Annotation of imach/src/imach.c, revision 1.211
1.211 ! brouard 1: /* $Id: imach.c,v 1.210 2015/11/18 17:41:20 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.211 ! brouard 4: Revision 1.210 2015/11/18 17:41:20 brouard
! 5: Summary: Start working on projected prevalences
! 6:
1.210 brouard 7: Revision 1.209 2015/11/17 22:12:03 brouard
8: Summary: Adding ftolpl parameter
9: Author: N Brouard
10:
11: We had difficulties to get smoothed confidence intervals. It was due
12: to the period prevalence which wasn't computed accurately. The inner
13: parameter ftolpl is now an outer parameter of the .imach parameter
14: file after estepm. If ftolpl is small 1.e-4 and estepm too,
15: computation are long.
16:
1.209 brouard 17: Revision 1.208 2015/11/17 14:31:57 brouard
18: Summary: temporary
19:
1.208 brouard 20: Revision 1.207 2015/10/27 17:36:57 brouard
21: *** empty log message ***
22:
1.207 brouard 23: Revision 1.206 2015/10/24 07:14:11 brouard
24: *** empty log message ***
25:
1.206 brouard 26: Revision 1.205 2015/10/23 15:50:53 brouard
27: Summary: 0.98r3 some clarification for graphs on likelihood contributions
28:
1.205 brouard 29: Revision 1.204 2015/10/01 16:20:26 brouard
30: Summary: Some new graphs of contribution to likelihood
31:
1.204 brouard 32: Revision 1.203 2015/09/30 17:45:14 brouard
33: Summary: looking at better estimation of the hessian
34:
35: Also a better criteria for convergence to the period prevalence And
36: therefore adding the number of years needed to converge. (The
37: prevalence in any alive state shold sum to one
38:
1.203 brouard 39: Revision 1.202 2015/09/22 19:45:16 brouard
40: Summary: Adding some overall graph on contribution to likelihood. Might change
41:
1.202 brouard 42: Revision 1.201 2015/09/15 17:34:58 brouard
43: Summary: 0.98r0
44:
45: - Some new graphs like suvival functions
46: - Some bugs fixed like model=1+age+V2.
47:
1.201 brouard 48: Revision 1.200 2015/09/09 16:53:55 brouard
49: Summary: Big bug thanks to Flavia
50:
51: Even model=1+age+V2. did not work anymore
52:
1.200 brouard 53: Revision 1.199 2015/09/07 14:09:23 brouard
54: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
55:
1.199 brouard 56: Revision 1.198 2015/09/03 07:14:39 brouard
57: Summary: 0.98q5 Flavia
58:
1.198 brouard 59: Revision 1.197 2015/09/01 18:24:39 brouard
60: *** empty log message ***
61:
1.197 brouard 62: Revision 1.196 2015/08/18 23:17:52 brouard
63: Summary: 0.98q5
64:
1.196 brouard 65: Revision 1.195 2015/08/18 16:28:39 brouard
66: Summary: Adding a hack for testing purpose
67:
68: After reading the title, ftol and model lines, if the comment line has
69: a q, starting with #q, the answer at the end of the run is quit. It
70: permits to run test files in batch with ctest. The former workaround was
71: $ echo q | imach foo.imach
72:
1.195 brouard 73: Revision 1.194 2015/08/18 13:32:00 brouard
74: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
75:
1.194 brouard 76: Revision 1.193 2015/08/04 07:17:42 brouard
77: Summary: 0.98q4
78:
1.193 brouard 79: Revision 1.192 2015/07/16 16:49:02 brouard
80: Summary: Fixing some outputs
81:
1.192 brouard 82: Revision 1.191 2015/07/14 10:00:33 brouard
83: Summary: Some fixes
84:
1.191 brouard 85: Revision 1.190 2015/05/05 08:51:13 brouard
86: Summary: Adding digits in output parameters (7 digits instead of 6)
87:
88: Fix 1+age+.
89:
1.190 brouard 90: Revision 1.189 2015/04/30 14:45:16 brouard
91: Summary: 0.98q2
92:
1.189 brouard 93: Revision 1.188 2015/04/30 08:27:53 brouard
94: *** empty log message ***
95:
1.188 brouard 96: Revision 1.187 2015/04/29 09:11:15 brouard
97: *** empty log message ***
98:
1.187 brouard 99: Revision 1.186 2015/04/23 12:01:52 brouard
100: Summary: V1*age is working now, version 0.98q1
101:
102: Some codes had been disabled in order to simplify and Vn*age was
103: working in the optimization phase, ie, giving correct MLE parameters,
104: but, as usual, outputs were not correct and program core dumped.
105:
1.186 brouard 106: Revision 1.185 2015/03/11 13:26:42 brouard
107: Summary: Inclusion of compile and links command line for Intel Compiler
108:
1.185 brouard 109: Revision 1.184 2015/03/11 11:52:39 brouard
110: Summary: Back from Windows 8. Intel Compiler
111:
1.184 brouard 112: Revision 1.183 2015/03/10 20:34:32 brouard
113: Summary: 0.98q0, trying with directest, mnbrak fixed
114:
115: We use directest instead of original Powell test; probably no
116: incidence on the results, but better justifications;
117: We fixed Numerical Recipes mnbrak routine which was wrong and gave
118: wrong results.
