __INTEL_COMPILER
7426: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 7427: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 7428: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 7429: #endif
1.169 brouard 7430: #endif
1.172 brouard 7431:
7432: // void main()
7433: // {
1.169 brouard 7434: #if defined(_MSC_VER)
1.174 brouard 7435: if (IsWow64()){
1.191 brouard 7436: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
7437: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 7438: }
7439: else{
1.191 brouard 7440: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
7441: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 7442: }
1.172 brouard 7443: // printf("\nPress Enter to continue...");
7444: // getchar();
7445: // }
7446:
1.169 brouard 7447: #endif
7448:
1.167 brouard 7449:
7450: }
1.136 brouard 7451:
1.209 brouard 7452: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.180 brouard 7453: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
7454: int i, j, k, i1 ;
1.202 brouard 7455: /* double ftolpl = 1.e-10; */
1.180 brouard 7456: double age, agebase, agelim;
1.203 brouard 7457: double tot;
1.180 brouard 7458:
1.202 brouard 7459: strcpy(filerespl,"PL_");
7460: strcat(filerespl,fileresu);
7461: if((ficrespl=fopen(filerespl,"w"))==NULL) {
7462: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
7463: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
7464: }
7465: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
7466: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
7467: pstamp(ficrespl);
1.203 brouard 7468: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 7469: fprintf(ficrespl,"#Age ");
7470: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
7471: fprintf(ficrespl,"\n");
1.180 brouard 7472:
7473: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
7474:
7475: agebase=ageminpar;
7476: agelim=agemaxpar;
7477:
7478: i1=pow(2,cptcoveff);
7479: if (cptcovn < 1){i1=1;}
7480:
7481: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7482: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
7483: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
7484: k=k+1;
7485: /* to clean */
1.198 brouard 7486: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
1.200 brouard 7487: fprintf(ficrespl,"#******");
7488: printf("#******");
7489: fprintf(ficlog,"#******");
1.180 brouard 7490: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 7491: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7492: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7493: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 7494: }
7495: fprintf(ficrespl,"******\n");
7496: printf("******\n");
7497: fprintf(ficlog,"******\n");
7498:
7499: fprintf(ficrespl,"#Age ");
7500: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 7501: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 7502: }
1.203 brouard 7503: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
7504: fprintf(ficrespl,"Total Years_to_converge\n");
1.180 brouard 7505:
7506: for (age=agebase; age<=agelim; age++){
7507: /* for (age=agebase; age<=agebase; age++){ */
1.209 brouard 7508: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
1.180 brouard 7509: fprintf(ficrespl,"%.0f ",age );
7510: for(j=1;j<=cptcoveff;j++)
1.198 brouard 7511: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.203 brouard 7512: tot=0.;
7513: for(i=1; i<=nlstate;i++){
7514: tot += prlim[i][i];
1.180 brouard 7515: fprintf(ficrespl," %.5f", prlim[i][i]);
1.203 brouard 7516: }
1.209 brouard 7517: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
1.180 brouard 7518: } /* Age */
7519: /* was end of cptcod */
7520: } /* cptcov */
1.184 brouard 7521: return 0;
1.180 brouard 7522: }
7523:
1.217 ! brouard 7524: int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
! 7525: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
! 7526: int i, j, k, i1 ;
! 7527: /* double ftolpl = 1.e-10; */
! 7528: double age, agebase, agelim;
! 7529: double tot;
! 7530:
! 7531: strcpy(fileresplb,"PLB_");
! 7532: strcat(fileresplb,fileresu);
! 7533: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
! 7534: printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
! 7535: fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
! 7536: }
! 7537: printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
! 7538: fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
! 7539: pstamp(ficresplb);
! 7540: fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
! 7541: fprintf(ficresplb,"#Age ");
! 7542: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
! 7543: fprintf(ficresplb,"\n");
! 7544:
! 7545: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
! 7546:
! 7547: agebase=ageminpar;
! 7548: agelim=agemaxpar;
! 7549:
! 7550: i1=pow(2,cptcoveff);
! 7551: if (cptcovn < 1){i1=1;}
! 7552:
! 7553: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
! 7554: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
! 7555: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
! 7556: k=k+1;
! 7557: /* to clean */
! 7558: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
! 7559: fprintf(ficresplb,"#******");
! 7560: printf("#******");
! 7561: fprintf(ficlog,"#******");
! 7562: for(j=1;j<=cptcoveff;j++) {
! 7563: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 7564: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 7565: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 7566: }
! 7567: fprintf(ficresplb,"******\n");
! 7568: printf("******\n");
! 7569: fprintf(ficlog,"******\n");
! 7570:
! 7571: fprintf(ficresplb,"#Age ");
! 7572: for(j=1;j<=cptcoveff;j++) {
! 7573: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 7574: }
! 7575: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
! 7576: fprintf(ficresplb,"Total Years_to_converge\n");
! 7577:
! 7578: for (age=agebase; age<=agelim; age++){
! 7579: /* for (age=agebase; age<=agebase; age++){ */
! 7580: bprevalim(bprlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
! 7581: fprintf(ficresplb,"%.0f ",age );
! 7582: for(j=1;j<=cptcoveff;j++)
! 7583: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 7584: tot=0.;
! 7585: for(i=1; i<=nlstate;i++){
! 7586: tot += bprlim[i][i];
! 7587: fprintf(ficresplb," %.5f", bprlim[i][i]);
! 7588: }
! 7589: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
! 7590: } /* Age */
! 7591: /* was end of cptcod */
! 7592: } /* cptcov */
! 7593: return 0;
! 7594: }
! 7595:
1.180 brouard 7596: int hPijx(double *p, int bage, int fage){
7597: /*------------- h Pij x at various ages ------------*/
7598:
7599: int stepsize;
7600: int agelim;
7601: int hstepm;
7602: int nhstepm;
7603: int h, i, i1, j, k;
7604:
7605: double agedeb;
7606: double ***p3mat;
7607:
1.201 brouard 7608: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 7609: if((ficrespij=fopen(filerespij,"w"))==NULL) {
7610: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
7611: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
7612: }
7613: printf("Computing pij: result on file '%s' \n", filerespij);
7614: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
7615:
7616: stepsize=(int) (stepm+YEARM-1)/YEARM;
7617: /*if (stepm<=24) stepsize=2;*/
7618:
7619: agelim=AGESUP;
7620: hstepm=stepsize*YEARM; /* Every year of age */
7621: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
7622:
7623: /* hstepm=1; aff par mois*/
7624: pstamp(ficrespij);
7625: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
7626: i1= pow(2,cptcoveff);
1.183 brouard 7627: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
7628: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
7629: /* k=k+1; */
7630: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7631: fprintf(ficrespij,"\n#****** ");
7632: for(j=1;j<=cptcoveff;j++)
1.198 brouard 7633: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.183 brouard 7634: fprintf(ficrespij,"******\n");
7635:
7636: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
7637: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
7638: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
7639:
7640: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 7641:
1.183 brouard 7642: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
7643: oldm=oldms;savm=savms;
7644: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
7645: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
7646: for(i=1; i<=nlstate;i++)
7647: for(j=1; j<=nlstate+ndeath;j++)
7648: fprintf(ficrespij," %1d-%1d",i,j);
7649: fprintf(ficrespij,"\n");
7650: for (h=0; h<=nhstepm; h++){
7651: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
7652: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 7653: for(i=1; i<=nlstate;i++)
7654: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 7655: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 7656: fprintf(ficrespij,"\n");
7657: }
1.183 brouard 7658: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
7659: fprintf(ficrespij,"\n");
7660: }
1.180 brouard 7661: /*}*/
7662: }
1.184 brouard 7663: return 0;
1.180 brouard 7664: }
7665:
1.217 ! brouard 7666: int hBijx(double *p, int bage, int fage){
! 7667: /*------------- h Bij x at various ages ------------*/
! 7668:
! 7669: int stepsize;
! 7670: int agelim;
! 7671: int hstepm;
! 7672: int nhstepm;
! 7673: int h, i, i1, j, k;
! 7674:
! 7675: double agedeb;
! 7676: double ***p3mat;
! 7677:
! 7678: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
! 7679: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
! 7680: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
! 7681: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
! 7682: }
! 7683: printf("Computing pij back: result on file '%s' \n", filerespijb);
! 7684: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
! 7685:
