Annotation of imach/src/imach.c, revision 1.219
1.219 ! brouard 1: /* $Id: imach.c,v 1.218 2016/02/12 11:29:23 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.219 ! brouard 4: Revision 1.218 2016/02/12 11:29:23 brouard
! 5: Summary: 0.99 Back projections
! 6:
1.218 brouard 7: Revision 1.217 2015/12/23 17:18:31 brouard
8: Summary: Experimental backcast
9:
1.217 brouard 10: Revision 1.216 2015/12/18 17:32:11 brouard
11: Summary: 0.98r4 Warning and status=-2
12:
13: Version 0.98r4 is now:
14: - displaying an error when status is -1, date of interview unknown and date of death known;
15: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
16: Older changes concerning s=-2, dating from 2005 have been supersed.
17:
1.216 brouard 18: Revision 1.215 2015/12/16 08:52:24 brouard
19: Summary: 0.98r4 working
20:
1.215 brouard 21: Revision 1.214 2015/12/16 06:57:54 brouard
22: Summary: temporary not working
23:
1.214 brouard 24: Revision 1.213 2015/12/11 18:22:17 brouard
25: Summary: 0.98r4
26:
1.213 brouard 27: Revision 1.212 2015/11/21 12:47:24 brouard
28: Summary: minor typo
29:
1.212 brouard 30: Revision 1.211 2015/11/21 12:41:11 brouard
31: Summary: 0.98r3 with some graph of projected cross-sectional
32:
33: Author: Nicolas Brouard
34:
1.211 brouard 35: Revision 1.210 2015/11/18 17:41:20 brouard
36: Summary: Start working on projected prevalences
37:
1.210 brouard 38: Revision 1.209 2015/11/17 22:12:03 brouard
39: Summary: Adding ftolpl parameter
40: Author: N Brouard
41:
42: We had difficulties to get smoothed confidence intervals. It was due
43: to the period prevalence which wasn't computed accurately. The inner
44: parameter ftolpl is now an outer parameter of the .imach parameter
45: file after estepm. If ftolpl is small 1.e-4 and estepm too,
46: computation are long.
47:
1.209 brouard 48: Revision 1.208 2015/11/17 14:31:57 brouard
49: Summary: temporary
50:
1.208 brouard 51: Revision 1.207 2015/10/27 17:36:57 brouard
52: *** empty log message ***
53:
1.207 brouard 54: Revision 1.206 2015/10/24 07:14:11 brouard
55: *** empty log message ***
56:
1.206 brouard 57: Revision 1.205 2015/10/23 15:50:53 brouard
58: Summary: 0.98r3 some clarification for graphs on likelihood contributions
59:
1.205 brouard 60: Revision 1.204 2015/10/01 16:20:26 brouard
61: Summary: Some new graphs of contribution to likelihood
62:
1.204 brouard 63: Revision 1.203 2015/09/30 17:45:14 brouard
64: Summary: looking at better estimation of the hessian
65:
66: Also a better criteria for convergence to the period prevalence And
67: therefore adding the number of years needed to converge. (The
68: prevalence in any alive state shold sum to one
69:
1.203 brouard 70: Revision 1.202 2015/09/22 19:45:16 brouard
71: Summary: Adding some overall graph on contribution to likelihood. Might change
72:
1.202 brouard 73: Revision 1.201 2015/09/15 17:34:58 brouard
74: Summary: 0.98r0
75:
76: - Some new graphs like suvival functions
77: - Some bugs fixed like model=1+age+V2.
78:
1.201 brouard 79: Revision 1.200 2015/09/09 16:53:55 brouard
80: Summary: Big bug thanks to Flavia
81:
82: Even model=1+age+V2. did not work anymore
83:
1.200 brouard 84: Revision 1.199 2015/09/07 14:09:23 brouard
85: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
86:
1.199 brouard 87: Revision 1.198 2015/09/03 07:14:39 brouard
88: Summary: 0.98q5 Flavia
89:
1.198 brouard 90: Revision 1.197 2015/09/01 18:24:39 brouard
91: *** empty log message ***
92:
1.197 brouard 93: Revision 1.196 2015/08/18 23:17:52 brouard
94: Summary: 0.98q5
95:
1.196 brouard 96: Revision 1.195 2015/08/18 16:28:39 brouard
97: Summary: Adding a hack for testing purpose
98:
99: After reading the title, ftol and model lines, if the comment line has
100: a q, starting with #q, the answer at the end of the run is quit. It
101: permits to run test files in batch with ctest. The former workaround was
102: $ echo q | imach foo.imach
103:
1.195 brouard 104: Revision 1.194 2015/08/18 13:32:00 brouard
105: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
106:
1.194 brouard 107: Revision 1.193 2015/08/04 07:17:42 brouard
108: Summary: 0.98q4
109:
1.193 brouard 110: Revision 1.192 2015/07/16 16:49:02 brouard
111: Summary: Fixing some outputs
112:
1.192 brouard 113: Revision 1.191 2015/07/14 10:00:33 brouard
114: Summary: Some fixes
115:
1.191 brouard 116: Revision 1.190 2015/05/05 08:51:13 brouard
117: Summary: Adding digits in output parameters (7 digits instead of 6)
118:
119: Fix 1+age+.
120:
1.190 brouard 121: Revision 1.189 2015/04/30 14:45:16 brouard
122: Summary: 0.98q2
123:
1.189 brouard 124: Revision 1.188 2015/04/30 08:27:53 brouard
125: *** empty log message ***
126:
1.188 brouard 127: Revision 1.187 2015/04/29 09:11:15 brouard
128: *** empty log message ***
129:
1.187 brouard 130: Revision 1.186 2015/04/23 12:01:52 brouard
131: Summary: V1*age is working now, version 0.98q1
132:
133: Some codes had been disabled in order to simplify and Vn*age was
134: working in the optimization phase, ie, giving correct MLE parameters,
135: but, as usual, outputs were not correct and program core dumped.
136:
1.186 brouard 137: Revision 1.185 2015/03/11 13:26:42 brouard
138: Summary: Inclusion of compile and links command line for Intel Compiler
139:
1.185 brouard 140: Revision 1.184 2015/03/11 11:52:39 brouard
141: Summary: Back from Windows 8. Intel Compiler
142:
1.184 brouard 143: Revision 1.183 2015/03/10 20:34:32 brouard
144: Summary: 0.98q0, trying with directest, mnbrak fixed
145:
146: We use directest instead of original Powell test; probably no
147: incidence on the results, but better justifications;
148: We fixed Numerical Recipes mnbrak routine which was wrong and gave
149: wrong results.
150:
1.183 brouard 151: Revision 1.182 2015/02/12 08:19:57 brouard
152: Summary: Trying to keep directest which seems simpler and more general
153: Author: Nicolas Brouard
154:
1.182 brouard 155: Revision 1.181 2015/02/11 23:22:24 brouard
156: Summary: Comments on Powell added
157:
158: Author:
159:
1.181 brouard 160: Revision 1.180 2015/02/11 17:33:45 brouard
161: Summary: Finishing move from main to function (hpijx and prevalence_limit)
162:
1.180 brouard 163: Revision 1.179 2015/01/04 09:57:06 brouard
164: Summary: back to OS/X
165:
1.179 brouard 166: Revision 1.178 2015/01/04 09:35:48 brouard
167: *** empty log message ***
168:
1.178 brouard 169: Revision 1.177 2015/01/03 18:40:56 brouard
170: Summary: Still testing ilc32 on OSX
171:
1.177 brouard 172: Revision 1.176 2015/01/03 16:45:04 brouard
173: *** empty log message ***
174:
1.176 brouard 175: Revision 1.175 2015/01/03 16:33:42 brouard
176: *** empty log message ***
177:
1.175 brouard 178: Revision 1.174 2015/01/03 16:15:49 brouard
179: Summary: Still in cross-compilation
180:
1.174 brouard 181: Revision 1.173 2015/01/03 12:06:26 brouard
182: Summary: trying to detect cross-compilation
183:
1.173 brouard 184: Revision 1.172 2014/12/27 12:07:47 brouard
185: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
186:
1.172 brouard 187: Revision 1.171 2014/12/23 13:26:59 brouard
188: Summary: Back from Visual C
189:
190: Still problem with utsname.h on Windows
191:
1.171 brouard 192: Revision 1.170 2014/12/23 11:17:12 brouard
193: Summary: Cleaning some \%% back to %%
194:
195: The escape was mandatory for a specific compiler (which one?), but too many warnings.
196:
1.170 brouard 197: Revision 1.169 2014/12/22 23:08:31 brouard
198: Summary: 0.98p
199:
200: Outputs some informations on compiler used, OS etc. Testing on different platforms.
201:
1.169 brouard 202: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 203: Summary: update
1.169 brouard 204:
1.168 brouard 205: Revision 1.167 2014/12/22 13:50:56 brouard
206: Summary: Testing uname and compiler version and if compiled 32 or 64
207:
208: Testing on Linux 64
209:
1.167 brouard 210: Revision 1.166 2014/12/22 11:40:47 brouard
211: *** empty log message ***
212:
1.166 brouard 213: Revision 1.165 2014/12/16 11:20:36 brouard
214: Summary: After compiling on Visual C
215:
216: * imach.c (Module): Merging 1.61 to 1.162
217:
1.165 brouard 218: Revision 1.164 2014/12/16 10:52:11 brouard
219: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
220:
221: * imach.c (Module): Merging 1.61 to 1.162
222:
1.164 brouard 223: Revision 1.163 2014/12/16 10:30:11 brouard
224: * imach.c (Module): Merging 1.61 to 1.162
225:
1.163 brouard 226: Revision 1.162 2014/09/25 11:43:39 brouard
227: Summary: temporary backup 0.99!
228:
1.162 brouard 229: Revision 1.1 2014/09/16 11:06:58 brouard
230: Summary: With some code (wrong) for nlopt
231:
232: Author:
233:
234: Revision 1.161 2014/09/15 20:41:41 brouard
235: Summary: Problem with macro SQR on Intel compiler
236:
1.161 brouard 237: Revision 1.160 2014/09/02 09:24:05 brouard
238: *** empty log message ***
239:
1.160 brouard 240: Revision 1.159 2014/09/01 10:34:10 brouard
241: Summary: WIN32
242: Author: Brouard
243:
1.159 brouard 244: Revision 1.158 2014/08/27 17:11:51 brouard
245: *** empty log message ***
246:
1.158 brouard 247: Revision 1.157 2014/08/27 16:26:55 brouard
248: Summary: Preparing windows Visual studio version
249: Author: Brouard
250:
251: In order to compile on Visual studio, time.h is now correct and time_t
252: and tm struct should be used. difftime should be used but sometimes I
253: just make the differences in raw time format (time(&now).
254: Trying to suppress #ifdef LINUX
255: Add xdg-open for __linux in order to open default browser.
256:
1.157 brouard 257: Revision 1.156 2014/08/25 20:10:10 brouard
258: *** empty log message ***
259:
1.156 brouard 260: Revision 1.155 2014/08/25 18:32:34 brouard
261: Summary: New compile, minor changes
262: Author: Brouard
263:
1.155 brouard 264: Revision 1.154 2014/06/20 17:32:08 brouard
265: Summary: Outputs now all graphs of convergence to period prevalence
266:
1.154 brouard 267: Revision 1.153 2014/06/20 16:45:46 brouard
268: Summary: If 3 live state, convergence to period prevalence on same graph
269: Author: Brouard
270:
1.153 brouard 271: Revision 1.152 2014/06/18 17:54:09 brouard
272: Summary: open browser, use gnuplot on same dir than imach if not found in the path
273:
1.152 brouard 274: Revision 1.151 2014/06/18 16:43:30 brouard
275: *** empty log message ***
276:
1.151 brouard 277: Revision 1.150 2014/06/18 16:42:35 brouard
278: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
279: Author: brouard
280:
1.150 brouard 281: Revision 1.149 2014/06/18 15:51:14 brouard
282: Summary: Some fixes in parameter files errors
283: Author: Nicolas Brouard
284:
1.149 brouard 285: Revision 1.148 2014/06/17 17:38:48 brouard
286: Summary: Nothing new
287: Author: Brouard
288:
289: Just a new packaging for OS/X version 0.98nS
290:
1.148 brouard 291: Revision 1.147 2014/06/16 10:33:11 brouard
292: *** empty log message ***
293:
1.147 brouard 294: Revision 1.146 2014/06/16 10:20:28 brouard
295: Summary: Merge
296: Author: Brouard
297:
298: Merge, before building revised version.
299:
1.146 brouard 300: Revision 1.145 2014/06/10 21:23:15 brouard
301: Summary: Debugging with valgrind
302: Author: Nicolas Brouard
303:
304: Lot of changes in order to output the results with some covariates
305: After the Edimburgh REVES conference 2014, it seems mandatory to
306: improve the code.
307: No more memory valgrind error but a lot has to be done in order to
308: continue the work of splitting the code into subroutines.
309: Also, decodemodel has been improved. Tricode is still not
310: optimal. nbcode should be improved. Documentation has been added in
311: the source code.
312:
1.144 brouard 313: Revision 1.143 2014/01/26 09:45:38 brouard
314: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
315:
316: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
317: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
318:
1.143 brouard 319: Revision 1.142 2014/01/26 03:57:36 brouard
320: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
321:
322: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
323:
1.142 brouard 324: Revision 1.141 2014/01/26 02:42:01 brouard
325: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
326:
1.141 brouard 327: Revision 1.140 2011/09/02 10:37:54 brouard
328: Summary: times.h is ok with mingw32 now.
329:
1.140 brouard 330: Revision 1.139 2010/06/14 07:50:17 brouard
331: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
332: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
333:
1.139 brouard 334: Revision 1.138 2010/04/30 18:19:40 brouard
335: *** empty log message ***
336:
1.138 brouard 337: Revision 1.137 2010/04/29 18:11:38 brouard
338: (Module): Checking covariates for more complex models
339: than V1+V2. A lot of change to be done. Unstable.
340:
1.137 brouard 341: Revision 1.136 2010/04/26 20:30:53 brouard
342: (Module): merging some libgsl code. Fixing computation
343: of likelione (using inter/intrapolation if mle = 0) in order to
344: get same likelihood as if mle=1.
345: Some cleaning of code and comments added.
346:
1.136 brouard 347: Revision 1.135 2009/10/29 15:33:14 brouard
348: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
349:
1.135 brouard 350: Revision 1.134 2009/10/29 13:18:53 brouard
351: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
352:
1.134 brouard 353: Revision 1.133 2009/07/06 10:21:25 brouard
354: just nforces
355:
1.133 brouard 356: Revision 1.132 2009/07/06 08:22:05 brouard
357: Many tings
358:
1.132 brouard 359: Revision 1.131 2009/06/20 16:22:47 brouard
360: Some dimensions resccaled
361:
1.131 brouard 362: Revision 1.130 2009/05/26 06:44:34 brouard
363: (Module): Max Covariate is now set to 20 instead of 8. A
364: lot of cleaning with variables initialized to 0. Trying to make
365: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
366:
1.130 brouard 367: Revision 1.129 2007/08/31 13:49:27 lievre
368: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
369:
1.129 lievre 370: Revision 1.128 2006/06/30 13:02:05 brouard
371: (Module): Clarifications on computing e.j
372:
1.128 brouard 373: Revision 1.127 2006/04/28 18:11:50 brouard
374: (Module): Yes the sum of survivors was wrong since
375: imach-114 because nhstepm was no more computed in the age
376: loop. Now we define nhstepma in the age loop.
377: (Module): In order to speed up (in case of numerous covariates) we
378: compute health expectancies (without variances) in a first step
379: and then all the health expectancies with variances or standard
380: deviation (needs data from the Hessian matrices) which slows the
381: computation.
382: In the future we should be able to stop the program is only health
383: expectancies and graph are needed without standard deviations.
384:
1.127 brouard 385: Revision 1.126 2006/04/28 17:23:28 brouard
386: (Module): Yes the sum of survivors was wrong since
387: imach-114 because nhstepm was no more computed in the age
388: loop. Now we define nhstepma in the age loop.
389: Version 0.98h
390:
1.126 brouard 391: Revision 1.125 2006/04/04 15:20:31 lievre
392: Errors in calculation of health expectancies. Age was not initialized.
393: Forecasting file added.
394:
395: Revision 1.124 2006/03/22 17:13:53 lievre
396: Parameters are printed with %lf instead of %f (more numbers after the comma).
397: The log-likelihood is printed in the log file
398:
399: Revision 1.123 2006/03/20 10:52:43 brouard
400: * imach.c (Module): <title> changed, corresponds to .htm file
401: name. <head> headers where missing.
402:
403: * imach.c (Module): Weights can have a decimal point as for
404: English (a comma might work with a correct LC_NUMERIC environment,
405: otherwise the weight is truncated).
406: Modification of warning when the covariates values are not 0 or
407: 1.
408: Version 0.98g
409:
410: Revision 1.122 2006/03/20 09:45:41 brouard
411: (Module): Weights can have a decimal point as for
412: English (a comma might work with a correct LC_NUMERIC environment,
413: otherwise the weight is truncated).
414: Modification of warning when the covariates values are not 0 or
415: 1.
416: Version 0.98g
417:
418: Revision 1.121 2006/03/16 17:45:01 lievre
419: * imach.c (Module): Comments concerning covariates added
420:
421: * imach.c (Module): refinements in the computation of lli if
422: status=-2 in order to have more reliable computation if stepm is
423: not 1 month. Version 0.98f
424:
425: Revision 1.120 2006/03/16 15:10:38 lievre
426: (Module): refinements in the computation of lli if
427: status=-2 in order to have more reliable computation if stepm is
428: not 1 month. Version 0.98f
429:
430: Revision 1.119 2006/03/15 17:42:26 brouard
431: (Module): Bug if status = -2, the loglikelihood was
432: computed as likelihood omitting the logarithm. Version O.98e
433:
434: Revision 1.118 2006/03/14 18:20:07 brouard
435: (Module): varevsij Comments added explaining the second
436: table of variances if popbased=1 .
437: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
438: (Module): Function pstamp added
439: (Module): Version 0.98d
440:
441: Revision 1.117 2006/03/14 17:16:22 brouard
442: (Module): varevsij Comments added explaining the second
443: table of variances if popbased=1 .
444: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
445: (Module): Function pstamp added
446: (Module): Version 0.98d
447:
448: Revision 1.116 2006/03/06 10:29:27 brouard
449: (Module): Variance-covariance wrong links and
450: varian-covariance of ej. is needed (Saito).
451:
452: Revision 1.115 2006/02/27 12:17:45 brouard
453: (Module): One freematrix added in mlikeli! 0.98c
454:
455: Revision 1.114 2006/02/26 12:57:58 brouard
456: (Module): Some improvements in processing parameter
457: filename with strsep.
458:
459: Revision 1.113 2006/02/24 14:20:24 brouard
460: (Module): Memory leaks checks with valgrind and:
461: datafile was not closed, some imatrix were not freed and on matrix
462: allocation too.
463:
464: Revision 1.112 2006/01/30 09:55:26 brouard
465: (Module): Back to gnuplot.exe instead of wgnuplot.exe
466:
467: Revision 1.111 2006/01/25 20:38:18 brouard
468: (Module): Lots of cleaning and bugs added (Gompertz)
469: (Module): Comments can be added in data file. Missing date values
470: can be a simple dot '.'.
471:
472: Revision 1.110 2006/01/25 00:51:50 brouard
473: (Module): Lots of cleaning and bugs added (Gompertz)
474:
475: Revision 1.109 2006/01/24 19:37:15 brouard
476: (Module): Comments (lines starting with a #) are allowed in data.
477:
478: Revision 1.108 2006/01/19 18:05:42 lievre
479: Gnuplot problem appeared...
480: To be fixed
481:
482: Revision 1.107 2006/01/19 16:20:37 brouard
483: Test existence of gnuplot in imach path
484:
485: Revision 1.106 2006/01/19 13:24:36 brouard
486: Some cleaning and links added in html output
487:
488: Revision 1.105 2006/01/05 20:23:19 lievre
489: *** empty log message ***
490:
491: Revision 1.104 2005/09/30 16:11:43 lievre
492: (Module): sump fixed, loop imx fixed, and simplifications.
493: (Module): If the status is missing at the last wave but we know
494: that the person is alive, then we can code his/her status as -2
495: (instead of missing=-1 in earlier versions) and his/her
496: contributions to the likelihood is 1 - Prob of dying from last
497: health status (= 1-p13= p11+p12 in the easiest case of somebody in
498: the healthy state at last known wave). Version is 0.98
499:
500: Revision 1.103 2005/09/30 15:54:49 lievre
501: (Module): sump fixed, loop imx fixed, and simplifications.
502:
503: Revision 1.102 2004/09/15 17:31:30 brouard
504: Add the possibility to read data file including tab characters.
505:
506: Revision 1.101 2004/09/15 10:38:38 brouard
507: Fix on curr_time
508:
509: Revision 1.100 2004/07/12 18:29:06 brouard
510: Add version for Mac OS X. Just define UNIX in Makefile
511:
512: Revision 1.99 2004/06/05 08:57:40 brouard
513: *** empty log message ***
514:
515: Revision 1.98 2004/05/16 15:05:56 brouard
516: New version 0.97 . First attempt to estimate force of mortality
517: directly from the data i.e. without the need of knowing the health
518: state at each age, but using a Gompertz model: log u =a + b*age .
519: This is the basic analysis of mortality and should be done before any
520: other analysis, in order to test if the mortality estimated from the
521: cross-longitudinal survey is different from the mortality estimated
522: from other sources like vital statistic data.
523:
524: The same imach parameter file can be used but the option for mle should be -3.
525:
1.133 brouard 526: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 527: former routines in order to include the new code within the former code.
528:
529: The output is very simple: only an estimate of the intercept and of
530: the slope with 95% confident intervals.
531:
532: Current limitations:
533: A) Even if you enter covariates, i.e. with the
534: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
535: B) There is no computation of Life Expectancy nor Life Table.
536:
537: Revision 1.97 2004/02/20 13:25:42 lievre
538: Version 0.96d. Population forecasting command line is (temporarily)
539: suppressed.
540:
541: Revision 1.96 2003/07/15 15:38:55 brouard
542: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
543: rewritten within the same printf. Workaround: many printfs.
544:
545: Revision 1.95 2003/07/08 07:54:34 brouard
546: * imach.c (Repository):
547: (Repository): Using imachwizard code to output a more meaningful covariance
548: matrix (cov(a12,c31) instead of numbers.
549:
550: Revision 1.94 2003/06/27 13:00:02 brouard
551: Just cleaning
552:
553: Revision 1.93 2003/06/25 16:33:55 brouard
554: (Module): On windows (cygwin) function asctime_r doesn't
555: exist so I changed back to asctime which exists.
556: (Module): Version 0.96b
557:
558: Revision 1.92 2003/06/25 16:30:45 brouard
559: (Module): On windows (cygwin) function asctime_r doesn't
560: exist so I changed back to asctime which exists.
561:
562: Revision 1.91 2003/06/25 15:30:29 brouard
563: * imach.c (Repository): Duplicated warning errors corrected.
564: (Repository): Elapsed time after each iteration is now output. It
565: helps to forecast when convergence will be reached. Elapsed time
566: is stamped in powell. We created a new html file for the graphs
567: concerning matrix of covariance. It has extension -cov.htm.
568:
569: Revision 1.90 2003/06/24 12:34:15 brouard
570: (Module): Some bugs corrected for windows. Also, when
571: mle=-1 a template is output in file "or"mypar.txt with the design
572: of the covariance matrix to be input.
573:
574: Revision 1.89 2003/06/24 12:30:52 brouard
575: (Module): Some bugs corrected for windows. Also, when
576: mle=-1 a template is output in file "or"mypar.txt with the design
577: of the covariance matrix to be input.
578:
579: Revision 1.88 2003/06/23 17:54:56 brouard
580: * 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.
581:
582: Revision 1.87 2003/06/18 12:26:01 brouard
583: Version 0.96
584:
585: Revision 1.86 2003/06/17 20:04:08 brouard
586: (Module): Change position of html and gnuplot routines and added
587: routine fileappend.
588:
589: Revision 1.85 2003/06/17 13:12:43 brouard
590: * imach.c (Repository): Check when date of death was earlier that
591: current date of interview. It may happen when the death was just
592: prior to the death. In this case, dh was negative and likelihood
593: was wrong (infinity). We still send an "Error" but patch by
594: assuming that the date of death was just one stepm after the
595: interview.
596: (Repository): Because some people have very long ID (first column)
597: we changed int to long in num[] and we added a new lvector for
598: memory allocation. But we also truncated to 8 characters (left
599: truncation)
600: (Repository): No more line truncation errors.
601:
602: Revision 1.84 2003/06/13 21:44:43 brouard
603: * imach.c (Repository): Replace "freqsummary" at a correct
604: place. It differs from routine "prevalence" which may be called
605: many times. Probs is memory consuming and must be used with
606: parcimony.
607: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
608:
609: Revision 1.83 2003/06/10 13:39:11 lievre
610: *** empty log message ***
611:
612: Revision 1.82 2003/06/05 15:57:20 brouard
613: Add log in imach.c and fullversion number is now printed.
614:
615: */
616: /*
617: Interpolated Markov Chain
618:
619: Short summary of the programme:
620:
621: This program computes Healthy Life Expectancies from
622: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
623: first survey ("cross") where individuals from different ages are
624: interviewed on their health status or degree of disability (in the
625: case of a health survey which is our main interest) -2- at least a
626: second wave of interviews ("longitudinal") which measure each change
627: (if any) in individual health status. Health expectancies are
628: computed from the time spent in each health state according to a
629: model. More health states you consider, more time is necessary to reach the
630: Maximum Likelihood of the parameters involved in the model. The
631: simplest model is the multinomial logistic model where pij is the
632: probability to be observed in state j at the second wave
633: conditional to be observed in state i at the first wave. Therefore
634: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
635: 'age' is age and 'sex' is a covariate. If you want to have a more
636: complex model than "constant and age", you should modify the program
637: where the markup *Covariates have to be included here again* invites
638: you to do it. More covariates you add, slower the
639: convergence.
640:
641: The advantage of this computer programme, compared to a simple
642: multinomial logistic model, is clear when the delay between waves is not
643: identical for each individual. Also, if a individual missed an
644: intermediate interview, the information is lost, but taken into
645: account using an interpolation or extrapolation.
646:
647: hPijx is the probability to be observed in state i at age x+h
648: conditional to the observed state i at age x. The delay 'h' can be
649: split into an exact number (nh*stepm) of unobserved intermediate
650: states. This elementary transition (by month, quarter,
651: semester or year) is modelled as a multinomial logistic. The hPx
652: matrix is simply the matrix product of nh*stepm elementary matrices
653: and the contribution of each individual to the likelihood is simply
654: hPijx.
655:
656: Also this programme outputs the covariance matrix of the parameters but also
1.218 brouard 657: of the life expectancies. It also computes the period (stable) prevalence.
658:
659: Back prevalence and projections:
660: - back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj)
661: Computes the back prevalence limit for any combination of covariate values k
662: at any age between ageminpar and agemaxpar and returns it in **bprlim. In the loops,
663: - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm, **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
664: - hBijx Back Probability to be in state i at age x-h being in j at x
665: Computes for any combination of covariates k and any age between bage and fage
666: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
667: oldm=oldms;savm=savms;
668: - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
669: Computes the transition matrix starting at age 'age' over
670: 'nhstepm*hstepm*stepm' months (i.e. until
671: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
672: nhstepm*hstepm matrices. Returns p3mat[i][j][h] after calling
673: p3mat[i][j][h]=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\
674: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
675:
1.133 brouard 676: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
677: Institut national d'études démographiques, Paris.
1.126 brouard 678: This software have been partly granted by Euro-REVES, a concerted action
679: from the European Union.
680: It is copyrighted identically to a GNU software product, ie programme and
681: software can be distributed freely for non commercial use. Latest version
682: can be accessed at http://euroreves.ined.fr/imach .
683:
684: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
685: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
686:
687: **********************************************************************/
688: /*
689: main
690: read parameterfile
691: read datafile
692: concatwav
693: freqsummary
694: if (mle >= 1)
695: mlikeli
696: print results files
697: if mle==1
698: computes hessian
699: read end of parameter file: agemin, agemax, bage, fage, estepm
700: begin-prev-date,...
701: open gnuplot file
702: open html file
1.145 brouard 703: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
704: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
705: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
706: freexexit2 possible for memory heap.
707:
708: h Pij x | pij_nom ficrestpij
709: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
710: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
711: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
712:
713: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
714: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
715: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
716: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
717: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
718:
1.126 brouard 719: forecasting if prevfcast==1 prevforecast call prevalence()
720: health expectancies
721: Variance-covariance of DFLE
722: prevalence()
723: movingaverage()
724: varevsij()
725: if popbased==1 varevsij(,popbased)
726: total life expectancies
727: Variance of period (stable) prevalence
728: end
729: */
730:
1.187 brouard 731: /* #define DEBUG */
732: /* #define DEBUGBRENT */
1.203 brouard 733: /* #define DEBUGLINMIN */
734: /* #define DEBUGHESS */
735: #define DEBUGHESSIJ
736: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan)*\/ */
1.165 brouard 737: #define POWELL /* Instead of NLOPT */
1.192 brouard 738: #define POWELLF1F3 /* Skip test */
1.186 brouard 739: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
740: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 741:
742: #include <math.h>
743: #include <stdio.h>
744: #include <stdlib.h>
745: #include <string.h>
1.159 brouard 746:
747: #ifdef _WIN32
748: #include <io.h>
1.172 brouard 749: #include <windows.h>
750: #include <tchar.h>
1.159 brouard 751: #else
1.126 brouard 752: #include <unistd.h>
1.159 brouard 753: #endif
1.126 brouard 754:
755: #include <limits.h>
756: #include <sys/types.h>
1.171 brouard 757:
758: #if defined(__GNUC__)
759: #include <sys/utsname.h> /* Doesn't work on Windows */
760: #endif
761:
1.126 brouard 762: #include <sys/stat.h>
763: #include <errno.h>
1.159 brouard 764: /* extern int errno; */
1.126 brouard 765:
1.157 brouard 766: /* #ifdef LINUX */
767: /* #include <time.h> */
768: /* #include "timeval.h" */
769: /* #else */
770: /* #include <sys/time.h> */
771: /* #endif */
772:
1.126 brouard 773: #include <time.h>
774:
1.136 brouard 775: #ifdef GSL
776: #include <gsl/gsl_errno.h>
777: #include <gsl/gsl_multimin.h>
778: #endif
779:
1.167 brouard 780:
1.162 brouard 781: #ifdef NLOPT
782: #include <nlopt.h>
783: typedef struct {
784: double (* function)(double [] );
785: } myfunc_data ;
786: #endif
787:
1.126 brouard 788: /* #include <libintl.h> */
789: /* #define _(String) gettext (String) */
790:
1.141 brouard 791: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 792:
793: #define GNUPLOTPROGRAM "gnuplot"
794: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
795: #define FILENAMELENGTH 132
796:
797: #define GLOCK_ERROR_NOPATH -1 /* empty path */
798: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
799:
1.144 brouard 800: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
801: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 802:
803: #define NINTERVMAX 8
1.144 brouard 804: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
805: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
806: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 807: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 808: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
809: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.126 brouard 810: #define MAXN 20000
1.144 brouard 811: #define YEARM 12. /**< Number of months per year */
1.218 brouard 812: /* #define AGESUP 130 */
813: #define AGESUP 150
814: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126 brouard 815: #define AGEBASE 40
1.194 brouard 816: #define AGEOVERFLOW 1.e20
1.164 brouard 817: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 818: #ifdef _WIN32
819: #define DIRSEPARATOR '\\'
820: #define CHARSEPARATOR "\\"
821: #define ODIRSEPARATOR '/'
822: #else
1.126 brouard 823: #define DIRSEPARATOR '/'
824: #define CHARSEPARATOR "/"
825: #define ODIRSEPARATOR '\\'
826: #endif
827:
1.219 ! brouard 828: /* $Id: imach.c,v 1.218 2016/02/12 11:29:23 brouard Exp $ */
1.126 brouard 829: /* $State: Exp $ */
1.196 brouard 830: #include "version.h"
831: char version[]=__IMACH_VERSION__;
1.204 brouard 832: 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";
1.219 ! brouard 833: char fullversion[]="$Revision: 1.218 $ $Date: 2016/02/12 11:29:23 $";
1.126 brouard 834: char strstart[80];
835: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 836: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 837: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 838: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
839: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
840: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
841: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
842: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
843: int cptcovprodnoage=0; /**< Number of covariate products without age */
844: int cptcoveff=0; /* Total number of covariates to vary for printing results */
845: int cptcov=0; /* Working variable */
1.218 brouard 846: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.126 brouard 847: int npar=NPARMAX;
848: int nlstate=2; /* Number of live states */
849: int ndeath=1; /* Number of dead states */
1.130 brouard 850: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 851: int popbased=0;
852:
853: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 854: int maxwav=0; /* Maxim number of waves */
855: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
856: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
857: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 858: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 859: int mle=1, weightopt=0;
1.126 brouard 860: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
861: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
862: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
863: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 864: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 865: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 866: double **matprod2(); /* test */
1.126 brouard 867: double **oldm, **newm, **savm; /* Working pointers to matrices */
868: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218 brouard 869: double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
870:
1.136 brouard 871: /*FILE *fic ; */ /* Used in readdata only */
1.217 brouard 872: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 873: FILE *ficlog, *ficrespow;
1.130 brouard 874: int globpr=0; /* Global variable for printing or not */
1.126 brouard 875: double fretone; /* Only one call to likelihood */
1.130 brouard 876: long ipmx=0; /* Number of contributions */
1.126 brouard 877: double sw; /* Sum of weights */
878: char filerespow[FILENAMELENGTH];
879: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
880: FILE *ficresilk;
881: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
882: FILE *ficresprobmorprev;
883: FILE *fichtm, *fichtmcov; /* Html File */
884: FILE *ficreseij;
885: char filerese[FILENAMELENGTH];
886: FILE *ficresstdeij;
887: char fileresstde[FILENAMELENGTH];
888: FILE *ficrescveij;
889: char filerescve[FILENAMELENGTH];
890: FILE *ficresvij;
891: char fileresv[FILENAMELENGTH];
892: FILE *ficresvpl;
893: char fileresvpl[FILENAMELENGTH];
894: char title[MAXLINE];
1.217 brouard 895: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 896: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
897: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
898: char command[FILENAMELENGTH];
899: int outcmd=0;
900:
1.217 brouard 901: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 902: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 903: char filelog[FILENAMELENGTH]; /* Log file */
904: char filerest[FILENAMELENGTH];
905: char fileregp[FILENAMELENGTH];
906: char popfile[FILENAMELENGTH];
907:
908: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
909:
1.157 brouard 910: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
911: /* struct timezone tzp; */
912: /* extern int gettimeofday(); */
913: struct tm tml, *gmtime(), *localtime();
914:
915: extern time_t time();
916:
917: struct tm start_time, end_time, curr_time, last_time, forecast_time;
918: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
919: struct tm tm;
920:
1.126 brouard 921: char strcurr[80], strfor[80];
922:
923: char *endptr;
924: long lval;
925: double dval;
926:
927: #define NR_END 1
928: #define FREE_ARG char*
929: #define FTOL 1.0e-10
930:
931: #define NRANSI
932: #define ITMAX 200
933:
934: #define TOL 2.0e-4
935:
936: #define CGOLD 0.3819660
937: #define ZEPS 1.0e-10
938: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
939:
940: #define GOLD 1.618034
941: #define GLIMIT 100.0
942: #define TINY 1.0e-20
943:
944: static double maxarg1,maxarg2;
945: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
946: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
947:
948: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
949: #define rint(a) floor(a+0.5)
1.166 brouard 950: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 951: #define mytinydouble 1.0e-16
1.166 brouard 952: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
953: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
954: /* static double dsqrarg; */
955: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 956: static double sqrarg;
957: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
958: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
959: int agegomp= AGEGOMP;
960:
961: int imx;
962: int stepm=1;
963: /* Stepm, step in month: minimum step interpolation*/
964:
965: int estepm;
966: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
967:
968: int m,nb;
969: long *num;
1.197 brouard 970: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 971: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
972: covariate for which somebody answered excluding
973: undefined. Usually 2: 0 and 1. */
974: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
975: covariate for which somebody answered including
976: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 977: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218 brouard 978: double **pmmij, ***probs; /* Global pointer */
1.219 ! brouard 979: double ***mobaverage, ***mobaverages; /* New global variable */
1.126 brouard 980: double *ageexmed,*agecens;
981: double dateintmean=0;
982:
983: double *weight;
984: int **s; /* Status */
1.141 brouard 985: double *agedc;
1.145 brouard 986: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 987: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 988: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 989: double idx;
990: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.197 brouard 991: int *Tage;
1.145 brouard 992: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 993: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.141 brouard 994: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 995: double *lsurv, *lpop, *tpop;
996:
1.143 brouard 997: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
998: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 999:
1000: /**************** split *************************/
1001: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1002: {
1003: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1004: the name of the file (name), its extension only (ext) and its first part of the name (finame)
1005: */
1006: char *ss; /* pointer */
1.186 brouard 1007: int l1=0, l2=0; /* length counters */
1.126 brouard 1008:
1009: l1 = strlen(path ); /* length of path */
1010: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1011: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1012: if ( ss == NULL ) { /* no directory, so determine current directory */
1013: strcpy( name, path ); /* we got the fullname name because no directory */
1014: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
1015: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1016: /* get current working directory */
1017: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 1018: #ifdef WIN32
1019: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
1020: #else
1021: if (getcwd(dirc, FILENAME_MAX) == NULL) {
1022: #endif
1.126 brouard 1023: return( GLOCK_ERROR_GETCWD );
1024: }
1025: /* got dirc from getcwd*/
1026: printf(" DIRC = %s \n",dirc);
1.205 brouard 1027: } else { /* strip directory from path */
1.126 brouard 1028: ss++; /* after this, the filename */
1029: l2 = strlen( ss ); /* length of filename */
1030: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1031: strcpy( name, ss ); /* save file name */
1032: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1033: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1034: printf(" DIRC2 = %s \n",dirc);
1035: }
1036: /* We add a separator at the end of dirc if not exists */
1037: l1 = strlen( dirc ); /* length of directory */
1038: if( dirc[l1-1] != DIRSEPARATOR ){
1039: dirc[l1] = DIRSEPARATOR;
1040: dirc[l1+1] = 0;
1041: printf(" DIRC3 = %s \n",dirc);
1042: }
1043: ss = strrchr( name, '.' ); /* find last / */
1044: if (ss >0){
1045: ss++;
1046: strcpy(ext,ss); /* save extension */
1047: l1= strlen( name);
1048: l2= strlen(ss)+1;
1049: strncpy( finame, name, l1-l2);
1050: finame[l1-l2]= 0;
1051: }
1052:
1053: return( 0 ); /* we're done */
1054: }
1055:
1056:
1057: /******************************************/
1058:
1059: void replace_back_to_slash(char *s, char*t)
1060: {
1061: int i;
1062: int lg=0;
1063: i=0;
1064: lg=strlen(t);
1065: for(i=0; i<= lg; i++) {
1066: (s[i] = t[i]);
1067: if (t[i]== '\\') s[i]='/';
1068: }
1069: }
1070:
1.132 brouard 1071: char *trimbb(char *out, char *in)
1.137 brouard 1072: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1073: char *s;
1074: s=out;
1075: while (*in != '\0'){
1.137 brouard 1076: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1077: in++;
1078: }
1079: *out++ = *in++;
1080: }
1081: *out='\0';
1082: return s;
1083: }
1084:
1.187 brouard 1085: /* char *substrchaine(char *out, char *in, char *chain) */
1086: /* { */
1087: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1088: /* char *s, *t; */
1089: /* t=in;s=out; */
1090: /* while ((*in != *chain) && (*in != '\0')){ */
1091: /* *out++ = *in++; */
1092: /* } */
1093:
1094: /* /\* *in matches *chain *\/ */
1095: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1096: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1097: /* } */
1098: /* in--; chain--; */
1099: /* while ( (*in != '\0')){ */
1100: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1101: /* *out++ = *in++; */
1102: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1103: /* } */
1104: /* *out='\0'; */
1105: /* out=s; */
1106: /* return out; */
1107: /* } */
1108: char *substrchaine(char *out, char *in, char *chain)
1109: {
1110: /* Substract chain 'chain' from 'in', return and output 'out' */
1111: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1112:
1113: char *strloc;
1114:
1115: strcpy (out, in);
1116: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1117: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1118: if(strloc != NULL){
1119: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1120: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1121: /* strcpy (strloc, strloc +strlen(chain));*/
1122: }
1123: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1124: return out;
1125: }
1126:
1127:
1.145 brouard 1128: char *cutl(char *blocc, char *alocc, char *in, char occ)
1129: {
1.187 brouard 1130: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1131: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1132: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1133: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1134: */
1.160 brouard 1135: char *s, *t;
1.145 brouard 1136: t=in;s=in;
1137: while ((*in != occ) && (*in != '\0')){
1138: *alocc++ = *in++;
1139: }
1140: if( *in == occ){
1141: *(alocc)='\0';
1142: s=++in;
1143: }
1144:
1145: if (s == t) {/* occ not found */
1146: *(alocc-(in-s))='\0';
1147: in=s;
1148: }
1149: while ( *in != '\0'){
1150: *blocc++ = *in++;
1151: }
1152:
1153: *blocc='\0';
1154: return t;
1155: }
1.137 brouard 1156: char *cutv(char *blocc, char *alocc, char *in, char occ)
1157: {
1.187 brouard 1158: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1159: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1160: gives blocc="abcdef2ghi" and alocc="j".