119:
1.183 brouard 120: Revision 1.182 2015/02/12 08:19:57 brouard
121: Summary: Trying to keep directest which seems simpler and more general
122: Author: Nicolas Brouard
123:
1.182 brouard 124: Revision 1.181 2015/02/11 23:22:24 brouard
125: Summary: Comments on Powell added
126:
127: Author:
128:
1.181 brouard 129: Revision 1.180 2015/02/11 17:33:45 brouard
130: Summary: Finishing move from main to function (hpijx and prevalence_limit)
131:
1.180 brouard 132: Revision 1.179 2015/01/04 09:57:06 brouard
133: Summary: back to OS/X
134:
1.179 brouard 135: Revision 1.178 2015/01/04 09:35:48 brouard
136: *** empty log message ***
137:
1.178 brouard 138: Revision 1.177 2015/01/03 18:40:56 brouard
139: Summary: Still testing ilc32 on OSX
140:
1.177 brouard 141: Revision 1.176 2015/01/03 16:45:04 brouard
142: *** empty log message ***
143:
1.176 brouard 144: Revision 1.175 2015/01/03 16:33:42 brouard
145: *** empty log message ***
146:
1.175 brouard 147: Revision 1.174 2015/01/03 16:15:49 brouard
148: Summary: Still in cross-compilation
149:
1.174 brouard 150: Revision 1.173 2015/01/03 12:06:26 brouard
151: Summary: trying to detect cross-compilation
152:
1.173 brouard 153: Revision 1.172 2014/12/27 12:07:47 brouard
154: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
155:
1.172 brouard 156: Revision 1.171 2014/12/23 13:26:59 brouard
157: Summary: Back from Visual C
158:
159: Still problem with utsname.h on Windows
160:
1.171 brouard 161: Revision 1.170 2014/12/23 11:17:12 brouard
162: Summary: Cleaning some \%% back to %%
163:
164: The escape was mandatory for a specific compiler (which one?), but too many warnings.
165:
1.170 brouard 166: Revision 1.169 2014/12/22 23:08:31 brouard
167: Summary: 0.98p
168:
169: Outputs some informations on compiler used, OS etc. Testing on different platforms.
170:
1.169 brouard 171: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 172: Summary: update
1.169 brouard 173:
1.168 brouard 174: Revision 1.167 2014/12/22 13:50:56 brouard
175: Summary: Testing uname and compiler version and if compiled 32 or 64
176:
177: Testing on Linux 64
178:
1.167 brouard 179: Revision 1.166 2014/12/22 11:40:47 brouard
180: *** empty log message ***
181:
1.166 brouard 182: Revision 1.165 2014/12/16 11:20:36 brouard
183: Summary: After compiling on Visual C
184:
185: * imach.c (Module): Merging 1.61 to 1.162
186:
1.165 brouard 187: Revision 1.164 2014/12/16 10:52:11 brouard
188: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
189:
190: * imach.c (Module): Merging 1.61 to 1.162
191:
1.164 brouard 192: Revision 1.163 2014/12/16 10:30:11 brouard
193: * imach.c (Module): Merging 1.61 to 1.162
194:
1.163 brouard 195: Revision 1.162 2014/09/25 11:43:39 brouard
196: Summary: temporary backup 0.99!
197:
1.162 brouard 198: Revision 1.1 2014/09/16 11:06:58 brouard
199: Summary: With some code (wrong) for nlopt
200:
201: Author:
202:
203: Revision 1.161 2014/09/15 20:41:41 brouard
204: Summary: Problem with macro SQR on Intel compiler
205:
1.161 brouard 206: Revision 1.160 2014/09/02 09:24:05 brouard
207: *** empty log message ***
208:
1.160 brouard 209: Revision 1.159 2014/09/01 10:34:10 brouard
210: Summary: WIN32
211: Author: Brouard
212:
1.159 brouard 213: Revision 1.158 2014/08/27 17:11:51 brouard
214: *** empty log message ***
215:
1.158 brouard 216: Revision 1.157 2014/08/27 16:26:55 brouard
217: Summary: Preparing windows Visual studio version
218: Author: Brouard
219:
220: In order to compile on Visual studio, time.h is now correct and time_t
221: and tm struct should be used. difftime should be used but sometimes I
222: just make the differences in raw time format (time(&now).
223: Trying to suppress #ifdef LINUX
224: Add xdg-open for __linux in order to open default browser.
225:
1.157 brouard 226: Revision 1.156 2014/08/25 20:10:10 brouard
227: *** empty log message ***
228:
1.156 brouard 229: Revision 1.155 2014/08/25 18:32:34 brouard
230: Summary: New compile, minor changes
231: Author: Brouard
232:
1.155 brouard 233: Revision 1.154 2014/06/20 17:32:08 brouard
234: Summary: Outputs now all graphs of convergence to period prevalence
235:
1.154 brouard 236: Revision 1.153 2014/06/20 16:45:46 brouard
237: Summary: If 3 live state, convergence to period prevalence on same graph
238: Author: Brouard
239:
1.153 brouard 240: Revision 1.152 2014/06/18 17:54:09 brouard
241: Summary: open browser, use gnuplot on same dir than imach if not found in the path
242:
1.152 brouard 243: Revision 1.151 2014/06/18 16:43:30 brouard
244: *** empty log message ***
245:
1.151 brouard 246: Revision 1.150 2014/06/18 16:42:35 brouard
247: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
248: Author: brouard
249:
1.150 brouard 250: Revision 1.149 2014/06/18 15:51:14 brouard
251: Summary: Some fixes in parameter files errors
252: Author: Nicolas Brouard
253:
1.149 brouard 254: Revision 1.148 2014/06/17 17:38:48 brouard
255: Summary: Nothing new
256: Author: Brouard
257:
258: Just a new packaging for OS/X version 0.98nS
259:
1.148 brouard 260: Revision 1.147 2014/06/16 10:33:11 brouard
261: *** empty log message ***
262:
1.147 brouard 263: Revision 1.146 2014/06/16 10:20:28 brouard
264: Summary: Merge
265: Author: Brouard
266:
267: Merge, before building revised version.
268:
1.146 brouard 269: Revision 1.145 2014/06/10 21:23:15 brouard
270: Summary: Debugging with valgrind
271: Author: Nicolas Brouard
272:
273: Lot of changes in order to output the results with some covariates
274: After the Edimburgh REVES conference 2014, it seems mandatory to
275: improve the code.
276: No more memory valgrind error but a lot has to be done in order to
277: continue the work of splitting the code into subroutines.
278: Also, decodemodel has been improved. Tricode is still not
279: optimal. nbcode should be improved. Documentation has been added in
280: the source code.