! 7686: stepsize=(int) (stepm+YEARM-1)/YEARM;
! 7687: /*if (stepm<=24) stepsize=2;*/
! 7688:
! 7689: agelim=AGESUP;
! 7690: hstepm=stepsize*YEARM; /* Every year of age */
! 7691: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
! 7692:
! 7693: /* hstepm=1; aff par mois*/
! 7694: pstamp(ficrespijb);
! 7695: fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");
! 7696: i1= pow(2,cptcoveff);
! 7697: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
! 7698: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
! 7699: /* k=k+1; */
! 7700: for (k=1; k <= (int) pow(2,cptcoveff); k++){
! 7701: fprintf(ficrespijb,"\n#****** ");
! 7702: for(j=1;j<=cptcoveff;j++)
! 7703: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 7704: fprintf(ficrespijb,"******\n");
! 7705:
! 7706: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
! 7707: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months */
! 7708: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
! 7709: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
! 7710:
! 7711: /* nhstepm=nhstepm*YEARM; aff par mois*/
! 7712:
! 7713: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 7714: oldm=oldms;savm=savms;
! 7715: hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
! 7716: fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
! 7717: for(i=1; i<=nlstate;i++)
! 7718: for(j=1; j<=nlstate+ndeath;j++)
! 7719: fprintf(ficrespijb," %1d-%1d",i,j);
! 7720: fprintf(ficrespijb,"\n");
! 7721: for (h=0; h<=nhstepm; h++){
! 7722: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
! 7723: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
! 7724: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
! 7725: for(i=1; i<=nlstate;i++)
! 7726: for(j=1; j<=nlstate+ndeath;j++)
! 7727: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
! 7728: fprintf(ficrespijb,"\n");
! 7729: }
! 7730: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 7731: fprintf(ficrespijb,"\n");
! 7732: }
! 7733: /*}*/
! 7734: }
! 7735: return 0;
! 7736: }
! 7737:
1.180 brouard 7738:
1.136 brouard 7739: /***********************************************/
7740: /**************** Main Program *****************/
7741: /***********************************************/
7742:
7743: int main(int argc, char *argv[])
7744: {
7745: #ifdef GSL
7746: const gsl_multimin_fminimizer_type *T;
7747: size_t iteri = 0, it;
7748: int rval = GSL_CONTINUE;
7749: int status = GSL_SUCCESS;
7750: double ssval;
7751: #endif
7752: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 7753: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.209 brouard 7754: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 7755: int jj, ll, li, lj, lk;
1.136 brouard 7756: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 7757: int num_filled;
1.136 brouard 7758: int itimes;
7759: int NDIM=2;
7760: int vpopbased=0;
7761:
1.164 brouard 7762: char ca[32], cb[32];
1.136 brouard 7763: /* FILE *fichtm; *//* Html File */
7764: /* FILE *ficgp;*/ /*Gnuplot File */
7765: struct stat info;
1.191 brouard 7766: double agedeb=0.;
1.194 brouard 7767:
7768: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.136 brouard 7769:
1.165 brouard 7770: double fret;
1.191 brouard 7771: double dum=0.; /* Dummy variable */
1.136 brouard 7772: double ***p3mat;
7773: double ***mobaverage;
1.164 brouard 7774:
7775: char line[MAXLINE];
1.197 brouard 7776: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
7777:
7778: char model[MAXLINE], modeltemp[MAXLINE];
1.136 brouard 7779: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 7780: char *tok, *val; /* pathtot */
1.136 brouard 7781: int firstobs=1, lastobs=10;
1.195 brouard 7782: int c, h , cpt, c2;
1.191 brouard 7783: int jl=0;
7784: int i1, j1, jk, stepsize=0;
1.194 brouard 7785: int count=0;
7786:
1.164 brouard 7787: int *tab;
1.136 brouard 7788: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.217 ! brouard 7789: int backcast=0;
1.136 brouard 7790: int mobilav=0,popforecast=0;
1.191 brouard 7791: int hstepm=0, nhstepm=0;
1.136 brouard 7792: int agemortsup;
7793: float sumlpop=0.;
7794: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
7795: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
7796:
1.191 brouard 7797: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 7798: double ftolpl=FTOL;
7799: double **prlim;
1.217 ! brouard 7800: double **bprlim;
1.136 brouard 7801: double ***param; /* Matrix of parameters */
7802: double *p;
7803: double **matcov; /* Matrix of covariance */
1.203 brouard 7804: double **hess; /* Hessian matrix */
1.136 brouard 7805: double ***delti3; /* Scale */
7806: double *delti; /* Scale */
7807: double ***eij, ***vareij;
7808: double **varpl; /* Variances of prevalence limits by age */
7809: double *epj, vepp;
1.164 brouard 7810:
1.136 brouard 7811: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.217 ! brouard 7812: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;
! 7813:
1.136 brouard 7814: double **ximort;
1.145 brouard 7815: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 7816: int *dcwave;
7817:
1.164 brouard 7818: char z[1]="c";
1.136 brouard 7819:
7820: /*char *strt;*/
7821: char strtend[80];
1.126 brouard 7822:
1.164 brouard 7823:
1.126 brouard 7824: /* setlocale (LC_ALL, ""); */
7825: /* bindtextdomain (PACKAGE, LOCALEDIR); */
7826: /* textdomain (PACKAGE); */
7827: /* setlocale (LC_CTYPE, ""); */
7828: /* setlocale (LC_MESSAGES, ""); */
7829:
7830: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 7831: rstart_time = time(NULL);
7832: /* (void) gettimeofday(&start_time,&tzp);*/
7833: start_time = *localtime(&rstart_time);
1.126 brouard 7834: curr_time=start_time;
1.157 brouard 7835: /*tml = *localtime(&start_time.tm_sec);*/
7836: /* strcpy(strstart,asctime(&tml)); */
7837: strcpy(strstart,asctime(&start_time));
1.126 brouard 7838:
7839: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 7840: /* tp.tm_sec = tp.tm_sec +86400; */
7841: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 7842: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
7843: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
7844: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 7845: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 7846: /* strt=asctime(&tmg); */
7847: /* printf("Time(after) =%s",strstart); */
7848: /* (void) time (&time_value);
7849: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
7850: * tm = *localtime(&time_value);
7851: * strstart=asctime(&tm);
7852: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
7853: */
7854:
7855: nberr=0; /* Number of errors and warnings */
7856: nbwarn=0;
1.184 brouard 7857: #ifdef WIN32
7858: _getcwd(pathcd, size);
7859: #else
1.126 brouard 7860: getcwd(pathcd, size);
1.184 brouard 7861: #endif
1.191 brouard 7862: syscompilerinfo(0);
1.196 brouard 7863: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 7864: if(argc <=1){
7865: printf("\nEnter the parameter file name: ");
1.205 brouard 7866: if(!fgets(pathr,FILENAMELENGTH,stdin)){
7867: printf("ERROR Empty parameter file name\n");
7868: goto end;
7869: }
1.126 brouard 7870: i=strlen(pathr);
7871: if(pathr[i-1]=='\n')
7872: pathr[i-1]='\0';
1.156 brouard 7873: i=strlen(pathr);
1.205 brouard 7874: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 7875: pathr[i-1]='\0';
1.205 brouard 7876: }
7877: i=strlen(pathr);
7878: if( i==0 ){
7879: printf("ERROR Empty parameter file name\n");
7880: goto end;
7881: }
7882: for (tok = pathr; tok != NULL; ){
1.126 brouard 7883: printf("Pathr |%s|\n",pathr);
7884: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
7885: printf("val= |%s| pathr=%s\n",val,pathr);
7886: strcpy (pathtot, val);
7887: if(pathr[0] == '\0') break; /* Dirty */
7888: }
7889: }
7890: else{
7891: strcpy(pathtot,argv[1]);
7892: }
7893: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
7894: /*cygwin_split_path(pathtot,path,optionfile);
7895: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
7896: /* cutv(path,optionfile,pathtot,'\\');*/
7897:
7898: /* Split argv[0], imach program to get pathimach */
7899: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
7900: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
7901: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
7902: /* strcpy(pathimach,argv[0]); */
7903: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
7904: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
7905: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 7906: #ifdef WIN32
7907: _chdir(path); /* Can be a relative path */
7908: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
7909: #else
1.126 brouard 7910: chdir(path); /* Can be a relative path */
1.184 brouard 7911: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
7912: #endif
7913: printf("Current directory %s!\n",pathcd);
1.126 brouard 7914: strcpy(command,"mkdir ");
7915: strcat(command,optionfilefiname);
7916: if((outcmd=system(command)) != 0){
1.169 brouard 7917: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 7918: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
7919: /* fclose(ficlog); */
7920: /* exit(1); */
7921: }
7922: /* if((imk=mkdir(optionfilefiname))<0){ */
7923: /* perror("mkdir"); */
7924: /* } */
7925:
7926: /*-------- arguments in the command line --------*/
7927:
1.186 brouard 7928: /* Main Log file */
1.126 brouard 7929: strcat(filelog, optionfilefiname);
7930: strcat(filelog,".log"); /* */
7931: if((ficlog=fopen(filelog,"w"))==NULL) {
7932: printf("Problem with logfile %s\n",filelog);
7933: goto end;
7934: }
7935: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 7936: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 7937: fprintf(ficlog,"\nEnter the parameter file name: \n");
7938: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
7939: path=%s \n\
7940: optionfile=%s\n\