1161: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1162: */
1163: char *s, *t;
1164: t=in;s=in;
1165: while (*in != '\0'){
1166: while( *in == occ){
1167: *blocc++ = *in++;
1168: s=in;
1169: }
1170: *blocc++ = *in++;
1171: }
1172: if (s == t) /* occ not found */
1173: *(blocc-(in-s))='\0';
1174: else
1175: *(blocc-(in-s)-1)='\0';
1176: in=s;
1177: while ( *in != '\0'){
1178: *alocc++ = *in++;
1179: }
1180:
1181: *alocc='\0';
1182: return s;
1183: }
1184:
1.126 brouard 1185: int nbocc(char *s, char occ)
1186: {
1187: int i,j=0;
1188: int lg=20;
1189: i=0;
1190: lg=strlen(s);
1191: for(i=0; i<= lg; i++) {
1192: if (s[i] == occ ) j++;
1193: }
1194: return j;
1195: }
1196:
1.137 brouard 1197: /* void cutv(char *u,char *v, char*t, char occ) */
1198: /* { */
1199: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1200: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1201: /* gives u="abcdef2ghi" and v="j" *\/ */
1202: /* int i,lg,j,p=0; */
1203: /* i=0; */
1204: /* lg=strlen(t); */
1205: /* for(j=0; j<=lg-1; j++) { */
1206: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1207: /* } */
1.126 brouard 1208:
1.137 brouard 1209: /* for(j=0; j<p; j++) { */
1210: /* (u[j] = t[j]); */
1211: /* } */
1212: /* u[p]='\0'; */
1.126 brouard 1213:
1.137 brouard 1214: /* for(j=0; j<= lg; j++) { */
1215: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1216: /* } */
1217: /* } */
1.126 brouard 1218:
1.160 brouard 1219: #ifdef _WIN32
1220: char * strsep(char **pp, const char *delim)
1221: {
1222: char *p, *q;
1223:
1224: if ((p = *pp) == NULL)
1225: return 0;
1226: if ((q = strpbrk (p, delim)) != NULL)
1227: {
1228: *pp = q + 1;
1229: *q = '\0';
1230: }
1231: else
1232: *pp = 0;
1233: return p;
1234: }
1235: #endif
1236:
1.126 brouard 1237: /********************** nrerror ********************/
1238:
1239: void nrerror(char error_text[])
1240: {
1241: fprintf(stderr,"ERREUR ...\n");
1242: fprintf(stderr,"%s\n",error_text);
1243: exit(EXIT_FAILURE);
1244: }
1245: /*********************** vector *******************/
1246: double *vector(int nl, int nh)
1247: {
1248: double *v;
1249: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1250: if (!v) nrerror("allocation failure in vector");
1251: return v-nl+NR_END;
1252: }
1253:
1254: /************************ free vector ******************/
1255: void free_vector(double*v, int nl, int nh)
1256: {
1257: free((FREE_ARG)(v+nl-NR_END));
1258: }
1259:
1260: /************************ivector *******************************/
1261: int *ivector(long nl,long nh)
1262: {
1263: int *v;
1264: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1265: if (!v) nrerror("allocation failure in ivector");
1266: return v-nl+NR_END;
1267: }
1268:
1269: /******************free ivector **************************/
1270: void free_ivector(int *v, long nl, long nh)
1271: {
1272: free((FREE_ARG)(v+nl-NR_END));
1273: }
1274:
1275: /************************lvector *******************************/
1276: long *lvector(long nl,long nh)
1277: {
1278: long *v;
1279: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1280: if (!v) nrerror("allocation failure in ivector");
1281: return v-nl+NR_END;
1282: }
1283:
1284: /******************free lvector **************************/
1285: void free_lvector(long *v, long nl, long nh)
1286: {
1287: free((FREE_ARG)(v+nl-NR_END));
1288: }
1289:
1290: /******************* imatrix *******************************/
1291: int **imatrix(long nrl, long nrh, long ncl, long nch)
1292: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1293: {
1294: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1295: int **m;
1296:
1297: /* allocate pointers to rows */
1298: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1299: if (!m) nrerror("allocation failure 1 in matrix()");
1300: m += NR_END;
1301: m -= nrl;
1302:
1303:
1304: /* allocate rows and set pointers to them */
1305: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1306: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1307: m[nrl] += NR_END;
1308: m[nrl] -= ncl;
1309:
1310: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1311:
1312: /* return pointer to array of pointers to rows */
1313: return m;
1314: }
1315:
1316: /****************** free_imatrix *************************/
1317: void free_imatrix(m,nrl,nrh,ncl,nch)
1318: int **m;
1319: long nch,ncl,nrh,nrl;
1320: /* free an int matrix allocated by imatrix() */
1321: {
1322: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1323: free((FREE_ARG) (m+nrl-NR_END));
1324: }
1325:
1326: /******************* matrix *******************************/
1327: double **matrix(long nrl, long nrh, long ncl, long nch)
1328: {
1329: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1330: double **m;
1331:
1332: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1333: if (!m) nrerror("allocation failure 1 in matrix()");
1334: m += NR_END;
1335: m -= nrl;
1336:
1337: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1338: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1339: m[nrl] += NR_END;
1340: m[nrl] -= ncl;
1341:
1342: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1343: return m;
1.145 brouard 1344: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1345: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1346: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1347: */
1348: }
1349:
1350: /*************************free matrix ************************/
1351: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1352: {
1353: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1354: free((FREE_ARG)(m+nrl-NR_END));
1355: }
1356:
1357: /******************* ma3x *******************************/
1358: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1359: {
1360: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1361: double ***m;
1362:
1363: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1364: if (!m) nrerror("allocation failure 1 in matrix()");
1365: m += NR_END;
1366: m -= nrl;
1367:
1368: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1369: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1370: m[nrl] += NR_END;
1371: m[nrl] -= ncl;
1372:
1373: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1374:
1375: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1376: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1377: m[nrl][ncl] += NR_END;
1378: m[nrl][ncl] -= nll;
1379: for (j=ncl+1; j<=nch; j++)
1380: m[nrl][j]=m[nrl][j-1]+nlay;
1381:
1382: for (i=nrl+1; i<=nrh; i++) {
1383: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1384: for (j=ncl+1; j<=nch; j++)
1385: m[i][j]=m[i][j-1]+nlay;
1386: }
1387: return m;
1388: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1389: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1390: */
1391: }
1392:
1393: /*************************free ma3x ************************/
1394: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1395: {
1396: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1397: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1398: free((FREE_ARG)(m+nrl-NR_END));
1399: }
1400:
1401: /*************** function subdirf ***********/
1402: char *subdirf(char fileres[])
1403: {
1404: /* Caution optionfilefiname is hidden */
1405: strcpy(tmpout,optionfilefiname);
1406: strcat(tmpout,"/"); /* Add to the right */
1407: strcat(tmpout,fileres);
1408: return tmpout;
1409: }
1410:
1411: /*************** function subdirf2 ***********/
1412: char *subdirf2(char fileres[], char *preop)
1413: {
1414:
1415: /* Caution optionfilefiname is hidden */
1416: strcpy(tmpout,optionfilefiname);
1417: strcat(tmpout,"/");
1418: strcat(tmpout,preop);
1419: strcat(tmpout,fileres);
1420: return tmpout;
1421: }
1422:
1423: /*************** function subdirf3 ***********/
1424: char *subdirf3(char fileres[], char *preop, char *preop2)
1425: {
1426:
1427: /* Caution optionfilefiname is hidden */
1428: strcpy(tmpout,optionfilefiname);
1429: strcat(tmpout,"/");
1430: strcat(tmpout,preop);
1431: strcat(tmpout,preop2);
1432: strcat(tmpout,fileres);
1433: return tmpout;
1434: }
1.213 brouard 1435:
1436: /*************** function subdirfext ***********/
1437: char *subdirfext(char fileres[], char *preop, char *postop)
1438: {
1439:
1440: strcpy(tmpout,preop);
1441: strcat(tmpout,fileres);
1442: strcat(tmpout,postop);
1443: return tmpout;
1444: }
1.126 brouard 1445:
1.213 brouard 1446: /*************** function subdirfext3 ***********/
1447: char *subdirfext3(char fileres[], char *preop, char *postop)
1448: {
1449:
1450: /* Caution optionfilefiname is hidden */
1451: strcpy(tmpout,optionfilefiname);
1452: strcat(tmpout,"/");
1453: strcat(tmpout,preop);
1454: strcat(tmpout,fileres);
1455: strcat(tmpout,postop);
1456: return tmpout;
1457: }
1458:
1.162 brouard 1459: char *asc_diff_time(long time_sec, char ascdiff[])
1460: {
1461: long sec_left, days, hours, minutes;
1462: days = (time_sec) / (60*60*24);
1463: sec_left = (time_sec) % (60*60*24);
1464: hours = (sec_left) / (60*60) ;
1465: sec_left = (sec_left) %(60*60);
1466: minutes = (sec_left) /60;
1467: sec_left = (sec_left) % (60);
1468: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1469: return ascdiff;
1470: }
1471:
1.126 brouard 1472: /***************** f1dim *************************/
1473: extern int ncom;
1474: extern double *pcom,*xicom;
1475: extern double (*nrfunc)(double []);
1476:
1477: double f1dim(double x)
1478: {
1479: int j;
1480: double f;
1481: double *xt;
1482:
1483: xt=vector(1,ncom);
1484: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1485: f=(*nrfunc)(xt);
1486: free_vector(xt,1,ncom);
1487: return f;
1488: }
1489:
1490: /*****************brent *************************/
1491: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1492: {
1493: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1494: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1495: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1496: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1497: * returned function value.
1498: */
1.126 brouard 1499: int iter;
1500: double a,b,d,etemp;
1.159 brouard 1501: double fu=0,fv,fw,fx;
1.164 brouard 1502: double ftemp=0.;
1.126 brouard 1503: double p,q,r,tol1,tol2,u,v,w,x,xm;
1504: double e=0.0;
1505:
1506: a=(ax < cx ? ax : cx);
1507: b=(ax > cx ? ax : cx);
1508: x=w=v=bx;
1509: fw=fv=fx=(*f)(x);
1510: for (iter=1;iter<=ITMAX;iter++) {
1511: xm=0.5*(a+b);
1512: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1513: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1514: printf(".");fflush(stdout);
1515: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1516: #ifdef DEBUGBRENT
1.126 brouard 1517: 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);
1518: 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);
1519: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1520: #endif
1521: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1522: *xmin=x;
1523: return fx;
1524: }
1525: ftemp=fu;
1526: if (fabs(e) > tol1) {
1527: r=(x-w)*(fx-fv);
1528: q=(x-v)*(fx-fw);
1529: p=(x-v)*q-(x-w)*r;
1530: q=2.0*(q-r);
1531: if (q > 0.0) p = -p;
1532: q=fabs(q);
1533: etemp=e;
1534: e=d;
1535: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1536: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1537: else {
1538: d=p/q;
1539: u=x+d;
1540: if (u-a < tol2 || b-u < tol2)
1541: d=SIGN(tol1,xm-x);
1542: }
1543: } else {
1544: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1545: }
1546: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1547: fu=(*f)(u);
1548: if (fu <= fx) {
1549: if (u >= x) a=x; else b=x;
1550: SHFT(v,w,x,u)
1.183 brouard 1551: SHFT(fv,fw,fx,fu)
1552: } else {
1553: if (u < x) a=u; else b=u;
1554: if (fu <= fw || w == x) {
1555: v=w;
1556: w=u;
1557: fv=fw;
1558: fw=fu;
1559: } else if (fu <= fv || v == x || v == w) {
1560: v=u;
1561: fv=fu;
1562: }
1563: }
1.126 brouard 1564: }
1565: nrerror("Too many iterations in brent");
1566: *xmin=x;
1567: return fx;
1568: }
1569:
1570: /****************** mnbrak ***********************/
1571:
1572: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1573: double (*func)(double))
1.183 brouard 1574: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1575: the downhill direction (defined by the function as evaluated at the initial points) and returns
1576: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1577: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1578: */
1.126 brouard 1579: double ulim,u,r,q, dum;
1580: double fu;
1.187 brouard 1581:
1582: double scale=10.;
1583: int iterscale=0;
1584:
1585: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1586: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1587:
1588:
1589: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1590: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1591: /* *bx = *ax - (*ax - *bx)/scale; */
1592: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1593: /* } */
1594:
1.126 brouard 1595: if (*fb > *fa) {
1596: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1597: SHFT(dum,*fb,*fa,dum)
1598: }
1.126 brouard 1599: *cx=(*bx)+GOLD*(*bx-*ax);
1600: *fc=(*func)(*cx);
1.183 brouard 1601: #ifdef DEBUG
1602: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1603: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1604: #endif
1605: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1606: r=(*bx-*ax)*(*fb-*fc);
1607: q=(*bx-*cx)*(*fb-*fa);
1608: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1609: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1610: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1611: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1612: fu=(*func)(u);
1.163 brouard 1613: #ifdef DEBUG
1614: /* f(x)=A(x-u)**2+f(u) */
1615: double A, fparabu;
1616: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1617: fparabu= *fa - A*(*ax-u)*(*ax-u);
1618: 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);
1619: 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 1620: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1621: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1622: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1623: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1624: #endif
1.184 brouard 1625: #ifdef MNBRAKORIGINAL
1.183 brouard 1626: #else
1.191 brouard 1627: /* if (fu > *fc) { */
1628: /* #ifdef DEBUG */
1629: /* printf("mnbrak4 fu > fc \n"); */
1630: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1631: /* #endif */
1632: /* /\* 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 *\\/ *\/ */
1633: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1634: /* dum=u; /\* Shifting c and u *\/ */
1635: /* u = *cx; */
1636: /* *cx = dum; */
1637: /* dum = fu; */
1638: /* fu = *fc; */
1639: /* *fc =dum; */
1640: /* } else { /\* end *\/ */
1641: /* #ifdef DEBUG */
1642: /* printf("mnbrak3 fu < fc \n"); */
1643: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1644: /* #endif */
1645: /* dum=u; /\* Shifting c and u *\/ */
1646: /* u = *cx; */
1647: /* *cx = dum; */
1648: /* dum = fu; */
1649: /* fu = *fc; */
1650: /* *fc =dum; */
1651: /* } */
1.183 brouard 1652: #ifdef DEBUG
1.191 brouard 1653: printf("mnbrak34 fu < or >= fc \n");
1654: fprintf(ficlog, "mnbrak34 fu < fc\n");
1.183 brouard 1655: #endif
1.191 brouard 1656: dum=u; /* Shifting c and u */
1657: u = *cx;
1658: *cx = dum;
1659: dum = fu;
1660: fu = *fc;
1661: *fc =dum;
1.183 brouard 1662: #endif
1.162 brouard 1663: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1664: #ifdef DEBUG
1665: printf("mnbrak2 u after c but before ulim\n");
1666: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1667: #endif
1.126 brouard 1668: fu=(*func)(u);
1669: if (fu < *fc) {
1.183 brouard 1670: #ifdef DEBUG
1671: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1672: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1673: #endif
1.126 brouard 1674: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1675: SHFT(*fb,*fc,fu,(*func)(u))
1676: }
1.162 brouard 1677: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1678: #ifdef DEBUG
1679: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1680: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1681: #endif
1.126 brouard 1682: u=ulim;
1683: fu=(*func)(u);
1.183 brouard 1684: } else { /* u could be left to b (if r > q parabola has a maximum) */
1685: #ifdef DEBUG
1686: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1687: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1688: #endif
1.126 brouard 1689: u=(*cx)+GOLD*(*cx-*bx);
1690: fu=(*func)(u);
1.183 brouard 1691: } /* end tests */
1.126 brouard 1692: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1693: SHFT(*fa,*fb,*fc,fu)
1694: #ifdef DEBUG
1695: 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);
1696: 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);
1697: #endif
1698: } /* 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 1699: }
1700:
1701: /*************** linmin ************************/
1.162 brouard 1702: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1703: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1704: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1705: the value of func at the returned location p . This is actually all accomplished by calling the
1706: routines mnbrak and brent .*/
1.126 brouard 1707: int ncom;
1708: double *pcom,*xicom;
1709: double (*nrfunc)(double []);
1710:
1711: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1712: {
1713: double brent(double ax, double bx, double cx,
1714: double (*f)(double), double tol, double *xmin);
1715: double f1dim(double x);
1716: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1717: double *fc, double (*func)(double));
1718: int j;
1719: double xx,xmin,bx,ax;
1720: double fx,fb,fa;
1.187 brouard 1721:
1.203 brouard 1722: #ifdef LINMINORIGINAL
1723: #else
1724: double scale=10., axs, xxs; /* Scale added for infinity */
1725: #endif
1726:
1.126 brouard 1727: ncom=n;
1728: pcom=vector(1,n);
1729: xicom=vector(1,n);
1730: nrfunc=func;
1731: for (j=1;j<=n;j++) {
1732: pcom[j]=p[j];
1.202 brouard 1733: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1734: }
1.187 brouard 1735:
1.203 brouard 1736: #ifdef LINMINORIGINAL
1737: xx=1.;
1738: #else
1739: axs=0.0;
1740: xxs=1.;
1741: do{
1742: xx= xxs;
1743: #endif
1.187 brouard 1744: ax=0.;
1745: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1746: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1747: /* 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)) */
1748: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1749: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1750: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1751: /* 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 1752: #ifdef LINMINORIGINAL
1753: #else
1754: if (fx != fx){
1755: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1756: printf("|");
1757: fprintf(ficlog,"|");
1758: #ifdef DEBUGLINMIN
1759: 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);
1760: #endif
1761: }
1762: }while(fx != fx);
1763: #endif
1764:
1.191 brouard 1765: #ifdef DEBUGLINMIN
1766: 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 1767: 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 1768: #endif
1.187 brouard 1769: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1770: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1771: /* fmin = f(p[j] + xmin * xi[j]) */
1772: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1773: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1774: #ifdef DEBUG
1775: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1776: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1777: #endif
1.191 brouard 1778: #ifdef DEBUGLINMIN
1779: printf("linmin end ");
1.202 brouard 1780: fprintf(ficlog,"linmin end ");
1.191 brouard 1781: #endif
1.126 brouard 1782: for (j=1;j<=n;j++) {
1.203 brouard 1783: #ifdef LINMINORIGINAL
1784: xi[j] *= xmin;
1785: #else
1786: #ifdef DEBUGLINMIN
1787: if(xxs <1.0)
1788: printf(" before xi[%d]=%12.8f", j,xi[j]);
1789: #endif
1790: 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) */
1791: #ifdef DEBUGLINMIN
1792: if(xxs <1.0)
1793: 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 );
1794: #endif
1795: #endif
1.187 brouard 1796: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1797: }
1.191 brouard 1798: #ifdef DEBUGLINMIN
1.203 brouard 1799: printf("\n");
1.191 brouard 1800: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 1801: 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 1802: for (j=1;j<=n;j++) {
1.202 brouard 1803: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1804: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1805: if(j % ncovmodel == 0){
1.191 brouard 1806: printf("\n");
1.202 brouard 1807: fprintf(ficlog,"\n");
1808: }
1.191 brouard 1809: }
1.203 brouard 1810: #else
1.191 brouard 1811: #endif
1.126 brouard 1812: free_vector(xicom,1,n);
1813: free_vector(pcom,1,n);
1814: }
1815:
1816:
1817: /*************** powell ************************/
1.162 brouard 1818: /*
1819: Minimization of a function func of n variables. Input consists of an initial starting point
1820: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1821: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1822: such that failure to decrease by more than this amount on one iteration signals doneness. On
1823: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1824: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1825: */
1.126 brouard 1826: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1827: double (*func)(double []))
1828: {
1829: void linmin(double p[], double xi[], int n, double *fret,
1830: double (*func)(double []));
1831: int i,ibig,j;
1832: double del,t,*pt,*ptt,*xit;
1.181 brouard 1833: double directest;
1.126 brouard 1834: double fp,fptt;
1835: double *xits;
1836: int niterf, itmp;
1837:
1838: pt=vector(1,n);
1839: ptt=vector(1,n);
1840: xit=vector(1,n);
1841: xits=vector(1,n);
1842: *fret=(*func)(p);
1843: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 1844: rcurr_time = time(NULL);
1.126 brouard 1845: for (*iter=1;;++(*iter)) {
1.187 brouard 1846: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1847: ibig=0;
1848: del=0.0;
1.157 brouard 1849: rlast_time=rcurr_time;
1850: /* (void) gettimeofday(&curr_time,&tzp); */
1851: rcurr_time = time(NULL);
1852: curr_time = *localtime(&rcurr_time);
1853: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1854: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1855: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1856: for (i=1;i<=n;i++) {
1.126 brouard 1857: printf(" %d %.12f",i, p[i]);
1858: fprintf(ficlog," %d %.12lf",i, p[i]);
1859: fprintf(ficrespow," %.12lf", p[i]);
1860: }
1861: printf("\n");
1862: fprintf(ficlog,"\n");
1863: fprintf(ficrespow,"\n");fflush(ficrespow);
1864: if(*iter <=3){
1.157 brouard 1865: tml = *localtime(&rcurr_time);
1866: strcpy(strcurr,asctime(&tml));
1867: rforecast_time=rcurr_time;
1.126 brouard 1868: itmp = strlen(strcurr);
1869: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1870: strcurr[itmp-1]='\0';
1.162 brouard 1871: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1872: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1873: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1874: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1875: forecast_time = *localtime(&rforecast_time);
1876: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1877: itmp = strlen(strfor);
1878: if(strfor[itmp-1]=='\n')
1879: strfor[itmp-1]='\0';
1.157 brouard 1880: 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);
1881: 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 1882: }
1883: }
1.187 brouard 1884: for (i=1;i<=n;i++) { /* For each direction i */
1885: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1886: fptt=(*fret);
1887: #ifdef DEBUG
1.203 brouard 1888: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1889: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1890: #endif
1.203 brouard 1891: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1892: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 brouard 1893: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1894: /* Outputs are fret(new point p) p is updated and xit rescaled */
1895: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1896: /* because that direction will be replaced unless the gain del is small */
1897: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1898: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1899: /* with the new direction. */
1.126 brouard 1900: del=fabs(fptt-(*fret));
1901: ibig=i;
1902: }
1903: #ifdef DEBUG
1904: printf("%d %.12e",i,(*fret));
1905: fprintf(ficlog,"%d %.12e",i,(*fret));
1906: for (j=1;j<=n;j++) {
1907: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1908: printf(" x(%d)=%.12e",j,xit[j]);
1909: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1910: }
1911: for(j=1;j<=n;j++) {
1.162 brouard 1912: printf(" p(%d)=%.12e",j,p[j]);
1913: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1914: }
1915: printf("\n");
1916: fprintf(ficlog,"\n");
1917: #endif
1.187 brouard 1918: } /* end loop on each direction i */
1919: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1920: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1921: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1922: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1923: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1924: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1925: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1926: /* decreased of more than 3.84 */
1927: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1928: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1929: /* By adding 10 parameters more the gain should be 18.31 */
1930:
1931: /* Starting the program with initial values given by a former maximization will simply change */
1932: /* the scales of the directions and the directions, because the are reset to canonical directions */
1933: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1934: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1935: #ifdef DEBUG
1936: int k[2],l;
1937: k[0]=1;
1938: k[1]=-1;
1939: printf("Max: %.12e",(*func)(p));
1940: fprintf(ficlog,"Max: %.12e",(*func)(p));
1941: for (j=1;j<=n;j++) {
1942: printf(" %.12e",p[j]);
1943: fprintf(ficlog," %.12e",p[j]);
1944: }
1945: printf("\n");
1946: fprintf(ficlog,"\n");
1947: for(l=0;l<=1;l++) {
1948: for (j=1;j<=n;j++) {
1949: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1950: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1951: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1952: }
1953: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1954: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1955: }
1956: #endif
1957:
1958:
1959: free_vector(xit,1,n);
1960: free_vector(xits,1,n);
1961: free_vector(ptt,1,n);
1962: free_vector(pt,1,n);
1963: return;
1.192 brouard 1964: } /* enough precision */
1.126 brouard 1965: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1966: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1967: ptt[j]=2.0*p[j]-pt[j];
1968: xit[j]=p[j]-pt[j];
1969: pt[j]=p[j];
1970: }
1.181 brouard 1971: fptt=(*func)(ptt); /* f_3 */
1.192 brouard 1972: #ifdef POWELLF1F3
1973: #else
1.161 brouard 1974: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 1975: #endif
1.162 brouard 1976: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1977: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1978: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1979: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1980: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1981: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1982: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1983: #ifdef NRCORIGINAL
1984: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1985: #else
1986: 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 1987: t= t- del*SQR(fp-fptt);
1.183 brouard 1988: #endif
1.202 brouard 1989: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 1990: #ifdef DEBUG
1.181 brouard 1991: 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);
1992: 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 1993: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1994: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1995: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1996: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1997: 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);
1998: 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);
1999: #endif
1.183 brouard 2000: #ifdef POWELLORIGINAL
2001: if (t < 0.0) { /* Then we use it for new direction */
2002: #else
1.182 brouard 2003: if (directest*t < 0.0) { /* Contradiction between both tests */
1.202 brouard 2004: 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 2005: 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 2006: 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 2007: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
2008: }
1.181 brouard 2009: if (directest < 0.0) { /* Then we use it for new direction */
2010: #endif
1.191 brouard 2011: #ifdef DEBUGLINMIN
2012: printf("Before linmin in direction P%d-P0\n",n);
2013: for (j=1;j<=n;j++) {
1.202 brouard 2014: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2015: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2016: if(j % ncovmodel == 0){
1.191 brouard 2017: printf("\n");
1.202 brouard 2018: fprintf(ficlog,"\n");
2019: }
1.191 brouard 2020: }
2021: #endif
1.187 brouard 2022: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.191 brouard 2023: #ifdef DEBUGLINMIN
2024: for (j=1;j<=n;j++) {
2025: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1.202 brouard 2026: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2027: if(j % ncovmodel == 0){
1.191 brouard 2028: printf("\n");
1.202 brouard 2029: fprintf(ficlog,"\n");
2030: }
1.191 brouard 2031: }
2032: #endif
1.126 brouard 2033: for (j=1;j<=n;j++) {
1.181 brouard 2034: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
2035: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 2036: }
1.181 brouard 2037: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2038: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 2039:
1.126 brouard 2040: #ifdef DEBUG
1.164 brouard 2041: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2042: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 2043: for(j=1;j<=n;j++){
2044: printf(" %.12e",xit[j]);
2045: fprintf(ficlog," %.12e",xit[j]);
2046: }
2047: printf("\n");
2048: fprintf(ficlog,"\n");
2049: #endif
1.192 brouard 2050: } /* end of t or directest negative */
2051: #ifdef POWELLF1F3
2052: #else
1.162 brouard 2053: } /* end if (fptt < fp) */
1.192 brouard 2054: #endif
2055: } /* loop iteration */
1.126 brouard 2056: }
2057:
2058: /**** Prevalence limit (stable or period prevalence) ****************/
2059:
1.203 brouard 2060: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
1.126 brouard 2061: {
1.218 brouard 2062: /* Computes the prevalence limit in each live state at age x and for covariate ij by left multiplying the unit
1.203 brouard 2063: matrix by transitions matrix until convergence is reached with precision ftolpl */
1.206 brouard 2064: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2065: /* Wx is row vector: population in state 1, population in state 2, population dead */
2066: /* or prevalence in state 1, prevalence in state 2, 0 */
2067: /* newm is the matrix after multiplications, its rows are identical at a factor */
2068: /* Initial matrix pimij */
2069: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2070: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2071: /* 0, 0 , 1} */
2072: /*
2073: * and after some iteration: */
2074: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2075: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2076: /* 0, 0 , 1} */
2077: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2078: /* {0.51571254859325999, 0.4842874514067399, */
2079: /* 0.51326036147820708, 0.48673963852179264} */
2080: /* If we start from prlim again, prlim tends to a constant matrix */
2081:
1.126 brouard 2082: int i, ii,j,k;
1.209 brouard 2083: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2084: /* double **matprod2(); */ /* test */
1.218 brouard 2085: double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126 brouard 2086: double **newm;
1.209 brouard 2087: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2088: int ncvloop=0;
1.169 brouard 2089:
1.209 brouard 2090: min=vector(1,nlstate);
2091: max=vector(1,nlstate);
2092: meandiff=vector(1,nlstate);
2093:
1.218 brouard 2094: /* Starting with matrix unity */
1.126 brouard 2095: for (ii=1;ii<=nlstate+ndeath;ii++)
2096: for (j=1;j<=nlstate+ndeath;j++){
2097: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2098: }
1.169 brouard 2099:
2100: cov[1]=1.;
2101:
2102: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2103: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2104: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2105: ncvloop++;
1.126 brouard 2106: newm=savm;
2107: /* Covariates have to be included here again */
1.138 brouard 2108: cov[2]=agefin;
1.187 brouard 2109: if(nagesqr==1)
2110: cov[3]= agefin*agefin;;
1.138 brouard 2111: for (k=1; k<=cptcovn;k++) {
1.200 brouard 2112: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.218 brouard 2113: /* Here comes the value of the covariate 'ij' */
1.200 brouard 2114: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
1.198 brouard 2115: /* 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 2116: }
1.186 brouard 2117: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2118: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2119: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
1.186 brouard 2120: for (k=1; k<=cptcovprod;k++) /* Useless */
1.200 brouard 2121: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2122: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.138 brouard 2123:
2124: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2125: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2126: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2127: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2128: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2129: /* age and covariate values of ij are in 'cov' */
1.142 brouard 2130: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2131:
1.126 brouard 2132: savm=oldm;
2133: oldm=newm;
1.209 brouard 2134:
2135: for(j=1; j<=nlstate; j++){
2136: max[j]=0.;
2137: min[j]=1.;
2138: }
2139: for(i=1;i<=nlstate;i++){
2140: sumnew=0;
2141: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2142: for(j=1; j<=nlstate; j++){
2143: prlim[i][j]= newm[i][j]/(1-sumnew);
2144: max[j]=FMAX(max[j],prlim[i][j]);
2145: min[j]=FMIN(min[j],prlim[i][j]);
2146: }
2147: }
2148:
1.126 brouard 2149: maxmax=0.;
1.209 brouard 2150: for(j=1; j<=nlstate; j++){
2151: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2152: maxmax=FMAX(maxmax,meandiff[j]);
2153: /* 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 2154: } /* j loop */
1.203 brouard 2155: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2156: /* 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 2157: if(maxmax < ftolpl){
1.209 brouard 2158: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2159: free_vector(min,1,nlstate);
2160: free_vector(max,1,nlstate);
2161: free_vector(meandiff,1,nlstate);
1.126 brouard 2162: return prlim;
2163: }
1.169 brouard 2164: } /* age loop */
1.208 brouard 2165: /* After some age loop it doesn't converge */
1.209 brouard 2166: 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 2167: 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 2168: /* 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); */
2169: free_vector(min,1,nlstate);
2170: free_vector(max,1,nlstate);
2171: free_vector(meandiff,1,nlstate);
1.208 brouard 2172:
1.169 brouard 2173: return prlim; /* should not reach here */
1.126 brouard 2174: }
2175:
1.217 brouard 2176:
2177: /**** Back Prevalence limit (stable or period prevalence) ****************/
2178:
1.218 brouard 2179: /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ageminpar, double agemaxpar, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
2180: /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
2181: double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij)
1.217 brouard 2182: {
1.218 brouard 2183: /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit
1.217 brouard 2184: matrix by transitions matrix until convergence is reached with precision ftolpl */
2185: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2186: /* Wx is row vector: population in state 1, population in state 2, population dead */
2187: /* or prevalence in state 1, prevalence in state 2, 0 */
2188: /* newm is the matrix after multiplications, its rows are identical at a factor */
2189: /* Initial matrix pimij */
2190: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2191: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2192: /* 0, 0 , 1} */
2193: /*
2194: * and after some iteration: */
2195: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2196: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2197: /* 0, 0 , 1} */
2198: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2199: /* {0.51571254859325999, 0.4842874514067399, */
2200: /* 0.51326036147820708, 0.48673963852179264} */
2201: /* If we start from prlim again, prlim tends to a constant matrix */
2202:
2203: int i, ii,j,k;
2204: double *min, *max, *meandiff, maxmax,sumnew=0.;
2205: /* double **matprod2(); */ /* test */
2206: double **out, cov[NCOVMAX+1], **bmij();
2207: double **newm;
1.218 brouard 2208: double **dnewm, **doldm, **dsavm; /* for use */
2209: double **oldm, **savm; /* for use */
2210:
1.217 brouard 2211: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
2212: int ncvloop=0;
2213:
2214: min=vector(1,nlstate);
2215: max=vector(1,nlstate);
2216: meandiff=vector(1,nlstate);
2217:
1.218 brouard 2218: dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
2219: oldm=oldms; savm=savms;
2220:
2221: /* Starting with matrix unity */
2222: for (ii=1;ii<=nlstate+ndeath;ii++)
2223: for (j=1;j<=nlstate+ndeath;j++){
1.217 brouard 2224: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2225: }
2226:
2227: cov[1]=1.;
2228:
2229: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2230: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218 brouard 2231: /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
2232: for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217 brouard 2233: ncvloop++;
1.218 brouard 2234: newm=savm; /* oldm should be kept from previous iteration or unity at start */
2235: /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217 brouard 2236: /* Covariates have to be included here again */
2237: cov[2]=agefin;
2238: if(nagesqr==1)
2239: cov[3]= agefin*agefin;;
2240: for (k=1; k<=cptcovn;k++) {
2241: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
2242: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2243: /* 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])]); */
2244: }
2245: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2246: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2247: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
2248: for (k=1; k<=cptcovprod;k++) /* Useless */
2249: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2250: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2251:
2252: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2253: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2254: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
2255: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2256: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2257: /* ij should be linked to the correct index of cov */
2258: /* age and covariate values ij are in 'cov', but we need to pass
2259: * ij for the observed prevalence at age and status and covariate
2260: * number: prevacurrent[(int)agefin][ii][ij]
2261: */
2262: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
2263: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
2264: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
1.217 brouard 2265: savm=oldm;
2266: oldm=newm;
2267: for(j=1; j<=nlstate; j++){
2268: max[j]=0.;
2269: min[j]=1.;
2270: }
2271: for(j=1; j<=nlstate; j++){
2272: for(i=1;i<=nlstate;i++){
1.218 brouard 2273: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
2274: bprlim[i][j]= newm[i][j];
2275: max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
2276: min[i]=FMIN(min[i],bprlim[i][j]);
1.217 brouard 2277: }
2278: }
1.218 brouard 2279:
1.217 brouard 2280: maxmax=0.;
2281: for(i=1; i<=nlstate; i++){
2282: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
2283: maxmax=FMAX(maxmax,meandiff[i]);
2284: /* 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); */
2285: } /* j loop */
2286: *ncvyear= -( (int)age- (int)agefin);
1.218 brouard 2287: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/
1.217 brouard 2288: if(maxmax < ftolpl){
2289: printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);
2290: free_vector(min,1,nlstate);
2291: free_vector(max,1,nlstate);
2292: free_vector(meandiff,1,nlstate);
2293: return bprlim;
2294: }
2295: } /* age loop */
2296: /* After some age loop it doesn't converge */
2297: 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\
2298: 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);
2299: /* 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); */
2300: free_vector(min,1,nlstate);
2301: free_vector(max,1,nlstate);
2302: free_vector(meandiff,1,nlstate);
2303:
2304: return bprlim; /* should not reach here */
2305: }
2306:
1.126 brouard 2307: /*************** transition probabilities ***************/
2308:
2309: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2310: {
1.138 brouard 2311: /* According to parameters values stored in x and the covariate's values stored in cov,
2312: computes the probability to be observed in state j being in state i by appying the
2313: model to the ncovmodel covariates (including constant and age).
2314: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2315: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2316: ncth covariate in the global vector x is given by the formula:
2317: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2318: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2319: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2320: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2321: Outputs ps[i][j] the probability to be observed in j being in j according to
2322: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2323: */
2324: double s1, lnpijopii;
1.126 brouard 2325: /*double t34;*/
1.164 brouard 2326: int i,j, nc, ii, jj;
1.126 brouard 2327:
1.218 brouard 2328: for(i=1; i<= nlstate; i++){
2329: for(j=1; j<i;j++){
2330: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2331: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2332: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2333: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2334: }
2335: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2336: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2337: }
2338: for(j=i+1; j<=nlstate+ndeath;j++){
2339: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2340: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2341: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2342: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2343: }
2344: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2345: }
2346: }
2347:
2348: for(i=1; i<= nlstate; i++){
2349: s1=0;
2350: for(j=1; j<i; j++){
2351: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2352: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2353: }
2354: for(j=i+1; j<=nlstate+ndeath; j++){
2355: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2356: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2357: }
2358: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2359: ps[i][i]=1./(s1+1.);
2360: /* Computing other pijs */
2361: for(j=1; j<i; j++)
2362: ps[i][j]= exp(ps[i][j])*ps[i][i];
2363: for(j=i+1; j<=nlstate+ndeath; j++)
2364: ps[i][j]= exp(ps[i][j])*ps[i][i];
2365: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2366: } /* end i */
2367:
2368: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2369: for(jj=1; jj<= nlstate+ndeath; jj++){
2370: ps[ii][jj]=0;
2371: ps[ii][ii]=1;
2372: }
2373: }
2374:
2375:
2376: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2377: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2378: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2379: /* } */
2380: /* printf("\n "); */
2381: /* } */
2382: /* printf("\n ");printf("%lf ",cov[2]);*/
2383: /*
2384: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2385: goto end;*/
2386: return ps;
1.126 brouard 2387: }
2388:
1.218 brouard 2389: /*************** backward transition probabilities ***************/
2390:
2391: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ageminpar, double agemaxpar, double ***dnewm, double **doldm, double **dsavm, int ij ) */
2392: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
2393: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij )
2394: {
2395: /* Computes the backward probability at age agefin and covariate ij
2396: * and returns in **ps as well as **bmij.
2397: */
2398: int i, ii, j,k;
2399:
2400: double **out, **pmij();
2401: double sumnew=0.;
2402: double agefin;
2403:
2404: double **dnewm, **dsavm, **doldm;
2405: double **bbmij;
2406:
2407: doldm=ddoldms; /* global pointers */
2408: dnewm=ddnewms;
2409: dsavm=ddsavms;
2410:
2411: agefin=cov[2];
2412: /* bmij *//* age is cov[2], ij is included in cov, but we need for
2413: the observed prevalence (with this covariate ij) */
2414: dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
2415: /* We do have the matrix Px in savm and we need pij */
2416: for (j=1;j<=nlstate+ndeath;j++){
2417: sumnew=0.; /* w1 p11 + w2 p21 only on live states */
2418: for (ii=1;ii<=nlstate;ii++){
2419: sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
2420: } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
2421: for (ii=1;ii<=nlstate+ndeath;ii++){
2422: if(sumnew >= 1.e-10){
2423: /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
2424: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
2425: /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
2426: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
2427: /* }else */
2428: doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
2429: }else{
2430: printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin);
2431: }
2432: } /*End ii */
2433: } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
2434: /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
2435: bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
2436: /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
2437: /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
2438: /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
2439: /* left Product of this matrix by diag matrix of prevalences (savm) */
2440: for (j=1;j<=nlstate+ndeath;j++){
2441: for (ii=1;ii<=nlstate+ndeath;ii++){
2442: dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
2443: }
2444: } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
2445: ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
2446: /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
2447: /* end bmij */
2448: return ps;
2449: }
1.217 brouard 2450: /*************** transition probabilities ***************/
2451:
1.218 brouard 2452: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217 brouard 2453: {
2454: /* According to parameters values stored in x and the covariate's values stored in cov,
2455: computes the probability to be observed in state j being in state i by appying the
2456: model to the ncovmodel covariates (including constant and age).