281:
1.144 brouard 282: Revision 1.143 2014/01/26 09:45:38 brouard
283: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
284:
285: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
286: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
287:
1.143 brouard 288: Revision 1.142 2014/01/26 03:57:36 brouard
289: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
290:
291: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
292:
1.142 brouard 293: Revision 1.141 2014/01/26 02:42:01 brouard
294: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
295:
1.141 brouard 296: Revision 1.140 2011/09/02 10:37:54 brouard
297: Summary: times.h is ok with mingw32 now.
298:
1.140 brouard 299: Revision 1.139 2010/06/14 07:50:17 brouard
300: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
301: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
302:
1.139 brouard 303: Revision 1.138 2010/04/30 18:19:40 brouard
304: *** empty log message ***
305:
1.138 brouard 306: Revision 1.137 2010/04/29 18:11:38 brouard
307: (Module): Checking covariates for more complex models
308: than V1+V2. A lot of change to be done. Unstable.
309:
1.137 brouard 310: Revision 1.136 2010/04/26 20:30:53 brouard
311: (Module): merging some libgsl code. Fixing computation
312: of likelione (using inter/intrapolation if mle = 0) in order to
313: get same likelihood as if mle=1.
314: Some cleaning of code and comments added.
315:
1.136 brouard 316: Revision 1.135 2009/10/29 15:33:14 brouard
317: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
318:
1.135 brouard 319: Revision 1.134 2009/10/29 13:18:53 brouard
320: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
321:
1.134 brouard 322: Revision 1.133 2009/07/06 10:21:25 brouard
323: just nforces
324:
1.133 brouard 325: Revision 1.132 2009/07/06 08:22:05 brouard
326: Many tings
327:
1.132 brouard 328: Revision 1.131 2009/06/20 16:22:47 brouard
329: Some dimensions resccaled
330:
1.131 brouard 331: Revision 1.130 2009/05/26 06:44:34 brouard
332: (Module): Max Covariate is now set to 20 instead of 8. A
333: lot of cleaning with variables initialized to 0. Trying to make
334: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
335:
1.130 brouard 336: Revision 1.129 2007/08/31 13:49:27 lievre
337: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
338:
1.129 lievre 339: Revision 1.128 2006/06/30 13:02:05 brouard
340: (Module): Clarifications on computing e.j
341:
1.128 brouard 342: Revision 1.127 2006/04/28 18:11:50 brouard
343: (Module): Yes the sum of survivors was wrong since
344: imach-114 because nhstepm was no more computed in the age
345: loop. Now we define nhstepma in the age loop.
346: (Module): In order to speed up (in case of numerous covariates) we
347: compute health expectancies (without variances) in a first step
348: and then all the health expectancies with variances or standard
349: deviation (needs data from the Hessian matrices) which slows the
350: computation.
351: In the future we should be able to stop the program is only health
352: expectancies and graph are needed without standard deviations.
353:
1.127 brouard 354: Revision 1.126 2006/04/28 17:23:28 brouard
355: (Module): Yes the sum of survivors was wrong since
356: imach-114 because nhstepm was no more computed in the age
357: loop. Now we define nhstepma in the age loop.
358: Version 0.98h
359:
1.126 brouard 360: Revision 1.125 2006/04/04 15:20:31 lievre
361: Errors in calculation of health expectancies. Age was not initialized.
362: Forecasting file added.
363:
364: Revision 1.124 2006/03/22 17:13:53 lievre
365: Parameters are printed with %lf instead of %f (more numbers after the comma).
366: The log-likelihood is printed in the log file
367:
368: Revision 1.123 2006/03/20 10:52:43 brouard
369: * imach.c (Module): <title> changed, corresponds to .htm file
370: name. <head> headers where missing.
371:
372: * imach.c (Module): Weights can have a decimal point as for
373: English (a comma might work with a correct LC_NUMERIC environment,
374: otherwise the weight is truncated).
375: Modification of warning when the covariates values are not 0 or
376: 1.
377: Version 0.98g
378:
379: Revision 1.122 2006/03/20 09:45:41 brouard
380: (Module): Weights can have a decimal point as for
381: English (a comma might work with a correct LC_NUMERIC environment,
382: otherwise the weight is truncated).
383: Modification of warning when the covariates values are not 0 or
384: 1.
385: Version 0.98g
386:
387: Revision 1.121 2006/03/16 17:45:01 lievre
388: * imach.c (Module): Comments concerning covariates added
389:
390: * imach.c (Module): refinements in the computation of lli if
391: status=-2 in order to have more reliable computation if stepm is
392: not 1 month. Version 0.98f
393:
394: Revision 1.120 2006/03/16 15:10:38 lievre
395: (Module): refinements in the computation of lli if
396: status=-2 in order to have more reliable computation if stepm is
397: not 1 month. Version 0.98f
398:
399: Revision 1.119 2006/03/15 17:42:26 brouard
400: (Module): Bug if status = -2, the loglikelihood was
401: computed as likelihood omitting the logarithm. Version O.98e
402:
403: Revision 1.118 2006/03/14 18:20:07 brouard
404: (Module): varevsij Comments added explaining the second
405: table of variances if popbased=1 .
406: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
407: (Module): Function pstamp added
408: (Module): Version 0.98d
409:
410: Revision 1.117 2006/03/14 17:16:22 brouard
411: (Module): varevsij Comments added explaining the second
412: table of variances if popbased=1 .
413: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
414: (Module): Function pstamp added
415: (Module): Version 0.98d
416:
417: Revision 1.116 2006/03/06 10:29:27 brouard
418: (Module): Variance-covariance wrong links and
419: varian-covariance of ej. is needed (Saito).
420:
421: Revision 1.115 2006/02/27 12:17:45 brouard
422: (Module): One freematrix added in mlikeli! 0.98c
423:
424: Revision 1.114 2006/02/26 12:57:58 brouard
425: (Module): Some improvements in processing parameter
426: filename with strsep.
427:
428: Revision 1.113 2006/02/24 14:20:24 brouard
429: (Module): Memory leaks checks with valgrind and:
430: datafile was not closed, some imatrix were not freed and on matrix
431: allocation too.