7941: optionfilext=%s\n\
1.156 brouard 7942: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 7943:
1.197 brouard 7944: syscompilerinfo(1);
1.167 brouard 7945:
1.126 brouard 7946: printf("Local time (at start):%s",strstart);
7947: fprintf(ficlog,"Local time (at start): %s",strstart);
7948: fflush(ficlog);
7949: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 7950: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 7951:
7952: /* */
7953: strcpy(fileres,"r");
7954: strcat(fileres, optionfilefiname);
1.201 brouard 7955: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 7956: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 7957: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 7958:
1.186 brouard 7959: /* Main ---------arguments file --------*/
1.126 brouard 7960:
7961: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 7962: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
7963: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 7964: fflush(ficlog);
1.149 brouard 7965: /* goto end; */
7966: exit(70);
1.126 brouard 7967: }
7968:
7969:
7970:
7971: strcpy(filereso,"o");
1.201 brouard 7972: strcat(filereso,fileresu);
1.126 brouard 7973: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
7974: printf("Problem with Output resultfile: %s\n", filereso);
7975: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
7976: fflush(ficlog);
7977: goto end;
7978: }
7979:
7980: /* Reads comments: lines beginning with '#' */
7981: numlinepar=0;
1.197 brouard 7982:
7983: /* First parameter line */
7984: while(fgets(line, MAXLINE, ficpar)) {
7985: /* If line starts with a # it is a comment */
7986: if (line[0] == '#') {
7987: numlinepar++;
7988: fputs(line,stdout);
7989: fputs(line,ficparo);
7990: fputs(line,ficlog);
7991: continue;
7992: }else
7993: break;
7994: }
7995: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
7996: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
7997: if (num_filled != 5) {
7998: printf("Should be 5 parameters\n");
7999: }
1.126 brouard 8000: numlinepar++;
1.197 brouard 8001: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
8002: }
8003: /* Second parameter line */
8004: while(fgets(line, MAXLINE, ficpar)) {
8005: /* If line starts with a # it is a comment */
8006: if (line[0] == '#') {
8007: numlinepar++;
8008: fputs(line,stdout);
8009: fputs(line,ficparo);
8010: fputs(line,ficlog);
8011: continue;
8012: }else
8013: break;
8014: }
8015: if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
8016: &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
8017: if (num_filled != 8) {
1.209 brouard 8018: printf("Not 8 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
8019: printf("but line=%s\n",line);
1.197 brouard 8020: }
8021: printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);
1.126 brouard 8022: }
1.203 brouard 8023: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 8024: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 8025: /* Third parameter line */
8026: while(fgets(line, MAXLINE, ficpar)) {
8027: /* If line starts with a # it is a comment */
8028: if (line[0] == '#') {
8029: numlinepar++;
8030: fputs(line,stdout);
8031: fputs(line,ficparo);
8032: fputs(line,ficlog);
8033: continue;
8034: }else
8035: break;
8036: }
1.201 brouard 8037: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
8038: if (num_filled == 0)
8039: model[0]='\0';
8040: else if (num_filled != 1){
1.197 brouard 8041: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
8042: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
8043: model[0]='\0';
8044: goto end;
8045: }
8046: else{
8047: if (model[0]=='+'){
8048: for(i=1; i<=strlen(model);i++)
8049: modeltemp[i-1]=model[i];
1.201 brouard 8050: strcpy(model,modeltemp);
1.197 brouard 8051: }
8052: }
1.199 brouard 8053: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 8054: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 8055: }
8056: /* 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); */
8057: /* numlinepar=numlinepar+3; /\* In general *\/ */
8058: /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
1.203 brouard 8059: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
8060: fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
1.126 brouard 8061: fflush(ficlog);
1.190 brouard 8062: /* if(model[0]=='#'|| model[0]== '\0'){ */
8063: if(model[0]=='#'){
1.187 brouard 8064: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
8065: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
8066: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
8067: if(mle != -1){
8068: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
8069: exit(1);
8070: }
8071: }
1.126 brouard 8072: while((c=getc(ficpar))=='#' && c!= EOF){
8073: ungetc(c,ficpar);
8074: fgets(line, MAXLINE, ficpar);
8075: numlinepar++;
1.195 brouard 8076: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
8077: z[0]=line[1];
8078: }
8079: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 8080: fputs(line, stdout);
8081: //puts(line);
1.126 brouard 8082: fputs(line,ficparo);
8083: fputs(line,ficlog);
8084: }
8085: ungetc(c,ficpar);
8086:
8087:
1.145 brouard 8088: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 8089: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
8090: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
8091: v1+v2*age+v2*v3 makes cptcovn = 3
8092: */
8093: if (strlen(model)>1)
1.187 brouard 8094: 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 8095: else
1.187 brouard 8096: ncovmodel=2; /* Constant and age */
1.133 brouard 8097: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
8098: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 8099: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
8100: 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);
8101: 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);
8102: fflush(stdout);
8103: fclose (ficlog);
8104: goto end;
8105: }
1.126 brouard 8106: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
8107: delti=delti3[1][1];
8108: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
8109: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
8110: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 8111: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
8112: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 8113: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8114: fclose (ficparo);
8115: fclose (ficlog);
8116: goto end;
8117: exit(0);
8118: }
1.186 brouard 8119: else if(mle==-3) { /* Main Wizard */
1.126 brouard 8120: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 8121: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
8122: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 8123: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
8124: matcov=matrix(1,npar,1,npar);
1.203 brouard 8125: hess=matrix(1,npar,1,npar);
1.126 brouard 8126: }
8127: else{
1.145 brouard 8128: /* Read guessed parameters */
1.126 brouard 8129: /* Reads comments: lines beginning with '#' */
8130: while((c=getc(ficpar))=='#' && c!= EOF){
8131: ungetc(c,ficpar);
8132: fgets(line, MAXLINE, ficpar);
8133: numlinepar++;
1.141 brouard 8134: fputs(line,stdout);
1.126 brouard 8135: fputs(line,ficparo);
8136: fputs(line,ficlog);
8137: }
8138: ungetc(c,ficpar);
8139:
8140: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
8141: for(i=1; i <=nlstate; i++){
8142: j=0;
8143: for(jj=1; jj <=nlstate+ndeath; jj++){
8144: if(jj==i) continue;
8145: j++;
8146: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.193 brouard 8147: if ((i1 != i) || (j1 != jj)){
1.126 brouard 8148: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
8149: It might be a problem of design; if ncovcol and the model are correct\n \
8150: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
8151: exit(1);
8152: }
8153: fprintf(ficparo,"%1d%1d",i1,j1);
8154: if(mle==1)
1.193 brouard 8155: printf("%1d%1d",i,jj);
8156: fprintf(ficlog,"%1d%1d",i,jj);
1.126 brouard 8157: for(k=1; k<=ncovmodel;k++){
8158: fscanf(ficpar," %lf",¶m[i][j][k]);
8159: if(mle==1){
8160: printf(" %lf",param[i][j][k]);
8161: fprintf(ficlog," %lf",param[i][j][k]);
8162: }
8163: else
8164: fprintf(ficlog," %lf",param[i][j][k]);
8165: fprintf(ficparo," %lf",param[i][j][k]);
8166: }
8167: fscanf(ficpar,"\n");
8168: numlinepar++;
8169: if(mle==1)
8170: printf("\n");
8171: fprintf(ficlog,"\n");
8172: fprintf(ficparo,"\n");
8173: }
8174: }
8175: fflush(ficlog);
8176:
1.145 brouard 8177: /* Reads scales values */
1.126 brouard 8178: p=param[1][1];
8179:
8180: /* Reads comments: lines beginning with '#' */
8181: while((c=getc(ficpar))=='#' && c!= EOF){
8182: ungetc(c,ficpar);
8183: fgets(line, MAXLINE, ficpar);
8184: numlinepar++;
1.141 brouard 8185: fputs(line,stdout);
1.126 brouard 8186: fputs(line,ficparo);
8187: fputs(line,ficlog);
8188: }
8189: ungetc(c,ficpar);
8190:
8191: for(i=1; i <=nlstate; i++){
8192: for(j=1; j <=nlstate+ndeath-1; j++){
8193: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 8194: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 8195: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
8196: exit(1);
8197: }
8198: printf("%1d%1d",i,j);
8199: fprintf(ficparo,"%1d%1d",i1,j1);
8200: fprintf(ficlog,"%1d%1d",i1,j1);
8201: for(k=1; k<=ncovmodel;k++){
8202: fscanf(ficpar,"%le",&delti3[i][j][k]);
8203: printf(" %le",delti3[i][j][k]);
8204: fprintf(ficparo," %le",delti3[i][j][k]);
8205: fprintf(ficlog," %le",delti3[i][j][k]);
8206: }
8207: fscanf(ficpar,"\n");
8208: numlinepar++;
8209: printf("\n");
8210: fprintf(ficparo,"\n");
8211: fprintf(ficlog,"\n");
8212: }
8213: }
8214: fflush(ficlog);
8215:
1.145 brouard 8216: /* Reads covariance matrix */
1.126 brouard 8217: delti=delti3[1][1];
8218:
8219:
8220: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