2457: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2458: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2459: ncth covariate in the global vector x is given by the formula:
2460: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2461: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2462: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2463: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2464: Outputs ps[i][j] the probability to be observed in j being in j according to
2465: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2466: */
2467: double s1, lnpijopii;
2468: /*double t34;*/
2469: int i,j, nc, ii, jj;
2470:
1.218 brouard 2471: for(i=1; i<= nlstate; i++){
2472: for(j=1; j<i;j++){
2473: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2474: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2475: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2476: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2477: }
2478: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2479: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2480: }
2481: for(j=i+1; j<=nlstate+ndeath;j++){
2482: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2483: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2484: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2485: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2486: }
2487: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2488: }
2489: }
2490:
2491: for(i=1; i<= nlstate; i++){
2492: s1=0;
2493: for(j=1; j<i; j++){
2494: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2495: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2496: }
2497: for(j=i+1; j<=nlstate+ndeath; j++){
2498: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2499: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2500: }
2501: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2502: ps[i][i]=1./(s1+1.);
2503: /* Computing other pijs */
2504: for(j=1; j<i; j++)
2505: ps[i][j]= exp(ps[i][j])*ps[i][i];
2506: for(j=i+1; j<=nlstate+ndeath; j++)
2507: ps[i][j]= exp(ps[i][j])*ps[i][i];
2508: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2509: } /* end i */
2510:
2511: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2512: for(jj=1; jj<= nlstate+ndeath; jj++){
2513: ps[ii][jj]=0;
2514: ps[ii][ii]=1;
2515: }
2516: }
2517: /* Added for backcast */ /* Transposed matrix too */
2518: for(jj=1; jj<= nlstate+ndeath; jj++){
2519: s1=0.;
2520: for(ii=1; ii<= nlstate+ndeath; ii++){
2521: s1+=ps[ii][jj];
2522: }
2523: for(ii=1; ii<= nlstate; ii++){
2524: ps[ii][jj]=ps[ii][jj]/s1;
2525: }
2526: }
2527: /* Transposition */
2528: for(jj=1; jj<= nlstate+ndeath; jj++){
2529: for(ii=jj; ii<= nlstate+ndeath; ii++){
2530: s1=ps[ii][jj];
2531: ps[ii][jj]=ps[jj][ii];
2532: ps[jj][ii]=s1;
2533: }
2534: }
2535: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2536: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2537: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2538: /* } */
2539: /* printf("\n "); */
2540: /* } */
2541: /* printf("\n ");printf("%lf ",cov[2]);*/
2542: /*
2543: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2544: goto end;*/
2545: return ps;
1.217 brouard 2546: }
2547:
2548:
1.126 brouard 2549: /**************** Product of 2 matrices ******************/
2550:
1.145 brouard 2551: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2552: {
2553: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2554: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2555: /* in, b, out are matrice of pointers which should have been initialized
2556: before: only the contents of out is modified. The function returns
2557: a pointer to pointers identical to out */
1.145 brouard 2558: int i, j, k;
1.126 brouard 2559: for(i=nrl; i<= nrh; i++)
1.145 brouard 2560: for(k=ncolol; k<=ncoloh; k++){
2561: out[i][k]=0.;
2562: for(j=ncl; j<=nch; j++)
2563: out[i][k] +=in[i][j]*b[j][k];
2564: }
1.126 brouard 2565: return out;
2566: }
2567:
2568:
2569: /************* Higher Matrix Product ***************/
2570:
2571: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2572: {
1.218 brouard 2573: /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
1.126 brouard 2574: 'nhstepm*hstepm*stepm' months (i.e. until
2575: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2576: nhstepm*hstepm matrices.
2577: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2578: (typically every 2 years instead of every month which is too big
2579: for the memory).
2580: Model is determined by parameters x and covariates have to be
2581: included manually here.
2582:
2583: */
2584:
2585: int i, j, d, h, k;
1.131 brouard 2586: double **out, cov[NCOVMAX+1];
1.126 brouard 2587: double **newm;
1.187 brouard 2588: double agexact;
1.214 brouard 2589: double agebegin, ageend;
1.126 brouard 2590:
2591: /* Hstepm could be zero and should return the unit matrix */
2592: for (i=1;i<=nlstate+ndeath;i++)
2593: for (j=1;j<=nlstate+ndeath;j++){
2594: oldm[i][j]=(i==j ? 1.0 : 0.0);
2595: po[i][j][0]=(i==j ? 1.0 : 0.0);
2596: }
2597: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2598: for(h=1; h <=nhstepm; h++){
2599: for(d=1; d <=hstepm; d++){
2600: newm=savm;
2601: /* Covariates have to be included here again */
2602: cov[1]=1.;
1.214 brouard 2603: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 2604: cov[2]=agexact;
2605: if(nagesqr==1)
1.218 brouard 2606: cov[3]= agexact*agexact;
1.131 brouard 2607: for (k=1; k<=cptcovn;k++)
1.218 brouard 2608: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2609: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.186 brouard 2610: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1.218 brouard 2611: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2612: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2613: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.145 brouard 2614: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.218 brouard 2615: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2616: /* 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 2617:
2618:
2619: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2620: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 2621: /* right multiplication of oldm by the current matrix */
1.126 brouard 2622: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2623: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 brouard 2624: /* if((int)age == 70){ */
2625: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
2626: /* for(i=1; i<=nlstate+ndeath; i++) { */
2627: /* printf("%d pmmij ",i); */
2628: /* for(j=1;j<=nlstate+ndeath;j++) { */
2629: /* printf("%f ",pmmij[i][j]); */
2630: /* } */
2631: /* printf(" oldm "); */
2632: /* for(j=1;j<=nlstate+ndeath;j++) { */
2633: /* printf("%f ",oldm[i][j]); */
2634: /* } */
2635: /* printf("\n"); */
2636: /* } */
2637: /* } */
1.126 brouard 2638: savm=oldm;
2639: oldm=newm;
2640: }
2641: for(i=1; i<=nlstate+ndeath; i++)
2642: for(j=1;j<=nlstate+ndeath;j++) {
1.218 brouard 2643: po[i][j][h]=newm[i][j];
2644: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2645: }
1.128 brouard 2646: /*printf("h=%d ",h);*/
1.126 brouard 2647: } /* end h */
1.218 brouard 2648: /* printf("\n H=%d \n",h); */
1.126 brouard 2649: return po;
2650: }
2651:
1.217 brouard 2652: /************* Higher Back Matrix Product ***************/
1.218 brouard 2653: /* double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */
2654: double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )
1.217 brouard 2655: {
1.218 brouard 2656: /* Computes the transition matrix starting at age 'age' over
1.217 brouard 2657: 'nhstepm*hstepm*stepm' months (i.e. until
1.218 brouard 2658: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2659: nhstepm*hstepm matrices.
2660: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2661: (typically every 2 years instead of every month which is too big
1.217 brouard 2662: for the memory).
1.218 brouard 2663: Model is determined by parameters x and covariates have to be
2664: included manually here.
1.217 brouard 2665:
2666: */
2667:
2668: int i, j, d, h, k;
2669: double **out, cov[NCOVMAX+1];
2670: double **newm;
2671: double agexact;
2672: double agebegin, ageend;
1.218 brouard 2673: double **oldm, **savm;
1.217 brouard 2674:
1.218 brouard 2675: oldm=oldms;savm=savms;
1.217 brouard 2676: /* Hstepm could be zero and should return the unit matrix */
2677: for (i=1;i<=nlstate+ndeath;i++)
2678: for (j=1;j<=nlstate+ndeath;j++){
2679: oldm[i][j]=(i==j ? 1.0 : 0.0);
2680: po[i][j][0]=(i==j ? 1.0 : 0.0);
2681: }
2682: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2683: for(h=1; h <=nhstepm; h++){
2684: for(d=1; d <=hstepm; d++){
2685: newm=savm;
2686: /* Covariates have to be included here again */
2687: cov[1]=1.;
2688: agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
2689: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
2690: cov[2]=agexact;
2691: if(nagesqr==1)
1.218 brouard 2692: cov[3]= agexact*agexact;
2693: for (k=1; k<=cptcovn;k++)
2694: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2695: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.217 brouard 2696: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1.218 brouard 2697: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2698: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2699: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.217 brouard 2700: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.218 brouard 2701: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2702: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2703:
2704:
1.217 brouard 2705: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2706: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 2707: /* Careful transposed matrix */
2708: /* age is in cov[2] */
2709: /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
2710: /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
2711: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
2712: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217 brouard 2713: /* if((int)age == 70){ */
2714: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
2715: /* for(i=1; i<=nlstate+ndeath; i++) { */
2716: /* printf("%d pmmij ",i); */
2717: /* for(j=1;j<=nlstate+ndeath;j++) { */
2718: /* printf("%f ",pmmij[i][j]); */
2719: /* } */
2720: /* printf(" oldm "); */
2721: /* for(j=1;j<=nlstate+ndeath;j++) { */
2722: /* printf("%f ",oldm[i][j]); */
2723: /* } */
2724: /* printf("\n"); */
2725: /* } */
2726: /* } */
2727: savm=oldm;
2728: oldm=newm;
2729: }
2730: for(i=1; i<=nlstate+ndeath; i++)
2731: for(j=1;j<=nlstate+ndeath;j++) {
1.218 brouard 2732: po[i][j][h]=newm[i][j];
2733: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.217 brouard 2734: }
2735: /*printf("h=%d ",h);*/
2736: } /* end h */
1.218 brouard 2737: /* printf("\n H=%d \n",h); */
1.217 brouard 2738: return po;
2739: }
2740:
2741:
1.162 brouard 2742: #ifdef NLOPT
2743: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2744: double fret;
2745: double *xt;
2746: int j;
2747: myfunc_data *d2 = (myfunc_data *) pd;
2748: /* xt = (p1-1); */
2749: xt=vector(1,n);
2750: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2751:
2752: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2753: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2754: printf("Function = %.12lf ",fret);
2755: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2756: printf("\n");
2757: free_vector(xt,1,n);
2758: return fret;
2759: }
2760: #endif
1.126 brouard 2761:
2762: /*************** log-likelihood *************/
2763: double func( double *x)
2764: {
2765: int i, ii, j, k, mi, d, kk;
1.131 brouard 2766: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2767: double **out;
2768: double sw; /* Sum of weights */
2769: double lli; /* Individual log likelihood */
2770: int s1, s2;
2771: double bbh, survp;
2772: long ipmx;
1.187 brouard 2773: double agexact;
1.126 brouard 2774: /*extern weight */
2775: /* We are differentiating ll according to initial status */
2776: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2777: /*for(i=1;i<imx;i++)
2778: printf(" %d\n",s[4][i]);
2779: */
1.162 brouard 2780:
2781: ++countcallfunc;
2782:
1.126 brouard 2783: cov[1]=1.;
2784:
2785: for(k=1; k<=nlstate; k++) ll[k]=0.;
2786:
2787: if(mle==1){
2788: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2789: /* Computes the values of the ncovmodel covariates of the model
2790: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2791: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2792: to be observed in j being in i according to the model.
2793: */
1.145 brouard 2794: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 brouard 2795: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2796: }
1.137 brouard 2797: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2798: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2799: has been calculated etc */
1.126 brouard 2800: for(mi=1; mi<= wav[i]-1; mi++){
2801: for (ii=1;ii<=nlstate+ndeath;ii++)
2802: for (j=1;j<=nlstate+ndeath;j++){
2803: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2804: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2805: }
2806: for(d=0; d<dh[mi][i]; d++){
2807: newm=savm;
1.187 brouard 2808: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2809: cov[2]=agexact;
2810: if(nagesqr==1)
2811: cov[3]= agexact*agexact;
1.126 brouard 2812: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2813: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2814: }
2815: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2816: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2817: savm=oldm;
2818: oldm=newm;
2819: } /* end mult */
2820:
2821: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2822: /* But now since version 0.9 we anticipate for bias at large stepm.
2823: * If stepm is larger than one month (smallest stepm) and if the exact delay
2824: * (in months) between two waves is not a multiple of stepm, we rounded to
2825: * the nearest (and in case of equal distance, to the lowest) interval but now
2826: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2827: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2828: * probability in order to take into account the bias as a fraction of the way
2829: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2830: * -stepm/2 to stepm/2 .
2831: * For stepm=1 the results are the same as for previous versions of Imach.
2832: * For stepm > 1 the results are less biased than in previous versions.
2833: */
2834: s1=s[mw[mi][i]][i];
2835: s2=s[mw[mi+1][i]][i];
2836: bbh=(double)bh[mi][i]/(double)stepm;
2837: /* bias bh is positive if real duration
2838: * is higher than the multiple of stepm and negative otherwise.
2839: */
2840: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2841: if( s2 > nlstate){
2842: /* i.e. if s2 is a death state and if the date of death is known
2843: then the contribution to the likelihood is the probability to
2844: die between last step unit time and current step unit time,
2845: which is also equal to probability to die before dh
2846: minus probability to die before dh-stepm .
2847: In version up to 0.92 likelihood was computed
2848: as if date of death was unknown. Death was treated as any other
2849: health state: the date of the interview describes the actual state
2850: and not the date of a change in health state. The former idea was
2851: to consider that at each interview the state was recorded
2852: (healthy, disable or death) and IMaCh was corrected; but when we
2853: introduced the exact date of death then we should have modified
2854: the contribution of an exact death to the likelihood. This new
2855: contribution is smaller and very dependent of the step unit
2856: stepm. It is no more the probability to die between last interview
2857: and month of death but the probability to survive from last
2858: interview up to one month before death multiplied by the
2859: probability to die within a month. Thanks to Chris
2860: Jackson for correcting this bug. Former versions increased
2861: mortality artificially. The bad side is that we add another loop
2862: which slows down the processing. The difference can be up to 10%
2863: lower mortality.
2864: */
1.183 brouard 2865: /* If, at the beginning of the maximization mostly, the
2866: cumulative probability or probability to be dead is
2867: constant (ie = 1) over time d, the difference is equal to
2868: 0. out[s1][3] = savm[s1][3]: probability, being at state
2869: s1 at precedent wave, to be dead a month before current
2870: wave is equal to probability, being at state s1 at
2871: precedent wave, to be dead at mont of the current
2872: wave. Then the observed probability (that this person died)
2873: is null according to current estimated parameter. In fact,
2874: it should be very low but not zero otherwise the log go to
2875: infinity.
2876: */
2877: /* #ifdef INFINITYORIGINAL */
2878: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2879: /* #else */
2880: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2881: /* lli=log(mytinydouble); */
2882: /* else */
2883: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2884: /* #endif */
1.216 brouard 2885: lli=log(out[s1][s2] - savm[s1][s2]);
2886:
2887: } else if ( s2==-1 ) { /* alive */
1.126 brouard 2888: for (j=1,survp=0. ; j<=nlstate; j++)
2889: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2890: /*survp += out[s1][j]; */
2891: lli= log(survp);
2892: }
2893: else if (s2==-4) {
2894: for (j=3,survp=0. ; j<=nlstate; j++)
2895: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2896: lli= log(survp);
2897: }
2898: else if (s2==-5) {
2899: for (j=1,survp=0. ; j<=2; j++)
2900: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2901: lli= log(survp);
2902: }
2903: else{
2904: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2905: /* 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 */
2906: }
2907: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2908: /*if(lli ==000.0)*/
2909: /*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); */
2910: ipmx +=1;
2911: sw += weight[i];
2912: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2913: /* if (lli < log(mytinydouble)){ */
2914: /* 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); */
2915: /* 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]); */
2916: /* } */
1.126 brouard 2917: } /* end of wave */
2918: } /* end of individual */
2919: } else if(mle==2){
2920: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2921: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2922: for(mi=1; mi<= wav[i]-1; mi++){
2923: for (ii=1;ii<=nlstate+ndeath;ii++)
2924: for (j=1;j<=nlstate+ndeath;j++){
2925: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2926: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2927: }
2928: for(d=0; d<=dh[mi][i]; d++){
2929: newm=savm;
1.187 brouard 2930: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2931: cov[2]=agexact;
2932: if(nagesqr==1)
2933: cov[3]= agexact*agexact;
1.126 brouard 2934: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2935: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2936: }
2937: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2938: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2939: savm=oldm;
2940: oldm=newm;
2941: } /* end mult */
2942:
2943: s1=s[mw[mi][i]][i];
2944: s2=s[mw[mi+1][i]][i];
2945: bbh=(double)bh[mi][i]/(double)stepm;
2946: 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 */
2947: ipmx +=1;
2948: sw += weight[i];
2949: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2950: } /* end of wave */
2951: } /* end of individual */
2952: } else if(mle==3){ /* exponential inter-extrapolation */
2953: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2954: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2955: for(mi=1; mi<= wav[i]-1; mi++){
2956: for (ii=1;ii<=nlstate+ndeath;ii++)
2957: for (j=1;j<=nlstate+ndeath;j++){
2958: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2959: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2960: }
2961: for(d=0; d<dh[mi][i]; d++){
2962: newm=savm;
1.187 brouard 2963: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2964: cov[2]=agexact;
2965: if(nagesqr==1)
2966: cov[3]= agexact*agexact;
1.126 brouard 2967: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2968: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2969: }
2970: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2971: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2972: savm=oldm;
2973: oldm=newm;
2974: } /* end mult */
2975:
2976: s1=s[mw[mi][i]][i];
2977: s2=s[mw[mi+1][i]][i];
2978: bbh=(double)bh[mi][i]/(double)stepm;
2979: 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 */
2980: ipmx +=1;
2981: sw += weight[i];
2982: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2983: } /* end of wave */
2984: } /* end of individual */
2985: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2986: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2987: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2988: for(mi=1; mi<= wav[i]-1; mi++){
2989: for (ii=1;ii<=nlstate+ndeath;ii++)
2990: for (j=1;j<=nlstate+ndeath;j++){
2991: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2992: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2993: }
2994: for(d=0; d<dh[mi][i]; d++){
2995: newm=savm;
1.187 brouard 2996: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2997: cov[2]=agexact;
2998: if(nagesqr==1)
2999: cov[3]= agexact*agexact;
1.126 brouard 3000: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 3001: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 3002: }
3003:
3004: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3005: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3006: savm=oldm;
3007: oldm=newm;
3008: } /* end mult */
3009:
3010: s1=s[mw[mi][i]][i];
3011: s2=s[mw[mi+1][i]][i];
3012: if( s2 > nlstate){
3013: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3014: } else if ( s2==-1 ) { /* alive */
3015: for (j=1,survp=0. ; j<=nlstate; j++)
3016: survp += out[s1][j];
3017: lli= log(survp);
1.126 brouard 3018: }else{
3019: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3020: }
3021: ipmx +=1;
3022: sw += weight[i];
3023: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3024: /* 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]); */
3025: } /* end of wave */
3026: } /* end of individual */
3027: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
3028: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 3029: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 3030: for(mi=1; mi<= wav[i]-1; mi++){
3031: for (ii=1;ii<=nlstate+ndeath;ii++)
3032: for (j=1;j<=nlstate+ndeath;j++){
3033: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3034: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3035: }
3036: for(d=0; d<dh[mi][i]; d++){
3037: newm=savm;
1.187 brouard 3038: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3039: cov[2]=agexact;
3040: if(nagesqr==1)
3041: cov[3]= agexact*agexact;
1.126 brouard 3042: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 3043: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 3044: }
3045:
3046: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3047: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3048: savm=oldm;
3049: oldm=newm;
3050: } /* end mult */
3051:
3052: s1=s[mw[mi][i]][i];
3053: s2=s[mw[mi+1][i]][i];
3054: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3055: ipmx +=1;
3056: sw += weight[i];
3057: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3058: /*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]);*/
3059: } /* end of wave */
3060: } /* end of individual */
3061: } /* End of if */
3062: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3063: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3064: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3065: return -l;
3066: }
3067:
3068: /*************** log-likelihood *************/
3069: double funcone( double *x)
3070: {
3071: /* Same as likeli but slower because of a lot of printf and if */
3072: int i, ii, j, k, mi, d, kk;
1.131 brouard 3073: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 3074: double **out;
3075: double lli; /* Individual log likelihood */
3076: double llt;
3077: int s1, s2;
3078: double bbh, survp;
1.187 brouard 3079: double agexact;
1.214 brouard 3080: double agebegin, ageend;
1.126 brouard 3081: /*extern weight */
3082: /* We are differentiating ll according to initial status */
3083: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3084: /*for(i=1;i<imx;i++)
3085: printf(" %d\n",s[4][i]);
3086: */
3087: cov[1]=1.;
3088:
3089: for(k=1; k<=nlstate; k++) ll[k]=0.;
3090:
3091: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 3092: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 3093: for(mi=1; mi<= wav[i]-1; mi++){
3094: for (ii=1;ii<=nlstate+ndeath;ii++)
3095: for (j=1;j<=nlstate+ndeath;j++){
3096: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3097: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3098: }
1.214 brouard 3099:
3100: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
3101: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
3102: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
3103: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3104: and mw[mi+1][i]. dh depends on stepm.*/
1.126 brouard 3105: newm=savm;
1.187 brouard 3106: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3107: cov[2]=agexact;
3108: if(nagesqr==1)
3109: cov[3]= agexact*agexact;
1.126 brouard 3110: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 3111: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 3112: }
1.187 brouard 3113:
1.145 brouard 3114: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 3115: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3116: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 3117: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
3118: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 3119: savm=oldm;
3120: oldm=newm;
3121: } /* end mult */
3122:
3123: s1=s[mw[mi][i]][i];
3124: s2=s[mw[mi+1][i]][i];
1.217 brouard 3125: /* if(s2==-1){ */
3126: /* printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */
3127: /* /\* exit(1); *\/ */
3128: /* } */
1.126 brouard 3129: bbh=(double)bh[mi][i]/(double)stepm;
3130: /* bias is positive if real duration
3131: * is higher than the multiple of stepm and negative otherwise.
3132: */
3133: if( s2 > nlstate && (mle <5) ){ /* Jackson */
3134: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3135: } else if ( s2==-1 ) { /* alive */
1.126 brouard 3136: for (j=1,survp=0. ; j<=nlstate; j++)
3137: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3138: lli= log(survp);
3139: }else if (mle==1){
3140: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3141: } else if(mle==2){
3142: 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 */
3143: } else if(mle==3){ /* exponential inter-extrapolation */
3144: 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 */
3145: } else if (mle==4){ /* mle=4 no inter-extrapolation */
3146: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 3147: } else{ /* mle=0 back to 1 */
3148: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3149: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 3150: } /* End of if */
3151: ipmx +=1;
3152: sw += weight[i];
3153: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 3154: /*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 3155: if(globpr){
1.214 brouard 3156: fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\
1.126 brouard 3157: %11.6f %11.6f %11.6f ", \
1.214 brouard 3158: 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 3159: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
3160: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
3161: llt +=ll[k]*gipmx/gsw;
3162: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
3163: }
3164: fprintf(ficresilk," %10.6f\n", -llt);
3165: }
3166: } /* end of wave */
3167: } /* end of individual */
3168: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3169: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3170: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3171: if(globpr==0){ /* First time we count the contributions and weights */
3172: gipmx=ipmx;
3173: gsw=sw;
3174: }
3175: return -l;
3176: }
3177:
3178:
3179: /*************** function likelione ***********/
3180: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
3181: {
3182: /* This routine should help understanding what is done with
3183: the selection of individuals/waves and
3184: to check the exact contribution to the likelihood.
3185: Plotting could be done.
3186: */
3187: int k;
3188:
3189: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 3190: strcpy(fileresilk,"ILK_");
1.202 brouard 3191: strcat(fileresilk,fileresu);
1.126 brouard 3192: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
3193: printf("Problem with resultfile: %s\n", fileresilk);
3194: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
3195: }
1.214 brouard 3196: 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");
3197: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 3198: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
3199: for(k=1; k<=nlstate; k++)
3200: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
3201: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
3202: }
3203:
3204: *fretone=(*funcone)(p);
3205: if(*globpri !=0){
3206: fclose(ficresilk);
1.205 brouard 3207: if (mle ==0)
3208: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
3209: else if(mle >=1)
3210: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
3211: 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 3212:
1.208 brouard 3213:
3214: for (k=1; k<= nlstate ; k++) {
1.211 brouard 3215: 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 3216: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
3217: }
1.207 brouard 3218: 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 3219: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3220: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 3221: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3222: fflush(fichtm);
1.205 brouard 3223: }
1.126 brouard 3224: return;
3225: }
3226:
3227:
3228: /*********** Maximum Likelihood Estimation ***************/
3229:
3230: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
3231: {
1.165 brouard 3232: int i,j, iter=0;
1.126 brouard 3233: double **xi;
3234: double fret;
3235: double fretone; /* Only one call to likelihood */
3236: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 3237:
3238: #ifdef NLOPT
3239: int creturn;
3240: nlopt_opt opt;
3241: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
3242: double *lb;
3243: double minf; /* the minimum objective value, upon return */
3244: double * p1; /* Shifted parameters from 0 instead of 1 */
3245: myfunc_data dinst, *d = &dinst;
3246: #endif
3247:
3248:
1.126 brouard 3249: xi=matrix(1,npar,1,npar);
3250: for (i=1;i<=npar;i++)
3251: for (j=1;j<=npar;j++)
3252: xi[i][j]=(i==j ? 1.0 : 0.0);
3253: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 3254: strcpy(filerespow,"POW_");
1.126 brouard 3255: strcat(filerespow,fileres);
3256: if((ficrespow=fopen(filerespow,"w"))==NULL) {
3257: printf("Problem with resultfile: %s\n", filerespow);
3258: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
3259: }
3260: fprintf(ficrespow,"# Powell\n# iter -2*LL");
3261: for (i=1;i<=nlstate;i++)
3262: for(j=1;j<=nlstate+ndeath;j++)
3263: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
3264: fprintf(ficrespow,"\n");
1.162 brouard 3265: #ifdef POWELL
1.126 brouard 3266: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 3267: #endif
1.126 brouard 3268:
1.162 brouard 3269: #ifdef NLOPT
3270: #ifdef NEWUOA
3271: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
3272: #else
3273: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
3274: #endif
3275: lb=vector(0,npar-1);
3276: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
3277: nlopt_set_lower_bounds(opt, lb);
3278: nlopt_set_initial_step1(opt, 0.1);
3279:
3280: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
3281: d->function = func;
3282: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
3283: nlopt_set_min_objective(opt, myfunc, d);
3284: nlopt_set_xtol_rel(opt, ftol);
3285: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
3286: printf("nlopt failed! %d\n",creturn);
3287: }
3288: else {
3289: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
3290: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
3291: iter=1; /* not equal */
3292: }
3293: nlopt_destroy(opt);
3294: #endif
1.126 brouard 3295: free_matrix(xi,1,npar,1,npar);
3296: fclose(ficrespow);
1.203 brouard 3297: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
3298: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 3299: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 3300:
3301: }
3302:
3303: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 3304: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 3305: {
3306: double **a,**y,*x,pd;
1.203 brouard 3307: /* double **hess; */
1.164 brouard 3308: int i, j;
1.126 brouard 3309: int *indx;
3310:
3311: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 3312: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 3313: void lubksb(double **a, int npar, int *indx, double b[]) ;
3314: void ludcmp(double **a, int npar, int *indx, double *d) ;
3315: double gompertz(double p[]);
1.203 brouard 3316: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 3317:
3318: printf("\nCalculation of the hessian matrix. Wait...\n");
3319: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
3320: for (i=1;i<=npar;i++){
1.203 brouard 3321: printf("%d-",i);fflush(stdout);
3322: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 3323:
3324: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
3325:
3326: /* printf(" %f ",p[i]);
3327: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
3328: }
3329:
3330: for (i=1;i<=npar;i++) {
3331: for (j=1;j<=npar;j++) {
3332: if (j>i) {
1.203 brouard 3333: printf(".%d-%d",i,j);fflush(stdout);
3334: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
3335: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 3336:
3337: hess[j][i]=hess[i][j];
3338: /*printf(" %lf ",hess[i][j]);*/
3339: }
3340: }
3341: }
3342: printf("\n");
3343: fprintf(ficlog,"\n");
3344:
3345: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
3346: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
3347:
3348: a=matrix(1,npar,1,npar);
3349: y=matrix(1,npar,1,npar);
3350: x=vector(1,npar);
3351: indx=ivector(1,npar);
3352: for (i=1;i<=npar;i++)
3353: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
3354: ludcmp(a,npar,indx,&pd);
3355:
3356: for (j=1;j<=npar;j++) {
3357: for (i=1;i<=npar;i++) x[i]=0;
3358: x[j]=1;
3359: lubksb(a,npar,indx,x);
3360: for (i=1;i<=npar;i++){
3361: matcov[i][j]=x[i];
3362: }
3363: }
3364:
3365: printf("\n#Hessian matrix#\n");
3366: fprintf(ficlog,"\n#Hessian matrix#\n");
3367: for (i=1;i<=npar;i++) {
3368: for (j=1;j<=npar;j++) {
1.203 brouard 3369: printf("%.6e ",hess[i][j]);
3370: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 3371: }
3372: printf("\n");
3373: fprintf(ficlog,"\n");
3374: }
3375:
1.203 brouard 3376: /* printf("\n#Covariance matrix#\n"); */
3377: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
3378: /* for (i=1;i<=npar;i++) { */
3379: /* for (j=1;j<=npar;j++) { */
3380: /* printf("%.6e ",matcov[i][j]); */
3381: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
3382: /* } */
3383: /* printf("\n"); */
3384: /* fprintf(ficlog,"\n"); */
3385: /* } */
3386:
1.126 brouard 3387: /* Recompute Inverse */
1.203 brouard 3388: /* for (i=1;i<=npar;i++) */
3389: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
3390: /* ludcmp(a,npar,indx,&pd); */
3391:
3392: /* printf("\n#Hessian matrix recomputed#\n"); */
3393:
3394: /* for (j=1;j<=npar;j++) { */
3395: /* for (i=1;i<=npar;i++) x[i]=0; */
3396: /* x[j]=1; */
3397: /* lubksb(a,npar,indx,x); */
3398: /* for (i=1;i<=npar;i++){ */
3399: /* y[i][j]=x[i]; */
3400: /* printf("%.3e ",y[i][j]); */
3401: /* fprintf(ficlog,"%.3e ",y[i][j]); */
3402: /* } */
3403: /* printf("\n"); */
3404: /* fprintf(ficlog,"\n"); */
3405: /* } */
3406:
3407: /* Verifying the inverse matrix */
3408: #ifdef DEBUGHESS
3409: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 3410:
1.203 brouard 3411: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
3412: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 3413:
3414: for (j=1;j<=npar;j++) {
3415: for (i=1;i<=npar;i++){
1.203 brouard 3416: printf("%.2f ",y[i][j]);
3417: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 3418: }
3419: printf("\n");
3420: fprintf(ficlog,"\n");
3421: }
1.203 brouard 3422: #endif
1.126 brouard 3423:
3424: free_matrix(a,1,npar,1,npar);
3425: free_matrix(y,1,npar,1,npar);
3426: free_vector(x,1,npar);
3427: free_ivector(indx,1,npar);
1.203 brouard 3428: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 3429:
3430:
3431: }
3432:
3433: /*************** hessian matrix ****************/
3434: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 3435: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 3436: int i;
3437: int l=1, lmax=20;
1.203 brouard 3438: double k1,k2, res, fx;
1.132 brouard 3439: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 3440: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
3441: int k=0,kmax=10;
3442: double l1;
3443:
3444: fx=func(x);
3445: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 3446: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 3447: l1=pow(10,l);
3448: delts=delt;
3449: for(k=1 ; k <kmax; k=k+1){
3450: delt = delta*(l1*k);
3451: p2[theta]=x[theta] +delt;
1.145 brouard 3452: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 3453: p2[theta]=x[theta]-delt;
3454: k2=func(p2)-fx;
3455: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 3456: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 3457:
1.203 brouard 3458: #ifdef DEBUGHESSII
1.126 brouard 3459: 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);
3460: 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);
3461: #endif
3462: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
3463: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
3464: k=kmax;
3465: }
3466: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 3467: k=kmax; l=lmax*10;
1.126 brouard 3468: }
3469: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
3470: delts=delt;
3471: }
1.203 brouard 3472: } /* End loop k */
1.126 brouard 3473: }
3474: delti[theta]=delts;
3475: return res;
3476:
3477: }
3478:
1.203 brouard 3479: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 3480: {
3481: int i;
1.164 brouard 3482: int l=1, lmax=20;
1.126 brouard 3483: double k1,k2,k3,k4,res,fx;
1.132 brouard 3484: double p2[MAXPARM+1];
1.203 brouard 3485: int k, kmax=1;
3486: double v1, v2, cv12, lc1, lc2;
1.208 brouard 3487:
3488: int firstime=0;
1.203 brouard 3489:
1.126 brouard 3490: fx=func(x);
1.203 brouard 3491: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 3492: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 3493: p2[thetai]=x[thetai]+delti[thetai]*k;
3494: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3495: k1=func(p2)-fx;
3496:
1.203 brouard 3497: p2[thetai]=x[thetai]+delti[thetai]*k;
3498: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3499: k2=func(p2)-fx;
3500:
1.203 brouard 3501: p2[thetai]=x[thetai]-delti[thetai]*k;
3502: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3503: k3=func(p2)-fx;
3504:
1.203 brouard 3505: p2[thetai]=x[thetai]-delti[thetai]*k;
3506: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3507: k4=func(p2)-fx;
1.203 brouard 3508: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
3509: if(k1*k2*k3*k4 <0.){
1.208 brouard 3510: firstime=1;
1.203 brouard 3511: kmax=kmax+10;
1.208 brouard 3512: }
3513: if(kmax >=10 || firstime ==1){
1.218 brouard 3514: printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);
3515: fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);
1.203 brouard 3516: 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);
3517: 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);
3518: }
3519: #ifdef DEBUGHESSIJ
3520: v1=hess[thetai][thetai];
3521: v2=hess[thetaj][thetaj];
3522: cv12=res;
3523: /* Computing eigen value of Hessian matrix */
3524: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3525: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3526: if ((lc2 <0) || (lc1 <0) ){
3527: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3528: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3529: 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);
3530: 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);
3531: }
1.126 brouard 3532: #endif
3533: }
3534: return res;
3535: }
3536:
1.203 brouard 3537: /* Not done yet: Was supposed to fix if not exactly at the maximum */
3538: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
3539: /* { */
3540: /* int i; */
3541: /* int l=1, lmax=20; */
3542: /* double k1,k2,k3,k4,res,fx; */
3543: /* double p2[MAXPARM+1]; */
3544: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
3545: /* int k=0,kmax=10; */
3546: /* double l1; */
3547:
3548: /* fx=func(x); */
3549: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
3550: /* l1=pow(10,l); */
3551: /* delts=delt; */
3552: /* for(k=1 ; k <kmax; k=k+1){ */
3553: /* delt = delti*(l1*k); */
3554: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
3555: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3556: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3557: /* k1=func(p2)-fx; */
3558:
3559: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3560: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3561: /* k2=func(p2)-fx; */
3562:
3563: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3564: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3565: /* k3=func(p2)-fx; */
3566:
3567: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3568: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3569: /* k4=func(p2)-fx; */
3570: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
3571: /* #ifdef DEBUGHESSIJ */
3572: /* 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); */
3573: /* 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); */
3574: /* #endif */
3575: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
3576: /* k=kmax; */
3577: /* } */
3578: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
3579: /* k=kmax; l=lmax*10; */
3580: /* } */
3581: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
3582: /* delts=delt; */
3583: /* } */
3584: /* } /\* End loop k *\/ */
3585: /* } */
3586: /* delti[theta]=delts; */
3587: /* return res; */
3588: /* } */
3589:
3590:
1.126 brouard 3591: /************** Inverse of matrix **************/
3592: void ludcmp(double **a, int n, int *indx, double *d)
3593: {
3594: int i,imax,j,k;
3595: double big,dum,sum,temp;
3596: double *vv;
3597:
3598: vv=vector(1,n);
3599: *d=1.0;
3600: for (i=1;i<=n;i++) {
3601: big=0.0;
3602: for (j=1;j<=n;j++)
3603: if ((temp=fabs(a[i][j])) > big) big=temp;
3604: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
3605: vv[i]=1.0/big;
3606: }
3607: for (j=1;j<=n;j++) {
3608: for (i=1;i<j;i++) {
3609: sum=a[i][j];
3610: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
3611: a[i][j]=sum;
3612: }
3613: big=0.0;
3614: for (i=j;i<=n;i++) {
3615: sum=a[i][j];
3616: for (k=1;k<j;k++)
3617: sum -= a[i][k]*a[k][j];
3618: a[i][j]=sum;
3619: if ( (dum=vv[i]*fabs(sum)) >= big) {
3620: big=dum;
3621: imax=i;
3622: }
3623: }
3624: if (j != imax) {
3625: for (k=1;k<=n;k++) {
3626: dum=a[imax][k];
3627: a[imax][k]=a[j][k];
3628: a[j][k]=dum;
3629: }
3630: *d = -(*d);
3631: vv[imax]=vv[j];
3632: }
3633: indx[j]=imax;
3634: if (a[j][j] == 0.0) a[j][j]=TINY;
3635: if (j != n) {
3636: dum=1.0/(a[j][j]);
3637: for (i=j+1;i<=n;i++) a[i][j] *= dum;
3638: }
3639: }
3640: free_vector(vv,1,n); /* Doesn't work */
3641: ;
3642: }
3643:
3644: void lubksb(double **a, int n, int *indx, double b[])
3645: {
3646: int i,ii=0,ip,j;
3647: double sum;
3648:
3649: for (i=1;i<=n;i++) {
3650: ip=indx[i];
3651: sum=b[ip];
3652: b[ip]=b[i];
3653: if (ii)
3654: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
3655: else if (sum) ii=i;
3656: b[i]=sum;
3657: }
3658: for (i=n;i>=1;i--) {
3659: sum=b[i];
3660: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
3661: b[i]=sum/a[i][i];
3662: }
3663: }
3664:
3665: void pstamp(FILE *fichier)
3666: {
1.196 brouard 3667: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 3668: }
3669:
3670: /************ Frequencies ********************/
1.214 brouard 3671: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
3672: int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[],\
3673: int firstpass, int lastpass, int stepm, int weightopt, char model[])
1.126 brouard 3674: { /* Some frequencies */
3675:
1.164 brouard 3676: int i, m, jk, j1, bool, z1,j;
1.214 brouard 3677: int mi; /* Effective wave */
1.126 brouard 3678: int first;
3679: double ***freq; /* Frequencies */
3680: double *pp, **prop;
3681: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.214 brouard 3682: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
3683: double agebegin, ageend;
3684:
1.126 brouard 3685: pp=vector(1,nlstate);
1.218 brouard 3686: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
3687: /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
1.201 brouard 3688: strcpy(fileresp,"P_");
3689: strcat(fileresp,fileresu);
1.213 brouard 3690: /*strcat(fileresphtm,fileresu);*/
1.126 brouard 3691: if((ficresp=fopen(fileresp,"w"))==NULL) {
3692: printf("Problem with prevalence resultfile: %s\n", fileresp);
3693: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
3694: exit(0);
3695: }
1.214 brouard 3696:
1.213 brouard 3697: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
3698: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
3699: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3700: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3701: fflush(ficlog);
3702: exit(70);
3703: }
1.214 brouard 3704: else{
3705: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
3706: <hr size=\"2\" color=\"#EC5E5E\"> \n\
3707: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
3708: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
3709: }
3710: 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);
3711:
3712: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
3713: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
3714: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
3715: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
3716: fflush(ficlog);
3717: exit(70);
3718: }
3719: else{
3720: fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
3721: <hr size=\"2\" color=\"#EC5E5E\"> \n\
3722: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
3723: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
3724: }
3725: 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);
3726:
1.218 brouard 3727: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
1.126 brouard 3728: j1=0;
3729:
3730: j=cptcoveff;
3731: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3732:
3733: first=1;
3734:
1.214 brouard 3735: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ /* Loop on covariates combination */
1.126 brouard 3736: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
3737: scanf("%d", i);*/
3738: for (i=-5; i<=nlstate+ndeath; i++)
3739: for (jk=-5; jk<=nlstate+ndeath; jk++)
3740: for(m=iagemin; m <= iagemax+3; m++)
3741: freq[i][jk][m]=0;
1.143 brouard 3742:
3743: for (i=1; i<=nlstate; i++)
3744: for(m=iagemin; m <= iagemax+3; m++)
3745: prop[i][m]=0;
1.126 brouard 3746:
3747: dateintsum=0;
3748: k2cpt=0;
1.214 brouard 3749: for (i=1; i<=imx; i++) { /* For each individual i */
1.126 brouard 3750: bool=1;
1.210 brouard 3751: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
1.144 brouard 3752: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 3753: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
1.145 brouard 3754: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 3755: bool=0;
1.198 brouard 3756: /* 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",
3757: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
3758: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
3759: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
1.144 brouard 3760: }
1.210 brouard 3761: } /* cptcovn > 0 */
1.214 brouard 3762:
1.126 brouard 3763: if (bool==1){
1.214 brouard 3764: /* for(m=firstpass; m<=lastpass; m++){ */
3765: for(mi=1; mi<wav[i];mi++){
3766: m=mw[mi][i];
3767: /* dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective (mi) waves m=mw[mi][i]
3768: and mw[mi+1][i]. dh depends on stepm. */
3769: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
3770: ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /* Age at end of wave and transition */
3771: if(m >=firstpass && m <=lastpass){
3772: k2=anint[m][i]+(mint[m][i]/12.);
3773: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
3774: if(agev[m][i]==0) agev[m][i]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
3775: if(agev[m][i]==1) agev[m][i]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
3776: if (s[m][i]>0 && s[m][i]<=nlstate) /* If status at wave m is known and a live state */
3777: prop[s[m][i]][(int)agev[m][i]] += weight[i]; /* At age of beginning of transition, where status is known */
1.126 brouard 3778: if (m<lastpass) {
1.214 brouard 3779: /* if(s[m][i]==4 && s[m+1][i]==4) */
3780: /* 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]); */
3781: if(s[m][i]==-1)
3782: 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.));
3783: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; /* At age of beginning of transition, where status is known */
3784: /* freq[s[m][i]][s[m+1][i]][(int)((agebegin+ageend)/2.)] += weight[i]; */
3785: 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 3786: }
1.214 brouard 3787: }
3788: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3)) && (anint[m][i]!=9999) && (mint[m][i]!=99)) {
3789: dateintsum=dateintsum+k2;
3790: k2cpt++;
3791: /* printf("i=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",i, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
3792: }
3793: /*}*/
1.210 brouard 3794: } /* end m */
3795: } /* end bool */
3796: } /* end i = 1 to imx */
1.126 brouard 3797:
3798: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
3799: pstamp(ficresp);
3800: if (cptcovn>0) {
3801: fprintf(ficresp, "\n#********** Variable ");
1.214 brouard 3802: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
3803: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
1.213 brouard 3804: for (z1=1; z1<=cptcoveff; z1++){
3805: fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
3806: fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.214 brouard 3807: fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.213 brouard 3808: }
3809: fprintf(ficresp, "**********\n#");
1.214 brouard 3810: fprintf(ficresphtm, "**********</h3>\n");
3811: fprintf(ficresphtmfr, "**********</h3>\n");
1.143 brouard 3812: fprintf(ficlog, "\n#********** Variable ");
1.198 brouard 3813: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.214 brouard 3814: fprintf(ficlog, "**********\n");
1.126 brouard 3815: }
1.214 brouard 3816: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
1.213 brouard 3817: for(i=1; i<=nlstate;i++) {
1.126 brouard 3818: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1.213 brouard 3819: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
3820: }
1.126 brouard 3821: fprintf(ficresp, "\n");
1.213 brouard 3822: fprintf(ficresphtm, "\n");
1.126 brouard 3823:
1.214 brouard 3824: /* Header of frequency table by age */
3825: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
3826: fprintf(ficresphtmfr,"<th>Age</th> ");
3827: for(jk=-1; jk <=nlstate+ndeath; jk++){
3828: for(m=-1; m <=nlstate+ndeath; m++){
3829: if(jk!=0 && m!=0)
3830: fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
3831: }
3832: }
3833: fprintf(ficresphtmfr, "\n");
3834:
3835: /* For each age */
1.126 brouard 3836: for(i=iagemin; i <= iagemax+3; i++){
1.213 brouard 3837: fprintf(ficresphtm,"<tr>");
1.214 brouard 3838: if(i==iagemax+1){
3839: fprintf(ficlog,"1");
3840: fprintf(ficresphtmfr,"<tr><th>0</th> ");
3841: }else if(i==iagemax+2){
3842: fprintf(ficlog,"0");
3843: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
3844: }else if(i==iagemax+3){
1.126 brouard 3845: fprintf(ficlog,"Total");
1.214 brouard 3846: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
1.126 brouard 3847: }else{
3848: if(first==1){
3849: first=0;
3850: printf("See log file for details...\n");
3851: }
1.214 brouard 3852: fprintf(ficresphtmfr,"<tr><th>%d</th> ",i);
1.126 brouard 3853: fprintf(ficlog,"Age %d", i);
3854: }
3855: for(jk=1; jk <=nlstate ; jk++){
3856: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
3857: pp[jk] += freq[jk][m][i];
3858: }
3859: for(jk=1; jk <=nlstate ; jk++){
3860: for(m=-1, pos=0; m <=0 ; m++)
3861: pos += freq[jk][m][i];
3862: if(pp[jk]>=1.e-10){
3863: if(first==1){
1.132 brouard 3864: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 3865: }
3866: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3867: }else{
3868: if(first==1)
3869: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3870: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3871: }
3872: }
3873:
3874: for(jk=1; jk <=nlstate ; jk++){
3875: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
3876: pp[jk] += freq[jk][m][i];
3877: }
3878: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
3879: pos += pp[jk];
3880: posprop += prop[jk][i];
3881: }
3882: for(jk=1; jk <=nlstate ; jk++){
3883: if(pos>=1.e-5){
3884: if(first==1)
3885: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3886: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3887: }else{
3888: if(first==1)
3889: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3890: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3891: }
3892: if( i <= iagemax){
3893: if(pos>=1.e-5){
3894: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.213 brouard 3895: 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 3896: /*probs[i][jk][j1]= pp[jk]/pos;*/
3897: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
3898: }
1.213 brouard 3899: else{
1.126 brouard 3900: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.213 brouard 3901: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",i, prop[jk][i],posprop);
3902: }
1.126 brouard 3903: }
3904: }
3905:
1.214 brouard 3906: for(jk=-1; jk <=nlstate+ndeath; jk++){
3907: for(m=-1; m <=nlstate+ndeath; m++){
3908: if(freq[jk][m][i] !=0 ) { /* minimizing output */
3909: if(first==1){
3910: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
3911: }
1.126 brouard 3912: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
3913: }
1.214 brouard 3914: if(jk!=0 && m!=0)
3915: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][i]);
3916: }
3917: }
3918: fprintf(ficresphtmfr,"</tr>\n ");
1.213 brouard 3919: if(i <= iagemax){
1.126 brouard 3920: fprintf(ficresp,"\n");
1.213 brouard 3921: fprintf(ficresphtm,"</tr>\n");
3922: }
1.126 brouard 3923: if(first==1)
3924: printf("Others in log...\n");
3925: fprintf(ficlog,"\n");
1.210 brouard 3926: } /* end loop i */
1.213 brouard 3927: fprintf(ficresphtm,"</table>\n");
1.214 brouard 3928: fprintf(ficresphtmfr,"</table>\n");
1.145 brouard 3929: /*}*/
1.210 brouard 3930: } /* end j1 */
1.126 brouard 3931: dateintmean=dateintsum/k2cpt;
3932:
3933: fclose(ficresp);
1.213 brouard 3934: fclose(ficresphtm);
1.214 brouard 3935: fclose(ficresphtmfr);
1.218 brouard 3936: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
1.126 brouard 3937: free_vector(pp,1,nlstate);
1.218 brouard 3938: free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
1.126 brouard 3939: /* End of Freq */
3940: }
3941:
3942: /************ Prevalence ********************/
3943: 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)
3944: {
3945: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3946: in each health status at the date of interview (if between dateprev1 and dateprev2).