432:
433: Revision 1.112 2006/01/30 09:55:26 brouard
434: (Module): Back to gnuplot.exe instead of wgnuplot.exe
435:
436: Revision 1.111 2006/01/25 20:38:18 brouard
437: (Module): Lots of cleaning and bugs added (Gompertz)
438: (Module): Comments can be added in data file. Missing date values
439: can be a simple dot '.'.
440:
441: Revision 1.110 2006/01/25 00:51:50 brouard
442: (Module): Lots of cleaning and bugs added (Gompertz)
443:
444: Revision 1.109 2006/01/24 19:37:15 brouard
445: (Module): Comments (lines starting with a #) are allowed in data.
446:
447: Revision 1.108 2006/01/19 18:05:42 lievre
448: Gnuplot problem appeared...
449: To be fixed
450:
451: Revision 1.107 2006/01/19 16:20:37 brouard
452: Test existence of gnuplot in imach path
453:
454: Revision 1.106 2006/01/19 13:24:36 brouard
455: Some cleaning and links added in html output
456:
457: Revision 1.105 2006/01/05 20:23:19 lievre
458: *** empty log message ***
459:
460: Revision 1.104 2005/09/30 16:11:43 lievre
461: (Module): sump fixed, loop imx fixed, and simplifications.
462: (Module): If the status is missing at the last wave but we know
463: that the person is alive, then we can code his/her status as -2
464: (instead of missing=-1 in earlier versions) and his/her
465: contributions to the likelihood is 1 - Prob of dying from last
466: health status (= 1-p13= p11+p12 in the easiest case of somebody in
467: the healthy state at last known wave). Version is 0.98
468:
469: Revision 1.103 2005/09/30 15:54:49 lievre
470: (Module): sump fixed, loop imx fixed, and simplifications.
471:
472: Revision 1.102 2004/09/15 17:31:30 brouard
473: Add the possibility to read data file including tab characters.
474:
475: Revision 1.101 2004/09/15 10:38:38 brouard
476: Fix on curr_time
477:
478: Revision 1.100 2004/07/12 18:29:06 brouard
479: Add version for Mac OS X. Just define UNIX in Makefile
480:
481: Revision 1.99 2004/06/05 08:57:40 brouard
482: *** empty log message ***
483:
484: Revision 1.98 2004/05/16 15:05:56 brouard
485: New version 0.97 . First attempt to estimate force of mortality
486: directly from the data i.e. without the need of knowing the health
487: state at each age, but using a Gompertz model: log u =a + b*age .
488: This is the basic analysis of mortality and should be done before any
489: other analysis, in order to test if the mortality estimated from the
490: cross-longitudinal survey is different from the mortality estimated
491: from other sources like vital statistic data.
492:
493: The same imach parameter file can be used but the option for mle should be -3.
494:
1.133 brouard 495: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 496: former routines in order to include the new code within the former code.
497:
498: The output is very simple: only an estimate of the intercept and of
499: the slope with 95% confident intervals.
500:
501: Current limitations:
502: A) Even if you enter covariates, i.e. with the
503: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
504: B) There is no computation of Life Expectancy nor Life Table.
505:
506: Revision 1.97 2004/02/20 13:25:42 lievre
507: Version 0.96d. Population forecasting command line is (temporarily)
508: suppressed.
509:
510: Revision 1.96 2003/07/15 15:38:55 brouard
511: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
512: rewritten within the same printf. Workaround: many printfs.
513:
514: Revision 1.95 2003/07/08 07:54:34 brouard
515: * imach.c (Repository):
516: (Repository): Using imachwizard code to output a more meaningful covariance
517: matrix (cov(a12,c31) instead of numbers.
518:
519: Revision 1.94 2003/06/27 13:00:02 brouard
520: Just cleaning
521:
522: Revision 1.93 2003/06/25 16:33:55 brouard
523: (Module): On windows (cygwin) function asctime_r doesn't
524: exist so I changed back to asctime which exists.
525: (Module): Version 0.96b
526:
527: Revision 1.92 2003/06/25 16:30:45 brouard
528: (Module): On windows (cygwin) function asctime_r doesn't
529: exist so I changed back to asctime which exists.
530:
531: Revision 1.91 2003/06/25 15:30:29 brouard
532: * imach.c (Repository): Duplicated warning errors corrected.
533: (Repository): Elapsed time after each iteration is now output. It
534: helps to forecast when convergence will be reached. Elapsed time
535: is stamped in powell. We created a new html file for the graphs
536: concerning matrix of covariance. It has extension -cov.htm.
537:
538: Revision 1.90 2003/06/24 12:34:15 brouard
539: (Module): Some bugs corrected for windows. Also, when
540: mle=-1 a template is output in file "or"mypar.txt with the design
541: of the covariance matrix to be input.
542:
543: Revision 1.89 2003/06/24 12:30:52 brouard
544: (Module): Some bugs corrected for windows. Also, when
545: mle=-1 a template is output in file "or"mypar.txt with the design
546: of the covariance matrix to be input.
547:
548: Revision 1.88 2003/06/23 17:54:56 brouard
549: * 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.
550:
551: Revision 1.87 2003/06/18 12:26:01 brouard
552: Version 0.96
553:
554: Revision 1.86 2003/06/17 20:04:08 brouard
555: (Module): Change position of html and gnuplot routines and added
556: routine fileappend.
557:
558: Revision 1.85 2003/06/17 13:12:43 brouard
559: * imach.c (Repository): Check when date of death was earlier that
560: current date of interview. It may happen when the death was just
561: prior to the death. In this case, dh was negative and likelihood
562: was wrong (infinity). We still send an "Error" but patch by
563: assuming that the date of death was just one stepm after the
564: interview.
565: (Repository): Because some people have very long ID (first column)
566: we changed int to long in num[] and we added a new lvector for
567: memory allocation. But we also truncated to 8 characters (left
568: truncation)
569: (Repository): No more line truncation errors.