8221:
8222: /* Reads comments: lines beginning with '#' */
8223: while((c=getc(ficpar))=='#' && c!= EOF){
8224: ungetc(c,ficpar);
8225: fgets(line, MAXLINE, ficpar);
8226: numlinepar++;
1.141 brouard 8227: fputs(line,stdout);
1.126 brouard 8228: fputs(line,ficparo);
8229: fputs(line,ficlog);
8230: }
8231: ungetc(c,ficpar);
8232:
8233: matcov=matrix(1,npar,1,npar);
1.203 brouard 8234: hess=matrix(1,npar,1,npar);
1.131 brouard 8235: for(i=1; i <=npar; i++)
8236: for(j=1; j <=npar; j++) matcov[i][j]=0.;
8237:
1.194 brouard 8238: /* Scans npar lines */
1.126 brouard 8239: for(i=1; i <=npar; i++){
1.194 brouard 8240: count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
8241: if(count != 3){
8242: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
8243: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
8244: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
8245: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
8246: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
8247: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
8248: exit(1);
8249: }else
1.126 brouard 8250: if(mle==1)
1.194 brouard 8251: printf("%1d%1d%1d",i1,j1,jk);
8252: fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
8253: fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
1.126 brouard 8254: for(j=1; j <=i; j++){
8255: fscanf(ficpar," %le",&matcov[i][j]);
8256: if(mle==1){
8257: printf(" %.5le",matcov[i][j]);
8258: }
8259: fprintf(ficlog," %.5le",matcov[i][j]);
8260: fprintf(ficparo," %.5le",matcov[i][j]);
8261: }
8262: fscanf(ficpar,"\n");
8263: numlinepar++;
8264: if(mle==1)
8265: printf("\n");
8266: fprintf(ficlog,"\n");
8267: fprintf(ficparo,"\n");
8268: }
1.194 brouard 8269: /* End of read covariance matrix npar lines */
1.126 brouard 8270: for(i=1; i <=npar; i++)
8271: for(j=i+1;j<=npar;j++)
8272: matcov[i][j]=matcov[j][i];
8273:
8274: if(mle==1)
8275: printf("\n");
8276: fprintf(ficlog,"\n");
8277:
8278: fflush(ficlog);
8279:
8280: /*-------- Rewriting parameter file ----------*/
8281: strcpy(rfileres,"r"); /* "Rparameterfile */
8282: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
8283: strcat(rfileres,"."); /* */
8284: strcat(rfileres,optionfilext); /* Other files have txt extension */
8285: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 8286: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
8287: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 8288: }
8289: fprintf(ficres,"#%s\n",version);
8290: } /* End of mle != -3 */
8291:
1.186 brouard 8292: /* Main data
8293: */
1.126 brouard 8294: n= lastobs;
8295: num=lvector(1,n);
8296: moisnais=vector(1,n);
8297: annais=vector(1,n);
8298: moisdc=vector(1,n);
8299: andc=vector(1,n);
8300: agedc=vector(1,n);
8301: cod=ivector(1,n);
8302: weight=vector(1,n);
8303: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
8304: mint=matrix(1,maxwav,1,n);
8305: anint=matrix(1,maxwav,1,n);
1.131 brouard 8306: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 8307: tab=ivector(1,NCOVMAX);
1.144 brouard 8308: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 8309: 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 8310:
1.136 brouard 8311: /* Reads data from file datafile */
8312: if (readdata(datafile, firstobs, lastobs, &imx)==1)
8313: goto end;
8314:
8315: /* Calculation of the number of parameters from char model */
1.137 brouard 8316: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
8317: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
8318: k=3 V4 Tvar[k=3]= 4 (from V4)
8319: k=2 V1 Tvar[k=2]= 1 (from V1)
8320: k=1 Tvar[1]=2 (from V2)
8321: */
8322: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
8323: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
8324: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
8325: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
8326: */
8327: /* For model-covariate k tells which data-covariate to use but
8328: because this model-covariate is a construction we invent a new column
8329: ncovcol + k1
8330: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
8331: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 8332: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 8333: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
8334: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
8335: */
1.145 brouard 8336: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
8337: 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 8338: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
8339: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 8340: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 8341: 4 covariates (3 plus signs)
8342: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
8343: */
1.136 brouard 8344:
1.186 brouard 8345: /* Main decodemodel */
8346:
1.187 brouard 8347:
1.136 brouard 8348: if(decodemodel(model, lastobs) == 1)
8349: goto end;
8350:
1.137 brouard 8351: if((double)(lastobs-imx)/(double)imx > 1.10){
8352: nbwarn++;
8353: 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);
8354: 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);
8355: }
1.136 brouard 8356: /* if(mle==1){*/
1.137 brouard 8357: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
8358: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 8359: }
8360:
8361: /*-calculation of age at interview from date of interview and age at death -*/
8362: agev=matrix(1,maxwav,1,imx);
8363:
8364: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
8365: goto end;
8366:
1.126 brouard 8367:
1.136 brouard 8368: agegomp=(int)agemin;
8369: free_vector(moisnais,1,n);
8370: free_vector(annais,1,n);
1.126 brouard 8371: /* free_matrix(mint,1,maxwav,1,n);
8372: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 8373: /* free_vector(moisdc,1,n); */
8374: /* free_vector(andc,1,n); */
1.145 brouard 8375: /* */
8376:
1.126 brouard 8377: wav=ivector(1,imx);
1.214 brouard 8378: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
8379: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
8380: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
8381: 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.*/
8382: bh=imatrix(1,lastpass-firstpass+2,1,imx);
8383: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 8384:
8385: /* Concatenates waves */
1.214 brouard 8386: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
8387: Death is a valid wave (if date is known).
8388: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
8389: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
8390: and mw[mi+1][i]. dh depends on stepm.
8391: */
8392:
1.126 brouard 8393: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 8394: /* */
8395:
1.215 brouard 8396: free_vector(moisdc,1,n);
8397: free_vector(andc,1,n);
8398:
1.126 brouard 8399: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
8400:
8401: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
8402: ncodemax[1]=1;
1.145 brouard 8403: Ndum =ivector(-1,NCOVMAX);
1.187 brouard 8404: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
1.145 brouard 8405: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.211 brouard 8406: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 8407: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 8408: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.145 brouard 8409:
1.200 brouard 8410: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 8411: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 8412: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 8413: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
8414: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
8415: * (currently 0 or 1) in the data.
8416: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
8417: * corresponding modality (h,j).
8418: */
8419:
1.145 brouard 8420: h=0;
8421:
8422:
8423: /*if (cptcovn > 0) */
1.126 brouard 8424:
1.145 brouard 8425:
1.126 brouard 8426: m=pow(2,cptcoveff);
8427:
1.144 brouard 8428: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 8429: * For k=4 covariates, h goes from 1 to m=2**k
8430: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
8431: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 8432: * h\k 1 2 3 4
1.143 brouard 8433: *______________________________
8434: * 1 i=1 1 i=1 1 i=1 1 i=1 1
8435: * 2 2 1 1 1
8436: * 3 i=2 1 2 1 1
8437: * 4 2 2 1 1
8438: * 5 i=3 1 i=2 1 2 1
8439: * 6 2 1 2 1
8440: * 7 i=4 1 2 2 1
8441: * 8 2 2 2 1
1.197 brouard 8442: * 9 i=5 1 i=3 1 i=2 1 2
8443: * 10 2 1 1 2
8444: * 11 i=6 1 2 1 2
8445: * 12 2 2 1 2
8446: * 13 i=7 1 i=4 1 2 2
8447: * 14 2 1 2 2
8448: * 15 i=8 1 2 2 2
8449: * 16 2 2 2 2
1.143 brouard 8450: */
1.212 brouard 8451: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 8452: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
8453: * and the value of each covariate?
8454: * V1=1, V2=1, V3=2, V4=1 ?
8455: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
8456: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
8457: * In order to get the real value in the data, we use nbcode
8458: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
8459: * We are keeping this crazy system in order to be able (in the future?)
8460: * to have more than 2 values (0 or 1) for a covariate.
8461: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
8462: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
8463: * bbbbbbbb
8464: * 76543210
8465: * h-1 00000101 (6-1=5)
8466: *(h-1)>>(k-1)= 00000001 >> (2-1) = 1 right shift
8467: * &
8468: * 1 00000001 (1)
8469: * 00000001 = 1 & ((h-1) >> (k-1))
8470: * +1= 00000010 =2
8471: *
8472: * h=14, k=3 => h'=h-1=13, k'=k-1=2
8473: * h' 1101 =2^3+2^2+0x2^1+2^0
8474: * >>k' 11
8475: * & 00000001
8476: * = 00000001
8477: * +1 = 00000010=2 = codtabm(14,3)
8478: * Reverse h=6 and m=16?