3947: We still use firstpass and lastpass as another selection.
3948: */
3949:
1.164 brouard 3950: int i, m, jk, j1, bool, z1,j;
1.214 brouard 3951: int mi; /* Effective wave */
3952: int iage;
3953: double agebegin, ageend;
1.164 brouard 3954:
3955: double **prop;
3956: double posprop;
1.126 brouard 3957: double y2; /* in fractional years */
3958: int iagemin, iagemax;
1.145 brouard 3959: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 3960:
3961: iagemin= (int) agemin;
3962: iagemax= (int) agemax;
3963: /*pp=vector(1,nlstate);*/
1.218 brouard 3964: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
1.126 brouard 3965: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3966: j1=0;
3967:
1.145 brouard 3968: /*j=cptcoveff;*/
1.126 brouard 3969: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3970:
1.145 brouard 3971: first=1;
1.219 ! brouard 3972: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
1.214 brouard 3973: for (i=1; i<=nlstate; i++)
1.218 brouard 3974: for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
3975: prop[i][iage]=0.0;
1.214 brouard 3976:
3977: for (i=1; i<=imx; i++) { /* Each individual */
3978: bool=1;
3979: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
1.219 ! brouard 3980: for (z1=1; z1<=cptcoveff; z1++) /* For each covariate, look at the value for individual i and checks if it is equal to the corresponding value of this covariate according to current combination j1*/
1.218 brouard 3981: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
3982: bool=0;
1.214 brouard 3983: }
1.219 ! brouard 3984: if (bool==1) { /* For this combination of covariates values, this individual fits */
1.218 brouard 3985: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
3986: for(mi=1; mi<wav[i];mi++){
3987: m=mw[mi][i];
3988: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
3989: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
3990: if(m >=firstpass && m <=lastpass){
3991: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3992: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3993: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3994: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3995: if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
3996: printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m);
3997: exit(1);
3998: }
3999: if (s[m][i]>0 && s[m][i]<=nlstate) {
4000: /*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]]);*/
4001: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
4002: prop[s[m][i]][iagemax+3] += weight[i];
4003: } /* end valid statuses */
4004: } /* end selection of dates */
4005: } /* end selection of waves */
4006: } /* end effective waves */
1.214 brouard 4007: } /* end bool */
4008: }
4009: for(i=iagemin; i <= iagemax+3; i++){
4010: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
1.218 brouard 4011: posprop += prop[jk][i];
1.214 brouard 4012: }
4013:
4014: for(jk=1; jk <=nlstate ; jk++){
1.218 brouard 4015: if( i <= iagemax){
4016: if(posprop>=1.e-5){
4017: probs[i][jk][j1]= prop[jk][i]/posprop;
4018: } else{
4019: if(first==1){
4020: first=0;
4021: 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]);
4022: }
4023: }
4024: }
1.214 brouard 4025: }/* end jk */
4026: }/* end i */
1.145 brouard 4027: /*} *//* end i1 */
4028: } /* end j1 */
1.126 brouard 4029:
4030: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
4031: /*free_vector(pp,1,nlstate);*/
1.218 brouard 4032: free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
1.126 brouard 4033: } /* End of prevalence */
4034:
4035: /************* Waves Concatenation ***************/
4036:
4037: 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)
4038: {
4039: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
4040: Death is a valid wave (if date is known).
4041: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
4042: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
4043: and mw[mi+1][i]. dh depends on stepm.
4044: */
4045:
4046: int i, mi, m;
4047: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
4048: double sum=0., jmean=0.;*/
1.218 brouard 4049: int first, firstwo, firsthree, firstfour;
1.126 brouard 4050: int j, k=0,jk, ju, jl;
4051: double sum=0.;
4052: first=0;
1.214 brouard 4053: firstwo=0;
1.217 brouard 4054: firsthree=0;
1.218 brouard 4055: firstfour=0;
1.164 brouard 4056: jmin=100000;
1.126 brouard 4057: jmax=-1;
4058: jmean=0.;
1.214 brouard 4059: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.126 brouard 4060: mi=0;
4061: m=firstpass;
1.214 brouard 4062: while(s[m][i] <= nlstate){ /* a live state */
1.216 brouard 4063: 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 4064: mw[++mi][i]=m;
1.216 brouard 4065: }
4066: if(m >=lastpass){
4067: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
1.217 brouard 4068: if(firsthree == 0){
4069: 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);
4070: firsthree=1;
4071: }
1.218 brouard 4072: fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
1.216 brouard 4073: mw[++mi][i]=m;
4074: }
4075: if(s[m][i]==-2){ /* Vital status is really unknown */
4076: nbwarn++;
4077: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */
4078: 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);
4079: 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);
4080: }
4081: break;
4082: }
1.126 brouard 4083: break;
1.216 brouard 4084: }
1.126 brouard 4085: else
4086: m++;
4087: }/* end while */
1.216 brouard 4088:
4089: /* After last pass */
1.214 brouard 4090: if (s[m][i] > nlstate){ /* In a death state */
1.126 brouard 4091: mi++; /* Death is another wave */
4092: /* if(mi==0) never been interviewed correctly before death */
4093: /* Only death is a correct wave */
4094: mw[mi][i]=m;
1.216 brouard 4095: }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 */
4096: /* m++; */
4097: /* mi++; */
4098: /* s[m][i]=nlstate+1; /\* We are setting the status to the last of non live state *\/ */
4099: /* mw[mi][i]=m; */
4100: nberr++;
1.218 brouard 4101: if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
4102: if(firstwo==0){
4103: 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 );
4104: firstwo=1;
4105: }
4106: fprintf(ficlog,"Error! Death for individual %ld line=%d occurred %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
4107: }else{ /* end date of interview is known */
4108: /* death is known but not confirmed by death status at any wave */
4109: if(firstfour==0){
4110: printf("Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
4111: firstfour=1;
4112: }
4113: fprintf(ficlog,"Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
1.214 brouard 4114: }
1.126 brouard 4115: }
4116: wav[i]=mi;
4117: if(mi==0){
4118: nbwarn++;
4119: if(first==0){
4120: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
4121: first=1;
4122: }
4123: if(first==1){
4124: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
4125: }
4126: } /* end mi==0 */
4127: } /* End individuals */
1.214 brouard 4128: /* wav and mw are no more changed */
1.126 brouard 4129:
1.214 brouard 4130:
1.126 brouard 4131: for(i=1; i<=imx; i++){
4132: for(mi=1; mi<wav[i];mi++){
4133: if (stepm <=0)
4134: dh[mi][i]=1;
4135: else{
4136: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
4137: if (agedc[i] < 2*AGESUP) {
4138: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
4139: if(j==0) j=1; /* Survives at least one month after exam */
4140: else if(j<0){
4141: nberr++;
4142: 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]);
4143: j=1; /* Temporary Dangerous patch */
4144: 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);
4145: 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]);
4146: 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);
4147: }
4148: k=k+1;
4149: if (j >= jmax){
4150: jmax=j;
4151: ijmax=i;
4152: }
4153: if (j <= jmin){
4154: jmin=j;
4155: ijmin=i;
4156: }
4157: sum=sum+j;
4158: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
4159: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
4160: }
4161: }
4162: else{
4163: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
4164: /* 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]); */
4165:
4166: k=k+1;
4167: if (j >= jmax) {
4168: jmax=j;
4169: ijmax=i;
4170: }
4171: else if (j <= jmin){
4172: jmin=j;
4173: ijmin=i;
4174: }
4175: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
4176: /*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]);*/
4177: if(j<0){
4178: nberr++;
4179: 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]);
4180: 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]);
4181: }
4182: sum=sum+j;
4183: }
4184: jk= j/stepm;
4185: jl= j -jk*stepm;
4186: ju= j -(jk+1)*stepm;
4187: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
4188: if(jl==0){
4189: dh[mi][i]=jk;
4190: bh[mi][i]=0;
4191: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 4192: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 4193: dh[mi][i]=jk+1;
4194: bh[mi][i]=ju;
4195: }
4196: }else{
4197: if(jl <= -ju){
4198: dh[mi][i]=jk;
4199: bh[mi][i]=jl; /* bias is positive if real duration
4200: * is higher than the multiple of stepm and negative otherwise.
4201: */
4202: }
4203: else{
4204: dh[mi][i]=jk+1;
4205: bh[mi][i]=ju;
4206: }
4207: if(dh[mi][i]==0){
4208: dh[mi][i]=1; /* At least one step */
4209: bh[mi][i]=ju; /* At least one step */
4210: /* 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);*/
4211: }
4212: } /* end if mle */
4213: }
4214: } /* end wave */
4215: }
4216: jmean=sum/k;
4217: 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 4218: 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 4219: }
4220:
4221: /*********** Tricode ****************************/
1.145 brouard 4222: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 4223: {
1.144 brouard 4224: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
4225: /* 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 4226: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 4227: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 4228: * nbcode[Tvar[j]][1]=
1.144 brouard 4229: */
1.130 brouard 4230:
1.145 brouard 4231: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 4232: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 4233: int cptcode=0; /* Modality max of covariates j */
4234: int modmincovj=0; /* Modality min of covariates j */
4235:
4236:
1.126 brouard 4237: cptcoveff=0;
4238:
1.144 brouard 4239: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 4240:
1.145 brouard 4241: /* Loop on covariates without age and products */
1.186 brouard 4242: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
1.192 brouard 4243: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.186 brouard 4244: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.219 ! brouard 4245: modality of this covariate Vj*/
1.145 brouard 4246: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
1.219 ! brouard 4247: * If product of Vn*Vm, still boolean *:
! 4248: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
! 4249: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
1.145 brouard 4250: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 4251: modality of the nth covariate of individual i. */
1.145 brouard 4252: if (ij > modmaxcovj)
4253: modmaxcovj=ij;
4254: else if (ij < modmincovj)
1.219 ! brouard 4255: modmincovj=ij;
1.145 brouard 4256: if ((ij < -1) && (ij > NCOVMAX)){
1.219 ! brouard 4257: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
! 4258: exit(1);
1.145 brouard 4259: }else
1.136 brouard 4260: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 4261: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 4262: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 4263: /* getting the maximum value of the modality of the covariate
4264: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
4265: female is 1, then modmaxcovj=1.*/
1.192 brouard 4266: } /* end for loop on individuals i */
1.145 brouard 4267: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.192 brouard 4268: 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 4269: cptcode=modmaxcovj;
1.137 brouard 4270: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 4271: /*for (i=0; i<=cptcode; i++) {*/
1.192 brouard 4272: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
4273: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
4274: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
4275: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
1.219 ! brouard 4276: if( k != -1){
! 4277: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
! 4278: covariate for which somebody answered excluding
! 4279: undefined. Usually 2: 0 and 1. */
! 4280: }
! 4281: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
! 4282: covariate for which somebody answered including
! 4283: undefined. Usually 3: -1, 0 and 1. */
1.145 brouard 4284: }
4285: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
1.219 ! brouard 4286: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 4287: } /* Ndum[-1] number of undefined modalities */
1.219 ! brouard 4288:
1.136 brouard 4289: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 4290: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
4291: 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 4292: modmincovj=3; modmaxcovj = 7;
1.186 brouard 4293: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
4294: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
4295: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 4296: nbcode[Tvar[j]][ij]=k;
4297: nbcode[Tvar[j]][1]=0;
4298: nbcode[Tvar[j]][2]=1;
4299: nbcode[Tvar[j]][3]=2;
1.197 brouard 4300: To be continued (not working yet).
1.145 brouard 4301: */
1.197 brouard 4302: ij=0; /* ij is similar to i but can jump over null modalities */
4303: 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*/
4304: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
1.219 ! brouard 4305: break;
! 4306: }
1.192 brouard 4307: ij++;
1.197 brouard 4308: 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 4309: cptcode = ij; /* New max modality for covar j */
4310: } /* end of loop on modality i=-1 to 1 or more */
4311:
4312: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
4313: /* /\*recode from 0 *\/ */
4314: /* k is a modality. If we have model=V1+V1*sex */
4315: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
4316: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
4317: /* } */
4318: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
4319: /* if (ij > ncodemax[j]) { */
4320: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4321: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4322: /* break; */
4323: /* } */
4324: /* } /\* end of loop on modality k *\/ */
1.137 brouard 4325: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
4326:
1.219 ! brouard 4327: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 4328:
1.187 brouard 4329: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.219 ! brouard 4330: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
! 4331: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
! 4332: Ndum[ij]++; /* Might be supersed V1 + V1*age */
! 4333: }
! 4334:
! 4335: ij=0;
! 4336: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
! 4337: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
! 4338: if((Ndum[i]!=0) && (i<=ncovcol)){
! 4339: ij++;
! 4340: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
! 4341: Tvaraff[ij]=i; /*For printing (unclear) */
! 4342: }else{
! 4343: /* Tvaraff[ij]=0; */
! 4344: }
! 4345: }
! 4346: /* ij--; */
! 4347: cptcoveff=ij; /*Number of total covariates*/
! 4348:
1.126 brouard 4349: }
4350:
1.145 brouard 4351:
1.126 brouard 4352: /*********** Health Expectancies ****************/
4353:
1.127 brouard 4354: 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 4355:
4356: {
4357: /* Health expectancies, no variances */
1.164 brouard 4358: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 4359: int nhstepma, nstepma; /* Decreasing with age */
4360: double age, agelim, hf;
4361: double ***p3mat;
4362: double eip;
4363:
4364: pstamp(ficreseij);
4365: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
4366: fprintf(ficreseij,"# Age");
4367: for(i=1; i<=nlstate;i++){
4368: for(j=1; j<=nlstate;j++){
4369: fprintf(ficreseij," e%1d%1d ",i,j);
4370: }
4371: fprintf(ficreseij," e%1d. ",i);
4372: }
4373: fprintf(ficreseij,"\n");
4374:
4375:
4376: if(estepm < stepm){
4377: printf ("Problem %d lower than %d\n",estepm, stepm);
4378: }
4379: else hstepm=estepm;
4380: /* We compute the life expectancy from trapezoids spaced every estepm months
4381: * This is mainly to measure the difference between two models: for example
4382: * if stepm=24 months pijx are given only every 2 years and by summing them
4383: * we are calculating an estimate of the Life Expectancy assuming a linear
4384: * progression in between and thus overestimating or underestimating according
4385: * to the curvature of the survival function. If, for the same date, we
4386: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4387: * to compare the new estimate of Life expectancy with the same linear
4388: * hypothesis. A more precise result, taking into account a more precise
4389: * curvature will be obtained if estepm is as small as stepm. */
4390:
4391: /* For example we decided to compute the life expectancy with the smallest unit */
4392: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4393: nhstepm is the number of hstepm from age to agelim
4394: nstepm is the number of stepm from age to agelin.
4395: Look at hpijx to understand the reason of that which relies in memory size
4396: and note for a fixed period like estepm months */
4397: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4398: survival function given by stepm (the optimization length). Unfortunately it
4399: means that if the survival funtion is printed only each two years of age and if
4400: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4401: results. So we changed our mind and took the option of the best precision.
4402: */
4403: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4404:
4405: agelim=AGESUP;
4406: /* If stepm=6 months */
4407: /* Computed by stepm unit matrices, product of hstepm matrices, stored
4408: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
4409:
4410: /* nhstepm age range expressed in number of stepm */
4411: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4412: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4413: /* if (stepm >= YEARM) hstepm=1;*/
4414: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4415: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4416:
4417: for (age=bage; age<=fage; age ++){
4418: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4419: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4420: /* if (stepm >= YEARM) hstepm=1;*/
4421: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
4422:
4423: /* If stepm=6 months */
4424: /* Computed by stepm unit matrices, product of hstepma matrices, stored
4425: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
4426:
4427: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
4428:
4429: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4430:
4431: printf("%d|",(int)age);fflush(stdout);
4432: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
4433:
4434: /* Computing expectancies */
4435: for(i=1; i<=nlstate;i++)
4436: for(j=1; j<=nlstate;j++)
4437: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
4438: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
4439:
4440: /* 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]);*/
4441:
4442: }
4443:
4444: fprintf(ficreseij,"%3.0f",age );
4445: for(i=1; i<=nlstate;i++){
4446: eip=0;
4447: for(j=1; j<=nlstate;j++){
4448: eip +=eij[i][j][(int)age];
4449: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
4450: }
4451: fprintf(ficreseij,"%9.4f", eip );
4452: }
4453: fprintf(ficreseij,"\n");
4454:
4455: }
4456: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4457: printf("\n");
4458: fprintf(ficlog,"\n");
4459:
4460: }
4461:
1.127 brouard 4462: 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 4463:
4464: {
4465: /* Covariances of health expectancies eij and of total life expectancies according
4466: to initial status i, ei. .
4467: */
4468: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
4469: int nhstepma, nstepma; /* Decreasing with age */
4470: double age, agelim, hf;
4471: double ***p3matp, ***p3matm, ***varhe;
4472: double **dnewm,**doldm;
4473: double *xp, *xm;
4474: double **gp, **gm;
4475: double ***gradg, ***trgradg;
4476: int theta;
4477:
4478: double eip, vip;
4479:
4480: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
4481: xp=vector(1,npar);
4482: xm=vector(1,npar);
4483: dnewm=matrix(1,nlstate*nlstate,1,npar);
4484: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
4485:
4486: pstamp(ficresstdeij);
4487: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
4488: fprintf(ficresstdeij,"# Age");
4489: for(i=1; i<=nlstate;i++){
4490: for(j=1; j<=nlstate;j++)
4491: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
4492: fprintf(ficresstdeij," e%1d. ",i);
4493: }
4494: fprintf(ficresstdeij,"\n");
4495:
4496: pstamp(ficrescveij);
4497: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
4498: fprintf(ficrescveij,"# Age");
4499: for(i=1; i<=nlstate;i++)
4500: for(j=1; j<=nlstate;j++){
4501: cptj= (j-1)*nlstate+i;
4502: for(i2=1; i2<=nlstate;i2++)
4503: for(j2=1; j2<=nlstate;j2++){
4504: cptj2= (j2-1)*nlstate+i2;
4505: if(cptj2 <= cptj)
4506: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
4507: }
4508: }
4509: fprintf(ficrescveij,"\n");
4510:
4511: if(estepm < stepm){
4512: printf ("Problem %d lower than %d\n",estepm, stepm);
4513: }
4514: else hstepm=estepm;
4515: /* We compute the life expectancy from trapezoids spaced every estepm months
4516: * This is mainly to measure the difference between two models: for example
4517: * if stepm=24 months pijx are given only every 2 years and by summing them
4518: * we are calculating an estimate of the Life Expectancy assuming a linear
4519: * progression in between and thus overestimating or underestimating according
4520: * to the curvature of the survival function. If, for the same date, we
4521: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4522: * to compare the new estimate of Life expectancy with the same linear
4523: * hypothesis. A more precise result, taking into account a more precise
4524: * curvature will be obtained if estepm is as small as stepm. */
4525:
4526: /* For example we decided to compute the life expectancy with the smallest unit */
4527: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4528: nhstepm is the number of hstepm from age to agelim
4529: nstepm is the number of stepm from age to agelin.
4530: Look at hpijx to understand the reason of that which relies in memory size
4531: and note for a fixed period like estepm months */
4532: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4533: survival function given by stepm (the optimization length). Unfortunately it
4534: means that if the survival funtion is printed only each two years of age and if
4535: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4536: results. So we changed our mind and took the option of the best precision.
4537: */
4538: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4539:
4540: /* If stepm=6 months */
4541: /* nhstepm age range expressed in number of stepm */
4542: agelim=AGESUP;
4543: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
4544: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4545: /* if (stepm >= YEARM) hstepm=1;*/
4546: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4547:
4548: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4549: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4550: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
4551: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
4552: gp=matrix(0,nhstepm,1,nlstate*nlstate);
4553: gm=matrix(0,nhstepm,1,nlstate*nlstate);
4554:
4555: for (age=bage; age<=fage; age ++){
4556: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4557: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4558: /* if (stepm >= YEARM) hstepm=1;*/
4559: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218 brouard 4560:
1.126 brouard 4561: /* If stepm=6 months */
4562: /* Computed by stepm unit matrices, product of hstepma matrices, stored
4563: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
4564:
4565: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.218 brouard 4566:
1.126 brouard 4567: /* Computing Variances of health expectancies */
4568: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
4569: decrease memory allocation */
4570: for(theta=1; theta <=npar; theta++){
4571: for(i=1; i<=npar; i++){
1.218 brouard 4572: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4573: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126 brouard 4574: }
4575: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
4576: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
1.218 brouard 4577:
1.126 brouard 4578: for(j=1; j<= nlstate; j++){
1.218 brouard 4579: for(i=1; i<=nlstate; i++){
4580: for(h=0; h<=nhstepm-1; h++){
4581: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
4582: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
4583: }
4584: }
1.126 brouard 4585: }
1.218 brouard 4586:
1.126 brouard 4587: for(ij=1; ij<= nlstate*nlstate; ij++)
1.218 brouard 4588: for(h=0; h<=nhstepm-1; h++){
4589: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
4590: }
1.126 brouard 4591: }/* End theta */
4592:
4593:
4594: for(h=0; h<=nhstepm-1; h++)
4595: for(j=1; j<=nlstate*nlstate;j++)
1.218 brouard 4596: for(theta=1; theta <=npar; theta++)
4597: trgradg[h][j][theta]=gradg[h][theta][j];
1.126 brouard 4598:
1.218 brouard 4599:
4600: for(ij=1;ij<=nlstate*nlstate;ij++)
1.126 brouard 4601: for(ji=1;ji<=nlstate*nlstate;ji++)
1.218 brouard 4602: varhe[ij][ji][(int)age] =0.;
4603:
4604: printf("%d|",(int)age);fflush(stdout);
4605: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
4606: for(h=0;h<=nhstepm-1;h++){
1.126 brouard 4607: for(k=0;k<=nhstepm-1;k++){
1.218 brouard 4608: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
4609: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
4610: for(ij=1;ij<=nlstate*nlstate;ij++)
4611: for(ji=1;ji<=nlstate*nlstate;ji++)
4612: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126 brouard 4613: }
4614: }
1.218 brouard 4615:
1.126 brouard 4616: /* Computing expectancies */
4617: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
4618: for(i=1; i<=nlstate;i++)
4619: for(j=1; j<=nlstate;j++)
1.218 brouard 4620: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
4621: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
4622:
4623: /* 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]);*/
4624:
4625: }
4626:
1.126 brouard 4627: fprintf(ficresstdeij,"%3.0f",age );
4628: for(i=1; i<=nlstate;i++){
4629: eip=0.;
4630: vip=0.;
4631: for(j=1; j<=nlstate;j++){
1.218 brouard 4632: eip += eij[i][j][(int)age];
4633: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
4634: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
4635: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
1.126 brouard 4636: }
4637: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
4638: }
4639: fprintf(ficresstdeij,"\n");
1.218 brouard 4640:
1.126 brouard 4641: fprintf(ficrescveij,"%3.0f",age );
4642: for(i=1; i<=nlstate;i++)
4643: for(j=1; j<=nlstate;j++){
1.218 brouard 4644: cptj= (j-1)*nlstate+i;
4645: for(i2=1; i2<=nlstate;i2++)
4646: for(j2=1; j2<=nlstate;j2++){
4647: cptj2= (j2-1)*nlstate+i2;
4648: if(cptj2 <= cptj)
4649: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
4650: }
1.126 brouard 4651: }
4652: fprintf(ficrescveij,"\n");
1.218 brouard 4653:
1.126 brouard 4654: }
4655: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
4656: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
4657: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
4658: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
4659: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4660: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4661: printf("\n");
4662: fprintf(ficlog,"\n");
1.218 brouard 4663:
1.126 brouard 4664: free_vector(xm,1,npar);
4665: free_vector(xp,1,npar);
4666: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
4667: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
4668: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
4669: }
1.218 brouard 4670:
1.126 brouard 4671: /************ Variance ******************/
1.209 brouard 4672: void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
1.218 brouard 4673: {
4674: /* Variance of health expectancies */
4675: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
4676: /* double **newm;*/
4677: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
4678:
4679: /* int movingaverage(); */
4680: double **dnewm,**doldm;
4681: double **dnewmp,**doldmp;
4682: int i, j, nhstepm, hstepm, h, nstepm ;
4683: int k;
4684: double *xp;
4685: double **gp, **gm; /* for var eij */
4686: double ***gradg, ***trgradg; /*for var eij */
4687: double **gradgp, **trgradgp; /* for var p point j */
4688: double *gpp, *gmp; /* for var p point j */
4689: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
4690: double ***p3mat;
4691: double age,agelim, hf;
4692: /* double ***mobaverage; */
4693: int theta;
4694: char digit[4];
4695: char digitp[25];
4696:
4697: char fileresprobmorprev[FILENAMELENGTH];
4698:
4699: if(popbased==1){
4700: if(mobilav!=0)
4701: strcpy(digitp,"-POPULBASED-MOBILAV_");
4702: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
4703: }
4704: else
4705: strcpy(digitp,"-STABLBASED_");
1.126 brouard 4706:
1.218 brouard 4707: /* if (mobilav!=0) { */
4708: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
4709: /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
4710: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
4711: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
4712: /* } */
4713: /* } */
4714:
4715: strcpy(fileresprobmorprev,"PRMORPREV-");
4716: sprintf(digit,"%-d",ij);
4717: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
4718: strcat(fileresprobmorprev,digit); /* Tvar to be done */
4719: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
4720: strcat(fileresprobmorprev,fileresu);
4721: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
4722: printf("Problem with resultfile: %s\n", fileresprobmorprev);
4723: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
4724: }
4725: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4726: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4727: pstamp(ficresprobmorprev);
4728: 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);
4729: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
4730: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4731: fprintf(ficresprobmorprev," p.%-d SE",j);
4732: for(i=1; i<=nlstate;i++)
4733: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
4734: }
4735: fprintf(ficresprobmorprev,"\n");
4736:
4737: fprintf(ficgp,"\n# Routine varevsij");
4738: fprintf(ficgp,"\nunset title \n");
4739: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
4740: 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");
4741: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
4742: /* } */
4743: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4744: pstamp(ficresvij);
4745: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
4746: if(popbased==1)
4747: 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);
4748: else
4749: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
4750: fprintf(ficresvij,"# Age");
4751: for(i=1; i<=nlstate;i++)
4752: for(j=1; j<=nlstate;j++)
4753: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
4754: fprintf(ficresvij,"\n");
4755:
4756: xp=vector(1,npar);
4757: dnewm=matrix(1,nlstate,1,npar);
4758: doldm=matrix(1,nlstate,1,nlstate);
4759: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
4760: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4761:
4762: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
4763: gpp=vector(nlstate+1,nlstate+ndeath);
4764: gmp=vector(nlstate+1,nlstate+ndeath);
4765: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126 brouard 4766:
1.218 brouard 4767: if(estepm < stepm){
4768: printf ("Problem %d lower than %d\n",estepm, stepm);
4769: }
4770: else hstepm=estepm;
4771: /* For example we decided to compute the life expectancy with the smallest unit */
4772: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4773: nhstepm is the number of hstepm from age to agelim
4774: nstepm is the number of stepm from age to agelim.
4775: Look at function hpijx to understand why because of memory size limitations,
4776: we decided (b) to get a life expectancy respecting the most precise curvature of the
4777: survival function given by stepm (the optimization length). Unfortunately it
4778: means that if the survival funtion is printed every two years of age and if
4779: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4780: results. So we changed our mind and took the option of the best precision.
4781: */
4782: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4783: agelim = AGESUP;
4784: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4785: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4786: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4787: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4788: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
4789: gp=matrix(0,nhstepm,1,nlstate);
4790: gm=matrix(0,nhstepm,1,nlstate);
4791:
4792:
4793: for(theta=1; theta <=npar; theta++){
4794: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
4795: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4796: }
4797:
4798: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
4799:
4800: if (popbased==1) {
4801: if(mobilav ==0){
4802: for(i=1; i<=nlstate;i++)
4803: prlim[i][i]=probs[(int)age][i][ij];
4804: }else{ /* mobilav */
4805: for(i=1; i<=nlstate;i++)
4806: prlim[i][i]=mobaverage[(int)age][i][ij];
4807: }
4808: }
4809:
4810: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); /* Returns p3mat[i][j][h] for h=1 to nhstepm */
4811: for(j=1; j<= nlstate; j++){
4812: for(h=0; h<=nhstepm; h++){
4813: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
4814: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
4815: }
4816: }
4817: /* Next for computing probability of death (h=1 means
4818: computed over hstepm matrices product = hstepm*stepm months)
4819: as a weighted average of prlim.
4820: */
4821: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4822: for(i=1,gpp[j]=0.; i<= nlstate; i++)
4823: gpp[j] += prlim[i][i]*p3mat[i][j][1];
4824: }
4825: /* end probability of death */
4826:
4827: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
4828: xp[i] = x[i] - (i==theta ?delti[theta]:0);
4829:
4830: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
4831:
4832: if (popbased==1) {
4833: if(mobilav ==0){
4834: for(i=1; i<=nlstate;i++)
4835: prlim[i][i]=probs[(int)age][i][ij];
4836: }else{ /* mobilav */
4837: for(i=1; i<=nlstate;i++)
4838: prlim[i][i]=mobaverage[(int)age][i][ij];
4839: }
4840: }
4841:
4842: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
4843:
4844: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
4845: for(h=0; h<=nhstepm; h++){
4846: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
4847: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
4848: }
4849: }
4850: /* This for computing probability of death (h=1 means
4851: computed over hstepm matrices product = hstepm*stepm months)
4852: as a weighted average of prlim.
4853: */
4854: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4855: for(i=1,gmp[j]=0.; i<= nlstate; i++)
4856: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4857: }
4858: /* end probability of death */
4859:
4860: for(j=1; j<= nlstate; j++) /* vareij */
4861: for(h=0; h<=nhstepm; h++){
4862: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
4863: }
4864:
4865: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
4866: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
4867: }
4868:
4869: } /* End theta */
4870:
4871: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
4872:
4873: for(h=0; h<=nhstepm; h++) /* veij */
4874: for(j=1; j<=nlstate;j++)
4875: for(theta=1; theta <=npar; theta++)
4876: trgradg[h][j][theta]=gradg[h][theta][j];
4877:
4878: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
4879: for(theta=1; theta <=npar; theta++)
4880: trgradgp[j][theta]=gradgp[theta][j];
4881:
4882:
4883: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4884: for(i=1;i<=nlstate;i++)
4885: for(j=1;j<=nlstate;j++)
4886: vareij[i][j][(int)age] =0.;
4887:
4888: for(h=0;h<=nhstepm;h++){
4889: for(k=0;k<=nhstepm;k++){
4890: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
4891: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
4892: for(i=1;i<=nlstate;i++)
4893: for(j=1;j<=nlstate;j++)
4894: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
4895: }
4896: }
4897:
4898: /* pptj */
4899: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
4900: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
4901: for(j=nlstate+1;j<=nlstate+ndeath;j++)
4902: for(i=nlstate+1;i<=nlstate+ndeath;i++)
4903: varppt[j][i]=doldmp[j][i];
4904: /* end ppptj */
4905: /* x centered again */
4906:
4907: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
4908:
4909: if (popbased==1) {
4910: if(mobilav ==0){
4911: for(i=1; i<=nlstate;i++)
4912: prlim[i][i]=probs[(int)age][i][ij];
4913: }else{ /* mobilav */
4914: for(i=1; i<=nlstate;i++)
4915: prlim[i][i]=mobaverage[(int)age][i][ij];
4916: }
4917: }
4918:
4919: /* This for computing probability of death (h=1 means
4920: computed over hstepm (estepm) matrices product = hstepm*stepm months)
4921: as a weighted average of prlim.