570:
571: Revision 1.84 2003/06/13 21:44:43 brouard
572: * imach.c (Repository): Replace "freqsummary" at a correct
573: place. It differs from routine "prevalence" which may be called
574: many times. Probs is memory consuming and must be used with
575: parcimony.
576: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
577:
578: Revision 1.83 2003/06/10 13:39:11 lievre
579: *** empty log message ***
580:
581: Revision 1.82 2003/06/05 15:57:20 brouard
582: Add log in imach.c and fullversion number is now printed.
583:
584: */
585: /*
586: Interpolated Markov Chain
587:
588: Short summary of the programme:
589:
590: This program computes Healthy Life Expectancies from
591: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
592: first survey ("cross") where individuals from different ages are
593: interviewed on their health status or degree of disability (in the
594: case of a health survey which is our main interest) -2- at least a
595: second wave of interviews ("longitudinal") which measure each change
596: (if any) in individual health status. Health expectancies are
597: computed from the time spent in each health state according to a
598: model. More health states you consider, more time is necessary to reach the
599: Maximum Likelihood of the parameters involved in the model. The
600: simplest model is the multinomial logistic model where pij is the
601: probability to be observed in state j at the second wave
602: conditional to be observed in state i at the first wave. Therefore
603: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
604: 'age' is age and 'sex' is a covariate. If you want to have a more
605: complex model than "constant and age", you should modify the program
606: where the markup *Covariates have to be included here again* invites
607: you to do it. More covariates you add, slower the
608: convergence.
609:
610: The advantage of this computer programme, compared to a simple
611: multinomial logistic model, is clear when the delay between waves is not
612: identical for each individual. Also, if a individual missed an
613: intermediate interview, the information is lost, but taken into
614: account using an interpolation or extrapolation.
615:
616: hPijx is the probability to be observed in state i at age x+h
617: conditional to the observed state i at age x. The delay 'h' can be
618: split into an exact number (nh*stepm) of unobserved intermediate
619: states. This elementary transition (by month, quarter,
620: semester or year) is modelled as a multinomial logistic. The hPx
621: matrix is simply the matrix product of nh*stepm elementary matrices
622: and the contribution of each individual to the likelihood is simply
623: hPijx.
624:
625: Also this programme outputs the covariance matrix of the parameters but also
626: of the life expectancies. It also computes the period (stable) prevalence.
627:
1.133 brouard 628: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
629: Institut national d'études démographiques, Paris.
1.126 brouard 630: This software have been partly granted by Euro-REVES, a concerted action
631: from the European Union.
632: It is copyrighted identically to a GNU software product, ie programme and
633: software can be distributed freely for non commercial use. Latest version
634: can be accessed at http://euroreves.ined.fr/imach .
635:
636: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
637: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
638:
639: **********************************************************************/
640: /*
641: main
642: read parameterfile
643: read datafile
644: concatwav
645: freqsummary
646: if (mle >= 1)
647: mlikeli
648: print results files
649: if mle==1
650: computes hessian
651: read end of parameter file: agemin, agemax, bage, fage, estepm
652: begin-prev-date,...
653: open gnuplot file
654: open html file
1.145 brouard 655: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
656: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
657: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
658: freexexit2 possible for memory heap.
659:
660: h Pij x | pij_nom ficrestpij
661: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
662: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
663: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
664:
665: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
666: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
667: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
668: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
669: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
670:
1.126 brouard 671: forecasting if prevfcast==1 prevforecast call prevalence()
672: health expectancies
673: Variance-covariance of DFLE
674: prevalence()
675: movingaverage()
676: varevsij()
677: if popbased==1 varevsij(,popbased)
678: total life expectancies
679: Variance of period (stable) prevalence
680: end
681: */
682:
1.187 brouard 683: /* #define DEBUG */
684: /* #define DEBUGBRENT */
1.203 brouard 685: /* #define DEBUGLINMIN */
686: /* #define DEBUGHESS */
687: #define DEBUGHESSIJ
688: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan)*\/ */
1.165 brouard 689: #define POWELL /* Instead of NLOPT */
1.192 brouard 690: #define POWELLF1F3 /* Skip test */
1.186 brouard 691: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
692: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 693:
694: #include <math.h>
695: #include <stdio.h>
696: #include <stdlib.h>
697: #include <string.h>
1.159 brouard 698:
699: #ifdef _WIN32
700: #include <io.h>
1.172 brouard 701: #include <windows.h>
702: #include <tchar.h>
1.159 brouard 703: #else
1.126 brouard 704: #include <unistd.h>
1.159 brouard 705: #endif
1.126 brouard 706:
707: #include <limits.h>
708: #include <sys/types.h>
1.171 brouard 709:
710: #if defined(__GNUC__)
711: #include <sys/utsname.h> /* Doesn't work on Windows */
712: #endif
713:
1.126 brouard 714: #include <sys/stat.h>
715: #include <errno.h>
1.159 brouard 716: /* extern int errno; */
1.126 brouard 717:
1.157 brouard 718: /* #ifdef LINUX */
719: /* #include <time.h> */
720: /* #include "timeval.h" */
721: /* #else */
722: /* #include <sys/time.h> */
723: /* #endif */
724:
1.126 brouard 725: #include <time.h>
726:
1.136 brouard 727: #ifdef GSL
728: #include <gsl/gsl_errno.h>
729: #include <gsl/gsl_multimin.h>
730: #endif
731:
1.167 brouard 732:
1.162 brouard 733: #ifdef NLOPT
734: #include <nlopt.h>
735: typedef struct {
736: double (* function)(double [] );
737: } myfunc_data ;
738: #endif
739:
1.126 brouard 740: /* #include <libintl.h> */
741: /* #define _(String) gettext (String) */
742:
1.141 brouard 743: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 744:
745: #define GNUPLOTPROGRAM "gnuplot"
746: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
747: #define FILENAMELENGTH 132
748:
749: #define GLOCK_ERROR_NOPATH -1 /* empty path */
750: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
751:
1.144 brouard 752: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
753: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 754:
755: #define NINTERVMAX 8
1.144 brouard 756: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
757: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
758: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 759: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 ! brouard 760: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
! 761: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.126 brouard 762: #define MAXN 20000
1.144 brouard 763: #define YEARM 12. /**< Number of months per year */
1.126 brouard 764: #define AGESUP 130
765: #define AGEBASE 40
1.194 brouard 766: #define AGEOVERFLOW 1.e20
1.164 brouard 767: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 768: #ifdef _WIN32
769: #define DIRSEPARATOR '\\'
770: #define CHARSEPARATOR "\\"
771: #define ODIRSEPARATOR '/'
772: #else
1.126 brouard 773: #define DIRSEPARATOR '/'
774: #define CHARSEPARATOR "/"
775: #define ODIRSEPARATOR '\\'
776: #endif
777:
1.211 ! brouard 778: /* $Id: imach.c,v 1.210 2015/11/18 17:41:20 brouard Exp $ */
1.126 brouard 779: /* $State: Exp $ */
1.196 brouard 780: #include "version.h"
781: char version[]=__IMACH_VERSION__;
1.204 brouard 782: 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";
1.211 ! brouard 783: char fullversion[]="$Revision: 1.210 $ $Date: 2015/11/18 17:41:20 $";
1.126 brouard 784: char strstart[80];
785: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 786: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 787: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 788: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
789: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
790: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
791: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
792: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
793: int cptcovprodnoage=0; /**< Number of covariate products without age */
794: int cptcoveff=0; /* Total number of covariates to vary for printing results */
795: int cptcov=0; /* Working variable */
1.126 brouard 796: int npar=NPARMAX;
797: int nlstate=2; /* Number of live states */
798: int ndeath=1; /* Number of dead states */
1.130 brouard 799: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 800: int popbased=0;
801:
802: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 803: int maxwav=0; /* Maxim number of waves */
804: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
805: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
806: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 807: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 808: int mle=1, weightopt=0;
1.126 brouard 809: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
810: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
811: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
812: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 813: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 814: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 815: double **matprod2(); /* test */
1.126 brouard 816: double **oldm, **newm, **savm; /* Working pointers to matrices */
817: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 818: /*FILE *fic ; */ /* Used in readdata only */
819: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 820: FILE *ficlog, *ficrespow;
1.130 brouard 821: int globpr=0; /* Global variable for printing or not */
1.126 brouard 822: double fretone; /* Only one call to likelihood */
1.130 brouard 823: long ipmx=0; /* Number of contributions */
1.126 brouard 824: double sw; /* Sum of weights */
825: char filerespow[FILENAMELENGTH];
826: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
827: FILE *ficresilk;
828: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
829: FILE *ficresprobmorprev;
830: FILE *fichtm, *fichtmcov; /* Html File */
831: FILE *ficreseij;
832: char filerese[FILENAMELENGTH];
833: FILE *ficresstdeij;
834: char fileresstde[FILENAMELENGTH];
835: FILE *ficrescveij;
836: char filerescve[FILENAMELENGTH];
837: FILE *ficresvij;
838: char fileresv[FILENAMELENGTH];
839: FILE *ficresvpl;
840: char fileresvpl[FILENAMELENGTH];
841: char title[MAXLINE];
842: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
843: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
844: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
845: char command[FILENAMELENGTH];
846: int outcmd=0;
847:
848: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 849: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 850: char filelog[FILENAMELENGTH]; /* Log file */
851: char filerest[FILENAMELENGTH];
852: char fileregp[FILENAMELENGTH];
853: char popfile[FILENAMELENGTH];
854:
855: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
856:
1.157 brouard 857: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
858: /* struct timezone tzp; */
859: /* extern int gettimeofday(); */
860: struct tm tml, *gmtime(), *localtime();
861:
862: extern time_t time();
863:
864: struct tm start_time, end_time, curr_time, last_time, forecast_time;
865: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
866: struct tm tm;
867:
1.126 brouard 868: char strcurr[80], strfor[80];
869:
870: char *endptr;
871: long lval;
872: double dval;
873:
874: #define NR_END 1
875: #define FREE_ARG char*
876: #define FTOL 1.0e-10
877:
878: #define NRANSI
879: #define ITMAX 200
880:
881: #define TOL 2.0e-4
882:
883: #define CGOLD 0.3819660
884: #define ZEPS 1.0e-10
885: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
886:
887: #define GOLD 1.618034
888: #define GLIMIT 100.0
889: #define TINY 1.0e-20
890:
891: static double maxarg1,maxarg2;
892: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
893: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
894:
895: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
896: #define rint(a) floor(a+0.5)
1.166 brouard 897: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 898: #define mytinydouble 1.0e-16
1.166 brouard 899: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
900: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
901: /* static double dsqrarg; */
902: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 903: static double sqrarg;
904: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
905: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
906: int agegomp= AGEGOMP;
907:
908: int imx;