8479: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
8480: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
8481: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
8482: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
8483: * V3=decodtabm(14,3,2**4)=2
8484: * h'=13 1101 =2^3+2^2+0x2^1+2^0
8485: *(h-1) >> (j-1) 0011 =13 >> 2
8486: * &1 000000001
8487: * = 000000001
8488: * +1= 000000010 =2
8489: * 2211
8490: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
8491: * V3=2
8492: */
8493:
1.202 brouard 8494: /* /\* for(h=1; h <=100 ;h++){ *\/ */
8495: /* /\* printf("h=%2d ", h); *\/ */
8496: /* /\* for(k=1; k <=10; k++){ *\/ */
8497: /* /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */
8498: /* /\* codtab[h][k]=codtabm(h,k); *\/ */
8499: /* /\* } *\/ */
8500: /* /\* printf("\n"); *\/ */
8501: /* } */
1.197 brouard 8502: /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
8503: /* for(i=1; i <=pow(2,cptcoveff-k);i++){ /\* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 *\/ */
8504: /* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
8505: /* for(cpt=1; cpt <=pow(2,k-1); cpt++){ /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/ */
8506: /* h++; */
8507: /* if (h>m) */
8508: /* h=1; */
8509: /* codtab[h][k]=j; */
8510: /* /\* codtab[12][3]=1; *\/ */
8511: /* /\*codtab[h][Tvar[k]]=j;*\/ */
8512: /* /\* printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]); *\/ */
8513: /* } */
8514: /* } */
8515: /* } */
8516: /* } */
1.126 brouard 8517: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
8518: codtab[1][2]=1;codtab[2][2]=2; */
1.197 brouard 8519: /* for(i=1; i <=m ;i++){ */
8520: /* for(k=1; k <=cptcovn; k++){ */
8521: /* printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
8522: /* } */
8523: /* printf("\n"); */
8524: /* } */
8525: /* scanf("%d",i);*/
1.145 brouard 8526:
8527: free_ivector(Ndum,-1,NCOVMAX);
8528:
8529:
1.126 brouard 8530:
1.186 brouard 8531: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 8532: strcpy(optionfilegnuplot,optionfilefiname);
8533: if(mle==-3)
1.201 brouard 8534: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 8535: strcat(optionfilegnuplot,".gp");
8536:
8537: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
8538: printf("Problem with file %s",optionfilegnuplot);
8539: }
8540: else{
1.204 brouard 8541: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 8542: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 8543: //fprintf(ficgp,"set missing 'NaNq'\n");
8544: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 8545: }
8546: /* fclose(ficgp);*/
1.186 brouard 8547:
8548:
8549: /* Initialisation of --------- index.htm --------*/
1.126 brouard 8550:
8551: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
8552: if(mle==-3)
1.201 brouard 8553: strcat(optionfilehtm,"-MORT_");
1.126 brouard 8554: strcat(optionfilehtm,".htm");
8555: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 8556: printf("Problem with %s \n",optionfilehtm);
8557: exit(0);
1.126 brouard 8558: }
8559:
8560: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
8561: strcat(optionfilehtmcov,"-cov.htm");
8562: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
8563: printf("Problem with %s \n",optionfilehtmcov), exit(0);
8564: }
8565: else{
8566: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
8567: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 8568: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 8569: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
8570: }
8571:
1.213 brouard 8572: 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 8573: <hr size=\"2\" color=\"#EC5E5E\"> \n\
8574: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 8575: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 8576: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 8577: \n\
8578: <hr size=\"2\" color=\"#EC5E5E\">\
8579: <ul><li><h4>Parameter files</h4>\n\
8580: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
8581: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
8582: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
8583: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
8584: - Date and time at start: %s</ul>\n",\
8585: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
8586: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
8587: fileres,fileres,\
8588: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
8589: fflush(fichtm);
8590:
8591: strcpy(pathr,path);
8592: strcat(pathr,optionfilefiname);
1.184 brouard 8593: #ifdef WIN32
8594: _chdir(optionfilefiname); /* Move to directory named optionfile */
8595: #else
1.126 brouard 8596: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 8597: #endif
8598:
1.126 brouard 8599:
8600: /* Calculates basic frequencies. Computes observed prevalence at single age
8601: and prints on file fileres'p'. */
1.214 brouard 8602: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\
8603: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 8604:
8605: fprintf(fichtm,"\n");
8606: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
8607: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
8608: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
8609: imx,agemin,agemax,jmin,jmax,jmean);
8610: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
8611: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
8612: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
8613: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
8614: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
8615:
8616:
8617: /* For Powell, parameters are in a vector p[] starting at p[1]
8618: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
8619: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
8620:
8621: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 8622: /* For mortality only */
1.126 brouard 8623: if (mle==-3){
1.136 brouard 8624: ximort=matrix(1,NDIM,1,NDIM);
1.186 brouard 8625: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 8626: cens=ivector(1,n);
8627: ageexmed=vector(1,n);
8628: agecens=vector(1,n);
8629: dcwave=ivector(1,n);
8630:
8631: for (i=1; i<=imx; i++){
8632: dcwave[i]=-1;
8633: for (m=firstpass; m<=lastpass; m++)
8634: if (s[m][i]>nlstate) {
8635: dcwave[i]=m;
8636: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
8637: break;
8638: }
8639: }
8640:
8641: for (i=1; i<=imx; i++) {
8642: if (wav[i]>0){
8643: ageexmed[i]=agev[mw[1][i]][i];
8644: j=wav[i];
8645: agecens[i]=1.;
8646:
8647: if (ageexmed[i]> 1 && wav[i] > 0){
8648: agecens[i]=agev[mw[j][i]][i];
8649: cens[i]= 1;
8650: }else if (ageexmed[i]< 1)
8651: cens[i]= -1;
8652: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
8653: cens[i]=0 ;
8654: }
8655: else cens[i]=-1;
8656: }
8657:
8658: for (i=1;i<=NDIM;i++) {
8659: for (j=1;j<=NDIM;j++)
8660: ximort[i][j]=(i == j ? 1.0 : 0.0);
8661: }
8662:
1.145 brouard 8663: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 8664: /*printf("%lf %lf", p[1], p[2]);*/
8665:
8666:
1.136 brouard 8667: #ifdef GSL
8668: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 8669: #else
1.126 brouard 8670: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 8671: #endif
1.201 brouard 8672: strcpy(filerespow,"POW-MORT_");
8673: strcat(filerespow,fileresu);
1.126 brouard 8674: if((ficrespow=fopen(filerespow,"w"))==NULL) {
8675: printf("Problem with resultfile: %s\n", filerespow);
8676: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
8677: }
1.136 brouard 8678: #ifdef GSL
8679: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 8680: #else
1.126 brouard 8681: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 8682: #endif
1.126 brouard 8683: /* for (i=1;i<=nlstate;i++)
8684: for(j=1;j<=nlstate+ndeath;j++)
8685: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
8686: */
8687: fprintf(ficrespow,"\n");
1.136 brouard 8688: #ifdef GSL
8689: /* gsl starts here */
8690: T = gsl_multimin_fminimizer_nmsimplex;
8691: gsl_multimin_fminimizer *sfm = NULL;
8692: gsl_vector *ss, *x;
8693: gsl_multimin_function minex_func;
8694:
8695: /* Initial vertex size vector */
8696: ss = gsl_vector_alloc (NDIM);
8697:
8698: if (ss == NULL){
8699: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
8700: }
8701: /* Set all step sizes to 1 */
8702: gsl_vector_set_all (ss, 0.001);
8703:
8704: /* Starting point */
1.126 brouard 8705:
1.136 brouard 8706: x = gsl_vector_alloc (NDIM);
8707:
8708: if (x == NULL){
8709: gsl_vector_free(ss);
8710: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
8711: }
8712:
8713: /* Initialize method and iterate */
8714: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 8715: /* gsl_vector_set(x, 0, 0.0268); */
8716: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 8717: gsl_vector_set(x, 0, p[1]);
8718: gsl_vector_set(x, 1, p[2]);
8719:
8720: minex_func.f = &gompertz_f;
8721: minex_func.n = NDIM;
8722: minex_func.params = (void *)&p; /* ??? */
8723:
8724: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
8725: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
8726:
8727: printf("Iterations beginning .....\n\n");
8728: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
8729:
8730: iteri=0;
8731: while (rval == GSL_CONTINUE){
8732: iteri++;
8733: status = gsl_multimin_fminimizer_iterate(sfm);
8734:
8735: if (status) printf("error: %s\n", gsl_strerror (status));
8736: fflush(0);
8737:
8738: if (status)
8739: break;
8740:
8741: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
8742: ssval = gsl_multimin_fminimizer_size (sfm);
8743:
8744: if (rval == GSL_SUCCESS)
8745: printf ("converged to a local maximum at\n");
8746:
8747: printf("%5d ", iteri);
8748: for (it = 0; it < NDIM; it++){
8749: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
8750: }
8751: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
8752: }
8753:
8754: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
8755:
8756: gsl_vector_free(x); /* initial values */
8757: gsl_vector_free(ss); /* inital step size */
8758: for (it=0; it<NDIM; it++){
8759: p[it+1]=gsl_vector_get(sfm->x,it);
8760: fprintf(ficrespow," %.12lf", p[it]);
8761: }
8762: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
8763: #endif
8764: #ifdef POWELL
8765: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
8766: #endif
1.126 brouard 8767: fclose(ficrespow);
8768:
1.203 brouard 8769: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 8770:
8771: for(i=1; i <=NDIM; i++)
8772: for(j=i+1;j<=NDIM;j++)
8773: matcov[i][j]=matcov[j][i];