4922: */
4923: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
4924: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4925: for(i=1,gmp[j]=0.;i<= nlstate; i++)
4926: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4927: }
4928: /* end probability of death */
4929:
4930: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
4931: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4932: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
4933: for(i=1; i<=nlstate;i++){
4934: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
4935: }
4936: }
4937: fprintf(ficresprobmorprev,"\n");
4938:
4939: fprintf(ficresvij,"%.0f ",age );
4940: for(i=1; i<=nlstate;i++)
4941: for(j=1; j<=nlstate;j++){
4942: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
4943: }
4944: fprintf(ficresvij,"\n");
4945: free_matrix(gp,0,nhstepm,1,nlstate);
4946: free_matrix(gm,0,nhstepm,1,nlstate);
4947: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
4948: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
4949: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4950: } /* End age */
4951: free_vector(gpp,nlstate+1,nlstate+ndeath);
4952: free_vector(gmp,nlstate+1,nlstate+ndeath);
4953: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
4954: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
4955: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
4956: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
4957: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
4958: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
4959: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
4960: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
4961: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
4962: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
4963: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
4964: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
4965: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
4966: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
4967: 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);
4968: /* 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 4969: */
1.218 brouard 4970: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
4971: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4972:
1.218 brouard 4973: free_vector(xp,1,npar);
4974: free_matrix(doldm,1,nlstate,1,nlstate);
4975: free_matrix(dnewm,1,nlstate,1,npar);
4976: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4977: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
4978: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4979: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
4980: fclose(ficresprobmorprev);
4981: fflush(ficgp);
4982: fflush(fichtm);
4983: } /* end varevsij */
1.126 brouard 4984:
4985: /************ Variance of prevlim ******************/
1.209 brouard 4986: 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 4987: {
1.205 brouard 4988: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 4989: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 4990:
1.126 brouard 4991: double **dnewm,**doldm;
4992: int i, j, nhstepm, hstepm;
4993: double *xp;
4994: double *gp, *gm;
4995: double **gradg, **trgradg;
1.208 brouard 4996: double **mgm, **mgp;
1.126 brouard 4997: double age,agelim;
4998: int theta;
4999:
5000: pstamp(ficresvpl);
5001: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
5002: fprintf(ficresvpl,"# Age");
5003: for(i=1; i<=nlstate;i++)
5004: fprintf(ficresvpl," %1d-%1d",i,i);
5005: fprintf(ficresvpl,"\n");
5006:
5007: xp=vector(1,npar);
5008: dnewm=matrix(1,nlstate,1,npar);
5009: doldm=matrix(1,nlstate,1,nlstate);
5010:
5011: hstepm=1*YEARM; /* Every year of age */
5012: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
5013: agelim = AGESUP;
5014: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5015: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5016: if (stepm >= YEARM) hstepm=1;
5017: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5018: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 5019: mgp=matrix(1,npar,1,nlstate);
5020: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 5021: gp=vector(1,nlstate);
5022: gm=vector(1,nlstate);
5023:
5024: for(theta=1; theta <=npar; theta++){
5025: for(i=1; i<=npar; i++){ /* Computes gradient */
5026: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5027: }
1.209 brouard 5028: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
5029: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5030: else
5031: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 5032: for(i=1;i<=nlstate;i++){
1.126 brouard 5033: gp[i] = prlim[i][i];
1.208 brouard 5034: mgp[theta][i] = prlim[i][i];
5035: }
1.126 brouard 5036: for(i=1; i<=npar; i++) /* Computes gradient */
5037: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 5038: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
5039: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5040: else
5041: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 5042: for(i=1;i<=nlstate;i++){
1.126 brouard 5043: gm[i] = prlim[i][i];
1.208 brouard 5044: mgm[theta][i] = prlim[i][i];
5045: }
1.126 brouard 5046: for(i=1;i<=nlstate;i++)
5047: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 5048: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 5049: } /* End theta */
5050:
5051: trgradg =matrix(1,nlstate,1,npar);
5052:
5053: for(j=1; j<=nlstate;j++)
5054: for(theta=1; theta <=npar; theta++)
5055: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 5056: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5057: /* printf("\nmgm mgp %d ",(int)age); */
5058: /* for(j=1; j<=nlstate;j++){ */
5059: /* printf(" %d ",j); */
5060: /* for(theta=1; theta <=npar; theta++) */
5061: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
5062: /* printf("\n "); */
5063: /* } */
5064: /* } */
5065: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5066: /* printf("\n gradg %d ",(int)age); */
5067: /* for(j=1; j<=nlstate;j++){ */
5068: /* printf("%d ",j); */
5069: /* for(theta=1; theta <=npar; theta++) */
5070: /* printf("%d %lf ",theta,gradg[theta][j]); */
5071: /* printf("\n "); */
5072: /* } */
5073: /* } */
1.126 brouard 5074:
5075: for(i=1;i<=nlstate;i++)
5076: varpl[i][(int)age] =0.;
1.209 brouard 5077: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.205 brouard 5078: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5079: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
5080: }else{
1.126 brouard 5081: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5082: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 5083: }
1.126 brouard 5084: for(i=1;i<=nlstate;i++)
5085: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
5086:
5087: fprintf(ficresvpl,"%.0f ",age );
5088: for(i=1; i<=nlstate;i++)
5089: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
5090: fprintf(ficresvpl,"\n");
5091: free_vector(gp,1,nlstate);
5092: free_vector(gm,1,nlstate);
1.208 brouard 5093: free_matrix(mgm,1,npar,1,nlstate);
5094: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 5095: free_matrix(gradg,1,npar,1,nlstate);
5096: free_matrix(trgradg,1,nlstate,1,npar);
5097: } /* End age */
5098:
5099: free_vector(xp,1,npar);
5100: free_matrix(doldm,1,nlstate,1,npar);
5101: free_matrix(dnewm,1,nlstate,1,nlstate);
5102:
5103: }
5104:
5105: /************ Variance of one-step probabilities ******************/
5106: 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[])
5107: {
1.164 brouard 5108: int i, j=0, k1, l1, tj;
1.126 brouard 5109: int k2, l2, j1, z1;
1.164 brouard 5110: int k=0, l;
1.145 brouard 5111: int first=1, first1, first2;
1.126 brouard 5112: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
5113: double **dnewm,**doldm;
5114: double *xp;
5115: double *gp, *gm;
5116: double **gradg, **trgradg;
5117: double **mu;
1.164 brouard 5118: double age, cov[NCOVMAX+1];
1.126 brouard 5119: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
5120: int theta;
5121: char fileresprob[FILENAMELENGTH];
5122: char fileresprobcov[FILENAMELENGTH];
5123: char fileresprobcor[FILENAMELENGTH];
5124: double ***varpij;
5125:
1.201 brouard 5126: strcpy(fileresprob,"PROB_");
1.126 brouard 5127: strcat(fileresprob,fileres);
5128: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
5129: printf("Problem with resultfile: %s\n", fileresprob);
5130: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
5131: }
1.201 brouard 5132: strcpy(fileresprobcov,"PROBCOV_");
1.202 brouard 5133: strcat(fileresprobcov,fileresu);
1.126 brouard 5134: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
5135: printf("Problem with resultfile: %s\n", fileresprobcov);
5136: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
5137: }
1.201 brouard 5138: strcpy(fileresprobcor,"PROBCOR_");
1.202 brouard 5139: strcat(fileresprobcor,fileresu);
1.126 brouard 5140: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
5141: printf("Problem with resultfile: %s\n", fileresprobcor);
5142: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
5143: }
5144: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
5145: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
5146: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
5147: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
5148: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
5149: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
5150: pstamp(ficresprob);
5151: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
5152: fprintf(ficresprob,"# Age");
5153: pstamp(ficresprobcov);
5154: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
5155: fprintf(ficresprobcov,"# Age");
5156: pstamp(ficresprobcor);
5157: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
5158: fprintf(ficresprobcor,"# Age");
5159:
5160:
5161: for(i=1; i<=nlstate;i++)
5162: for(j=1; j<=(nlstate+ndeath);j++){
5163: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
5164: fprintf(ficresprobcov," p%1d-%1d ",i,j);
5165: fprintf(ficresprobcor," p%1d-%1d ",i,j);
5166: }
5167: /* fprintf(ficresprob,"\n");
5168: fprintf(ficresprobcov,"\n");
5169: fprintf(ficresprobcor,"\n");
5170: */
1.131 brouard 5171: xp=vector(1,npar);
1.126 brouard 5172: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
5173: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
5174: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
5175: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
5176: first=1;
5177: fprintf(ficgp,"\n# Routine varprob");
5178: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
5179: fprintf(fichtm,"\n");
5180:
1.200 brouard 5181: 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 5182: 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);
5183: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 5184: and drawn. It helps understanding how is the covariance between two incidences.\
5185: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
5186: 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. \
5187: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
5188: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
5189: standard deviations wide on each axis. <br>\
5190: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
5191: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
5192: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
5193:
5194: cov[1]=1;
1.145 brouard 5195: /* tj=cptcoveff; */
5196: tj = (int) pow(2,cptcoveff);
1.126 brouard 5197: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
5198: j1=0;
1.145 brouard 5199: for(j1=1; j1<=tj;j1++){
5200: /*for(i1=1; i1<=ncodemax[t];i1++){ */
5201: /*j1++;*/
1.126 brouard 5202: if (cptcovn>0) {
5203: fprintf(ficresprob, "\n#********** Variable ");
1.198 brouard 5204: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 5205: fprintf(ficresprob, "**********\n#\n");
5206: fprintf(ficresprobcov, "\n#********** Variable ");
1.198 brouard 5207: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 5208: fprintf(ficresprobcov, "**********\n#\n");
5209:
5210: fprintf(ficgp, "\n#********** Variable ");
1.198 brouard 5211: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 5212: fprintf(ficgp, "**********\n#\n");
5213:
5214:
5215: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.198 brouard 5216: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 5217: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
5218:
5219: fprintf(ficresprobcor, "\n#********** Variable ");
1.198 brouard 5220: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 5221: fprintf(ficresprobcor, "**********\n#");
5222: }
5223:
1.145 brouard 5224: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
5225: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
5226: gp=vector(1,(nlstate)*(nlstate+ndeath));
5227: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 5228: for (age=bage; age<=fage; age ++){
5229: cov[2]=age;
1.187 brouard 5230: if(nagesqr==1)
5231: cov[3]= age*age;
1.126 brouard 5232: for (k=1; k<=cptcovn;k++) {
1.200 brouard 5233: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
5234: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
1.145 brouard 5235: * 1 1 1 1 1
5236: * 2 2 1 1 1
5237: * 3 1 2 1 1
5238: */
5239: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 5240: }
1.186 brouard 5241: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 5242: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
1.126 brouard 5243: for (k=1; k<=cptcovprod;k++)
1.200 brouard 5244: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.126 brouard 5245:
5246:
5247: for(theta=1; theta <=npar; theta++){
5248: for(i=1; i<=npar; i++)
5249: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
5250:
5251: pmij(pmmij,cov,ncovmodel,xp,nlstate);
5252:
5253: k=0;
5254: for(i=1; i<= (nlstate); i++){
5255: for(j=1; j<=(nlstate+ndeath);j++){
5256: k=k+1;
5257: gp[k]=pmmij[i][j];
5258: }
5259: }
5260:
5261: for(i=1; i<=npar; i++)
5262: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
5263:
5264: pmij(pmmij,cov,ncovmodel,xp,nlstate);
5265: k=0;
5266: for(i=1; i<=(nlstate); i++){
5267: for(j=1; j<=(nlstate+ndeath);j++){
5268: k=k+1;
5269: gm[k]=pmmij[i][j];
5270: }
5271: }
5272:
5273: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
5274: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
5275: }
5276:
5277: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
5278: for(theta=1; theta <=npar; theta++)
5279: trgradg[j][theta]=gradg[theta][j];
5280:
5281: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
5282: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
5283:
5284: pmij(pmmij,cov,ncovmodel,x,nlstate);
5285:
5286: k=0;
5287: for(i=1; i<=(nlstate); i++){
5288: for(j=1; j<=(nlstate+ndeath);j++){
5289: k=k+1;
5290: mu[k][(int) age]=pmmij[i][j];
5291: }
5292: }
5293: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
5294: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
5295: varpij[i][j][(int)age] = doldm[i][j];
5296:
5297: /*printf("\n%d ",(int)age);
5298: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
5299: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
5300: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
5301: }*/
5302:
5303: fprintf(ficresprob,"\n%d ",(int)age);
5304: fprintf(ficresprobcov,"\n%d ",(int)age);
5305: fprintf(ficresprobcor,"\n%d ",(int)age);
5306:
5307: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
5308: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
5309: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
5310: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
5311: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
5312: }
5313: i=0;
5314: for (k=1; k<=(nlstate);k++){
5315: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 5316: i++;
1.126 brouard 5317: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
5318: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
5319: for (j=1; j<=i;j++){
1.145 brouard 5320: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 5321: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
5322: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
5323: }
5324: }
5325: }/* end of loop for state */
5326: } /* end of loop for age */
1.145 brouard 5327: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
5328: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
5329: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
5330: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
5331:
1.126 brouard 5332: /* Confidence intervalle of pij */
5333: /*
1.131 brouard 5334: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 5335: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
5336: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
5337: 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);
5338: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
5339: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
5340: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
5341: */
5342:
5343: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 5344: first1=1;first2=2;
1.126 brouard 5345: for (k2=1; k2<=(nlstate);k2++){
5346: for (l2=1; l2<=(nlstate+ndeath);l2++){
5347: if(l2==k2) continue;
5348: j=(k2-1)*(nlstate+ndeath)+l2;
5349: for (k1=1; k1<=(nlstate);k1++){
5350: for (l1=1; l1<=(nlstate+ndeath);l1++){
5351: if(l1==k1) continue;
5352: i=(k1-1)*(nlstate+ndeath)+l1;
5353: if(i<=j) continue;
5354: for (age=bage; age<=fage; age ++){
5355: if ((int)age %5==0){
5356: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
5357: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
5358: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
5359: mu1=mu[i][(int) age]/stepm*YEARM ;
5360: mu2=mu[j][(int) age]/stepm*YEARM;
5361: c12=cv12/sqrt(v1*v2);
5362: /* Computing eigen value of matrix of covariance */
5363: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
5364: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 5365: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 5366: if(first2==1){
5367: first1=0;
5368: 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);
5369: }
5370: 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);
5371: /* lc1=fabs(lc1); */ /* If we want to have them positive */
5372: /* lc2=fabs(lc2); */
1.135 brouard 5373: }
5374:
1.126 brouard 5375: /* Eigen vectors */
5376: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
5377: /*v21=sqrt(1.-v11*v11); *//* error */
5378: v21=(lc1-v1)/cv12*v11;
5379: v12=-v21;
5380: v22=v11;
5381: tnalp=v21/v11;
5382: if(first1==1){
5383: first1=0;
5384: 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);
5385: }
5386: 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);
5387: /*printf(fignu*/
5388: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
5389: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
5390: if(first==1){
5391: first=0;
1.200 brouard 5392: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
1.126 brouard 5393: fprintf(ficgp,"\nset parametric;unset label");
5394: 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 5395: fprintf(ficgp,"\nset ter svg size 640, 480");
1.126 brouard 5396: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.201 brouard 5397: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">\
5398: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
5399: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\
5400: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5401: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 5402: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.201 brouard 5403: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 5404: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
5405: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
5406: 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",\
5407: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
5408: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
5409: }else{
5410: first=0;
5411: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
5412: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
5413: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
5414: 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",\
5415: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
5416: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
5417: }/* if first */
5418: } /* age mod 5 */
5419: } /* end loop age */
1.201 brouard 5420: 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 5421: first=1;
5422: } /*l12 */
5423: } /* k12 */
5424: } /*l1 */
5425: }/* k1 */
1.169 brouard 5426: /* } */ /* loop covariates */
1.126 brouard 5427: }
5428: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
5429: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
5430: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
5431: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
5432: free_vector(xp,1,npar);
5433: fclose(ficresprob);
5434: fclose(ficresprobcov);
5435: fclose(ficresprobcor);
5436: fflush(ficgp);
5437: fflush(fichtmcov);
5438: }
5439:
5440:
5441: /******************* Printing html file ***********/
1.201 brouard 5442: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 5443: int lastpass, int stepm, int weightopt, char model[],\
5444: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.217 brouard 5445: int popforecast, int prevfcast, int backcast, int estepm , \
1.213 brouard 5446: double jprev1, double mprev1,double anprev1, double dateprev1, \
5447: double jprev2, double mprev2,double anprev2, double dateprev2){
1.126 brouard 5448: int jj1, k1, i1, cpt;
5449:
5450: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
5451: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
5452: </ul>");
1.214 brouard 5453: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
5454: 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",
5455: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
5456: 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 5457: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
5458: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 5459: fprintf(fichtm,"\
5460: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 5461: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 5462: fprintf(fichtm,"\
1.217 brouard 5463: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
5464: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
5465: fprintf(fichtm,"\
1.126 brouard 5466: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5467: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 5468: fprintf(fichtm,"\
1.217 brouard 5469: - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
5470: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
5471: fprintf(fichtm,"\
1.211 brouard 5472: - (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 5473: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5474: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 5475: if(prevfcast==1){
5476: fprintf(fichtm,"\
5477: - Prevalence projections by age and states: \
1.201 brouard 5478: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 5479: }
1.126 brouard 5480:
5481: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
5482:
1.145 brouard 5483: m=pow(2,cptcoveff);
1.126 brouard 5484: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
5485:
5486: jj1=0;
5487: for(k1=1; k1<=m;k1++){
1.192 brouard 5488: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 5489: jj1++;
5490: if (cptcovn > 0) {
5491: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.192 brouard 5492: for (cpt=1; cpt<=cptcoveff;cpt++){
1.198 brouard 5493: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
5494: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
1.192 brouard 5495: }
1.126 brouard 5496: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
5497: }
1.201 brouard 5498: /* aij, bij */
1.211 brouard 5499: 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> \
5500: <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 5501: /* Pij */
1.211 brouard 5502: 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 5503: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 5504: /* Quasi-incidences */
1.211 brouard 5505: 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 5506: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\
1.211 brouard 5507: incidence (rates) are the limit when h tends to zero of the ratio of the probability <sub>h</sub>P<sub>ij</sub> \
5508: 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 5509: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
5510: /* Survival functions (period) in state j */
5511: for(cpt=1; cpt<=nlstate;cpt++){
5512: 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> \
5513: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
5514: }
5515: /* State specific survival functions (period) */
5516: for(cpt=1; cpt<=nlstate;cpt++){
1.208 brouard 5517: fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
1.201 brouard 5518: Or probability to survive in various states (1 to %d) being in state %d at different ages.\
5519: <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);
5520: }
5521: /* Period (stable) prevalence in each health state */
5522: for(cpt=1; cpt<=nlstate;cpt++){
1.217 brouard 5523: 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 5524: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
5525: }
1.217 brouard 5526: if(backcast==1){
5527: /* Period (stable) back prevalence in each health state */
5528: for(cpt=1; cpt<=nlstate;cpt++){
5529: 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> \
5530: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);
5531: }
5532: }
1.211 brouard 5533: if(prevfcast==1){
5534: /* Projection of prevalence up to period (stable) prevalence in each health state */
5535: for(cpt=1; cpt<=nlstate;cpt++){
1.214 brouard 5536: 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 5537: <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 5538: }
5539: }
5540:
1.126 brouard 5541: for(cpt=1; cpt<=nlstate;cpt++) {
1.205 brouard 5542: 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 5543: <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 5544: }
1.192 brouard 5545: /* } /\* end i1 *\/ */
1.126 brouard 5546: }/* End k1 */
5547: fprintf(fichtm,"</ul>");
5548:
5549: fprintf(fichtm,"\
5550: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 5551: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 5552: - 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 5553: But because parameters are usually highly correlated (a higher incidence of disability \
5554: and a higher incidence of recovery can give very close observed transition) it might \
5555: be very useful to look not only at linear confidence intervals estimated from the \
5556: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
5557: (parameters) of the logistic regression, it might be more meaningful to visualize the \
5558: covariance matrix of the one-step probabilities. \
5559: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 5560:
1.193 brouard 5561: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5562: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
1.126 brouard 5563: fprintf(fichtm,"\
5564: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5565: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 5566:
5567: fprintf(fichtm,"\
5568: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5569: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
1.126 brouard 5570: fprintf(fichtm,"\
5571: - 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): \
5572: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5573: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.126 brouard 5574: fprintf(fichtm,"\
5575: - (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): \
5576: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5577: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.126 brouard 5578: fprintf(fichtm,"\
1.128 brouard 5579: - 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 5580: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
1.126 brouard 5581: fprintf(fichtm,"\
1.128 brouard 5582: - 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 5583: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
1.126 brouard 5584: fprintf(fichtm,"\
5585: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.201 brouard 5586: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 5587:
5588: /* if(popforecast==1) fprintf(fichtm,"\n */
5589: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
5590: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
5591: /* <br>",fileres,fileres,fileres,fileres); */
5592: /* else */
5593: /* 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); */
5594: fflush(fichtm);
5595: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
5596:
1.145 brouard 5597: m=pow(2,cptcoveff);
1.126 brouard 5598: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
5599:
5600: jj1=0;
5601: for(k1=1; k1<=m;k1++){
1.192 brouard 5602: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 5603: jj1++;
5604: if (cptcovn > 0) {
5605: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
5606: for (cpt=1; cpt<=cptcoveff;cpt++)
1.198 brouard 5607: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 5608: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
5609: }
5610: for(cpt=1; cpt<=nlstate;cpt++) {
1.218 brouard 5611: fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
5612: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d.svg\"> %s_%d-%d.svg</a>\n <br>\
1.205 brouard 5613: <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 5614: }
5615: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 5616: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
5617: true period expectancies (those weighted with period prevalences are also\
5618: drawn in addition to the population based expectancies computed using\
1.218 brouard 5619: observed and cahotic prevalences: <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\
1.205 brouard 5620: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.192 brouard 5621: /* } /\* end i1 *\/ */
1.126 brouard 5622: }/* End k1 */
5623: fprintf(fichtm,"</ul>");
5624: fflush(fichtm);
5625: }
5626:
5627: /******************* Gnuplot file **************/
1.218 brouard 5628: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
1.126 brouard 5629:
5630: char dirfileres[132],optfileres[132];
1.164 brouard 5631: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.211 brouard 5632: int lv=0, vlv=0, kl=0;
1.130 brouard 5633: int ng=0;
1.201 brouard 5634: int vpopbased;
1.219 ! brouard 5635: int ioffset; /* variable offset for columns */
! 5636:
1.126 brouard 5637: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
5638: /* printf("Problem with file %s",optionfilegnuplot); */
5639: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
5640: /* } */
5641:
5642: /*#ifdef windows */
5643: fprintf(ficgp,"cd \"%s\" \n",pathc);
5644: /*#endif */
5645: m=pow(2,cptcoveff);
5646:
1.202 brouard 5647: /* Contribution to likelihood */
5648: /* Plot the probability implied in the likelihood */
5649: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
5650: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
5651: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
1.205 brouard 5652: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 5653: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 5654: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
5655: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
5656: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
1.204 brouard 5657: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
1.214 brouard 5658: 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 5659: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
1.214 brouard 5660: 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 5661: for (i=1; i<= nlstate ; i ++) {
5662: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
1.205 brouard 5663: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
1.214 brouard 5664: 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 5665: for (j=2; j<= nlstate+ndeath ; j ++) {
1.219 ! brouard 5666: 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 5667: }
5668: fprintf(ficgp,";\nset out; unset ylabel;\n");
5669: }
5670: /* 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 */
5671: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
5672: /* 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 5673: fprintf(ficgp,"\nset out;unset log\n");
1.202 brouard 5674: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
5675:
1.126 brouard 5676: strcpy(dirfileres,optionfilefiname);
5677: strcpy(optfileres,"vpl");
5678: /* 1eme*/
1.211 brouard 5679: for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
5680: for (k1=1; k1<= m ; k1 ++) { /* For each combination of covariate */
5681: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
5682: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
1.219 ! brouard 5683: for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
! 5684: lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
! 5685: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
! 5686: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
! 5687: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
! 5688: vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
! 5689: /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
! 5690: fprintf(ficgp," V%d=%d ",k,vlv);
1.211 brouard 5691: }
5692: fprintf(ficgp,"\n#\n");
5693:
1.219 ! brouard 5694: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
! 5695: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
! 5696: fprintf(ficgp,"set xlabel \"Age\" \n\
! 5697: set ylabel \"Probability\" \n \
! 5698: set ter svg size 640, 480\n \
1.201 brouard 5699: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.219 ! brouard 5700:
! 5701: for (i=1; i<= nlstate ; i ++) {
! 5702: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
! 5703: else fprintf(ficgp," %%*lf (%%*lf)");
! 5704: }
! 5705: 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);
! 5706: for (i=1; i<= nlstate ; i ++) {
! 5707: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
! 5708: else fprintf(ficgp," %%*lf (%%*lf)");
! 5709: }
! 5710: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
! 5711: for (i=1; i<= nlstate ; i ++) {
! 5712: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
! 5713: else fprintf(ficgp," %%*lf (%%*lf)");
! 5714: }
! 5715: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
! 5716: if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
! 5717: /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
! 5718: fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
! 5719: kl=0;
! 5720: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
! 5721: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
! 5722: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
! 5723: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
! 5724: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
! 5725: vlv= nbcode[Tvaraff[k]][lv];
! 5726: kl++;
! 5727: /* 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 *\/ */
! 5728: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
! 5729: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
! 5730: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
! 5731: if(k==cptcoveff){
! 5732: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, k,kl+1+1,nbcode[Tvaraff[k]][lv], \
! 5733: 4+(cpt-1), cpt );
! 5734: }else{
! 5735: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, k,kl+1+1,nbcode[Tvaraff[k]][lv]);
! 5736: kl++;
! 5737: }
! 5738: } /* end covariate */
! 5739: }
! 5740: fprintf(ficgp,"\nset out \n");
1.201 brouard 5741: } /* k1 */
5742: } /* cpt */
1.126 brouard 5743: /*2 eme*/
5744: for (k1=1; k1<= m ; k1 ++) {
1.211 brouard 5745: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
5746: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.219 ! brouard 5747: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
! 5748: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
! 5749: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
! 5750: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
! 5751: vlv= nbcode[Tvaraff[k]][lv];
! 5752: fprintf(ficgp," V%d=%d ",k,vlv);
1.211 brouard 5753: }
5754: fprintf(ficgp,"\n#\n");
1.219 ! brouard 5755:
! 5756: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
! 5757: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
! 5758: if(vpopbased==0)
! 5759: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
! 5760: else
! 5761: fprintf(ficgp,"\nreplot ");
! 5762: for (i=1; i<= nlstate+1 ; i ++) {
! 5763: k=2*i;
! 5764: 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);
! 5765: for (j=1; j<= nlstate+1 ; j ++) {
! 5766: if (j==i) fprintf(ficgp," %%lf (%%lf)");
! 5767: else fprintf(ficgp," %%*lf (%%*lf)");
! 5768: }
! 5769: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
! 5770: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
! 5771: 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);
! 5772: for (j=1; j<= nlstate+1 ; j ++) {
! 5773: if (j==i) fprintf(ficgp," %%lf (%%lf)");
! 5774: else fprintf(ficgp," %%*lf (%%*lf)");
! 5775: }
! 5776: fprintf(ficgp,"\" t\"\" w l lt 0,");
! 5777: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
! 5778: for (j=1; j<= nlstate+1 ; j ++) {
! 5779: if (j==i) fprintf(ficgp," %%lf (%%lf)");
! 5780: else fprintf(ficgp," %%*lf (%%*lf)");
! 5781: }
! 5782: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
! 5783: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
! 5784: } /* state */
! 5785: } /* vpopbased */
! 5786: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
1.201 brouard 5787: } /* k1 */
1.219 ! brouard 5788:
! 5789:
1.126 brouard 5790: /*3eme*/
5791: for (k1=1; k1<= m ; k1 ++) {
5792: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.211 brouard 5793: fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt);
5794: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.219 ! brouard 5795: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
! 5796: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
! 5797: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
! 5798: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
! 5799: vlv= nbcode[Tvaraff[k]][lv];
! 5800: fprintf(ficgp," V%d=%d ",k,vlv);
1.211 brouard 5801: }
5802: fprintf(ficgp,"\n#\n");
1.219 ! brouard 5803:
1.126 brouard 5804: /* k=2+nlstate*(2*cpt-2); */
5805: k=2+(nlstate+1)*(cpt-1);
1.201 brouard 5806: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
1.199 brouard 5807: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 5808: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.126 brouard 5809: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
1.219 ! brouard 5810: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
! 5811: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
! 5812: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
! 5813: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
! 5814: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
! 5815:
1.126 brouard 5816: */
5817: for (i=1; i< nlstate ; i ++) {
1.219 ! brouard 5818: 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);
! 5819: /* 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);*/
! 5820:
1.126 brouard 5821: }
1.201 brouard 5822: 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 5823: }
5824: }
5825:
1.201 brouard 5826: /* Survival functions (period) from state i in state j by initial state i */
5827: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
5828: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.211 brouard 5829: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
5830: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5831: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5832: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5833: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5834: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.219 ! brouard 5835: vlv= nbcode[Tvaraff[k]][lv];
1.211 brouard 5836: fprintf(ficgp," V%d=%d ",k,vlv);
5837: }
5838: fprintf(ficgp,"\n#\n");
5839:
1.201 brouard 5840: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
5841: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
5842: set ter svg size 640, 480\n\
5843: unset log y\n\
5844: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 5845: k=3;
1.201 brouard 5846: for (i=1; i<= nlstate ; i ++){
1.217 brouard 5847: if(i==1){
1.201 brouard 5848: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
1.217 brouard 5849: }else{
1.201 brouard 5850: fprintf(ficgp,", '' ");
1.217 brouard 5851: }
1.201 brouard 5852: l=(nlstate+ndeath)*(i-1)+1;
5853: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
5854: for (j=2; j<= nlstate+ndeath ; j ++)
5855: fprintf(ficgp,"+$%d",k+l+j-1);
5856: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
5857: } /* nlstate */
5858: fprintf(ficgp,"\nset out\n");
5859: } /* end cpt state*/
5860: } /* end covariate */
5861:
5862: /* Survival functions (period) from state i in state j by final state j */
1.202 brouard 5863: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.201 brouard 5864: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
5865: 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 5866: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5867: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5868: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5869: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5870: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.219 ! brouard 5871: vlv= nbcode[Tvaraff[k]][lv];
1.211 brouard 5872: fprintf(ficgp," V%d=%d ",k,vlv);
5873: }
5874: fprintf(ficgp,"\n#\n");
5875:
1.201 brouard 5876: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
5877: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
5878: set ter svg size 640, 480\n\
5879: unset log y\n\
5880: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 5881: k=3;
1.201 brouard 5882: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
5883: if(j==1)
5884: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5885: else
5886: fprintf(ficgp,", '' ");
5887: l=(nlstate+ndeath)*(cpt-1) +j;
5888: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
5889: /* for (i=2; i<= nlstate+ndeath ; i ++) */
5890: /* fprintf(ficgp,"+$%d",k+l+i-1); */
5891: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
5892: } /* nlstate */
5893: fprintf(ficgp,", '' ");
5894: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
5895: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
5896: l=(nlstate+ndeath)*(cpt-1) +j;
5897: if(j < nlstate)
5898: fprintf(ficgp,"$%d +",k+l);
5899: else
5900: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
5901: }
5902: fprintf(ficgp,"\nset out\n");
5903: } /* end cpt state*/
5904: } /* end covariate */
5905:
1.202 brouard 5906: /* CV preval stable (period) for each covariate */
1.211 brouard 5907: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.153 brouard 5908: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.211 brouard 5909: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
5910: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5911: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5912: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5913: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5914: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.219 ! brouard 5915: vlv= nbcode[Tvaraff[k]][lv];
1.211 brouard 5916: fprintf(ficgp," V%d=%d ",k,vlv);
5917: }
5918: fprintf(ficgp,"\n#\n");
5919:
1.201 brouard 5920: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 5921: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.199 brouard 5922: set ter svg size 640, 480\n\
1.126 brouard 5923: unset log y\n\
1.153 brouard 5924: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 5925: k=3; /* Offset */
1.153 brouard 5926: for (i=1; i<= nlstate ; i ++){
5927: if(i==1)
1.201 brouard 5928: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
1.153 brouard 5929: else
5930: fprintf(ficgp,", '' ");
1.154 brouard 5931: l=(nlstate+ndeath)*(i-1)+1;
5932: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.201 brouard 5933: for (j=2; j<= nlstate ; j ++)
5934: fprintf(ficgp,"+$%d",k+l+j-1);
1.153 brouard 5935: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
5936: } /* nlstate */
1.201 brouard 5937: fprintf(ficgp,"\nset out\n");
1.153 brouard 5938: } /* end cpt state*/
5939: } /* end covariate */
1.218 brouard 5940: if(backcast == 1){
1.217 brouard 5941: /* CV back preval stable (period) for each covariate */
1.218 brouard 5942: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
5943: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
5944: fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
5945: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5946: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5947: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5948: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5949: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.219 ! brouard 5950: vlv= nbcode[Tvaraff[k]][lv];
1.218 brouard 5951: fprintf(ficgp," V%d=%d ",k,vlv);
5952: }
5953: fprintf(ficgp,"\n#\n");
5954:
5955: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
5956: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
5957: set ter svg size 640, 480\n \
5958: unset log y\n \
5959: plot [%.f:%.f] ", ageminpar, agemaxpar);
5960: k=3; /* Offset */
5961: for (i=1; i<= nlstate ; i ++){
5962: if(i==1)
5963: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
5964: else
5965: fprintf(ficgp,", '' ");
5966: /* l=(nlstate+ndeath)*(i-1)+1; */
5967: l=(nlstate+ndeath)*(cpt-1)+1;
5968: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
5969: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
5970: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
5971: /* for (j=2; j<= nlstate ; j ++) */
5972: /* fprintf(ficgp,"+$%d",k+l+j-1); */
5973: /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
5974: fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
5975: } /* nlstate */
5976: fprintf(ficgp,"\nset out\n");
5977: } /* end cpt state*/
5978: } /* end covariate */
5979: } /* End if backcast */
5980:
5981: if(prevfcast==1){
5982: /* Projection from cross-sectional to stable (period) for each covariate */
5983:
5984: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.211 brouard 5985: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.219 ! brouard 5986: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
! 5987: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
! 5988: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
! 5989: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
! 5990: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
! 5991: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
! 5992: vlv= nbcode[Tvaraff[k]][lv];
! 5993: fprintf(ficgp," V%d=%d ",k,vlv);
! 5994: }
! 5995: fprintf(ficgp,"\n#\n");
! 5996:
! 5997: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
! 5998: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
! 5999: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
! 6000: set ter svg size 640, 480\n \
! 6001: unset log y\n \
! 6002: plot [%.f:%.f] ", ageminpar, agemaxpar);
! 6003: for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
! 6004: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
! 6005: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
! 6006: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
! 6007: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
! 6008: if(i==1){
! 6009: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
! 6010: }else{
! 6011: fprintf(ficgp,",\\\n '' ");
! 6012: }
! 6013: if(cptcoveff ==0){ /* No covariate */
! 6014: ioffset=2; /* Age is in 2 */
! 6015: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
! 6016: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
! 6017: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
! 6018: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
! 6019: fprintf(ficgp," u %d:(", ioffset);
! 6020: if(i==nlstate+1)
! 6021: fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ", \
! 6022: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
! 6023: else
! 6024: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
! 6025: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
! 6026: }else{ /* more than 2 covariates */
! 6027: if(cptcoveff ==1){
! 6028: ioffset=4; /* Age is in 4 */
! 6029: }else{
! 6030: ioffset=6; /* Age is in 6 */
! 6031: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
! 6032: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
! 6033: }
! 6034: fprintf(ficgp," u %d:((",ioffset);
! 6035: kl=0;
! 6036: for (k=1; k<=cptcoveff; k++){ /* For each covariate */
! 6037: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
! 6038: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
! 6039: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
! 6040: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
! 6041: vlv= nbcode[Tvaraff[k]][lv];
! 6042: kl++;
! 6043: /* 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 *\/ */
! 6044: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
! 6045: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
! 6046: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
! 6047: if(k==cptcoveff){
! 6048: if(i==nlstate+1){
! 6049: if(cptcoveff ==1){
! 6050: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ",kl, k,kl+1,nbcode[Tvaraff[k]][lv], \
! 6051: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
! 6052: }else{
! 6053: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ",kl, k,kl+1,nbcode[Tvaraff[k]][lv], \
! 6054: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
! 6055: }
! 6056: }else{
! 6057: if(cptcoveff ==1){
! 6058: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ",kl, k,kl+1,nbcode[Tvaraff[k]][lv], \
! 6059: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
! 6060: }else{
! 6061: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ",kl, k,kl+1,nbcode[Tvaraff[k]][lv], \
! 6062: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
! 6063: }
! 6064: }
! 6065: }else{ /* k < cptcoveff */
! 6066: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl, k,kl+1,nbcode[Tvaraff[k]][lv]);
! 6067: kl++;
! 6068: }
! 6069: } /* end covariate */
! 6070: } /* end if covariate */
! 6071: } /* nlstate */
! 6072: fprintf(ficgp,"\nset out\n");
! 6073: } /* end cpt state*/
! 6074: } /* end covariate */
! 6075: } /* End if prevfcast */
! 6076:
1.211 brouard 6077:
1.219 ! brouard 6078: /* proba elementaires */
! 6079: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 6080: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 6081: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 6082: for(k=1; k <=(nlstate+ndeath); k++){
6083: if (k != i) {
1.187 brouard 6084: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 6085: for(j=1; j <=ncovmodel; j++){
1.187 brouard 6086: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 6087: jk++;
6088: }
1.187 brouard 6089: fprintf(ficgp,"\n");
1.126 brouard 6090: }
6091: }
6092: }
1.187 brouard 6093: fprintf(ficgp,"##############\n#\n");
6094:
1.145 brouard 6095: /*goto avoid;*/
1.200 brouard 6096: fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
1.187 brouard 6097: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
6098: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
6099: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
6100: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
6101: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6102: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
6103: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6104: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
6105: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
6106: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6107: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
6108: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
6109: fprintf(ficgp,"#\n");
1.201 brouard 6110: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.187 brouard 6111: fprintf(ficgp,"# ng=%d\n",ng);
6112: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 6113: for(jk=1; jk <=m; jk++) {
1.187 brouard 6114: fprintf(ficgp,"# jk=%d\n",jk);
1.201 brouard 6115: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
6116: fprintf(ficgp,"\nset ter svg size 640, 480 ");
6117: if (ng==1){
6118: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
6119: fprintf(ficgp,"\nunset log y");
6120: }else if (ng==2){
6121: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
6122: fprintf(ficgp,"\nset log y");
6123: }else if (ng==3){
1.126 brouard 6124: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
1.201 brouard 6125: fprintf(ficgp,"\nset log y");
6126: }else
6127: fprintf(ficgp,"\nunset title ");
6128: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 6129: i=1;
6130: for(k2=1; k2<=nlstate; k2++) {
6131: k3=i;
6132: for(k=1; k<=(nlstate+ndeath); k++) {
6133: if (k != k2){
1.201 brouard 6134: switch( ng) {
6135: case 1:
1.187 brouard 6136: if(nagesqr==0)
1.201 brouard 6137: fprintf(ficgp," p%d+p%d*x",i,i+1);
1.187 brouard 6138: else /* nagesqr =1 */
1.201 brouard 6139: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
6140: break;
6141: case 2: /* ng=2 */
1.187 brouard 6142: if(nagesqr==0)
6143: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
6144: else /* nagesqr =1 */
1.201 brouard 6145: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
6146: break;
6147: case 3:
6148: if(nagesqr==0)
6149: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
6150: else /* nagesqr =1 */
6151: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
6152: break;
6153: }
1.141 brouard 6154: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 brouard 6155: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.197 brouard 6156: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
6157: if(ij <=cptcovage) { /* Bug valgrind */
6158: if((j-2)==Tage[ij]) { /* Bug valgrind */
1.200 brouard 6159: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
6160: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
1.197 brouard 6161: ij++;
6162: }
1.186 brouard 6163: }
6164: else
1.198 brouard 6165: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.126 brouard 6166: }
1.217 brouard 6167: }else{
6168: i=i-ncovmodel;
6169: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
6170: fprintf(ficgp," (1.");
6171: }
6172:
6173: if(ng != 1){
6174: fprintf(ficgp,")/(1");
1.126 brouard 6175:
1.217 brouard 6176: for(k1=1; k1 <=nlstate; k1++){
6177: if(nagesqr==0)
6178: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
6179: else /* nagesqr =1 */
6180: 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);
6181:
6182: ij=1;
6183: for(j=3; j <=ncovmodel-nagesqr; j++){
6184: if(ij <=cptcovage) { /* Bug valgrind */
6185: if((j-2)==Tage[ij]) { /* Bug valgrind */
6186: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
6187: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
6188: ij++;
1.197 brouard 6189: }
1.186 brouard 6190: }
1.217 brouard 6191: else
6192: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.126 brouard 6193: }
6194: fprintf(ficgp,")");
1.217 brouard 6195: }
6196: fprintf(ficgp,")");
6197: if(ng ==2)
6198: fprintf(ficgp," t \"p%d%d\" ", k2,k);
6199: else /* ng= 3 */
6200: fprintf(ficgp," t \"i%d%d\" ", k2,k);
6201: }else{ /* end ng <> 1 */
6202: if( k !=k2) /* logit p11 is hard to draw */
1.201 brouard 6203: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
1.126 brouard 6204: }
1.217 brouard 6205: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
6206: fprintf(ficgp,",");
6207: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
6208: fprintf(ficgp,",");
6209: i=i+ncovmodel;
1.126 brouard 6210: } /* end k */
6211: } /* end k2 */
1.201 brouard 6212: fprintf(ficgp,"\n set out\n");
1.126 brouard 6213: } /* end jk */
6214: } /* end ng */
1.164 brouard 6215: /* avoid: */
1.126 brouard 6216: fflush(ficgp);
6217: } /* end gnuplot */
6218:
6219:
6220: /*************** Moving average **************/
1.219 ! brouard 6221: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.218 brouard 6222: int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
6223:
1.126 brouard 6224: int i, cpt, cptcod;
6225: int modcovmax =1;
6226: int mobilavrange, mob;
1.219 ! brouard 6227: int iage=0;
! 6228:
! 6229: double sum=0.;
1.126 brouard 6230: double age;
1.218 brouard 6231: double *sumnewp, *sumnewm;
6232: double *agemingood, *agemaxgood; /* Currently identical for all covariates */
6233:
1.219 ! brouard 6234:
! 6235: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
! 6236: a covariate has 2 modalities, should be equal to ncovcombmax */
! 6237:
1.218 brouard 6238: sumnewp = vector(1,modcovmax);
6239: sumnewm = vector(1,modcovmax);
6240: agemingood = vector(1,modcovmax);
6241: agemaxgood = vector(1,modcovmax);
1.219 ! brouard 6242:
! 6243: for (cptcod=1;cptcod<=modcovmax;cptcod++){
! 6244: sumnewm[cptcod]=0.;
! 6245: sumnewp[cptcod]=0.;
! 6246: agemingood[cptcod]=0;
! 6247: agemaxgood[cptcod]=0;
! 6248: }
1.126 brouard 6249: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
1.218 brouard 6250:
1.126 brouard 6251: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
6252: if(mobilav==1) mobilavrange=5; /* default */
6253: else mobilavrange=mobilav;
6254: for (age=bage; age<=fage; age++)
6255: for (i=1; i<=nlstate;i++)
1.219 ! brouard 6256: for (cptcod=1;cptcod<=modcovmax;cptcod++)
! 6257: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
1.126 brouard 6258: /* We keep the original values on the extreme ages bage, fage and for
6259: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
6260: we use a 5 terms etc. until the borders are no more concerned.