909: int stepm=1;
910: /* Stepm, step in month: minimum step interpolation*/
911:
912: int estepm;
913: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
914:
915: int m,nb;
916: long *num;
1.197 brouard 917: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 918: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
919: covariate for which somebody answered excluding
920: undefined. Usually 2: 0 and 1. */
921: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
922: covariate for which somebody answered including
923: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 924: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
925: double **pmmij, ***probs;
926: double *ageexmed,*agecens;
927: double dateintmean=0;
928:
929: double *weight;
930: int **s; /* Status */
1.141 brouard 931: double *agedc;
1.145 brouard 932: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 933: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 934: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 935: double idx;
936: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.197 brouard 937: int *Tage;
1.145 brouard 938: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 939: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.141 brouard 940: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 941: double *lsurv, *lpop, *tpop;
942:
1.143 brouard 943: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
944: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 945:
946: /**************** split *************************/
947: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
948: {
949: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
950: the name of the file (name), its extension only (ext) and its first part of the name (finame)
951: */
952: char *ss; /* pointer */
1.186 brouard 953: int l1=0, l2=0; /* length counters */
1.126 brouard 954:
955: l1 = strlen(path ); /* length of path */
956: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
957: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
958: if ( ss == NULL ) { /* no directory, so determine current directory */
959: strcpy( name, path ); /* we got the fullname name because no directory */
960: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
961: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
962: /* get current working directory */
963: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 964: #ifdef WIN32
965: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
966: #else
967: if (getcwd(dirc, FILENAME_MAX) == NULL) {
968: #endif
1.126 brouard 969: return( GLOCK_ERROR_GETCWD );
970: }
971: /* got dirc from getcwd*/
972: printf(" DIRC = %s \n",dirc);
1.205 brouard 973: } else { /* strip directory from path */
1.126 brouard 974: ss++; /* after this, the filename */
975: l2 = strlen( ss ); /* length of filename */
976: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
977: strcpy( name, ss ); /* save file name */
978: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 979: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 980: printf(" DIRC2 = %s \n",dirc);
981: }
982: /* We add a separator at the end of dirc if not exists */
983: l1 = strlen( dirc ); /* length of directory */
984: if( dirc[l1-1] != DIRSEPARATOR ){
985: dirc[l1] = DIRSEPARATOR;
986: dirc[l1+1] = 0;
987: printf(" DIRC3 = %s \n",dirc);
988: }
989: ss = strrchr( name, '.' ); /* find last / */
990: if (ss >0){
991: ss++;
992: strcpy(ext,ss); /* save extension */
993: l1= strlen( name);
994: l2= strlen(ss)+1;
995: strncpy( finame, name, l1-l2);
996: finame[l1-l2]= 0;
997: }
998:
999: return( 0 ); /* we're done */
1000: }
1001:
1002:
1003: /******************************************/
1004:
1005: void replace_back_to_slash(char *s, char*t)
1006: {
1007: int i;
1008: int lg=0;
1009: i=0;
1010: lg=strlen(t);
1011: for(i=0; i<= lg; i++) {
1012: (s[i] = t[i]);
1013: if (t[i]== '\\') s[i]='/';
1014: }
1015: }
1016:
1.132 brouard 1017: char *trimbb(char *out, char *in)
1.137 brouard 1018: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1019: char *s;
1020: s=out;
1021: while (*in != '\0'){
1.137 brouard 1022: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1023: in++;
1024: }
1025: *out++ = *in++;
1026: }
1027: *out='\0';
1028: return s;
1029: }
1030:
1.187 brouard 1031: /* char *substrchaine(char *out, char *in, char *chain) */
1032: /* { */
1033: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1034: /* char *s, *t; */
1035: /* t=in;s=out; */
1036: /* while ((*in != *chain) && (*in != '\0')){ */
1037: /* *out++ = *in++; */
1038: /* } */
1039:
1040: /* /\* *in matches *chain *\/ */
1041: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1042: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1043: /* } */
1044: /* in--; chain--; */
1045: /* while ( (*in != '\0')){ */
1046: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1047: /* *out++ = *in++; */
1048: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1049: /* } */
1050: /* *out='\0'; */
1051: /* out=s; */
1052: /* return out; */
1053: /* } */
1054: char *substrchaine(char *out, char *in, char *chain)
1055: {
1056: /* Substract chain 'chain' from 'in', return and output 'out' */
1057: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1058:
1059: char *strloc;
1060:
1061: strcpy (out, in);
1062: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1063: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1064: if(strloc != NULL){
1065: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1066: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1067: /* strcpy (strloc, strloc +strlen(chain));*/
1068: }
1069: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1070: return out;
1071: }
1072:
1073:
1.145 brouard 1074: char *cutl(char *blocc, char *alocc, char *in, char occ)
1075: {
1.187 brouard 1076: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1077: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1078: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1079: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1080: */
1.160 brouard 1081: char *s, *t;
1.145 brouard 1082: t=in;s=in;
1083: while ((*in != occ) && (*in != '\0')){
1084: *alocc++ = *in++;
1085: }
1086: if( *in == occ){
1087: *(alocc)='\0';
1088: s=++in;
1089: }
1090:
1091: if (s == t) {/* occ not found */
1092: *(alocc-(in-s))='\0';
1093: in=s;
1094: }
1095: while ( *in != '\0'){
1096: *blocc++ = *in++;
1097: }
1098:
1099: *blocc='\0';
1100: return t;
1101: }
1.137 brouard 1102: char *cutv(char *blocc, char *alocc, char *in, char occ)
1103: {
1.187 brouard 1104: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1105: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1106: gives blocc="abcdef2ghi" and alocc="j".