8774:
8775: printf("\nCovariance matrix\n ");
1.203 brouard 8776: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 8777: for(i=1; i <=NDIM; i++) {
8778: for(j=1;j<=NDIM;j++){
8779: printf("%f ",matcov[i][j]);
1.203 brouard 8780: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 8781: }
1.203 brouard 8782: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 8783: }
8784:
8785: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 8786: for (i=1;i<=NDIM;i++) {
1.126 brouard 8787: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 8788: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
8789: }
1.126 brouard 8790: lsurv=vector(1,AGESUP);
8791: lpop=vector(1,AGESUP);
8792: tpop=vector(1,AGESUP);
8793: lsurv[agegomp]=100000;
8794:
8795: for (k=agegomp;k<=AGESUP;k++) {
8796: agemortsup=k;
8797: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
8798: }
8799:
8800: for (k=agegomp;k<agemortsup;k++)
8801: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
8802:
8803: for (k=agegomp;k<agemortsup;k++){
8804: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
8805: sumlpop=sumlpop+lpop[k];
8806: }
8807:
8808: tpop[agegomp]=sumlpop;
8809: for (k=agegomp;k<(agemortsup-3);k++){
8810: /* tpop[k+1]=2;*/
8811: tpop[k+1]=tpop[k]-lpop[k];
8812: }
8813:
8814:
8815: printf("\nAge lx qx dx Lx Tx e(x)\n");
8816: for (k=agegomp;k<(agemortsup-2);k++)
8817: 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]);
8818:
8819:
8820: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 8821: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
8822: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
8823: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
8824: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
8825: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
8826: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
8827: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
8828: }else
1.201 brouard 8829: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
8830: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 8831: stepm, weightopt,\
8832: model,imx,p,matcov,agemortsup);
8833:
8834: free_vector(lsurv,1,AGESUP);
8835: free_vector(lpop,1,AGESUP);
8836: free_vector(tpop,1,AGESUP);
1.136 brouard 8837: #ifdef GSL
8838: free_ivector(cens,1,n);
8839: free_vector(agecens,1,n);
8840: free_ivector(dcwave,1,n);
8841: free_matrix(ximort,1,NDIM,1,NDIM);
8842: #endif
1.186 brouard 8843: } /* Endof if mle==-3 mortality only */
1.205 brouard 8844: /* Standard */
8845: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
8846: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
8847: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 8848: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 8849: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
8850: for (k=1; k<=npar;k++)
8851: printf(" %d %8.5f",k,p[k]);
8852: printf("\n");
1.205 brouard 8853: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
8854: /* mlikeli uses func not funcone */
8855: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
8856: }
8857: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
8858: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
8859: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
8860: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
8861: }
8862: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 8863: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
8864: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
8865: for (k=1; k<=npar;k++)
8866: printf(" %d %8.5f",k,p[k]);
8867: printf("\n");
8868:
8869: /*--------- results files --------------*/
1.192 brouard 8870: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
1.126 brouard 8871:
8872:
8873: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8874: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8875: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8876: for(i=1,jk=1; i <=nlstate; i++){
8877: for(k=1; k <=(nlstate+ndeath); k++){
8878: if (k != i) {
8879: printf("%d%d ",i,k);
8880: fprintf(ficlog,"%d%d ",i,k);
8881: fprintf(ficres,"%1d%1d ",i,k);
8882: for(j=1; j <=ncovmodel; j++){
1.190 brouard 8883: printf("%12.7f ",p[jk]);
8884: fprintf(ficlog,"%12.7f ",p[jk]);
8885: fprintf(ficres,"%12.7f ",p[jk]);
1.126 brouard 8886: jk++;
8887: }
8888: printf("\n");
8889: fprintf(ficlog,"\n");
8890: fprintf(ficres,"\n");
8891: }
8892: }
8893: }
1.203 brouard 8894: if(mle != 0){
8895: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 8896: ftolhess=ftol; /* Usually correct */
1.203 brouard 8897: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
8898: 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");
8899: 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");
8900: for(i=1,jk=1; i <=nlstate; i++){
8901: for(k=1; k <=(nlstate+ndeath); k++){
8902: if (k != i) {
8903: printf("%d%d ",i,k);
8904: fprintf(ficlog,"%d%d ",i,k);
8905: for(j=1; j <=ncovmodel; j++){
8906: 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]));
8907: 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]));
8908: jk++;
8909: }
8910: printf("\n");
8911: fprintf(ficlog,"\n");
1.193 brouard 8912: }
8913: }
8914: }
1.203 brouard 8915: } /* end of hesscov and Wald tests */
1.193 brouard 8916:
1.203 brouard 8917: /* */
1.126 brouard 8918: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
8919: printf("# Scales (for hessian or gradient estimation)\n");
8920: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
8921: for(i=1,jk=1; i <=nlstate; i++){
8922: for(j=1; j <=nlstate+ndeath; j++){
8923: if (j!=i) {
8924: fprintf(ficres,"%1d%1d",i,j);
8925: printf("%1d%1d",i,j);
8926: fprintf(ficlog,"%1d%1d",i,j);
8927: for(k=1; k<=ncovmodel;k++){
8928: printf(" %.5e",delti[jk]);
8929: fprintf(ficlog," %.5e",delti[jk]);
8930: fprintf(ficres," %.5e",delti[jk]);
8931: jk++;
8932: }
8933: printf("\n");
8934: fprintf(ficlog,"\n");
8935: fprintf(ficres,"\n");
8936: }
8937: }
8938: }
8939:
8940: 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 8941: if(mle >= 1) /* To big for the screen */
1.126 brouard 8942: 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");
8943: 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");
8944: /* # 121 Var(a12)\n\ */
8945: /* # 122 Cov(b12,a12) Var(b12)\n\ */
8946: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
8947: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
8948: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
8949: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
8950: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
8951: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
8952:
8953:
8954: /* Just to have a covariance matrix which will be more understandable
8955: even is we still don't want to manage dictionary of variables
8956: */
8957: for(itimes=1;itimes<=2;itimes++){
8958: jj=0;
8959: for(i=1; i <=nlstate; i++){
8960: for(j=1; j <=nlstate+ndeath; j++){
8961: if(j==i) continue;
8962: for(k=1; k<=ncovmodel;k++){
8963: jj++;
8964: ca[0]= k+'a'-1;ca[1]='\0';
8965: if(itimes==1){
8966: if(mle>=1)
8967: printf("#%1d%1d%d",i,j,k);
8968: fprintf(ficlog,"#%1d%1d%d",i,j,k);
8969: fprintf(ficres,"#%1d%1d%d",i,j,k);
8970: }else{
8971: if(mle>=1)
8972: printf("%1d%1d%d",i,j,k);
8973: fprintf(ficlog,"%1d%1d%d",i,j,k);
8974: fprintf(ficres,"%1d%1d%d",i,j,k);
8975: }
8976: ll=0;
8977: for(li=1;li <=nlstate; li++){
8978: for(lj=1;lj <=nlstate+ndeath; lj++){
8979: if(lj==li) continue;
8980: for(lk=1;lk<=ncovmodel;lk++){
8981: ll++;
8982: if(ll<=jj){
8983: cb[0]= lk +'a'-1;cb[1]='\0';
8984: if(ll<jj){
8985: if(itimes==1){
8986: if(mle>=1)
8987: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
8988: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
8989: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
8990: }else{
8991: if(mle>=1)
8992: printf(" %.5e",matcov[jj][ll]);
8993: fprintf(ficlog," %.5e",matcov[jj][ll]);
8994: fprintf(ficres," %.5e",matcov[jj][ll]);
8995: }
8996: }else{
8997: if(itimes==1){
8998: if(mle>=1)
8999: printf(" Var(%s%1d%1d)",ca,i,j);
9000: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
9001: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
9002: }else{
9003: if(mle>=1)
1.203 brouard 9004: printf(" %.7e",matcov[jj][ll]);
9005: fprintf(ficlog," %.7e",matcov[jj][ll]);
9006: fprintf(ficres," %.7e",matcov[jj][ll]);
1.126 brouard 9007: }
9008: }
9009: }
9010: } /* end lk */
9011: } /* end lj */
9012: } /* end li */
9013: if(mle>=1)
9014: printf("\n");
9015: fprintf(ficlog,"\n");
9016: fprintf(ficres,"\n");
9017: numlinepar++;
9018: } /* end k*/
9019: } /*end j */
9020: } /* end i */
9021: } /* end itimes */
9022:
9023: fflush(ficlog);
9024: fflush(ficres);
1.209 brouard 9025: while(fgets(line, MAXLINE, ficpar)) {
9026: /* If line starts with a # it is a comment */
9027: if (line[0] == '#') {
9028: numlinepar++;
1.141 brouard 9029: fputs(line,stdout);
1.126 brouard 9030: fputs(line,ficparo);
1.209 brouard 9031: fputs(line,ficlog);
9032: continue;
9033: }else
9034: break;
9035: }
9036:
9037: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
9038: /* ungetc(c,ficpar); */
9039: /* fgets(line, MAXLINE, ficpar); */
9040: /* fputs(line,stdout); */
9041: /* fputs(line,ficparo); */
9042: /* } */
9043: /* ungetc(c,ficpar); */
1.126 brouard 9044:
9045: estepm=0;
1.209 brouard 9046: 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){
9047:
9048: if (num_filled != 6) {
9049: printf("Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n");
9050: printf("but line=%s\n",line);
9051: goto end;
9052: }
9053: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
9054: }
9055: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
9056: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
9057:
9058: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 9059: if (estepm==0 || estepm < stepm) estepm=stepm;
9060: if (fage <= 2) {
9061: bage = ageminpar;
9062: fage = agemaxpar;
9063: }
9064:
9065: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 9066: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
9067: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.186 brouard 9068:
9069: /* Other stuffs, more or less useful */
1.126 brouard 9070: while((c=getc(ficpar))=='#' && c!= EOF){
9071: ungetc(c,ficpar);
9072: fgets(line, MAXLINE, ficpar);
1.141 brouard 9073: fputs(line,stdout);
1.126 brouard 9074: fputs(line,ficparo);
9075: }
9076: ungetc(c,ficpar);
9077:
9078: 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);