6261: */
6262: for (mob=3;mob <=mobilavrange;mob=mob+2){
6263: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
1.219 ! brouard 6264: for (i=1; i<=nlstate;i++){
! 6265: for (cptcod=1;cptcod<=modcovmax;cptcod++){
! 6266: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
! 6267: for (cpt=1;cpt<=(mob-1)/2;cpt++){
! 6268: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
! 6269: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
! 6270: }
! 6271: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
! 6272: }
! 6273: }
1.126 brouard 6274: }/* end age */
6275: }/* end mob */
1.218 brouard 6276: }else
6277: return -1;
6278: for (cptcod=1;cptcod<=modcovmax;cptcod++){
6279: /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
1.219 ! brouard 6280: agemingood[cptcod]=fage-(mob-1)/2;
1.218 brouard 6281: for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
6282: sumnewm[cptcod]=0.;
6283: for (i=1; i<=nlstate;i++){
6284: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6285: }
6286: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
1.219 ! brouard 6287: agemingood[cptcod]=age;
1.218 brouard 6288: }else{ /* bad */
1.219 ! brouard 6289: for (i=1; i<=nlstate;i++){
! 6290: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
! 6291: } /* i */
1.218 brouard 6292: } /* end bad */
6293: }/* age */
1.219 ! brouard 6294: sum=0.;
! 6295: for (i=1; i<=nlstate;i++){
! 6296: sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
1.218 brouard 6297: }
1.219 ! brouard 6298: if(fabs(sum - 1.) > 1.e-3) { /* bad */
! 6299: printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);
! 6300: /* for (i=1; i<=nlstate;i++){ */
! 6301: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
! 6302: /* } /\* i *\/ */
! 6303: } /* end bad */
! 6304: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
! 6305: /* From youngest, finding the oldest wrong */
! 6306: agemaxgood[cptcod]=bage+(mob-1)/2;
! 6307: for (age=bage+(mob-1)/2; age<=fage; age++){
! 6308: sumnewm[cptcod]=0.;
! 6309: for (i=1; i<=nlstate;i++){
! 6310: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
! 6311: }
! 6312: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
! 6313: agemaxgood[cptcod]=age;
! 6314: }else{ /* bad */
! 6315: for (i=1; i<=nlstate;i++){
! 6316: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
! 6317: } /* i */
! 6318: } /* end bad */
! 6319: }/* age */
! 6320: sum=0.;
! 6321: for (i=1; i<=nlstate;i++){
! 6322: sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
! 6323: }
! 6324: if(fabs(sum - 1.) > 1.e-3) { /* bad */
! 6325: printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod);
! 6326: /* for (i=1; i<=nlstate;i++){ */
! 6327: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
! 6328: /* } /\* i *\/ */
! 6329: } /* end bad */
! 6330:
! 6331: for (age=bage; age<=fage; age++){
! 6332: printf("%d %d ", cptcod, (int)age);
! 6333: sumnewp[cptcod]=0.;
! 6334: sumnewm[cptcod]=0.;
! 6335: for (i=1; i<=nlstate;i++){
! 6336: sumnewp[cptcod]+=probs[(int)age][i][cptcod];
! 6337: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
! 6338: /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
! 6339: }
! 6340: /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
! 6341: }
! 6342: /* printf("\n"); */
! 6343: /* } */
1.218 brouard 6344: /* brutal averaging */
6345: for (i=1; i<=nlstate;i++){
6346: for (age=1; age<=bage; age++){
1.219 ! brouard 6347: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
! 6348: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
1.218 brouard 6349: }
6350: for (age=fage; age<=AGESUP; age++){
1.219 ! brouard 6351: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
! 6352: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
1.218 brouard 6353: }
6354: } /* end i status */
6355: for (i=nlstate+1; i<=nlstate+ndeath;i++){
6356: for (age=1; age<=AGESUP; age++){
1.219 ! brouard 6357: /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
! 6358: mobaverage[(int)age][i][cptcod]=0.;
1.218 brouard 6359: }
6360: }
6361: }/* end cptcod */
6362: free_vector(sumnewm,1, modcovmax);
6363: free_vector(sumnewp,1, modcovmax);
6364: free_vector(agemaxgood,1, modcovmax);
6365: free_vector(agemingood,1, modcovmax);
1.126 brouard 6366: return 0;
6367: }/* End movingaverage */
1.218 brouard 6368:
1.126 brouard 6369:
6370: /************** Forecasting ******************/
1.169 brouard 6371: 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 6372: /* proj1, year, month, day of starting projection
6373: agemin, agemax range of age
6374: dateprev1 dateprev2 range of dates during which prevalence is computed
6375: anproj2 year of en of projection (same day and month as proj1).
6376: */
1.164 brouard 6377: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 6378: double agec; /* generic age */
6379: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
6380: double *popeffectif,*popcount;
6381: double ***p3mat;
1.218 brouard 6382: /* double ***mobaverage; */
1.126 brouard 6383: char fileresf[FILENAMELENGTH];
6384:
6385: agelim=AGESUP;
1.211 brouard 6386: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
6387: in each health status at the date of interview (if between dateprev1 and dateprev2).
6388: We still use firstpass and lastpass as another selection.
6389: */
1.214 brouard 6390: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
6391: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 6392:
1.201 brouard 6393: strcpy(fileresf,"F_");
6394: strcat(fileresf,fileresu);
1.126 brouard 6395: if((ficresf=fopen(fileresf,"w"))==NULL) {
6396: printf("Problem with forecast resultfile: %s\n", fileresf);
6397: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
6398: }
1.215 brouard 6399: printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
6400: fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 6401:
6402: if (cptcoveff==0) ncodemax[cptcoveff]=1;
6403:
6404:
6405: stepsize=(int) (stepm+YEARM-1)/YEARM;
6406: if (stepm<=12) stepsize=1;
6407: if(estepm < stepm){
6408: printf ("Problem %d lower than %d\n",estepm, stepm);
6409: }
6410: else hstepm=estepm;
6411:
6412: hstepm=hstepm/stepm;
6413: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
6414: fractional in yp1 */
6415: anprojmean=yp;
6416: yp2=modf((yp1*12),&yp);
6417: mprojmean=yp;
6418: yp1=modf((yp2*30.5),&yp);
6419: jprojmean=yp;
6420: if(jprojmean==0) jprojmean=1;
6421: if(mprojmean==0) jprojmean=1;
6422:
6423: i1=cptcoveff;
6424: if (cptcovn < 1){i1=1;}
6425:
6426: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
6427:
6428: fprintf(ficresf,"#****** Routine prevforecast **\n");
6429:
6430: /* if (h==(int)(YEARM*yearp)){ */
6431: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
6432: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
6433: k=k+1;
1.211 brouard 6434: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
1.126 brouard 6435: for(j=1;j<=cptcoveff;j++) {
1.219 ! brouard 6436: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 6437: }
1.211 brouard 6438: fprintf(ficresf," yearproj age");
1.126 brouard 6439: for(j=1; j<=nlstate+ndeath;j++){
1.219 ! brouard 6440: for(i=1; i<=nlstate;i++)
1.126 brouard 6441: fprintf(ficresf," p%d%d",i,j);
1.219 ! brouard 6442: fprintf(ficresf," wp.%d",j);
1.126 brouard 6443: }
1.217 brouard 6444: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.219 ! brouard 6445: fprintf(ficresf,"\n");
! 6446: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
! 6447: for (agec=fage; agec>=(ageminpar-1); agec--){
! 6448: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
! 6449: nhstepm = nhstepm/hstepm;
! 6450: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 6451: oldm=oldms;savm=savms;
! 6452: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
! 6453:
! 6454: for (h=0; h<=nhstepm; h++){
! 6455: if (h*hstepm/YEARM*stepm ==yearp) {
1.126 brouard 6456: fprintf(ficresf,"\n");
6457: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6458: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.219 ! brouard 6459: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
! 6460: }
! 6461: for(j=1; j<=nlstate+ndeath;j++) {
! 6462: ppij=0.;
! 6463: for(i=1; i<=nlstate;i++) {
! 6464: if (mobilav==1)
! 6465: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
! 6466: else {
! 6467: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
! 6468: }
! 6469: if (h*hstepm/YEARM*stepm== yearp) {
! 6470: fprintf(ficresf," %.3f", p3mat[i][j][h]);
! 6471: }
! 6472: } /* end i */
! 6473: if (h*hstepm/YEARM*stepm==yearp) {
! 6474: fprintf(ficresf," %.3f", ppij);
! 6475: }
! 6476: }/* end j */
! 6477: } /* end h */
! 6478: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 6479: } /* end agec */
1.126 brouard 6480: } /* end yearp */
6481: } /* end cptcod */
6482: } /* end cptcov */
1.219 ! brouard 6483:
1.126 brouard 6484: fclose(ficresf);
1.215 brouard 6485: printf("End of Computing forecasting \n");
6486: fprintf(ficlog,"End of Computing forecasting\n");
6487:
1.126 brouard 6488: }
6489:
1.218 brouard 6490: /* /\************** Back Forecasting ******************\/ */
6491: /* 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){ */
6492: /* /\* back1, year, month, day of starting backection */
6493: /* agemin, agemax range of age */
6494: /* dateprev1 dateprev2 range of dates during which prevalence is computed */
6495: /* anback2 year of en of backection (same day and month as back1). */
6496: /* *\/ */
6497: /* int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */
6498: /* double agec; /\* generic age *\/ */
6499: /* double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */
6500: /* double *popeffectif,*popcount; */
6501: /* double ***p3mat; */
6502: /* /\* double ***mobaverage; *\/ */
6503: /* char fileresfb[FILENAMELENGTH]; */
6504:
6505: /* agelim=AGESUP; */
6506: /* /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */
6507: /* in each health status at the date of interview (if between dateprev1 and dateprev2). */
6508: /* We still use firstpass and lastpass as another selection. */
6509: /* *\/ */
6510: /* /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */
6511: /* /\* firstpass, lastpass, stepm, weightopt, model); *\/ */
6512: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
6513:
6514: /* strcpy(fileresfb,"FB_"); */
6515: /* strcat(fileresfb,fileresu); */
6516: /* if((ficresfb=fopen(fileresfb,"w"))==NULL) { */
6517: /* printf("Problem with back forecast resultfile: %s\n", fileresfb); */
6518: /* fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */
6519: /* } */
6520: /* printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
6521: /* fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
6522:
6523: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
6524:
6525: /* /\* if (mobilav!=0) { *\/ */
6526: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
6527: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
6528: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
6529: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
6530: /* /\* } *\/ */
6531: /* /\* } *\/ */
6532:
6533: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
6534: /* if (stepm<=12) stepsize=1; */
6535: /* if(estepm < stepm){ */
6536: /* printf ("Problem %d lower than %d\n",estepm, stepm); */
6537: /* } */
6538: /* else hstepm=estepm; */
6539:
6540: /* hstepm=hstepm/stepm; */
6541: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
6542: /* fractional in yp1 *\/ */
6543: /* anprojmean=yp; */
6544: /* yp2=modf((yp1*12),&yp); */
6545: /* mprojmean=yp; */
6546: /* yp1=modf((yp2*30.5),&yp); */
6547: /* jprojmean=yp; */
6548: /* if(jprojmean==0) jprojmean=1; */
6549: /* if(mprojmean==0) jprojmean=1; */
6550:
6551: /* i1=cptcoveff; */
6552: /* if (cptcovn < 1){i1=1;} */
1.217 brouard 6553:
1.218 brouard 6554: /* fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); */
1.217 brouard 6555:
1.218 brouard 6556: /* fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */
6557:
6558: /* /\* if (h==(int)(YEARM*yearp)){ *\/ */
6559: /* for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
6560: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
6561: /* k=k+1; */
6562: /* fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
6563: /* for(j=1;j<=cptcoveff;j++) { */
6564: /* fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
6565: /* } */
6566: /* fprintf(ficresfb," yearbproj age"); */
6567: /* for(j=1; j<=nlstate+ndeath;j++){ */
6568: /* for(i=1; i<=nlstate;i++) */
6569: /* fprintf(ficresfb," p%d%d",i,j); */
6570: /* fprintf(ficresfb," p.%d",j); */
6571: /* } */
6572: /* for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) { */
6573: /* /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { *\/ */
6574: /* fprintf(ficresfb,"\n"); */
6575: /* fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
6576: /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
6577: /* nhstepm=(int) rint((agelim-agec)*YEARM/stepm); */
6578: /* nhstepm = nhstepm/hstepm; */
6579: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
6580: /* oldm=oldms;savm=savms; */
6581: /* hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k); */
6582: /* for (h=0; h<=nhstepm; h++){ */
6583: /* if (h*hstepm/YEARM*stepm ==yearp) { */
6584: /* fprintf(ficresfb,"\n"); */
6585: /* for(j=1;j<=cptcoveff;j++) */
6586: /* fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
6587: /* fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */
6588: /* } */
6589: /* for(j=1; j<=nlstate+ndeath;j++) { */
6590: /* ppij=0.; */
6591: /* for(i=1; i<=nlstate;i++) { */
6592: /* if (mobilav==1) */
6593: /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */
6594: /* else { */
6595: /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */
6596: /* } */
6597: /* if (h*hstepm/YEARM*stepm== yearp) { */
6598: /* fprintf(ficresfb," %.3f", p3mat[i][j][h]); */
6599: /* } */
6600: /* } /\* end i *\/ */
6601: /* if (h*hstepm/YEARM*stepm==yearp) { */
6602: /* fprintf(ficresfb," %.3f", ppij); */
6603: /* } */
6604: /* }/\* end j *\/ */
6605: /* } /\* end h *\/ */
6606: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
6607: /* } /\* end agec *\/ */
6608: /* } /\* end yearp *\/ */
6609: /* } /\* end cptcod *\/ */
6610: /* } /\* end cptcov *\/ */
6611:
6612: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
6613:
6614: /* fclose(ficresfb); */
6615: /* printf("End of Computing Back forecasting \n"); */
6616: /* fprintf(ficlog,"End of Computing Back forecasting\n"); */
1.217 brouard 6617:
1.218 brouard 6618: /* } */
1.217 brouard 6619:
1.126 brouard 6620: /************** Forecasting *****not tested NB*************/
1.169 brouard 6621: 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 6622:
6623: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
6624: int *popage;
6625: double calagedatem, agelim, kk1, kk2;
6626: double *popeffectif,*popcount;
6627: double ***p3mat,***tabpop,***tabpopprev;
1.218 brouard 6628: /* double ***mobaverage; */
1.126 brouard 6629: char filerespop[FILENAMELENGTH];
6630:
6631: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6632: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6633: agelim=AGESUP;
6634: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
6635:
6636: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6637:
6638:
1.201 brouard 6639: strcpy(filerespop,"POP_");
6640: strcat(filerespop,fileresu);
1.126 brouard 6641: if((ficrespop=fopen(filerespop,"w"))==NULL) {
6642: printf("Problem with forecast resultfile: %s\n", filerespop);
6643: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
6644: }
6645: printf("Computing forecasting: result on file '%s' \n", filerespop);
6646: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
6647:
6648: if (cptcoveff==0) ncodemax[cptcoveff]=1;
6649:
1.218 brouard 6650: /* if (mobilav!=0) { */
6651: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
6652: /* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ */
6653: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
6654: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
6655: /* } */
6656: /* } */
1.126 brouard 6657:
6658: stepsize=(int) (stepm+YEARM-1)/YEARM;
6659: if (stepm<=12) stepsize=1;
6660:
6661: agelim=AGESUP;
6662:
6663: hstepm=1;
6664: hstepm=hstepm/stepm;
1.218 brouard 6665:
1.126 brouard 6666: if (popforecast==1) {
6667: if((ficpop=fopen(popfile,"r"))==NULL) {
6668: printf("Problem with population file : %s\n",popfile);exit(0);
6669: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
6670: }
6671: popage=ivector(0,AGESUP);
6672: popeffectif=vector(0,AGESUP);
6673: popcount=vector(0,AGESUP);
6674:
6675: i=1;
6676: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
1.218 brouard 6677:
1.126 brouard 6678: imx=i;
6679: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
6680: }
1.218 brouard 6681:
1.126 brouard 6682: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.218 brouard 6683: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
1.126 brouard 6684: k=k+1;
6685: fprintf(ficrespop,"\n#******");
6686: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 6687: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 6688: }
6689: fprintf(ficrespop,"******\n");
6690: fprintf(ficrespop,"# Age");
6691: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
6692: if (popforecast==1) fprintf(ficrespop," [Population]");
6693:
6694: for (cpt=0; cpt<=0;cpt++) {
6695: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
6696:
1.218 brouard 6697: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.126 brouard 6698: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
6699: nhstepm = nhstepm/hstepm;
6700:
6701: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6702: oldm=oldms;savm=savms;
6703: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.218 brouard 6704:
1.126 brouard 6705: for (h=0; h<=nhstepm; h++){
6706: if (h==(int) (calagedatem+YEARM*cpt)) {
6707: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
6708: }
6709: for(j=1; j<=nlstate+ndeath;j++) {
6710: kk1=0.;kk2=0;
6711: for(i=1; i<=nlstate;i++) {
6712: if (mobilav==1)
6713: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
6714: else {
6715: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
6716: }
6717: }
6718: if (h==(int)(calagedatem+12*cpt)){
6719: tabpop[(int)(agedeb)][j][cptcod]=kk1;
1.218 brouard 6720: /*fprintf(ficrespop," %.3f", kk1);
6721: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
1.126 brouard 6722: }
6723: }
6724: for(i=1; i<=nlstate;i++){
6725: kk1=0.;
1.218 brouard 6726: for(j=1; j<=nlstate;j++){
6727: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
6728: }
6729: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.126 brouard 6730: }
1.218 brouard 6731:
6732: if (h==(int)(calagedatem+12*cpt))
6733: for(j=1; j<=nlstate;j++)
6734: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
1.126 brouard 6735: }
6736: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6737: }
6738: }
1.218 brouard 6739:
6740: /******/
6741:
1.126 brouard 6742: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
6743: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
6744: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
6745: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
6746: nhstepm = nhstepm/hstepm;
6747:
6748: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6749: oldm=oldms;savm=savms;
6750: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6751: for (h=0; h<=nhstepm; h++){
6752: if (h==(int) (calagedatem+YEARM*cpt)) {
6753: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
6754: }
6755: for(j=1; j<=nlstate+ndeath;j++) {
6756: kk1=0.;kk2=0;
6757: for(i=1; i<=nlstate;i++) {
6758: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
6759: }
6760: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
6761: }
6762: }
6763: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6764: }
6765: }
1.218 brouard 6766: }
1.126 brouard 6767: }
1.218 brouard 6768:
6769: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
6770:
1.126 brouard 6771: if (popforecast==1) {
6772: free_ivector(popage,0,AGESUP);
6773: free_vector(popeffectif,0,AGESUP);
6774: free_vector(popcount,0,AGESUP);
6775: }
6776: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6777: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6778: fclose(ficrespop);
6779: } /* End of popforecast */
1.218 brouard 6780:
1.126 brouard 6781: int fileappend(FILE *fichier, char *optionfich)
6782: {
6783: if((fichier=fopen(optionfich,"a"))==NULL) {
6784: printf("Problem with file: %s\n", optionfich);
6785: fprintf(ficlog,"Problem with file: %s\n", optionfich);
6786: return (0);
6787: }
6788: fflush(fichier);
6789: return (1);
6790: }
6791:
6792:
6793: /**************** function prwizard **********************/
6794: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
6795: {
6796:
6797: /* Wizard to print covariance matrix template */
6798:
1.164 brouard 6799: char ca[32], cb[32];
6800: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 6801: int numlinepar;
6802:
6803: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6804: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6805: for(i=1; i <=nlstate; i++){
6806: jj=0;
6807: for(j=1; j <=nlstate+ndeath; j++){
6808: if(j==i) continue;
6809: jj++;
6810: /*ca[0]= k+'a'-1;ca[1]='\0';*/
6811: printf("%1d%1d",i,j);
6812: fprintf(ficparo,"%1d%1d",i,j);
6813: for(k=1; k<=ncovmodel;k++){
6814: /* printf(" %lf",param[i][j][k]); */
6815: /* fprintf(ficparo," %lf",param[i][j][k]); */
6816: printf(" 0.");
6817: fprintf(ficparo," 0.");
6818: }
6819: printf("\n");
6820: fprintf(ficparo,"\n");
6821: }
6822: }
6823: printf("# Scales (for hessian or gradient estimation)\n");
6824: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
6825: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
6826: for(i=1; i <=nlstate; i++){
6827: jj=0;
6828: for(j=1; j <=nlstate+ndeath; j++){
6829: if(j==i) continue;
6830: jj++;
6831: fprintf(ficparo,"%1d%1d",i,j);
6832: printf("%1d%1d",i,j);
6833: fflush(stdout);
6834: for(k=1; k<=ncovmodel;k++){
6835: /* printf(" %le",delti3[i][j][k]); */
6836: /* fprintf(ficparo," %le",delti3[i][j][k]); */
6837: printf(" 0.");
6838: fprintf(ficparo," 0.");
6839: }
6840: numlinepar++;
6841: printf("\n");
6842: fprintf(ficparo,"\n");
6843: }
6844: }
6845: printf("# Covariance matrix\n");
6846: /* # 121 Var(a12)\n\ */
6847: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6848: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6849: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6850: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6851: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6852: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6853: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6854: fflush(stdout);
6855: fprintf(ficparo,"# Covariance matrix\n");
6856: /* # 121 Var(a12)\n\ */
6857: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6858: /* # ...\n\ */
6859: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6860:
6861: for(itimes=1;itimes<=2;itimes++){
6862: jj=0;
6863: for(i=1; i <=nlstate; i++){
6864: for(j=1; j <=nlstate+ndeath; j++){
6865: if(j==i) continue;
6866: for(k=1; k<=ncovmodel;k++){
6867: jj++;
6868: ca[0]= k+'a'-1;ca[1]='\0';
6869: if(itimes==1){
6870: printf("#%1d%1d%d",i,j,k);
6871: fprintf(ficparo,"#%1d%1d%d",i,j,k);
6872: }else{
6873: printf("%1d%1d%d",i,j,k);
6874: fprintf(ficparo,"%1d%1d%d",i,j,k);
6875: /* printf(" %.5le",matcov[i][j]); */
6876: }
6877: ll=0;
6878: for(li=1;li <=nlstate; li++){
6879: for(lj=1;lj <=nlstate+ndeath; lj++){
6880: if(lj==li) continue;
6881: for(lk=1;lk<=ncovmodel;lk++){
6882: ll++;
6883: if(ll<=jj){
6884: cb[0]= lk +'a'-1;cb[1]='\0';
6885: if(ll<jj){
6886: if(itimes==1){
6887: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6888: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6889: }else{
6890: printf(" 0.");
6891: fprintf(ficparo," 0.");
6892: }
6893: }else{
6894: if(itimes==1){
6895: printf(" Var(%s%1d%1d)",ca,i,j);
6896: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
6897: }else{
6898: printf(" 0.");
6899: fprintf(ficparo," 0.");
6900: }
6901: }
6902: }
6903: } /* end lk */
6904: } /* end lj */
6905: } /* end li */
6906: printf("\n");
6907: fprintf(ficparo,"\n");
6908: numlinepar++;
6909: } /* end k*/
6910: } /*end j */
6911: } /* end i */
6912: } /* end itimes */
6913:
6914: } /* end of prwizard */
6915: /******************* Gompertz Likelihood ******************************/
6916: double gompertz(double x[])
6917: {
6918: double A,B,L=0.0,sump=0.,num=0.;
6919: int i,n=0; /* n is the size of the sample */
6920:
6921: for (i=0;i<=imx-1 ; i++) {
6922: sump=sump+weight[i];
6923: /* sump=sump+1;*/
6924: num=num+1;
6925: }
6926:
6927:
6928: /* for (i=0; i<=imx; i++)
6929: 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]);*/
6930:
6931: for (i=1;i<=imx ; i++)
6932: {
6933: if (cens[i] == 1 && wav[i]>1)
6934: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
6935:
6936: if (cens[i] == 0 && wav[i]>1)
6937: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
6938: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
6939:
6940: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
6941: if (wav[i] > 1 ) { /* ??? */
6942: L=L+A*weight[i];
6943: /* 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]);*/
6944: }
6945: }
6946:
6947: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
6948:
6949: return -2*L*num/sump;
6950: }
6951:
1.136 brouard 6952: #ifdef GSL
6953: /******************* Gompertz_f Likelihood ******************************/
6954: double gompertz_f(const gsl_vector *v, void *params)
6955: {
6956: double A,B,LL=0.0,sump=0.,num=0.;
6957: double *x= (double *) v->data;
6958: int i,n=0; /* n is the size of the sample */
6959:
6960: for (i=0;i<=imx-1 ; i++) {
6961: sump=sump+weight[i];
6962: /* sump=sump+1;*/
6963: num=num+1;
6964: }
6965:
6966:
6967: /* for (i=0; i<=imx; i++)
6968: 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]);*/
6969: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
6970: for (i=1;i<=imx ; i++)
6971: {
6972: if (cens[i] == 1 && wav[i]>1)
6973: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
6974:
6975: if (cens[i] == 0 && wav[i]>1)
6976: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
6977: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
6978:
6979: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
6980: if (wav[i] > 1 ) { /* ??? */
6981: LL=LL+A*weight[i];
6982: /* 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]);*/
6983: }
6984: }
6985:
6986: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
6987: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
6988:
6989: return -2*LL*num/sump;
6990: }
6991: #endif
6992:
1.126 brouard 6993: /******************* Printing html file ***********/
1.201 brouard 6994: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 6995: int lastpass, int stepm, int weightopt, char model[],\
6996: int imx, double p[],double **matcov,double agemortsup){
6997: int i,k;
6998:
6999: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
7000: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
7001: for (i=1;i<=2;i++)
7002: 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 7003: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 7004: fprintf(fichtm,"</ul>");
7005:
7006: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
7007:
7008: 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>");
7009:
7010: for (k=agegomp;k<(agemortsup-2);k++)
7011: 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]);
7012:
7013:
7014: fflush(fichtm);
7015: }
7016:
7017: /******************* Gnuplot file **************/
1.201 brouard 7018: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 7019:
7020: char dirfileres[132],optfileres[132];
1.164 brouard 7021:
1.126 brouard 7022: int ng;
7023:
7024:
7025: /*#ifdef windows */
7026: fprintf(ficgp,"cd \"%s\" \n",pathc);
7027: /*#endif */
7028:
7029:
7030: strcpy(dirfileres,optionfilefiname);
7031: strcpy(optfileres,"vpl");
1.199 brouard 7032: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 7033: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 7034: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 7035: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 7036: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
7037:
7038: }
7039:
1.136 brouard 7040: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
7041: {
1.126 brouard 7042:
1.136 brouard 7043: /*-------- data file ----------*/
7044: FILE *fic;
7045: char dummy[]=" ";
1.164 brouard 7046: int i=0, j=0, n=0;
1.136 brouard 7047: int linei, month, year,iout;
7048: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 7049: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 7050: char *stratrunc;
7051: int lstra;
1.126 brouard 7052:
7053:
1.136 brouard 7054: if((fic=fopen(datafile,"r"))==NULL) {
1.218 brouard 7055: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
7056: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136 brouard 7057: }
1.126 brouard 7058:
1.136 brouard 7059: i=1;
7060: linei=0;
7061: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
7062: linei=linei+1;
7063: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
7064: if(line[j] == '\t')
7065: line[j] = ' ';
7066: }
7067: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
7068: ;
7069: };
7070: line[j+1]=0; /* Trims blanks at end of line */
7071: if(line[0]=='#'){
7072: fprintf(ficlog,"Comment line\n%s\n",line);
7073: printf("Comment line\n%s\n",line);
7074: continue;
7075: }
7076: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 7077: strcpy(line, linetmp);
1.136 brouard 7078:
1.126 brouard 7079:
1.136 brouard 7080: for (j=maxwav;j>=1;j--){
1.137 brouard 7081: cutv(stra, strb, line, ' ');
1.136 brouard 7082: if(strb[0]=='.') { /* Missing status */
7083: lval=-1;
7084: }else{
7085: errno=0;
7086: lval=strtol(strb,&endptr,10);
7087: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
7088: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 7089: 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);
7090: 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 7091: return 1;
7092: }
7093: }
7094: s[j][i]=lval;
7095:
7096: strcpy(line,stra);
7097: cutv(stra, strb,line,' ');
1.169 brouard 7098: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7099: }
1.169 brouard 7100: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 7101: month=99;
7102: year=9999;
7103: }else{
1.141 brouard 7104: 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);
7105: 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 7106: return 1;
7107: }
7108: anint[j][i]= (double) year;
7109: mint[j][i]= (double)month;
7110: strcpy(line,stra);
7111: } /* ENd Waves */
7112:
7113: cutv(stra, strb,line,' ');
1.169 brouard 7114: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7115: }
1.169 brouard 7116: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 7117: month=99;
7118: year=9999;
7119: }else{
1.141 brouard 7120: 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);
7121: 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 7122: return 1;
7123: }
7124: andc[i]=(double) year;
7125: moisdc[i]=(double) month;
7126: strcpy(line,stra);
7127:
7128: cutv(stra, strb,line,' ');
1.169 brouard 7129: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7130: }
1.169 brouard 7131: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 7132: month=99;
7133: year=9999;
7134: }else{
1.141 brouard 7135: 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);
7136: 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 7137: return 1;
7138: }
7139: if (year==9999) {
1.141 brouard 7140: 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);
7141: 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 7142: return 1;
1.126 brouard 7143:
1.136 brouard 7144: }
7145: annais[i]=(double)(year);
7146: moisnais[i]=(double)(month);
7147: strcpy(line,stra);
7148:
7149: cutv(stra, strb,line,' ');
7150: errno=0;
7151: dval=strtod(strb,&endptr);
7152: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 7153: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
7154: 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 7155: fflush(ficlog);
7156: return 1;
7157: }
7158: weight[i]=dval;
7159: strcpy(line,stra);
7160:
7161: for (j=ncovcol;j>=1;j--){
7162: cutv(stra, strb,line,' ');
7163: if(strb[0]=='.') { /* Missing status */
7164: lval=-1;
7165: }else{
7166: errno=0;
7167: lval=strtol(strb,&endptr,10);
7168: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 7169: 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);
7170: 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 7171: return 1;
7172: }
7173: }
7174: if(lval <-1 || lval >1){
1.141 brouard 7175: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 7176: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7177: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
7178: For example, for multinomial values like 1, 2 and 3,\n \
7179: build V1=0 V2=0 for the reference value (1),\n \
7180: V1=1 V2=0 for (2) \n \
7181: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
7182: output of IMaCh is often meaningless.\n \
7183: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 7184: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 7185: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7186: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
7187: For example, for multinomial values like 1, 2 and 3,\n \
7188: build V1=0 V2=0 for the reference value (1),\n \
7189: V1=1 V2=0 for (2) \n \
7190: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
7191: output of IMaCh is often meaningless.\n \
7192: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
7193: return 1;
7194: }
7195: covar[j][i]=(double)(lval);
7196: strcpy(line,stra);
7197: }
7198: lstra=strlen(stra);
7199:
7200: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
7201: stratrunc = &(stra[lstra-9]);
7202: num[i]=atol(stratrunc);
7203: }
7204: else
7205: num[i]=atol(stra);
7206: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
7207: 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;}*/
7208:
7209: i=i+1;
7210: } /* End loop reading data */
1.126 brouard 7211:
1.136 brouard 7212: *imax=i-1; /* Number of individuals */
7213: fclose(fic);
7214:
7215: return (0);
1.164 brouard 7216: /* endread: */
1.136 brouard 7217: printf("Exiting readdata: ");
7218: fclose(fic);
7219: return (1);
1.126 brouard 7220:
7221:
7222:
1.136 brouard 7223: }
1.145 brouard 7224: void removespace(char *str) {
7225: char *p1 = str, *p2 = str;
7226: do
7227: while (*p2 == ' ')
7228: p2++;
1.169 brouard 7229: while (*p1++ == *p2++);
1.145 brouard 7230: }
7231:
7232: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 7233: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
7234: * - nagesqr = 1 if age*age in the model, otherwise 0.
7235: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
7236: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 7237: * - cptcovage number of covariates with age*products =2
7238: * - cptcovs number of simple covariates
7239: * - 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
7240: * which is a new column after the 9 (ncovcol) variables.
7241: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
7242: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
7243: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
7244: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
7245: */
1.136 brouard 7246: {
1.145 brouard 7247: int i, j, k, ks;
1.164 brouard 7248: int j1, k1, k2;
1.136 brouard 7249: char modelsav[80];
1.145 brouard 7250: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 7251: char *strpt;
1.136 brouard 7252:
1.145 brouard 7253: /*removespace(model);*/
1.136 brouard 7254: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 7255: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 7256: if (strstr(model,"AGE") !=0){
1.192 brouard 7257: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
7258: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 7259: return 1;
7260: }
1.141 brouard 7261: if (strstr(model,"v") !=0){
7262: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
7263: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
7264: return 1;
7265: }
1.187 brouard 7266: strcpy(modelsav,model);
7267: if ((strpt=strstr(model,"age*age")) !=0){
7268: printf(" strpt=%s, model=%s\n",strpt, model);
7269: if(strpt != model){
7270: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 7271: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 7272: corresponding column of parameters.\n",model);
7273: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 7274: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 7275: corresponding column of parameters.\n",model); fflush(ficlog);
7276: return 1;
7277: }
7278:
7279: nagesqr=1;
7280: if (strstr(model,"+age*age") !=0)
7281: substrchaine(modelsav, model, "+age*age");
7282: else if (strstr(model,"age*age+") !=0)
7283: substrchaine(modelsav, model, "age*age+");
7284: else
7285: substrchaine(modelsav, model, "age*age");
7286: }else
7287: nagesqr=0;
7288: if (strlen(modelsav) >1){
7289: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
7290: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
7291: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
7292: cptcovt= j+1; /* Number of total covariates in the model, not including
7293: * cst, age and age*age
7294: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
7295: /* including age products which are counted in cptcovage.
7296: * but the covariates which are products must be treated
7297: * separately: ncovn=4- 2=2 (V1+V3). */
7298: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
7299: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
7300:
7301:
7302: /* Design
7303: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
7304: * < ncovcol=8 >
7305: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
7306: * k= 1 2 3 4 5 6 7 8
7307: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
7308: * covar[k,i], value of kth covariate if not including age for individual i:
7309: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
7310: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
7311: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
7312: * Tage[++cptcovage]=k
7313: * if products, new covar are created after ncovcol with k1
7314: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
7315: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
7316: * 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
7317: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
7318: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
7319: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
7320: * < ncovcol=8 >
7321: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
7322: * k= 1 2 3 4 5 6 7 8 9 10 11 12
7323: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
7324: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
7325: * p Tprod[1]@2={ 6, 5}
7326: *p Tvard[1][1]@4= {7, 8, 5, 6}
7327: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
7328: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
7329: *How to reorganize?
7330: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
7331: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
7332: * {2, 1, 4, 8, 5, 6, 3, 7}
7333: * Struct []
7334: */
1.145 brouard 7335:
1.187 brouard 7336: /* This loop fills the array Tvar from the string 'model'.*/
7337: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
7338: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
7339: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
7340: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
7341: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
7342: /* k=1 Tvar[1]=2 (from V2) */
7343: /* k=5 Tvar[5] */
7344: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 7345: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 7346: /* } */
1.198 brouard 7347: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 7348: /*
7349: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
7350: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 7351: Tvar[k]=0;
1.187 brouard 7352: cptcovage=0;
7353: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
7354: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
7355: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
7356: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
7357: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
7358: /*scanf("%d",i);*/
7359: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
7360: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
7361: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
7362: /* covar is not filled and then is empty */
7363: cptcovprod--;
7364: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
7365: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
7366: cptcovage++; /* Sums the number of covariates which include age as a product */
7367: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
7368: /*printf("stre=%s ", stre);*/
7369: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
7370: cptcovprod--;
7371: cutl(stre,strb,strc,'V');
7372: Tvar[k]=atoi(stre);
7373: cptcovage++;
7374: Tage[cptcovage]=k;
7375: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
7376: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
7377: cptcovn++;
7378: cptcovprodnoage++;k1++;
7379: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
7380: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
7381: because this model-covariate is a construction we invent a new column
7382: ncovcol + k1
7383: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
7384: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
7385: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
7386: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
7387: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
7388: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
7389: k2=k2+2;
7390: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
7391: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
7392: for (i=1; i<=lastobs;i++){
7393: /* Computes the new covariate which is a product of
7394: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
7395: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
7396: }
7397: } /* End age is not in the model */
7398: } /* End if model includes a product */
7399: else { /* no more sum */
7400: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
7401: /* scanf("%d",i);*/
7402: cutl(strd,strc,strb,'V');
7403: ks++; /**< Number of simple covariates */
1.145 brouard 7404: cptcovn++;
1.187 brouard 7405: Tvar[k]=atoi(strd);
7406: }
7407: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
7408: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
7409: scanf("%d",i);*/
7410: } /* end of loop + on total covariates */
7411: } /* end if strlen(modelsave == 0) age*age might exist */
7412: } /* end if strlen(model == 0) */
1.136 brouard 7413:
7414: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
7415: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
7416:
7417: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
7418: printf("cptcovprod=%d ", cptcovprod);
7419: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
7420:
7421: scanf("%d ",i);*/
7422:
7423:
1.137 brouard 7424: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 7425: /*endread:*/
1.136 brouard 7426: printf("Exiting decodemodel: ");
7427: return (1);
7428: }
7429:
1.169 brouard 7430: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 7431: {
7432: int i, m;
1.218 brouard 7433: int firstone=0;
7434:
1.136 brouard 7435: for (i=1; i<=imx; i++) {
7436: for(m=2; (m<= maxwav); m++) {
7437: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
7438: anint[m][i]=9999;
1.216 brouard 7439: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
7440: s[m][i]=-1;
1.136 brouard 7441: }
7442: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 7443: *nberr = *nberr + 1;
1.218 brouard 7444: if(firstone == 0){
7445: firstone=1;
7446: printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\nOther similar cases in log file\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
7447: }
7448: fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
1.136 brouard 7449: s[m][i]=-1;
7450: }
7451: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 7452: (*nberr)++;
1.136 brouard 7453: 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]);
7454: 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]);
7455: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
7456: }
7457: }
7458: }
7459:
7460: for (i=1; i<=imx; i++) {
7461: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
7462: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 7463: 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 7464: if (s[m][i] >= nlstate+1) {
1.169 brouard 7465: if(agedc[i]>0){
7466: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 7467: agev[m][i]=agedc[i];
1.214 brouard 7468: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 7469: }else {
1.136 brouard 7470: if ((int)andc[i]!=9999){
7471: nbwarn++;
7472: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
7473: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
7474: agev[m][i]=-1;
7475: }
7476: }
1.169 brouard 7477: } /* agedc > 0 */
1.214 brouard 7478: } /* end if */
1.136 brouard 7479: else if(s[m][i] !=9){ /* Standard case, age in fractional
7480: years but with the precision of a month */
7481: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
7482: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
7483: agev[m][i]=1;
7484: else if(agev[m][i] < *agemin){
7485: *agemin=agev[m][i];
7486: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
7487: }
7488: else if(agev[m][i] >*agemax){
7489: *agemax=agev[m][i];
1.156 brouard 7490: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 7491: }
7492: /*agev[m][i]=anint[m][i]-annais[i];*/
7493: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 7494: } /* en if 9*/
1.136 brouard 7495: else { /* =9 */
1.214 brouard 7496: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 7497: agev[m][i]=1;
7498: s[m][i]=-1;
7499: }
7500: }
1.214 brouard 7501: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 7502: agev[m][i]=1;
1.214 brouard 7503: else{
7504: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
7505: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
7506: agev[m][i]=0;
7507: }
7508: } /* End for lastpass */
7509: }
1.136 brouard 7510:
7511: for (i=1; i<=imx; i++) {
7512: for(m=firstpass; (m<=lastpass); m++){
7513: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 7514: (*nberr)++;
1.136 brouard 7515: 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);
7516: 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);
7517: return 1;
7518: }
7519: }
7520: }
7521:
7522: /*for (i=1; i<=imx; i++){
7523: for (m=firstpass; (m<lastpass); m++){
7524: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
7525: }
7526:
7527: }*/
7528:
7529:
1.139 brouard 7530: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
7531: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 7532:
7533: return (0);
1.164 brouard 7534: /* endread:*/
1.136 brouard 7535: printf("Exiting calandcheckages: ");
7536: return (1);
7537: }
7538:
1.172 brouard 7539: #if defined(_MSC_VER)
7540: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
7541: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
7542: //#include "stdafx.h"
7543: //#include <stdio.h>
7544: //#include <tchar.h>
7545: //#include <windows.h>
7546: //#include <iostream>
7547: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
7548:
7549: LPFN_ISWOW64PROCESS fnIsWow64Process;
7550:
7551: BOOL IsWow64()
7552: {
7553: BOOL bIsWow64 = FALSE;
7554:
7555: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
7556: // (HANDLE, PBOOL);
7557:
7558: //LPFN_ISWOW64PROCESS fnIsWow64Process;
7559:
7560: HMODULE module = GetModuleHandle(_T("kernel32"));
7561: const char funcName[] = "IsWow64Process";
7562: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
7563: GetProcAddress(module, funcName);
7564:
7565: if (NULL != fnIsWow64Process)
7566: {
7567: if (!fnIsWow64Process(GetCurrentProcess(),
7568: &bIsWow64))
7569: //throw std::exception("Unknown error");
7570: printf("Unknown error\n");
7571: }
7572: return bIsWow64 != FALSE;
7573: }
7574: #endif
1.177 brouard 7575:
1.191 brouard 7576: void syscompilerinfo(int logged)
1.167 brouard 7577: {
7578: /* #include "syscompilerinfo.h"*/
1.185 brouard 7579: /* command line Intel compiler 32bit windows, XP compatible:*/
7580: /* /GS /W3 /Gy
7581: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
7582: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
7583: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 7584: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
7585: */
7586: /* 64 bits */
1.185 brouard 7587: /*
7588: /GS /W3 /Gy
7589: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
7590: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
7591: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
7592: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
7593: /* Optimization are useless and O3 is slower than O2 */
7594: /*
7595: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
7596: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
7597: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
7598: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
7599: */
1.186 brouard 7600: /* Link is */ /* /OUT:"visual studio
1.185 brouard 7601: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
7602: /PDB:"visual studio
7603: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
7604: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
7605: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
7606: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
7607: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
7608: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
7609: uiAccess='false'"
7610: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
7611: /NOLOGO /TLBID:1
7612: */
1.177 brouard 7613: #if defined __INTEL_COMPILER
1.178 brouard 7614: #if defined(__GNUC__)
7615: struct utsname sysInfo; /* For Intel on Linux and OS/X */
7616: #endif
1.177 brouard 7617: #elif defined(__GNUC__)
1.179 brouard 7618: #ifndef __APPLE__
1.174 brouard 7619: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 7620: #endif
1.177 brouard 7621: struct utsname sysInfo;
1.178 brouard 7622: int cross = CROSS;
7623: if (cross){
7624: printf("Cross-");
1.191 brouard 7625: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 7626: }
1.174 brouard 7627: #endif
7628:
1.171 brouard 7629: #include <stdint.h>
1.178 brouard 7630:
1.191 brouard 7631: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 7632: #if defined(__clang__)
1.191 brouard 7633: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 7634: #endif
7635: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 7636: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 7637: #endif
7638: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 7639: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 7640: #endif
7641: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 7642: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 7643: #endif
7644: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 7645: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 7646: #endif
7647: #if defined(_MSC_VER)
1.191 brouard 7648: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 7649: #endif
7650: #if defined(__PGI)
1.191 brouard 7651: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 7652: #endif
7653: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 7654: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 7655: #endif
1.191 brouard 7656: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 7657:
1.167 brouard 7658: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
7659: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
7660: // Windows (x64 and x86)
1.191 brouard 7661: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 7662: #elif __unix__ // all unices, not all compilers
7663: // Unix
1.191 brouard 7664: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 7665: #elif __linux__
7666: // linux
1.191 brouard 7667: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 7668: #elif __APPLE__
1.174 brouard 7669: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 7670: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 7671: #endif
7672:
7673: /* __MINGW32__ */
7674: /* __CYGWIN__ */
7675: /* __MINGW64__ */
7676: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
7677: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
7678: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
7679: /* _WIN64 // Defined for applications for Win64. */
7680: /* _M_X64 // Defined for compilations that target x64 processors. */
7681: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 7682:
1.167 brouard 7683: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 7684: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 7685: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 7686: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 7687: #else
1.191 brouard 7688: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 7689: #endif
7690:
1.169 brouard 7691: #if defined(__GNUC__)
7692: # if defined(__GNUC_PATCHLEVEL__)
7693: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
7694: + __GNUC_MINOR__ * 100 \
7695: + __GNUC_PATCHLEVEL__)
7696: # else
7697: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
7698: + __GNUC_MINOR__ * 100)
7699: # endif
1.174 brouard 7700: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 7701: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 7702:
7703: if (uname(&sysInfo) != -1) {
7704: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 7705: 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 7706: }
7707: else
7708: perror("uname() error");
1.179 brouard 7709: //#ifndef __INTEL_COMPILER
7710: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 7711: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 7712: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 7713: #endif
1.169 brouard 7714: #endif
1.172 brouard 7715:
7716: // void main()
7717: // {
1.169 brouard 7718: #if defined(_MSC_VER)
1.174 brouard 7719: if (IsWow64()){
1.191 brouard 7720: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
7721: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 7722: }
7723: else{
1.191 brouard 7724: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
7725: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 7726: }
1.172 brouard 7727: // printf("\nPress Enter to continue...");
7728: // getchar();
7729: // }
7730:
1.169 brouard 7731: #endif
7732:
1.167 brouard 7733:
1.219 ! brouard 7734: }
1.136 brouard 7735:
1.219 ! brouard 7736: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.180 brouard 7737: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
7738: int i, j, k, i1 ;
1.202 brouard 7739: /* double ftolpl = 1.e-10; */
1.180 brouard 7740: double age, agebase, agelim;
1.203 brouard 7741: double tot;
1.180 brouard 7742:
1.202 brouard 7743: strcpy(filerespl,"PL_");
7744: strcat(filerespl,fileresu);
7745: if((ficrespl=fopen(filerespl,"w"))==NULL) {
7746: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
7747: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
7748: }
7749: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
7750: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
7751: pstamp(ficrespl);
1.203 brouard 7752: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 7753: fprintf(ficrespl,"#Age ");
7754: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
7755: fprintf(ficrespl,"\n");
1.180 brouard 7756:
1.219 ! brouard 7757: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180 brouard 7758:
1.219 ! brouard 7759: agebase=ageminpar;
! 7760: agelim=agemaxpar;
1.180 brouard 7761:
1.219 ! brouard 7762: i1=pow(2,cptcoveff);
! 7763: if (cptcovn < 1){i1=1;}
1.180 brouard 7764:
1.219 ! brouard 7765: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.180 brouard 7766: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
1.219 ! brouard 7767: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
! 7768: k=k+1;
! 7769: /* to clean */
! 7770: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
! 7771: fprintf(ficrespl,"#******");
! 7772: printf("#******");
! 7773: fprintf(ficlog,"#******");
! 7774: for(j=1;j<=cptcoveff;j++) {
! 7775: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 7776: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 7777: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 7778: }
! 7779: fprintf(ficrespl,"******\n");
! 7780: printf("******\n");
! 7781: fprintf(ficlog,"******\n");
! 7782:
! 7783: fprintf(ficrespl,"#Age ");
! 7784: for(j=1;j<=cptcoveff;j++) {
! 7785: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 7786: }
! 7787: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
! 7788: fprintf(ficrespl,"Total Years_to_converge\n");
! 7789:
! 7790: for (age=agebase; age<=agelim; age++){
! 7791: /* for (age=agebase; age<=agebase; age++){ */
! 7792: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
! 7793: fprintf(ficrespl,"%.0f ",age );
! 7794: for(j=1;j<=cptcoveff;j++)
! 7795: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 7796: tot=0.;
! 7797: for(i=1; i<=nlstate;i++){
! 7798: tot += prlim[i][i];
! 7799: fprintf(ficrespl," %.5f", prlim[i][i]);
! 7800: }
! 7801: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
! 7802: } /* Age */
! 7803: /* was end of cptcod */
! 7804: } /* cptcov */
! 7805: return 0;
1.180 brouard 7806: }
7807:
1.218 brouard 7808: int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){
7809: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
7810:
7811: /* Computes the back prevalence limit for any combination of covariate values
7812: * at any age between ageminpar and agemaxpar
7813: */
1.217 brouard 7814: int i, j, k, i1 ;
7815: /* double ftolpl = 1.e-10; */
7816: double age, agebase, agelim;
7817: double tot;
1.218 brouard 7818: /* double ***mobaverage; */
7819: /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
1.217 brouard 7820:
7821: strcpy(fileresplb,"PLB_");
7822: strcat(fileresplb,fileresu);
7823: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
7824: printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
7825: fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
7826: }
7827: printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
7828: fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
7829: pstamp(ficresplb);
7830: fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
7831: fprintf(ficresplb,"#Age ");
7832: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
7833: fprintf(ficresplb,"\n");
7834:
1.218 brouard 7835:
7836: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
7837:
7838: agebase=ageminpar;
7839: agelim=agemaxpar;
7840:
7841:
7842: i1=pow(2,cptcoveff);
7843: if (cptcovn < 1){i1=1;}
7844:
7845: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.217 brouard 7846: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
1.218 brouard 7847: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
7848: k=k+1;
7849: /* to clean */
7850: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
7851: fprintf(ficresplb,"#******");
7852: printf("#******");
7853: fprintf(ficlog,"#******");
7854: for(j=1;j<=cptcoveff;j++) {
7855: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7856: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7857: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7858: }
7859: fprintf(ficresplb,"******\n");
7860: printf("******\n");
7861: fprintf(ficlog,"******\n");
7862:
7863: fprintf(ficresplb,"#Age ");
7864: for(j=1;j<=cptcoveff;j++) {
7865: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7866: }
7867: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
7868: fprintf(ficresplb,"Total Years_to_converge\n");
7869:
7870:
7871: for (age=agebase; age<=agelim; age++){
7872: /* for (age=agebase; age<=agebase; age++){ */
7873: if(mobilavproj > 0){
7874: /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
7875: /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.219 ! brouard 7876: bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);
1.218 brouard 7877: }else if (mobilavproj == 0){
1.219 ! brouard 7878: printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
! 7879: fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
! 7880: exit(1);
1.218 brouard 7881: }else{
1.219 ! brouard 7882: /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
! 7883: bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);
1.218 brouard 7884: }
7885: fprintf(ficresplb,"%.0f ",age );
7886: for(j=1;j<=cptcoveff;j++)
1.219 ! brouard 7887: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.218 brouard 7888: tot=0.;
7889: for(i=1; i<=nlstate;i++){
1.219 ! brouard 7890: tot += bprlim[i][i];
! 7891: fprintf(ficresplb," %.5f", bprlim[i][i]);
1.218 brouard 7892: }
7893: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
7894: } /* Age */
7895: /* was end of cptcod */
7896: } /* cptcov */
7897:
7898: /* hBijx(p, bage, fage); */
7899: /* fclose(ficrespijb); */
7900:
7901: return 0;
1.217 brouard 7902: }
1.218 brouard 7903:
1.180 brouard 7904: int hPijx(double *p, int bage, int fage){
7905: /*------------- h Pij x at various ages ------------*/
7906:
7907: int stepsize;
7908: int agelim;
7909: int hstepm;
7910: int nhstepm;
7911: int h, i, i1, j, k;
7912:
7913: double agedeb;
7914: double ***p3mat;
7915:
1.201 brouard 7916: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 7917: if((ficrespij=fopen(filerespij,"w"))==NULL) {
7918: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
7919: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
7920: }
7921: printf("Computing pij: result on file '%s' \n", filerespij);
7922: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
7923:
7924: stepsize=(int) (stepm+YEARM-1)/YEARM;
7925: /*if (stepm<=24) stepsize=2;*/
7926:
7927: agelim=AGESUP;
7928: hstepm=stepsize*YEARM; /* Every year of age */
7929: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.218 brouard 7930:
1.180 brouard 7931: /* hstepm=1; aff par mois*/
7932: pstamp(ficrespij);
7933: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
7934: i1= pow(2,cptcoveff);
1.218 brouard 7935: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
7936: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
7937: /* k=k+1; */
1.183 brouard 7938: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7939: fprintf(ficrespij,"\n#****** ");
7940: for(j=1;j<=cptcoveff;j++)
1.198 brouard 7941: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.183 brouard 7942: fprintf(ficrespij,"******\n");
7943:
7944: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
7945: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
7946: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
7947:
7948: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 7949:
1.183 brouard 7950: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
7951: oldm=oldms;savm=savms;
7952: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
7953: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
7954: for(i=1; i<=nlstate;i++)
7955: for(j=1; j<=nlstate+ndeath;j++)
7956: fprintf(ficrespij," %1d-%1d",i,j);
7957: fprintf(ficrespij,"\n");
7958: for (h=0; h<=nhstepm; h++){
7959: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
7960: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 7961: for(i=1; i<=nlstate;i++)
7962: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 7963: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 7964: fprintf(ficrespij,"\n");
7965: }
1.183 brouard 7966: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
7967: fprintf(ficrespij,"\n");
7968: }
1.180 brouard 7969: /*}*/
7970: }
1.218 brouard 7971: return 0;
1.180 brouard 7972: }
1.218 brouard 7973:
7974: int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217 brouard 7975: /*------------- h Bij x at various ages ------------*/
7976:
7977: int stepsize;
1.218 brouard 7978: /* int agelim; */
7979: int ageminl;
1.217 brouard 7980: int hstepm;
7981: int nhstepm;
7982: int h, i, i1, j, k;
1.218 brouard 7983:
1.217 brouard 7984: double agedeb;
7985: double ***p3mat;
1.218 brouard 7986:
7987: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
7988: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
7989: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
7990: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
7991: }
7992: printf("Computing pij back: result on file '%s' \n", filerespijb);
7993: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
7994:
7995: stepsize=(int) (stepm+YEARM-1)/YEARM;
7996: /*if (stepm<=24) stepsize=2;*/
1.217 brouard 7997:
1.218 brouard 7998: /* agelim=AGESUP; */
7999: ageminl=30;
8000: hstepm=stepsize*YEARM; /* Every year of age */
8001: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
8002:
8003: /* hstepm=1; aff par mois*/
8004: pstamp(ficrespijb);
8005: fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");
8006: i1= pow(2,cptcoveff);
8007: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
8008: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
8009: /* k=k+1; */
8010: for (k=1; k <= (int) pow(2,cptcoveff); k++){
8011: fprintf(ficrespijb,"\n#****** ");
8012: for(j=1;j<=cptcoveff;j++)
8013: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8014: fprintf(ficrespijb,"******\n");
8015:
8016: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
8017: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
8018: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
8019: nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
8020: nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
8021:
8022: /* nhstepm=nhstepm*YEARM; aff par mois*/
8023:
8024: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8025: /* oldm=oldms;savm=savms; */
8026: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
8027: hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
8028: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
8029: fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
8030: for(i=1; i<=nlstate;i++)
8031: for(j=1; j<=nlstate+ndeath;j++)
8032: fprintf(ficrespijb," %1d-%1d",i,j);
8033: fprintf(ficrespijb,"\n");
8034: for (h=0; h<=nhstepm; h++){
8035: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
8036: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
8037: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
1.217 brouard 8038: for(i=1; i<=nlstate;i++)
8039: for(j=1; j<=nlstate+ndeath;j++)
1.218 brouard 8040: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
1.217 brouard 8041: fprintf(ficrespijb,"\n");
8042: }
1.218 brouard 8043: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8044: fprintf(ficrespijb,"\n");
1.217 brouard 8045: }
1.218 brouard 8046: /*}*/
8047: }
8048: return 0;
8049: } /* hBijx */
1.217 brouard 8050:
1.180 brouard 8051:
1.136 brouard 8052: /***********************************************/
8053: /**************** Main Program *****************/
8054: /***********************************************/
8055:
8056: int main(int argc, char *argv[])
8057: {
8058: #ifdef GSL
8059: const gsl_multimin_fminimizer_type *T;
8060: size_t iteri = 0, it;
8061: int rval = GSL_CONTINUE;
8062: int status = GSL_SUCCESS;
8063: double ssval;
8064: #endif
8065: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 8066: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.209 brouard 8067: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 8068: int jj, ll, li, lj, lk;
1.136 brouard 8069: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 8070: int num_filled;
1.136 brouard 8071: int itimes;
8072: int NDIM=2;
8073: int vpopbased=0;
8074:
1.164 brouard 8075: char ca[32], cb[32];
1.136 brouard 8076: /* FILE *fichtm; *//* Html File */
8077: /* FILE *ficgp;*/ /*Gnuplot File */
8078: struct stat info;
1.191 brouard 8079: double agedeb=0.;
1.194 brouard 8080:
8081: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219 ! brouard 8082: double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136 brouard 8083:
1.165 brouard 8084: double fret;
1.191 brouard 8085: double dum=0.; /* Dummy variable */
1.136 brouard 8086: double ***p3mat;
1.218 brouard 8087: /* double ***mobaverage; */
1.164 brouard 8088:
8089: char line[MAXLINE];
1.197 brouard 8090: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
8091:
8092: char model[MAXLINE], modeltemp[MAXLINE];
1.136 brouard 8093: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 8094: char *tok, *val; /* pathtot */
1.136 brouard 8095: int firstobs=1, lastobs=10;
1.195 brouard 8096: int c, h , cpt, c2;
1.191 brouard 8097: int jl=0;
8098: int i1, j1, jk, stepsize=0;
1.194 brouard 8099: int count=0;
8100:
1.164 brouard 8101: int *tab;
1.136 brouard 8102: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.217 brouard 8103: int backcast=0;
1.136 brouard 8104: int mobilav=0,popforecast=0;
1.191 brouard 8105: int hstepm=0, nhstepm=0;
1.136 brouard 8106: int agemortsup;
8107: float sumlpop=0.;
8108: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
8109: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
8110:
1.191 brouard 8111: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 8112: double ftolpl=FTOL;
8113: double **prlim;
1.217 brouard 8114: double **bprlim;
1.136 brouard 8115: double ***param; /* Matrix of parameters */
8116: double *p;
8117: double **matcov; /* Matrix of covariance */
1.203 brouard 8118: double **hess; /* Hessian matrix */
1.136 brouard 8119: double ***delti3; /* Scale */
8120: double *delti; /* Scale */
8121: double ***eij, ***vareij;
8122: double **varpl; /* Variances of prevalence limits by age */
8123: double *epj, vepp;
1.164 brouard 8124:
1.136 brouard 8125: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.217 brouard 8126: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;
8127:
1.136 brouard 8128: double **ximort;
1.145 brouard 8129: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 8130: int *dcwave;
8131:
1.164 brouard 8132: char z[1]="c";
1.136 brouard 8133:
8134: /*char *strt;*/
8135: char strtend[80];
1.126 brouard 8136:
1.164 brouard 8137:
1.126 brouard 8138: /* setlocale (LC_ALL, ""); */
8139: /* bindtextdomain (PACKAGE, LOCALEDIR); */
8140: /* textdomain (PACKAGE); */
8141: /* setlocale (LC_CTYPE, ""); */
8142: /* setlocale (LC_MESSAGES, ""); */
8143:
8144: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 8145: rstart_time = time(NULL);
8146: /* (void) gettimeofday(&start_time,&tzp);*/
8147: start_time = *localtime(&rstart_time);
1.126 brouard 8148: curr_time=start_time;
1.157 brouard 8149: /*tml = *localtime(&start_time.tm_sec);*/
8150: /* strcpy(strstart,asctime(&tml)); */
8151: strcpy(strstart,asctime(&start_time));
1.126 brouard 8152:
8153: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 8154: /* tp.tm_sec = tp.tm_sec +86400; */
8155: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 8156: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
8157: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
8158: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 8159: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 8160: /* strt=asctime(&tmg); */
8161: /* printf("Time(after) =%s",strstart); */
8162: /* (void) time (&time_value);
8163: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
8164: * tm = *localtime(&time_value);
8165: * strstart=asctime(&tm);
8166: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
8167: */
8168:
8169: nberr=0; /* Number of errors and warnings */
8170: nbwarn=0;
1.184 brouard 8171: #ifdef WIN32
8172: _getcwd(pathcd, size);
8173: #else
1.126 brouard 8174: getcwd(pathcd, size);
1.184 brouard 8175: #endif
1.191 brouard 8176: syscompilerinfo(0);
1.196 brouard 8177: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 8178: if(argc <=1){
8179: printf("\nEnter the parameter file name: ");
1.205 brouard 8180: if(!fgets(pathr,FILENAMELENGTH,stdin)){
8181: printf("ERROR Empty parameter file name\n");
8182: goto end;
8183: }
1.126 brouard 8184: i=strlen(pathr);
8185: if(pathr[i-1]=='\n')
8186: pathr[i-1]='\0';
1.156 brouard 8187: i=strlen(pathr);
1.205 brouard 8188: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 8189: pathr[i-1]='\0';
1.205 brouard 8190: }
8191: i=strlen(pathr);
8192: if( i==0 ){
8193: printf("ERROR Empty parameter file name\n");
8194: goto end;
8195: }
8196: for (tok = pathr; tok != NULL; ){
1.126 brouard 8197: printf("Pathr |%s|\n",pathr);
8198: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
8199: printf("val= |%s| pathr=%s\n",val,pathr);
8200: strcpy (pathtot, val);
8201: if(pathr[0] == '\0') break; /* Dirty */
8202: }
8203: }
8204: else{
8205: strcpy(pathtot,argv[1]);
8206: }
8207: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
8208: /*cygwin_split_path(pathtot,path,optionfile);
8209: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
8210: /* cutv(path,optionfile,pathtot,'\\');*/
8211:
8212: /* Split argv[0], imach program to get pathimach */
8213: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
8214: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
8215: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
8216: /* strcpy(pathimach,argv[0]); */
8217: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
8218: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
8219: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 8220: #ifdef WIN32
8221: _chdir(path); /* Can be a relative path */
8222: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
8223: #else
1.126 brouard 8224: chdir(path); /* Can be a relative path */
1.184 brouard 8225: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
8226: #endif
8227: printf("Current directory %s!\n",pathcd);
1.126 brouard 8228: strcpy(command,"mkdir ");
8229: strcat(command,optionfilefiname);
8230: if((outcmd=system(command)) != 0){
1.169 brouard 8231: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 8232: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
8233: /* fclose(ficlog); */
8234: /* exit(1); */
8235: }
8236: /* if((imk=mkdir(optionfilefiname))<0){ */
8237: /* perror("mkdir"); */
8238: /* } */
8239:
8240: /*-------- arguments in the command line --------*/
8241:
1.186 brouard 8242: /* Main Log file */
1.126 brouard 8243: strcat(filelog, optionfilefiname);
8244: strcat(filelog,".log"); /* */
8245: if((ficlog=fopen(filelog,"w"))==NULL) {
8246: printf("Problem with logfile %s\n",filelog);
8247: goto end;
8248: }
8249: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 8250: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 8251: fprintf(ficlog,"\nEnter the parameter file name: \n");
8252: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
8253: path=%s \n\
8254: optionfile=%s\n\
8255: optionfilext=%s\n\
1.156 brouard 8256: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 8257:
1.197 brouard 8258: syscompilerinfo(1);
1.167 brouard 8259:
1.126 brouard 8260: printf("Local time (at start):%s",strstart);
8261: fprintf(ficlog,"Local time (at start): %s",strstart);
8262: fflush(ficlog);
8263: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 8264: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 8265:
8266: /* */
8267: strcpy(fileres,"r");
8268: strcat(fileres, optionfilefiname);
1.201 brouard 8269: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 8270: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 8271: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 8272:
1.186 brouard 8273: /* Main ---------arguments file --------*/
1.126 brouard 8274:
8275: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 8276: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
8277: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 8278: fflush(ficlog);
1.149 brouard 8279: /* goto end; */
8280: exit(70);
1.126 brouard 8281: }
8282:
8283:
8284:
8285: strcpy(filereso,"o");
1.201 brouard 8286: strcat(filereso,fileresu);
1.126 brouard 8287: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
8288: printf("Problem with Output resultfile: %s\n", filereso);
8289: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
8290: fflush(ficlog);
8291: goto end;
8292: }
8293:
8294: /* Reads comments: lines beginning with '#' */
8295: numlinepar=0;
1.197 brouard 8296:
8297: /* First parameter line */
8298: while(fgets(line, MAXLINE, ficpar)) {
8299: /* If line starts with a # it is a comment */
8300: if (line[0] == '#') {
8301: numlinepar++;
8302: fputs(line,stdout);
8303: fputs(line,ficparo);
8304: fputs(line,ficlog);
8305: continue;
8306: }else
8307: break;
8308: }
8309: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
8310: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
8311: if (num_filled != 5) {
8312: printf("Should be 5 parameters\n");
8313: }
1.126 brouard 8314: numlinepar++;
1.197 brouard 8315: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
8316: }
8317: /* Second parameter line */
8318: while(fgets(line, MAXLINE, ficpar)) {
8319: /* If line starts with a # it is a comment */
8320: if (line[0] == '#') {
8321: numlinepar++;
8322: fputs(line,stdout);
8323: fputs(line,ficparo);
8324: fputs(line,ficlog);
8325: continue;
8326: }else
8327: break;
8328: }
8329: if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
8330: &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
8331: if (num_filled != 8) {
1.209 brouard 8332: 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");
8333: printf("but line=%s\n",line);
1.197 brouard 8334: }
8335: 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 8336: }
1.203 brouard 8337: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 8338: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 8339: /* Third parameter line */
8340: while(fgets(line, MAXLINE, ficpar)) {
8341: /* If line starts with a # it is a comment */
8342: if (line[0] == '#') {
8343: numlinepar++;
8344: fputs(line,stdout);
8345: fputs(line,ficparo);
8346: fputs(line,ficlog);
8347: continue;
8348: }else
8349: break;
8350: }
1.201 brouard 8351: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
8352: if (num_filled == 0)
8353: model[0]='\0';
8354: else if (num_filled != 1){
1.197 brouard 8355: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
8356: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
8357: model[0]='\0';
8358: goto end;
8359: }
8360: else{
8361: if (model[0]=='+'){
8362: for(i=1; i<=strlen(model);i++)
8363: modeltemp[i-1]=model[i];
1.201 brouard 8364: strcpy(model,modeltemp);
1.197 brouard 8365: }
8366: }
1.199 brouard 8367: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 8368: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 8369: }
8370: /* 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); */
8371: /* numlinepar=numlinepar+3; /\* In general *\/ */
8372: /* 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 8373: 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);
8374: 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 8375: fflush(ficlog);
1.190 brouard 8376: /* if(model[0]=='#'|| model[0]== '\0'){ */
8377: if(model[0]=='#'){
1.187 brouard 8378: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
8379: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
8380: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
8381: if(mle != -1){
8382: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
8383: exit(1);
8384: }
8385: }
1.126 brouard 8386: while((c=getc(ficpar))=='#' && c!= EOF){
8387: ungetc(c,ficpar);
8388: fgets(line, MAXLINE, ficpar);
8389: numlinepar++;
1.195 brouard 8390: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
8391: z[0]=line[1];
8392: }
8393: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 8394: fputs(line, stdout);
8395: //puts(line);
1.126 brouard 8396: fputs(line,ficparo);
8397: fputs(line,ficlog);
8398: }
8399: ungetc(c,ficpar);
8400:
8401:
1.145 brouard 8402: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 8403: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
8404: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
8405: v1+v2*age+v2*v3 makes cptcovn = 3
8406: */
8407: if (strlen(model)>1)
1.187 brouard 8408: 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 8409: else
1.187 brouard 8410: ncovmodel=2; /* Constant and age */
1.133 brouard 8411: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
8412: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 8413: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
8414: 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);
8415: 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);
8416: fflush(stdout);
8417: fclose (ficlog);
8418: goto end;
8419: }
1.126 brouard 8420: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
8421: delti=delti3[1][1];
8422: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
8423: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
8424: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 8425: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
8426: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 8427: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8428: fclose (ficparo);
8429: fclose (ficlog);
8430: goto end;
8431: exit(0);
8432: }
1.186 brouard 8433: else if(mle==-3) { /* Main Wizard */
1.126 brouard 8434: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 8435: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
8436: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 8437: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
8438: matcov=matrix(1,npar,1,npar);
1.203 brouard 8439: hess=matrix(1,npar,1,npar);
1.126 brouard 8440: }
8441: else{
1.145 brouard 8442: /* Read guessed parameters */
1.126 brouard 8443: /* Reads comments: lines beginning with '#' */
8444: while((c=getc(ficpar))=='#' && c!= EOF){
8445: ungetc(c,ficpar);
8446: fgets(line, MAXLINE, ficpar);
8447: numlinepar++;
1.141 brouard 8448: fputs(line,stdout);
1.126 brouard 8449: fputs(line,ficparo);
8450: fputs(line,ficlog);
8451: }
8452: ungetc(c,ficpar);
8453:
8454: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
8455: for(i=1; i <=nlstate; i++){
8456: j=0;
8457: for(jj=1; jj <=nlstate+ndeath; jj++){
8458: if(jj==i) continue;
8459: j++;
8460: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.193 brouard 8461: if ((i1 != i) || (j1 != jj)){
1.126 brouard 8462: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
8463: It might be a problem of design; if ncovcol and the model are correct\n \
8464: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
8465: exit(1);
8466: }
8467: fprintf(ficparo,"%1d%1d",i1,j1);
8468: if(mle==1)
1.193 brouard 8469: printf("%1d%1d",i,jj);
8470: fprintf(ficlog,"%1d%1d",i,jj);
1.126 brouard 8471: for(k=1; k<=ncovmodel;k++){
8472: fscanf(ficpar," %lf",¶m[i][j][k]);
8473: if(mle==1){
8474: printf(" %lf",param[i][j][k]);
8475: fprintf(ficlog," %lf",param[i][j][k]);
8476: }
8477: else
8478: fprintf(ficlog," %lf",param[i][j][k]);
8479: fprintf(ficparo," %lf",param[i][j][k]);
8480: }
8481: fscanf(ficpar,"\n");
8482: numlinepar++;
8483: if(mle==1)
8484: printf("\n");
8485: fprintf(ficlog,"\n");
8486: fprintf(ficparo,"\n");
8487: }
8488: }
8489: fflush(ficlog);
8490:
1.145 brouard 8491: /* Reads scales values */
1.126 brouard 8492: p=param[1][1];
8493:
8494: /* Reads comments: lines beginning with '#' */
8495: while((c=getc(ficpar))=='#' && c!= EOF){
8496: ungetc(c,ficpar);
8497: fgets(line, MAXLINE, ficpar);
8498: numlinepar++;
1.141 brouard 8499: fputs(line,stdout);
1.126 brouard 8500: fputs(line,ficparo);
8501: fputs(line,ficlog);
8502: }
8503: ungetc(c,ficpar);
8504:
8505: for(i=1; i <=nlstate; i++){
8506: for(j=1; j <=nlstate+ndeath-1; j++){
8507: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 8508: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 8509: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
8510: exit(1);
8511: }
8512: printf("%1d%1d",i,j);
8513: fprintf(ficparo,"%1d%1d",i1,j1);
8514: fprintf(ficlog,"%1d%1d",i1,j1);
8515: for(k=1; k<=ncovmodel;k++){
8516: fscanf(ficpar,"%le",&delti3[i][j][k]);
8517: printf(" %le",delti3[i][j][k]);
8518: fprintf(ficparo," %le",delti3[i][j][k]);
8519: fprintf(ficlog," %le",delti3[i][j][k]);
8520: }
8521: fscanf(ficpar,"\n");
8522: numlinepar++;
8523: printf("\n");
8524: fprintf(ficparo,"\n");
8525: fprintf(ficlog,"\n");
8526: }
8527: }
8528: fflush(ficlog);
8529:
1.145 brouard 8530: /* Reads covariance matrix */
1.126 brouard 8531: delti=delti3[1][1];
8532:
8533:
8534: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
8535:
8536: /* Reads comments: lines beginning with '#' */
8537: while((c=getc(ficpar))=='#' && c!= EOF){
8538: ungetc(c,ficpar);
8539: fgets(line, MAXLINE, ficpar);
8540: numlinepar++;
1.141 brouard 8541: fputs(line,stdout);
1.126 brouard 8542: fputs(line,ficparo);
8543: fputs(line,ficlog);
8544: }
8545: ungetc(c,ficpar);
8546:
8547: matcov=matrix(1,npar,1,npar);
1.203 brouard 8548: hess=matrix(1,npar,1,npar);
1.131 brouard 8549: for(i=1; i <=npar; i++)
8550: for(j=1; j <=npar; j++) matcov[i][j]=0.;
8551:
1.194 brouard 8552: /* Scans npar lines */
1.126 brouard 8553: for(i=1; i <=npar; i++){
1.194 brouard 8554: count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
8555: if(count != 3){
8556: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
8557: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
8558: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
8559: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
8560: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
8561: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
8562: exit(1);
8563: }else
1.218 brouard 8564: if(mle==1)
8565: printf("%1d%1d%1d",i1,j1,jk);
1.194 brouard 8566: fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
8567: fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
1.126 brouard 8568: for(j=1; j <=i; j++){
8569: fscanf(ficpar," %le",&matcov[i][j]);
8570: if(mle==1){
8571: printf(" %.5le",matcov[i][j]);
8572: }
8573: fprintf(ficlog," %.5le",matcov[i][j]);
8574: fprintf(ficparo," %.5le",matcov[i][j]);
8575: }
8576: fscanf(ficpar,"\n");
8577: numlinepar++;
8578: if(mle==1)
8579: printf("\n");
8580: fprintf(ficlog,"\n");
8581: fprintf(ficparo,"\n");
8582: }
1.194 brouard 8583: /* End of read covariance matrix npar lines */
1.126 brouard 8584: for(i=1; i <=npar; i++)
8585: for(j=i+1;j<=npar;j++)
8586: matcov[i][j]=matcov[j][i];
8587:
8588: if(mle==1)
8589: printf("\n");
8590: fprintf(ficlog,"\n");
8591:
8592: fflush(ficlog);
8593:
8594: /*-------- Rewriting parameter file ----------*/
8595: strcpy(rfileres,"r"); /* "Rparameterfile */
8596: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
8597: strcat(rfileres,"."); /* */
8598: strcat(rfileres,optionfilext); /* Other files have txt extension */
8599: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 8600: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
8601: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 8602: }
8603: fprintf(ficres,"#%s\n",version);
8604: } /* End of mle != -3 */
1.218 brouard 8605:
1.186 brouard 8606: /* Main data
8607: */
1.126 brouard 8608: n= lastobs;
8609: num=lvector(1,n);
8610: moisnais=vector(1,n);
8611: annais=vector(1,n);
8612: moisdc=vector(1,n);
8613: andc=vector(1,n);
8614: agedc=vector(1,n);
8615: cod=ivector(1,n);
8616: weight=vector(1,n);
8617: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
8618: mint=matrix(1,maxwav,1,n);
8619: anint=matrix(1,maxwav,1,n);
1.131 brouard 8620: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 8621: tab=ivector(1,NCOVMAX);
1.144 brouard 8622: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 8623: 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 8624:
1.136 brouard 8625: /* Reads data from file datafile */
8626: if (readdata(datafile, firstobs, lastobs, &imx)==1)
8627: goto end;
8628:
8629: /* Calculation of the number of parameters from char model */
1.137 brouard 8630: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
8631: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
8632: k=3 V4 Tvar[k=3]= 4 (from V4)
8633: k=2 V1 Tvar[k=2]= 1 (from V1)
8634: k=1 Tvar[1]=2 (from V2)
8635: */
8636: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
8637: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
8638: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
8639: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
8640: */
8641: /* For model-covariate k tells which data-covariate to use but
8642: because this model-covariate is a construction we invent a new column
8643: ncovcol + k1
8644: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
8645: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 8646: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 8647: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
8648: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
8649: */
1.145 brouard 8650: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
8651: 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 8652: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
8653: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 8654: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 8655: 4 covariates (3 plus signs)
8656: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
8657: */
1.136 brouard 8658:
1.186 brouard 8659: /* Main decodemodel */
8660:
1.187 brouard 8661:
1.136 brouard 8662: if(decodemodel(model, lastobs) == 1)
8663: goto end;
8664:
1.137 brouard 8665: if((double)(lastobs-imx)/(double)imx > 1.10){
8666: nbwarn++;
8667: 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);
8668: 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);
8669: }
1.136 brouard 8670: /* if(mle==1){*/
1.137 brouard 8671: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
8672: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 8673: }
8674:
8675: /*-calculation of age at interview from date of interview and age at death -*/
8676: agev=matrix(1,maxwav,1,imx);
8677:
8678: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
8679: goto end;
8680:
1.126 brouard 8681:
1.136 brouard 8682: agegomp=(int)agemin;
8683: free_vector(moisnais,1,n);
8684: free_vector(annais,1,n);
1.126 brouard 8685: /* free_matrix(mint,1,maxwav,1,n);
8686: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 8687: /* free_vector(moisdc,1,n); */
8688: /* free_vector(andc,1,n); */
1.145 brouard 8689: /* */
8690:
1.126 brouard 8691: wav=ivector(1,imx);
1.214 brouard 8692: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
8693: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
8694: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
8695: 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.*/
8696: bh=imatrix(1,lastpass-firstpass+2,1,imx);
8697: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 8698:
8699: /* Concatenates waves */
1.214 brouard 8700: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
8701: Death is a valid wave (if date is known).