9079: 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);
9080: 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);
9081: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
9082: 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);
9083:
9084: while((c=getc(ficpar))=='#' && c!= EOF){
9085: ungetc(c,ficpar);
9086: fgets(line, MAXLINE, ficpar);
1.141 brouard 9087: fputs(line,stdout);
1.126 brouard 9088: fputs(line,ficparo);
9089: }
9090: ungetc(c,ficpar);
9091:
9092:
9093: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
9094: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
9095:
9096: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 9097: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 9098: fprintf(ficparo,"pop_based=%d\n",popbased);
9099: fprintf(ficres,"pop_based=%d\n",popbased);
9100:
9101: while((c=getc(ficpar))=='#' && c!= EOF){
9102: ungetc(c,ficpar);
9103: fgets(line, MAXLINE, ficpar);
1.141 brouard 9104: fputs(line,stdout);
1.126 brouard 9105: fputs(line,ficparo);
9106: }
9107: ungetc(c,ficpar);
9108:
9109: 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);
9110: 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);
9111: 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);
9112: 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);
9113: 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);
9114: /* day and month of proj2 are not used but only year anproj2.*/
9115:
1.217 ! brouard 9116: while((c=getc(ficpar))=='#' && c!= EOF){
! 9117: ungetc(c,ficpar);
! 9118: fgets(line, MAXLINE, ficpar);
! 9119: fputs(line,stdout);
! 9120: fputs(line,ficparo);
! 9121: }
! 9122: ungetc(c,ficpar);
! 9123:
! 9124: 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);
! 9125: fscanf(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);
! 9126: fscanf(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);
! 9127: fscanf(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);
! 9128: /* day and month of proj2 are not used but only year anproj2.*/
1.126 brouard 9129:
9130:
1.145 brouard 9131: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
9132: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 9133:
9134: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 9135: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
9136: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
9137: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9138: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
9139: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
9140: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9141: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
9142: }else
1.211 brouard 9143: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, pathc,p);
1.126 brouard 9144:
1.201 brouard 9145: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\
1.217 ! brouard 9146: model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
1.213 brouard 9147: jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
1.126 brouard 9148:
9149: /*------------ free_vector -------------*/
9150: /* chdir(path); */
9151:
1.215 brouard 9152: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
9153: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
9154: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
9155: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.126 brouard 9156: free_lvector(num,1,n);
9157: free_vector(agedc,1,n);
9158: /*free_matrix(covar,0,NCOVMAX,1,n);*/
9159: /*free_matrix(covar,1,NCOVMAX,1,n);*/
9160: fclose(ficparo);
9161: fclose(ficres);
9162:
9163:
1.186 brouard 9164: /* Other results (useful)*/
9165:
9166:
1.126 brouard 9167: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 9168: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
9169: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 9170: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 9171: fclose(ficrespl);
9172:
1.217 ! brouard 9173: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
! 9174: /*#include "prevlim.h"*/ /* Use ficresplb, ficlog */
! 9175: bprlim=matrix(1,nlstate,1,nlstate);
! 9176: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
! 9177: fclose(ficresplb);
! 9178:
! 9179:
1.145 brouard 9180: #ifdef FREEEXIT2
9181: #include "freeexit2.h"
9182: #endif
9183:
1.126 brouard 9184: /*------------- h Pij x at various ages ------------*/
1.180 brouard 9185: /*#include "hpijx.h"*/
9186: hPijx(p, bage, fage);
1.145 brouard 9187: fclose(ficrespij);
1.126 brouard 9188:
1.217 ! brouard 9189: hBijx(p, bage, fage);
! 9190: fclose(ficrespijb);
! 9191:
1.145 brouard 9192: /*-------------- Variance of one-step probabilities---*/
9193: k=1;
1.126 brouard 9194: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
9195:
9196:
9197: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
9198: for(i=1;i<=AGESUP;i++)
9199: for(j=1;j<=NCOVMAX;j++)
9200: for(k=1;k<=NCOVMAX;k++)
9201: probs[i][j][k]=0.;
9202:
9203: /*---------- Forecasting ------------------*/
9204: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
9205: if(prevfcast==1){
9206: /* if(stepm ==1){*/
1.201 brouard 9207: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 9208: }
1.217 ! brouard 9209: if(backcast==1){
! 9210: prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff);
! 9211: }
! 9212: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
! 9213: /* } */
! 9214: /* else{ */
! 9215: /* erreur=108; */
! 9216: /* printf("Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
! 9217: /* fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
! 9218: /* } */
! 9219:
1.186 brouard 9220:
9221: /* ------ Other prevalence ratios------------ */
1.126 brouard 9222:
1.127 brouard 9223: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
9224:
9225: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
9226: /* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
9227: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
9228: */
1.215 brouard 9229: free_ivector(wav,1,imx);
9230: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
9231: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
9232: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
9233:
1.126 brouard 9234:
1.127 brouard 9235: if (mobilav!=0) {
9236: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
9237: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
9238: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
9239: printf(" Error in movingaverage mobilav=%d\n",mobilav);
9240: }
1.126 brouard 9241: }
9242:
9243:
1.127 brouard 9244: /*---------- Health expectancies, no variances ------------*/
9245:
1.201 brouard 9246: strcpy(filerese,"E_");
9247: strcat(filerese,fileresu);
1.126 brouard 9248: if((ficreseij=fopen(filerese,"w"))==NULL) {
9249: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
9250: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
9251: }
1.208 brouard 9252: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
9253: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.145 brouard 9254: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
9255: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
9256:
9257: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 9258: fprintf(ficreseij,"\n#****** ");
9259: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 9260: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.127 brouard 9261: }
9262: fprintf(ficreseij,"******\n");
9263:
9264: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
9265: oldm=oldms;savm=savms;
9266: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
9267:
9268: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 9269: /*}*/
1.127 brouard 9270: }
9271: fclose(ficreseij);
1.208 brouard 9272: printf("done evsij\n");fflush(stdout);
9273: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.127 brouard 9274:
9275: /*---------- Health expectancies and variances ------------*/
9276:
9277:
1.201 brouard 9278: strcpy(filerest,"T_");
9279: strcat(filerest,fileresu);
1.127 brouard 9280: if((ficrest=fopen(filerest,"w"))==NULL) {
9281: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
9282: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
9283: }
1.208 brouard 9284: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
9285: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.127 brouard 9286:
1.126 brouard 9287:
1.201 brouard 9288: strcpy(fileresstde,"STDE_");
9289: strcat(fileresstde,fileresu);
1.126 brouard 9290: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
9291: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
9292: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
9293: }
1.208 brouard 9294: printf(" Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
9295: fprintf(ficlog," Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 9296:
1.201 brouard 9297: strcpy(filerescve,"CVE_");
9298: strcat(filerescve,fileresu);
1.126 brouard 9299: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
9300: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
9301: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
9302: }
1.208 brouard 9303: printf(" Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
9304: fprintf(ficlog," Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 9305:
1.201 brouard 9306: strcpy(fileresv,"V_");
9307: strcat(fileresv,fileresu);
1.126 brouard 9308: if((ficresvij=fopen(fileresv,"w"))==NULL) {
9309: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
9310: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
9311: }
1.208 brouard 9312: printf(" Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(stdout);
9313: fprintf(ficlog," Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 9314:
1.145 brouard 9315: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
9316: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
9317:
9318: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.208 brouard 9319: fprintf(ficrest,"\n#****** ");
9320: for(j=1;j<=cptcoveff;j++)
9321: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9322: fprintf(ficrest,"******\n");
9323:
9324: fprintf(ficresstdeij,"\n#****** ");
9325: fprintf(ficrescveij,"\n#****** ");
9326: for(j=1;j<=cptcoveff;j++) {
9327: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9328: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9329: }
9330: fprintf(ficresstdeij,"******\n");
9331: fprintf(ficrescveij,"******\n");
9332:
9333: fprintf(ficresvij,"\n#****** ");
9334: for(j=1;j<=cptcoveff;j++)