8702: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
8703: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
8704: and mw[mi+1][i]. dh depends on stepm.
8705: */
8706:
1.126 brouard 8707: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 8708: /* */
8709:
1.215 brouard 8710: free_vector(moisdc,1,n);
8711: free_vector(andc,1,n);
8712:
1.126 brouard 8713: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
8714:
8715: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
8716: ncodemax[1]=1;
1.145 brouard 8717: Ndum =ivector(-1,NCOVMAX);
1.187 brouard 8718: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
1.145 brouard 8719: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.211 brouard 8720: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 8721: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 8722: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.145 brouard 8723:
1.200 brouard 8724: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 8725: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 8726: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 8727: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
8728: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
8729: * (currently 0 or 1) in the data.
8730: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
8731: * corresponding modality (h,j).
8732: */
8733:
1.145 brouard 8734: h=0;
8735:
8736:
8737: /*if (cptcovn > 0) */
1.126 brouard 8738:
1.145 brouard 8739:
1.126 brouard 8740: m=pow(2,cptcoveff);
8741:
1.144 brouard 8742: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 8743: * For k=4 covariates, h goes from 1 to m=2**k
8744: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
8745: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 8746: * h\k 1 2 3 4
1.143 brouard 8747: *______________________________
8748: * 1 i=1 1 i=1 1 i=1 1 i=1 1
8749: * 2 2 1 1 1
8750: * 3 i=2 1 2 1 1
8751: * 4 2 2 1 1
8752: * 5 i=3 1 i=2 1 2 1
8753: * 6 2 1 2 1
8754: * 7 i=4 1 2 2 1
8755: * 8 2 2 2 1
1.197 brouard 8756: * 9 i=5 1 i=3 1 i=2 1 2
8757: * 10 2 1 1 2
8758: * 11 i=6 1 2 1 2
8759: * 12 2 2 1 2
8760: * 13 i=7 1 i=4 1 2 2
8761: * 14 2 1 2 2
8762: * 15 i=8 1 2 2 2
8763: * 16 2 2 2 2
1.143 brouard 8764: */
1.212 brouard 8765: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 8766: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
8767: * and the value of each covariate?
8768: * V1=1, V2=1, V3=2, V4=1 ?
8769: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
8770: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
8771: * In order to get the real value in the data, we use nbcode
8772: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
8773: * We are keeping this crazy system in order to be able (in the future?)
8774: * to have more than 2 values (0 or 1) for a covariate.
8775: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
8776: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
8777: * bbbbbbbb
8778: * 76543210
8779: * h-1 00000101 (6-1=5)
1.219 ! brouard 8780: *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211 brouard 8781: * &
8782: * 1 00000001 (1)
1.219 ! brouard 8783: * 00000000 = 1 & ((h-1) >> (k-1))
! 8784: * +1= 00000001 =1
1.211 brouard 8785: *
8786: * h=14, k=3 => h'=h-1=13, k'=k-1=2
8787: * h' 1101 =2^3+2^2+0x2^1+2^0
8788: * >>k' 11
8789: * & 00000001
8790: * = 00000001
8791: * +1 = 00000010=2 = codtabm(14,3)
8792: * Reverse h=6 and m=16?
8793: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
8794: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
8795: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
8796: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
8797: * V3=decodtabm(14,3,2**4)=2
8798: * h'=13 1101 =2^3+2^2+0x2^1+2^0
8799: *(h-1) >> (j-1) 0011 =13 >> 2
8800: * &1 000000001
8801: * = 000000001
8802: * +1= 000000010 =2
8803: * 2211
8804: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
8805: * V3=2
8806: */
8807:
1.202 brouard 8808: /* /\* for(h=1; h <=100 ;h++){ *\/ */
8809: /* /\* printf("h=%2d ", h); *\/ */
8810: /* /\* for(k=1; k <=10; k++){ *\/ */
8811: /* /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */
8812: /* /\* codtab[h][k]=codtabm(h,k); *\/ */
8813: /* /\* } *\/ */
8814: /* /\* printf("\n"); *\/ */
8815: /* } */
1.197 brouard 8816: /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
8817: /* 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 *\/ */
8818: /* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
8819: /* for(cpt=1; cpt <=pow(2,k-1); cpt++){ /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/ */
8820: /* h++; */
8821: /* if (h>m) */
8822: /* h=1; */
8823: /* codtab[h][k]=j; */
8824: /* /\* codtab[12][3]=1; *\/ */
8825: /* /\*codtab[h][Tvar[k]]=j;*\/ */
8826: /* /\* 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]]); *\/ */
8827: /* } */
8828: /* } */
8829: /* } */
8830: /* } */
1.126 brouard 8831: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
8832: codtab[1][2]=1;codtab[2][2]=2; */
1.197 brouard 8833: /* for(i=1; i <=m ;i++){ */
8834: /* for(k=1; k <=cptcovn; k++){ */
8835: /* printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
8836: /* } */
8837: /* printf("\n"); */
8838: /* } */
8839: /* scanf("%d",i);*/
1.145 brouard 8840:
8841: free_ivector(Ndum,-1,NCOVMAX);
8842:
8843:
1.126 brouard 8844:
1.186 brouard 8845: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 8846: strcpy(optionfilegnuplot,optionfilefiname);
8847: if(mle==-3)
1.201 brouard 8848: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 8849: strcat(optionfilegnuplot,".gp");
8850:
8851: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
8852: printf("Problem with file %s",optionfilegnuplot);
8853: }
8854: else{
1.204 brouard 8855: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 8856: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 8857: //fprintf(ficgp,"set missing 'NaNq'\n");
8858: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 8859: }
8860: /* fclose(ficgp);*/
1.186 brouard 8861:
8862:
8863: /* Initialisation of --------- index.htm --------*/
1.126 brouard 8864:
8865: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
8866: if(mle==-3)
1.201 brouard 8867: strcat(optionfilehtm,"-MORT_");
1.126 brouard 8868: strcat(optionfilehtm,".htm");
8869: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 8870: printf("Problem with %s \n",optionfilehtm);
8871: exit(0);
1.126 brouard 8872: }
8873:
8874: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
8875: strcat(optionfilehtmcov,"-cov.htm");
8876: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
8877: printf("Problem with %s \n",optionfilehtmcov), exit(0);
8878: }
8879: else{
8880: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
8881: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 8882: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 8883: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
8884: }
8885:
1.213 brouard 8886: 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 8887: <hr size=\"2\" color=\"#EC5E5E\"> \n\
8888: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 8889: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 8890: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 8891: \n\
8892: <hr size=\"2\" color=\"#EC5E5E\">\
8893: <ul><li><h4>Parameter files</h4>\n\
8894: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
8895: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
8896: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
8897: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
8898: - Date and time at start: %s</ul>\n",\
8899: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
8900: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
8901: fileres,fileres,\
8902: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
8903: fflush(fichtm);
8904:
8905: strcpy(pathr,path);
8906: strcat(pathr,optionfilefiname);
1.184 brouard 8907: #ifdef WIN32
8908: _chdir(optionfilefiname); /* Move to directory named optionfile */
8909: #else
1.126 brouard 8910: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 8911: #endif
8912:
1.126 brouard 8913:
8914: /* Calculates basic frequencies. Computes observed prevalence at single age
8915: and prints on file fileres'p'. */
1.214 brouard 8916: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\
8917: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 8918:
8919: fprintf(fichtm,"\n");
8920: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
8921: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
8922: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
8923: imx,agemin,agemax,jmin,jmax,jmean);
8924: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
8925: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
8926: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
8927: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
8928: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218 brouard 8929:
1.126 brouard 8930: /* For Powell, parameters are in a vector p[] starting at p[1]
8931: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
8932: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
8933:
8934: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 8935: /* For mortality only */
1.126 brouard 8936: if (mle==-3){
1.136 brouard 8937: ximort=matrix(1,NDIM,1,NDIM);
1.186 brouard 8938: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 8939: cens=ivector(1,n);
8940: ageexmed=vector(1,n);
8941: agecens=vector(1,n);
8942: dcwave=ivector(1,n);
8943:
8944: for (i=1; i<=imx; i++){
8945: dcwave[i]=-1;
8946: for (m=firstpass; m<=lastpass; m++)
1.218 brouard 8947: if (s[m][i]>nlstate) {
8948: dcwave[i]=m;
8949: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
8950: break;
8951: }
1.126 brouard 8952: }
1.218 brouard 8953:
1.126 brouard 8954: for (i=1; i<=imx; i++) {
8955: if (wav[i]>0){
1.218 brouard 8956: ageexmed[i]=agev[mw[1][i]][i];
8957: j=wav[i];
8958: agecens[i]=1.;
8959:
8960: if (ageexmed[i]> 1 && wav[i] > 0){
8961: agecens[i]=agev[mw[j][i]][i];
8962: cens[i]= 1;
8963: }else if (ageexmed[i]< 1)
8964: cens[i]= -1;
8965: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
8966: cens[i]=0 ;
1.126 brouard 8967: }
8968: else cens[i]=-1;
8969: }
8970:
8971: for (i=1;i<=NDIM;i++) {
8972: for (j=1;j<=NDIM;j++)
1.218 brouard 8973: ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126 brouard 8974: }
8975:
1.145 brouard 8976: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 8977: /*printf("%lf %lf", p[1], p[2]);*/
8978:
8979:
1.136 brouard 8980: #ifdef GSL
8981: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 8982: #else
1.126 brouard 8983: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 8984: #endif
1.201 brouard 8985: strcpy(filerespow,"POW-MORT_");
8986: strcat(filerespow,fileresu);
1.126 brouard 8987: if((ficrespow=fopen(filerespow,"w"))==NULL) {
8988: printf("Problem with resultfile: %s\n", filerespow);
8989: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
8990: }
1.136 brouard 8991: #ifdef GSL
8992: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 8993: #else
1.126 brouard 8994: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 8995: #endif
1.126 brouard 8996: /* for (i=1;i<=nlstate;i++)
8997: for(j=1;j<=nlstate+ndeath;j++)
8998: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
8999: */
9000: fprintf(ficrespow,"\n");
1.136 brouard 9001: #ifdef GSL
9002: /* gsl starts here */
9003: T = gsl_multimin_fminimizer_nmsimplex;
9004: gsl_multimin_fminimizer *sfm = NULL;
9005: gsl_vector *ss, *x;
9006: gsl_multimin_function minex_func;
9007:
9008: /* Initial vertex size vector */
9009: ss = gsl_vector_alloc (NDIM);
9010:
9011: if (ss == NULL){
9012: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
9013: }
9014: /* Set all step sizes to 1 */
9015: gsl_vector_set_all (ss, 0.001);
9016:
9017: /* Starting point */
1.126 brouard 9018:
1.136 brouard 9019: x = gsl_vector_alloc (NDIM);
9020:
9021: if (x == NULL){
9022: gsl_vector_free(ss);
9023: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
9024: }
9025:
9026: /* Initialize method and iterate */
9027: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 9028: /* gsl_vector_set(x, 0, 0.0268); */
9029: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 9030: gsl_vector_set(x, 0, p[1]);
9031: gsl_vector_set(x, 1, p[2]);
9032:
9033: minex_func.f = &gompertz_f;
9034: minex_func.n = NDIM;
9035: minex_func.params = (void *)&p; /* ??? */
9036:
9037: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
9038: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
9039:
9040: printf("Iterations beginning .....\n\n");
9041: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
9042:
9043: iteri=0;
9044: while (rval == GSL_CONTINUE){
9045: iteri++;
9046: status = gsl_multimin_fminimizer_iterate(sfm);
9047:
9048: if (status) printf("error: %s\n", gsl_strerror (status));
9049: fflush(0);
9050:
9051: if (status)
9052: break;
9053:
9054: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
9055: ssval = gsl_multimin_fminimizer_size (sfm);
9056:
9057: if (rval == GSL_SUCCESS)
9058: printf ("converged to a local maximum at\n");
9059:
9060: printf("%5d ", iteri);
9061: for (it = 0; it < NDIM; it++){
9062: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
9063: }
9064: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
9065: }
9066:
9067: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
9068:
9069: gsl_vector_free(x); /* initial values */
9070: gsl_vector_free(ss); /* inital step size */
9071: for (it=0; it<NDIM; it++){
9072: p[it+1]=gsl_vector_get(sfm->x,it);
9073: fprintf(ficrespow," %.12lf", p[it]);
9074: }
9075: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
9076: #endif
9077: #ifdef POWELL
9078: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
9079: #endif
1.126 brouard 9080: fclose(ficrespow);
9081:
1.203 brouard 9082: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 9083:
9084: for(i=1; i <=NDIM; i++)
9085: for(j=i+1;j<=NDIM;j++)
9086: matcov[i][j]=matcov[j][i];
9087:
9088: printf("\nCovariance matrix\n ");
1.203 brouard 9089: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 9090: for(i=1; i <=NDIM; i++) {
9091: for(j=1;j<=NDIM;j++){
9092: printf("%f ",matcov[i][j]);
1.203 brouard 9093: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 9094: }
1.203 brouard 9095: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 9096: }
9097:
9098: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 9099: for (i=1;i<=NDIM;i++) {
1.126 brouard 9100: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 9101: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
9102: }
1.126 brouard 9103: lsurv=vector(1,AGESUP);
9104: lpop=vector(1,AGESUP);
9105: tpop=vector(1,AGESUP);
9106: lsurv[agegomp]=100000;
9107:
9108: for (k=agegomp;k<=AGESUP;k++) {
9109: agemortsup=k;
9110: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
9111: }
9112:
9113: for (k=agegomp;k<agemortsup;k++)
9114: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
9115:
9116: for (k=agegomp;k<agemortsup;k++){
9117: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
9118: sumlpop=sumlpop+lpop[k];
9119: }
9120:
9121: tpop[agegomp]=sumlpop;
9122: for (k=agegomp;k<(agemortsup-3);k++){
9123: /* tpop[k+1]=2;*/
9124: tpop[k+1]=tpop[k]-lpop[k];
9125: }
9126:
9127:
9128: printf("\nAge lx qx dx Lx Tx e(x)\n");
9129: for (k=agegomp;k<(agemortsup-2);k++)
9130: 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]);
9131:
9132:
9133: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 9134: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
9135: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
9136: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9137: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
9138: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
9139: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9140: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
9141: }else
1.201 brouard 9142: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
9143: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 9144: stepm, weightopt,\
9145: model,imx,p,matcov,agemortsup);
9146:
9147: free_vector(lsurv,1,AGESUP);
9148: free_vector(lpop,1,AGESUP);
9149: free_vector(tpop,1,AGESUP);
1.136 brouard 9150: #ifdef GSL
9151: free_ivector(cens,1,n);
9152: free_vector(agecens,1,n);
9153: free_ivector(dcwave,1,n);
9154: free_matrix(ximort,1,NDIM,1,NDIM);
9155: #endif
1.186 brouard 9156: } /* Endof if mle==-3 mortality only */
1.205 brouard 9157: /* Standard */
9158: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
9159: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
9160: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 9161: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 9162: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
9163: for (k=1; k<=npar;k++)
9164: printf(" %d %8.5f",k,p[k]);
9165: printf("\n");
1.205 brouard 9166: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
9167: /* mlikeli uses func not funcone */
9168: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
9169: }
9170: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
9171: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
9172: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
9173: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
9174: }
9175: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 9176: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
9177: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
9178: for (k=1; k<=npar;k++)
9179: printf(" %d %8.5f",k,p[k]);
9180: printf("\n");
9181:
9182: /*--------- results files --------------*/
1.192 brouard 9183: 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 9184:
9185:
9186: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9187: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9188: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9189: for(i=1,jk=1; i <=nlstate; i++){
9190: for(k=1; k <=(nlstate+ndeath); k++){
9191: if (k != i) {
9192: printf("%d%d ",i,k);
9193: fprintf(ficlog,"%d%d ",i,k);
9194: fprintf(ficres,"%1d%1d ",i,k);
9195: for(j=1; j <=ncovmodel; j++){
1.190 brouard 9196: printf("%12.7f ",p[jk]);
9197: fprintf(ficlog,"%12.7f ",p[jk]);
9198: fprintf(ficres,"%12.7f ",p[jk]);
1.126 brouard 9199: jk++;
9200: }
9201: printf("\n");
9202: fprintf(ficlog,"\n");
9203: fprintf(ficres,"\n");
9204: }
9205: }
9206: }
1.203 brouard 9207: if(mle != 0){
9208: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 9209: ftolhess=ftol; /* Usually correct */
1.203 brouard 9210: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
9211: 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");
9212: 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");
9213: for(i=1,jk=1; i <=nlstate; i++){
9214: for(k=1; k <=(nlstate+ndeath); k++){
9215: if (k != i) {
9216: printf("%d%d ",i,k);
9217: fprintf(ficlog,"%d%d ",i,k);
9218: for(j=1; j <=ncovmodel; j++){
9219: 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]));
9220: 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]));
9221: jk++;
9222: }
9223: printf("\n");
9224: fprintf(ficlog,"\n");
1.193 brouard 9225: }
9226: }
9227: }
1.203 brouard 9228: } /* end of hesscov and Wald tests */
1.193 brouard 9229:
1.203 brouard 9230: /* */
1.126 brouard 9231: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
9232: printf("# Scales (for hessian or gradient estimation)\n");
9233: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
9234: for(i=1,jk=1; i <=nlstate; i++){
9235: for(j=1; j <=nlstate+ndeath; j++){
9236: if (j!=i) {
9237: fprintf(ficres,"%1d%1d",i,j);
9238: printf("%1d%1d",i,j);
9239: fprintf(ficlog,"%1d%1d",i,j);
9240: for(k=1; k<=ncovmodel;k++){
9241: printf(" %.5e",delti[jk]);
9242: fprintf(ficlog," %.5e",delti[jk]);
9243: fprintf(ficres," %.5e",delti[jk]);
9244: jk++;
9245: }
9246: printf("\n");
9247: fprintf(ficlog,"\n");
9248: fprintf(ficres,"\n");
9249: }
9250: }
9251: }
9252:
9253: 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 9254: if(mle >= 1) /* To big for the screen */
1.126 brouard 9255: 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");
9256: 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");
9257: /* # 121 Var(a12)\n\ */
9258: /* # 122 Cov(b12,a12) Var(b12)\n\ */
9259: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
9260: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
9261: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
9262: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
9263: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
9264: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
9265:
9266:
9267: /* Just to have a covariance matrix which will be more understandable
9268: even is we still don't want to manage dictionary of variables
9269: */
9270: for(itimes=1;itimes<=2;itimes++){
9271: jj=0;
9272: for(i=1; i <=nlstate; i++){
9273: for(j=1; j <=nlstate+ndeath; j++){
9274: if(j==i) continue;
9275: for(k=1; k<=ncovmodel;k++){
9276: jj++;
9277: ca[0]= k+'a'-1;ca[1]='\0';
9278: if(itimes==1){
9279: if(mle>=1)
9280: printf("#%1d%1d%d",i,j,k);
9281: fprintf(ficlog,"#%1d%1d%d",i,j,k);
9282: fprintf(ficres,"#%1d%1d%d",i,j,k);
9283: }else{
9284: if(mle>=1)
9285: printf("%1d%1d%d",i,j,k);
9286: fprintf(ficlog,"%1d%1d%d",i,j,k);
9287: fprintf(ficres,"%1d%1d%d",i,j,k);
9288: }
9289: ll=0;
9290: for(li=1;li <=nlstate; li++){
9291: for(lj=1;lj <=nlstate+ndeath; lj++){
9292: if(lj==li) continue;
9293: for(lk=1;lk<=ncovmodel;lk++){
9294: ll++;
9295: if(ll<=jj){
9296: cb[0]= lk +'a'-1;cb[1]='\0';
9297: if(ll<jj){
9298: if(itimes==1){
9299: if(mle>=1)
9300: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9301: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9302: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9303: }else{
9304: if(mle>=1)
9305: printf(" %.5e",matcov[jj][ll]);
9306: fprintf(ficlog," %.5e",matcov[jj][ll]);
9307: fprintf(ficres," %.5e",matcov[jj][ll]);
9308: }
9309: }else{
9310: if(itimes==1){
9311: if(mle>=1)
9312: printf(" Var(%s%1d%1d)",ca,i,j);
9313: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
9314: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
9315: }else{
9316: if(mle>=1)
1.203 brouard 9317: printf(" %.7e",matcov[jj][ll]);
9318: fprintf(ficlog," %.7e",matcov[jj][ll]);
9319: fprintf(ficres," %.7e",matcov[jj][ll]);
1.126 brouard 9320: }
9321: }
9322: }
9323: } /* end lk */
9324: } /* end lj */
9325: } /* end li */
9326: if(mle>=1)
9327: printf("\n");
9328: fprintf(ficlog,"\n");
9329: fprintf(ficres,"\n");
9330: numlinepar++;
9331: } /* end k*/
9332: } /*end j */
9333: } /* end i */
9334: } /* end itimes */
9335:
9336: fflush(ficlog);
9337: fflush(ficres);
1.209 brouard 9338: while(fgets(line, MAXLINE, ficpar)) {
9339: /* If line starts with a # it is a comment */
9340: if (line[0] == '#') {
9341: numlinepar++;
1.141 brouard 9342: fputs(line,stdout);
1.126 brouard 9343: fputs(line,ficparo);
1.209 brouard 9344: fputs(line,ficlog);
9345: continue;
9346: }else
9347: break;
9348: }
9349:
9350: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
9351: /* ungetc(c,ficpar); */
9352: /* fgets(line, MAXLINE, ficpar); */
9353: /* fputs(line,stdout); */
9354: /* fputs(line,ficparo); */
9355: /* } */
9356: /* ungetc(c,ficpar); */
1.126 brouard 9357:
9358: estepm=0;
1.209 brouard 9359: 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){
9360:
9361: if (num_filled != 6) {
1.219 ! brouard 9362: printf("Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
! 9363: fprintf(ficlog,"Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
1.209 brouard 9364: goto end;
9365: }
9366: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
9367: }
9368: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
9369: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
9370:
9371: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 9372: if (estepm==0 || estepm < stepm) estepm=stepm;
9373: if (fage <= 2) {
9374: bage = ageminpar;
9375: fage = agemaxpar;
9376: }
9377:
9378: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 9379: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
9380: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.186 brouard 9381:
9382: /* Other stuffs, more or less useful */
1.126 brouard 9383: while((c=getc(ficpar))=='#' && c!= EOF){
9384: ungetc(c,ficpar);
9385: fgets(line, MAXLINE, ficpar);
1.141 brouard 9386: fputs(line,stdout);
1.126 brouard 9387: fputs(line,ficparo);
9388: }
9389: ungetc(c,ficpar);
9390:
9391: 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);
9392: 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);
9393: 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);
9394: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
9395: 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);
9396:
9397: while((c=getc(ficpar))=='#' && c!= EOF){
9398: ungetc(c,ficpar);
9399: fgets(line, MAXLINE, ficpar);
1.141 brouard 9400: fputs(line,stdout);
1.126 brouard 9401: fputs(line,ficparo);
9402: }
9403: ungetc(c,ficpar);
9404:
9405:
9406: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
9407: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
9408:
9409: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 9410: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 9411: fprintf(ficparo,"pop_based=%d\n",popbased);
9412: fprintf(ficres,"pop_based=%d\n",popbased);
9413:
9414: while((c=getc(ficpar))=='#' && c!= EOF){
9415: ungetc(c,ficpar);
9416: fgets(line, MAXLINE, ficpar);
1.141 brouard 9417: fputs(line,stdout);
1.126 brouard 9418: fputs(line,ficparo);
9419: }
9420: ungetc(c,ficpar);
9421:
9422: 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);
9423: 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);
9424: 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);
9425: 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);
9426: 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);
9427: /* day and month of proj2 are not used but only year anproj2.*/
9428:
1.217 brouard 9429: while((c=getc(ficpar))=='#' && c!= EOF){
9430: ungetc(c,ficpar);
9431: fgets(line, MAXLINE, ficpar);
9432: fputs(line,stdout);
9433: fputs(line,ficparo);
9434: }
9435: ungetc(c,ficpar);
9436:
9437: fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);
1.219 ! brouard 9438: fprintf(ficparo,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
! 9439: fprintf(ficlog,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
! 9440: fprintf(ficres,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
1.217 brouard 9441: /* day and month of proj2 are not used but only year anproj2.*/
1.126 brouard 9442:
9443:
1.145 brouard 9444: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
9445: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 9446:
9447: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 9448: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
9449: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
9450: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9451: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
9452: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
9453: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9454: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
9455: }else
1.218 brouard 9456: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
1.126 brouard 9457:
1.201 brouard 9458: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\
1.217 brouard 9459: model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
1.213 brouard 9460: jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
1.126 brouard 9461:
9462: /*------------ free_vector -------------*/
9463: /* chdir(path); */
9464:
1.215 brouard 9465: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
9466: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
9467: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
9468: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.126 brouard 9469: free_lvector(num,1,n);
9470: free_vector(agedc,1,n);
9471: /*free_matrix(covar,0,NCOVMAX,1,n);*/
9472: /*free_matrix(covar,1,NCOVMAX,1,n);*/
9473: fclose(ficparo);
9474: fclose(ficres);
9475:
9476:
1.186 brouard 9477: /* Other results (useful)*/
9478:
9479:
1.126 brouard 9480: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 9481: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
9482: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 9483: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 9484: fclose(ficrespl);
9485:
9486: /*------------- h Pij x at various ages ------------*/
1.180 brouard 9487: /*#include "hpijx.h"*/
9488: hPijx(p, bage, fage);
1.145 brouard 9489: fclose(ficrespij);
1.126 brouard 9490:
1.219 ! brouard 9491: ncovcombmax= pow(2,cptcoveff);
! 9492: /*-------------- Variance of one-step probabilities---*/
1.145 brouard 9493: k=1;
1.126 brouard 9494: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
9495:
1.219 ! brouard 9496: /* Prevalence for each covariates in probs[age][status][cov] */
1.218 brouard 9497: probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.126 brouard 9498: for(i=1;i<=AGESUP;i++)
1.219 ! brouard 9499: for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.218 brouard 9500: for(k=1;k<=ncovcombmax;k++)
9501: probs[i][j][k]=0.;
1.219 ! brouard 9502: prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
! 9503: if (mobilav!=0 ||mobilavproj !=0 ) {
! 9504: mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
! 9505: for(i=1;i<=AGESUP;i++)
! 9506: for(j=1;j<=nlstate;j++)
! 9507: for(k=1;k<=ncovcombmax;k++)
! 9508: mobaverages[i][j][k]=0.;
! 9509: mobaverage=mobaverages;
! 9510: if (mobilav!=0) {
1.218 brouard 9511: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
9512: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
9513: printf(" Error in movingaverage mobilav=%d\n",mobilav);
9514: }
1.219 ! brouard 9515: }
! 9516: /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
! 9517: /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
! 9518: else if (mobilavproj !=0) {
1.218 brouard 9519: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
9520: fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
9521: printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
9522: }
1.219 ! brouard 9523: }
! 9524: }/* end if moving average */
! 9525:
1.126 brouard 9526: /*---------- Forecasting ------------------*/
9527: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
9528: if(prevfcast==1){
9529: /* if(stepm ==1){*/
1.201 brouard 9530: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 9531: }
1.217 brouard 9532: if(backcast==1){
1.219 ! brouard 9533: ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
! 9534: ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
! 9535: ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
! 9536:
! 9537: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
! 9538:
! 9539: bprlim=matrix(1,nlstate,1,nlstate);
! 9540: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
! 9541: fclose(ficresplb);
! 9542:
! 9543: hBijx(p, bage, fage, mobaverage);
! 9544: fclose(ficrespijb);
! 9545: free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
! 9546:
! 9547: /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
! 9548: bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
! 9549: free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
! 9550: free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
! 9551: free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
! 9552: }
1.217 brouard 9553:
1.186 brouard 9554:
9555: /* ------ Other prevalence ratios------------ */
1.126 brouard 9556:
1.215 brouard 9557: free_ivector(wav,1,imx);
9558: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
9559: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
9560: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.218 brouard 9561:
9562:
1.127 brouard 9563: /*---------- Health expectancies, no variances ------------*/
1.218 brouard 9564:
1.201 brouard 9565: strcpy(filerese,"E_");
9566: strcat(filerese,fileresu);
1.126 brouard 9567: if((ficreseij=fopen(filerese,"w"))==NULL) {
9568: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
9569: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
9570: }
1.208 brouard 9571: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
9572: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.219 ! brouard 9573:
1.145 brouard 9574: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.219 ! brouard 9575: fprintf(ficreseij,"\n#****** ");
! 9576: for(j=1;j<=cptcoveff;j++) {
! 9577: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 9578: }
! 9579: fprintf(ficreseij,"******\n");
! 9580:
! 9581: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
! 9582: oldm=oldms;savm=savms;
! 9583: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
1.127 brouard 9584:
1.219 ! brouard 9585: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127 brouard 9586: }
9587: fclose(ficreseij);
1.208 brouard 9588: printf("done evsij\n");fflush(stdout);
9589: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.218 brouard 9590:
1.127 brouard 9591: /*---------- Health expectancies and variances ------------*/
1.218 brouard 9592:
9593:
1.201 brouard 9594: strcpy(filerest,"T_");
9595: strcat(filerest,fileresu);
1.127 brouard 9596: if((ficrest=fopen(filerest,"w"))==NULL) {
9597: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
9598: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
9599: }
1.208 brouard 9600: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
9601: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.218 brouard 9602:
1.126 brouard 9603:
1.201 brouard 9604: strcpy(fileresstde,"STDE_");
9605: strcat(fileresstde,fileresu);
1.126 brouard 9606: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
9607: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
9608: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
9609: }
1.208 brouard 9610: printf(" Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
9611: fprintf(ficlog," Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 9612:
1.201 brouard 9613: strcpy(filerescve,"CVE_");
9614: strcat(filerescve,fileresu);
1.126 brouard 9615: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
9616: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
9617: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
9618: }
1.208 brouard 9619: printf(" Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
9620: fprintf(ficlog," Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 9621:
1.201 brouard 9622: strcpy(fileresv,"V_");
9623: strcat(fileresv,fileresu);
1.126 brouard 9624: if((ficresvij=fopen(fileresv,"w"))==NULL) {
9625: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
9626: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
9627: }
1.208 brouard 9628: printf(" Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(stdout);
9629: fprintf(ficlog," Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 9630:
1.145 brouard 9631: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
9632: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
9633:
9634: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.208 brouard 9635: fprintf(ficrest,"\n#****** ");
9636: for(j=1;j<=cptcoveff;j++)
1.218 brouard 9637: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 9638: fprintf(ficrest,"******\n");
9639:
9640: fprintf(ficresstdeij,"\n#****** ");
9641: fprintf(ficrescveij,"\n#****** ");
9642: for(j=1;j<=cptcoveff;j++) {
1.218 brouard 9643: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9644: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 9645: }
9646: fprintf(ficresstdeij,"******\n");
9647: fprintf(ficrescveij,"******\n");
9648:
9649: fprintf(ficresvij,"\n#****** ");
9650: for(j=1;j<=cptcoveff;j++)
1.218 brouard 9651: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 9652: fprintf(ficresvij,"******\n");
9653:
9654: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
9655: oldm=oldms;savm=savms;
9656: printf(" cvevsij %d, ",k);
9657: fprintf(ficlog, " cvevsij %d, ",k);
9658: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
9659: printf(" end cvevsij \n ");
9660: fprintf(ficlog, " end cvevsij \n ");
9661:
9662: /*
9663: */
9664: /* goto endfree; */
9665:
9666: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
9667: pstamp(ficrest);
9668:
9669:
9670: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.219 ! brouard 9671: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
! 9672: cptcod= 0; /* To be deleted */
! 9673: printf("varevsij %d \n",vpopbased);
! 9674: fprintf(ficlog, "varevsij %d \n",vpopbased);
! 9675: 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 */
! 9676: 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 ");
! 9677: if(vpopbased==1)
! 9678: 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);
! 9679: else
! 9680: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
! 9681: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
! 9682: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
! 9683: fprintf(ficrest,"\n");
! 9684: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
! 9685: epj=vector(1,nlstate+1);
! 9686: printf("Computing age specific period (stable) prevalences in each health state \n");
! 9687: fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
! 9688: for(age=bage; age <=fage ;age++){
! 9689: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
! 9690: if (vpopbased==1) {
! 9691: if(mobilav ==0){
! 9692: for(i=1; i<=nlstate;i++)
! 9693: prlim[i][i]=probs[(int)age][i][k];
! 9694: }else{ /* mobilav */
! 9695: for(i=1; i<=nlstate;i++)
! 9696: prlim[i][i]=mobaverage[(int)age][i][k];
! 9697: }
! 9698: }
! 9699:
! 9700: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
! 9701: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
! 9702: /* printf(" age %4.0f ",age); */
! 9703: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
! 9704: for(i=1, epj[j]=0.;i <=nlstate;i++) {
! 9705: epj[j] += prlim[i][i]*eij[i][j][(int)age];
! 9706: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
! 9707: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
! 9708: }
! 9709: epj[nlstate+1] +=epj[j];
! 9710: }
! 9711: /* printf(" age %4.0f \n",age); */
! 9712:
! 9713: for(i=1, vepp=0.;i <=nlstate;i++)
! 9714: for(j=1;j <=nlstate;j++)
! 9715: vepp += vareij[i][j][(int)age];
! 9716: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
! 9717: for(j=1;j <=nlstate;j++){
! 9718: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
! 9719: }
! 9720: fprintf(ficrest,"\n");
! 9721: }
1.208 brouard 9722: } /* End vpopbased */
9723: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
9724: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
9725: free_vector(epj,1,nlstate+1);
9726: printf("done \n");fflush(stdout);
9727: fprintf(ficlog,"done\n");fflush(ficlog);
9728:
1.145 brouard 9729: /*}*/
1.208 brouard 9730: } /* End k */
1.126 brouard 9731: free_vector(weight,1,n);
1.145 brouard 9732: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 9733: free_imatrix(s,1,maxwav+1,1,n);
9734: free_matrix(anint,1,maxwav,1,n);
9735: free_matrix(mint,1,maxwav,1,n);
9736: free_ivector(cod,1,n);
9737: free_ivector(tab,1,NCOVMAX);
9738: fclose(ficresstdeij);
9739: fclose(ficrescveij);
9740: fclose(ficresvij);
9741: fclose(ficrest);
1.208 brouard 9742: printf("done Health expectancies\n");fflush(stdout);
9743: fprintf(ficlog,"done Health expectancies\n");fflush(ficlog);
1.126 brouard 9744: fclose(ficpar);
9745:
9746: /*------- Variance of period (stable) prevalence------*/
9747:
1.201 brouard 9748: strcpy(fileresvpl,"VPL_");
9749: strcat(fileresvpl,fileresu);
1.126 brouard 9750: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
9751: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
9752: exit(0);
9753: }
1.208 brouard 9754: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
9755: fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.126 brouard 9756:
1.145 brouard 9757: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
9758: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
9759:
9760: for (k=1; k <= (int) pow(2,cptcoveff); k++){
9761: fprintf(ficresvpl,"\n#****** ");
1.218 brouard 9762: for(j=1;j<=cptcoveff;j++)
9763: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9764: fprintf(ficresvpl,"******\n");
9765:
9766: varpl=matrix(1,nlstate,(int) bage, (int) fage);
9767: oldm=oldms;savm=savms;
9768: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
9769: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 9770: /*}*/
1.126 brouard 9771: }
1.218 brouard 9772:
1.126 brouard 9773: fclose(ficresvpl);
1.208 brouard 9774: printf("done variance-covariance of period prevalence\n");fflush(stdout);
9775: fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
1.126 brouard 9776:
9777: /*---------- End : free ----------------*/
1.219 ! brouard 9778: if (mobilav!=0 ||mobilavproj !=0)
! 9779: free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
1.218 brouard 9780: free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.126 brouard 9781: } /* mle==-3 arrives here for freeing */
1.164 brouard 9782: /* endfree:*/
1.141 brouard 9783: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 9784: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
9785: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
9786: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
9787: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
9788: free_matrix(covar,0,NCOVMAX,1,n);
9789: free_matrix(matcov,1,npar,1,npar);
1.203 brouard 9790: free_matrix(hess,1,npar,1,npar);
1.126 brouard 9791: /*free_vector(delti,1,npar);*/
9792: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
9793: free_matrix(agev,1,maxwav,1,imx);
9794: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
9795:
1.145 brouard 9796: free_ivector(ncodemax,1,NCOVMAX);
1.192 brouard 9797: free_ivector(ncodemaxwundef,1,NCOVMAX);
1.145 brouard 9798: free_ivector(Tvar,1,NCOVMAX);
9799: free_ivector(Tprod,1,NCOVMAX);
9800: free_ivector(Tvaraff,1,NCOVMAX);
9801: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 9802:
9803: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
1.200 brouard 9804: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 9805: fflush(fichtm);
9806: fflush(ficgp);
9807:
9808:
9809: if((nberr >0) || (nbwarn>0)){
1.216 brouard 9810: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
9811: 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 9812: }else{
9813: printf("End of Imach\n");
9814: fprintf(ficlog,"End of Imach\n");
9815: }
9816: printf("See log file on %s\n",filelog);
9817: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 9818: /*(void) gettimeofday(&end_time,&tzp);*/
9819: rend_time = time(NULL);
9820: end_time = *localtime(&rend_time);
9821: /* tml = *localtime(&end_time.tm_sec); */
9822: strcpy(strtend,asctime(&end_time));
1.126 brouard 9823: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
9824: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 9825: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 9826:
1.157 brouard 9827: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
9828: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
9829: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 9830: /* printf("Total time was %d uSec.\n", total_usecs);*/
9831: /* if(fileappend(fichtm,optionfilehtm)){ */
9832: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
9833: fclose(fichtm);
9834: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
9835: fclose(fichtmcov);
9836: fclose(ficgp);
9837: fclose(ficlog);
9838: /*------ End -----------*/
9839:
9840:
9841: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 9842: #ifdef WIN32
9843: if (_chdir(pathcd) != 0)
9844: printf("Can't move to directory %s!\n",path);
9845: if(_getcwd(pathcd,MAXLINE) > 0)
9846: #else
1.126 brouard 9847: if(chdir(pathcd) != 0)
1.184 brouard 9848: printf("Can't move to directory %s!\n", path);
9849: if (getcwd(pathcd, MAXLINE) > 0)
9850: #endif
1.126 brouard 9851: printf("Current directory %s!\n",pathcd);
9852: /*strcat(plotcmd,CHARSEPARATOR);*/
9853: sprintf(plotcmd,"gnuplot");
1.157 brouard 9854: #ifdef _WIN32
1.126 brouard 9855: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
9856: #endif
9857: if(!stat(plotcmd,&info)){
1.158 brouard 9858: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 9859: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 9860: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 9861: }else
9862: strcpy(pplotcmd,plotcmd);
1.157 brouard 9863: #ifdef __unix
1.126 brouard 9864: strcpy(plotcmd,GNUPLOTPROGRAM);
9865: if(!stat(plotcmd,&info)){
1.158 brouard 9866: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 9867: }else
9868: strcpy(pplotcmd,plotcmd);
9869: #endif
9870: }else
9871: strcpy(pplotcmd,plotcmd);
9872:
9873: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 9874: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 9875:
9876: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 9877: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 9878: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 9879: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 9880: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 9881: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 9882: }
1.158 brouard 9883: printf(" Successful, please wait...");
1.126 brouard 9884: while (z[0] != 'q') {
9885: /* chdir(path); */
1.154 brouard 9886: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 9887: scanf("%s",z);
9888: /* if (z[0] == 'c') system("./imach"); */
9889: if (z[0] == 'e') {
1.158 brouard 9890: #ifdef __APPLE__
1.152 brouard 9891: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 9892: #elif __linux
9893: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 9894: #else
1.152 brouard 9895: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 9896: #endif
9897: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
9898: system(pplotcmd);
1.126 brouard 9899: }
9900: else if (z[0] == 'g') system(plotcmd);
9901: else if (z[0] == 'q') exit(0);
9902: }
9903: end:
9904: while (z[0] != 'q') {
1.195 brouard 9905: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 9906: scanf("%s",z);
9907: }
9908: }
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