9335: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9336: fprintf(ficresvij,"******\n");
9337:
9338: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
9339: oldm=oldms;savm=savms;
9340: printf(" cvevsij %d, ",k);
9341: fprintf(ficlog, " cvevsij %d, ",k);
9342: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
9343: printf(" end cvevsij \n ");
9344: fprintf(ficlog, " end cvevsij \n ");
9345:
9346: /*
9347: */
9348: /* goto endfree; */
9349:
9350: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
9351: pstamp(ficrest);
9352:
9353:
9354: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
9355: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
9356: cptcod= 0; /* To be deleted */
9357: printf("varevsij %d \n",vpopbased);
9358: fprintf(ficlog, "varevsij %d \n",vpopbased);
1.209 brouard 9359: 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 */
1.208 brouard 9360: 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 ");
9361: if(vpopbased==1)
9362: 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);
9363: else
9364: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
9365: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
9366: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
9367: fprintf(ficrest,"\n");
9368: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
9369: epj=vector(1,nlstate+1);
9370: printf("Computing age specific period (stable) prevalences in each health state \n");
9371: fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
9372: for(age=bage; age <=fage ;age++){
1.209 brouard 9373: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
1.208 brouard 9374: if (vpopbased==1) {
9375: if(mobilav ==0){
9376: for(i=1; i<=nlstate;i++)
9377: prlim[i][i]=probs[(int)age][i][k];
9378: }else{ /* mobilav */
9379: for(i=1; i<=nlstate;i++)
9380: prlim[i][i]=mobaverage[(int)age][i][k];
1.126 brouard 9381: }
1.208 brouard 9382: }
9383:
9384: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
9385: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
9386: /* printf(" age %4.0f ",age); */
9387: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
9388: for(i=1, epj[j]=0.;i <=nlstate;i++) {
9389: epj[j] += prlim[i][i]*eij[i][j][(int)age];
9390: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
9391: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
1.126 brouard 9392: }
1.208 brouard 9393: epj[nlstate+1] +=epj[j];
9394: }
9395: /* printf(" age %4.0f \n",age); */
9396:
9397: for(i=1, vepp=0.;i <=nlstate;i++)
9398: for(j=1;j <=nlstate;j++)
9399: vepp += vareij[i][j][(int)age];
9400: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
9401: for(j=1;j <=nlstate;j++){
9402: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
1.126 brouard 9403: }
1.208 brouard 9404: fprintf(ficrest,"\n");
1.126 brouard 9405: }
1.208 brouard 9406: } /* End vpopbased */
9407: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
9408: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
9409: free_vector(epj,1,nlstate+1);
9410: printf("done \n");fflush(stdout);
9411: fprintf(ficlog,"done\n");fflush(ficlog);
9412:
1.145 brouard 9413: /*}*/
1.208 brouard 9414: } /* End k */
1.126 brouard 9415: free_vector(weight,1,n);
1.145 brouard 9416: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 9417: free_imatrix(s,1,maxwav+1,1,n);
9418: free_matrix(anint,1,maxwav,1,n);
9419: free_matrix(mint,1,maxwav,1,n);
9420: free_ivector(cod,1,n);
9421: free_ivector(tab,1,NCOVMAX);
9422: fclose(ficresstdeij);
9423: fclose(ficrescveij);
9424: fclose(ficresvij);
9425: fclose(ficrest);
1.208 brouard 9426: printf("done Health expectancies\n");fflush(stdout);
9427: fprintf(ficlog,"done Health expectancies\n");fflush(ficlog);
1.126 brouard 9428: fclose(ficpar);
9429:
9430: /*------- Variance of period (stable) prevalence------*/
9431:
1.201 brouard 9432: strcpy(fileresvpl,"VPL_");
9433: strcat(fileresvpl,fileresu);
1.126 brouard 9434: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
9435: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
9436: exit(0);
9437: }
1.208 brouard 9438: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
9439: fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.126 brouard 9440:
1.145 brouard 9441: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
9442: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
9443:
9444: for (k=1; k <= (int) pow(2,cptcoveff); k++){
9445: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 9446: for(j=1;j<=cptcoveff;j++)
1.200 brouard 9447: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 9448: fprintf(ficresvpl,"******\n");
9449:
9450: varpl=matrix(1,nlstate,(int) bage, (int) fage);
9451: oldm=oldms;savm=savms;
1.209 brouard 9452: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
1.126 brouard 9453: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 9454: /*}*/
1.126 brouard 9455: }
9456:
9457: fclose(ficresvpl);
1.208 brouard 9458: printf("done variance-covariance of period prevalence\n");fflush(stdout);
9459: fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
1.126 brouard 9460:
9461: /*---------- End : free ----------------*/
9462: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
9463: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
9464: } /* mle==-3 arrives here for freeing */
1.164 brouard 9465: /* endfree:*/
1.141 brouard 9466: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 9467: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
9468: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
9469: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
9470: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
9471: free_matrix(covar,0,NCOVMAX,1,n);
9472: free_matrix(matcov,1,npar,1,npar);
1.203 brouard 9473: free_matrix(hess,1,npar,1,npar);
1.126 brouard 9474: /*free_vector(delti,1,npar);*/
9475: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
9476: free_matrix(agev,1,maxwav,1,imx);
9477: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
9478:
1.145 brouard 9479: free_ivector(ncodemax,1,NCOVMAX);
1.192 brouard 9480: free_ivector(ncodemaxwundef,1,NCOVMAX);
1.145 brouard 9481: free_ivector(Tvar,1,NCOVMAX);
9482: free_ivector(Tprod,1,NCOVMAX);
9483: free_ivector(Tvaraff,1,NCOVMAX);
9484: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 9485:
9486: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
1.200 brouard 9487: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 9488: fflush(fichtm);
9489: fflush(ficgp);
9490:
9491:
9492: if((nberr >0) || (nbwarn>0)){
1.216 brouard 9493: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
9494: 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 9495: }else{
9496: printf("End of Imach\n");
9497: fprintf(ficlog,"End of Imach\n");
9498: }
9499: printf("See log file on %s\n",filelog);
9500: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 9501: /*(void) gettimeofday(&end_time,&tzp);*/
9502: rend_time = time(NULL);
9503: end_time = *localtime(&rend_time);
9504: /* tml = *localtime(&end_time.tm_sec); */
9505: strcpy(strtend,asctime(&end_time));
1.126 brouard 9506: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
9507: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 9508: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 9509:
1.157 brouard 9510: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
9511: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
9512: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 9513: /* printf("Total time was %d uSec.\n", total_usecs);*/
9514: /* if(fileappend(fichtm,optionfilehtm)){ */
9515: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
9516: fclose(fichtm);
9517: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
9518: fclose(fichtmcov);
9519: fclose(ficgp);
9520: fclose(ficlog);
9521: /*------ End -----------*/
9522:
9523:
9524: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 9525: #ifdef WIN32
9526: if (_chdir(pathcd) != 0)
9527: printf("Can't move to directory %s!\n",path);
9528: if(_getcwd(pathcd,MAXLINE) > 0)
9529: #else
1.126 brouard 9530: if(chdir(pathcd) != 0)
1.184 brouard 9531: printf("Can't move to directory %s!\n", path);
9532: if (getcwd(pathcd, MAXLINE) > 0)
9533: #endif
1.126 brouard 9534: printf("Current directory %s!\n",pathcd);
9535: /*strcat(plotcmd,CHARSEPARATOR);*/
9536: sprintf(plotcmd,"gnuplot");
1.157 brouard 9537: #ifdef _WIN32
1.126 brouard 9538: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
9539: #endif
9540: if(!stat(plotcmd,&info)){
1.158 brouard 9541: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 9542: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 9543: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 9544: }else
9545: strcpy(pplotcmd,plotcmd);
1.157 brouard 9546: #ifdef __unix
1.126 brouard 9547: strcpy(plotcmd,GNUPLOTPROGRAM);
9548: if(!stat(plotcmd,&info)){
1.158 brouard 9549: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 9550: }else
9551: strcpy(pplotcmd,plotcmd);
9552: #endif
9553: }else
9554: strcpy(pplotcmd,plotcmd);
9555:
9556: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 9557: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 9558:
9559: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 9560: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 9561: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 9562: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 9563: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 9564: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 9565: }
1.158 brouard 9566: printf(" Successful, please wait...");
1.126 brouard 9567: while (z[0] != 'q') {
9568: /* chdir(path); */
1.154 brouard 9569: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 9570: scanf("%s",z);
9571: /* if (z[0] == 'c') system("./imach"); */
9572: if (z[0] == 'e') {
1.158 brouard 9573: #ifdef __APPLE__
1.152 brouard 9574: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 9575: #elif __linux
9576: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 9577: #else
1.152 brouard 9578: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 9579: #endif
9580: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
9581: system(pplotcmd);
1.126 brouard 9582: }
9583: else if (z[0] == 'g') system(plotcmd);
9584: else if (z[0] == 'q') exit(0);
9585: }
9586: end:
9587: while (z[0] != 'q') {
1.195 brouard 9588: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 9589: scanf("%s",z);
9590: }
9591: }
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