1107: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1108: */
1109: char *s, *t;
1110: t=in;s=in;
1111: while (*in != '\0'){
1112: while( *in == occ){
1113: *blocc++ = *in++;
1114: s=in;
1115: }
1116: *blocc++ = *in++;
1117: }
1118: if (s == t) /* occ not found */
1119: *(blocc-(in-s))='\0';
1120: else
1121: *(blocc-(in-s)-1)='\0';
1122: in=s;
1123: while ( *in != '\0'){
1124: *alocc++ = *in++;
1125: }
1126:
1127: *alocc='\0';
1128: return s;
1129: }
1130:
1.126 brouard 1131: int nbocc(char *s, char occ)
1132: {
1133: int i,j=0;
1134: int lg=20;
1135: i=0;
1136: lg=strlen(s);
1137: for(i=0; i<= lg; i++) {
1138: if (s[i] == occ ) j++;
1139: }
1140: return j;
1141: }
1142:
1.137 brouard 1143: /* void cutv(char *u,char *v, char*t, char occ) */
1144: /* { */
1145: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1146: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1147: /* gives u="abcdef2ghi" and v="j" *\/ */
1148: /* int i,lg,j,p=0; */
1149: /* i=0; */
1150: /* lg=strlen(t); */
1151: /* for(j=0; j<=lg-1; j++) { */
1152: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1153: /* } */
1.126 brouard 1154:
1.137 brouard 1155: /* for(j=0; j<p; j++) { */
1156: /* (u[j] = t[j]); */
1157: /* } */
1158: /* u[p]='\0'; */
1.126 brouard 1159:
1.137 brouard 1160: /* for(j=0; j<= lg; j++) { */
1161: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1162: /* } */
1163: /* } */
1.126 brouard 1164:
1.160 brouard 1165: #ifdef _WIN32
1166: char * strsep(char **pp, const char *delim)
1167: {
1168: char *p, *q;
1169:
1170: if ((p = *pp) == NULL)
1171: return 0;
1172: if ((q = strpbrk (p, delim)) != NULL)
1173: {
1174: *pp = q + 1;
1175: *q = '\0';
1176: }
1177: else
1178: *pp = 0;
1179: return p;
1180: }
1181: #endif
1182:
1.126 brouard 1183: /********************** nrerror ********************/
1184:
1185: void nrerror(char error_text[])
1186: {
1187: fprintf(stderr,"ERREUR ...\n");
1188: fprintf(stderr,"%s\n",error_text);
1189: exit(EXIT_FAILURE);
1190: }
1191: /*********************** vector *******************/
1192: double *vector(int nl, int nh)
1193: {
1194: double *v;
1195: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1196: if (!v) nrerror("allocation failure in vector");
1197: return v-nl+NR_END;
1198: }
1199:
1200: /************************ free vector ******************/
1201: void free_vector(double*v, int nl, int nh)
1202: {
1203: free((FREE_ARG)(v+nl-NR_END));
1204: }
1205:
1206: /************************ivector *******************************/
1207: int *ivector(long nl,long nh)
1208: {
1209: int *v;
1210: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1211: if (!v) nrerror("allocation failure in ivector");
1212: return v-nl+NR_END;
1213: }
1214:
1215: /******************free ivector **************************/
1216: void free_ivector(int *v, long nl, long nh)
1217: {
1218: free((FREE_ARG)(v+nl-NR_END));
1219: }
1220:
1221: /************************lvector *******************************/
1222: long *lvector(long nl,long nh)
1223: {
1224: long *v;
1225: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1226: if (!v) nrerror("allocation failure in ivector");
1227: return v-nl+NR_END;
1228: }
1229:
1230: /******************free lvector **************************/
1231: void free_lvector(long *v, long nl, long nh)
1232: {
1233: free((FREE_ARG)(v+nl-NR_END));
1234: }
1235:
1236: /******************* imatrix *******************************/
1237: int **imatrix(long nrl, long nrh, long ncl, long nch)
1238: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1239: {
1240: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1241: int **m;
1242:
1243: /* allocate pointers to rows */
1244: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1245: if (!m) nrerror("allocation failure 1 in matrix()");
1246: m += NR_END;
1247: m -= nrl;
1248:
1249:
1250: /* allocate rows and set pointers to them */
1251: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1252: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1253: m[nrl] += NR_END;
1254: m[nrl] -= ncl;
1255:
1256: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1257:
1258: /* return pointer to array of pointers to rows */
1259: return m;
1260: }
1261:
1262: /****************** free_imatrix *************************/
1263: void free_imatrix(m,nrl,nrh,ncl,nch)
1264: int **m;
1265: long nch,ncl,nrh,nrl;
1266: /* free an int matrix allocated by imatrix() */
1267: {
1268: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1269: free((FREE_ARG) (m+nrl-NR_END));
1270: }
1271:
1272: /******************* matrix *******************************/
1273: double **matrix(long nrl, long nrh, long ncl, long nch)
1274: {
1275: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1276: double **m;
1277:
1278: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1279: if (!m) nrerror("allocation failure 1 in matrix()");
1280: m += NR_END;
1281: m -= nrl;
1282:
1283: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1284: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1285: m[nrl] += NR_END;
1286: m[nrl] -= ncl;
1287:
1288: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1289: return m;
1.145 brouard 1290: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1291: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1292: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1293: */
1294: }
1295:
1296: /*************************free matrix ************************/
1297: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1298: {
1299: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1300: free((FREE_ARG)(m+nrl-NR_END));
1301: }
1302:
1303: /******************* ma3x *******************************/
1304: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1305: {
1306: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1307: double ***m;
1308:
1309: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1310: if (!m) nrerror("allocation failure 1 in matrix()");
1311: m += NR_END;
1312: m -= nrl;
1313:
1314: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1315: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1316: m[nrl] += NR_END;
1317: m[nrl] -= ncl;
1318:
1319: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1320:
1321: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1322: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1323: m[nrl][ncl] += NR_END;
1324: m[nrl][ncl] -= nll;
1325: for (j=ncl+1; j<=nch; j++)
1326: m[nrl][j]=m[nrl][j-1]+nlay;
1327:
1328: for (i=nrl+1; i<=nrh; i++) {
1329: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1330: for (j=ncl+1; j<=nch; j++)
1331: m[i][j]=m[i][j-1]+nlay;
1332: }
1333: return m;
1334: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1335: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1336: */
1337: }
1338:
1339: /*************************free ma3x ************************/
1340: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1341: {
1342: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1343: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1344: free((FREE_ARG)(m+nrl-NR_END));
1345: }
1346:
1347: /*************** function subdirf ***********/
1348: char *subdirf(char fileres[])
1349: {
1350: /* Caution optionfilefiname is hidden */
1351: strcpy(tmpout,optionfilefiname);
1352: strcat(tmpout,"/"); /* Add to the right */
1353: strcat(tmpout,fileres);
1354: return tmpout;
1355: }
1356:
1357: /*************** function subdirf2 ***********/
1358: char *subdirf2(char fileres[], char *preop)
1359: {
1360:
1361: /* Caution optionfilefiname is hidden */
1362: strcpy(tmpout,optionfilefiname);
1363: strcat(tmpout,"/");
1364: strcat(tmpout,preop);
1365: strcat(tmpout,fileres);
1366: return tmpout;
1367: }
1368:
1369: /*************** function subdirf3 ***********/
1370: char *subdirf3(char fileres[], char *preop, char *preop2)
1371: {
1372:
1373: /* Caution optionfilefiname is hidden */
1374: strcpy(tmpout,optionfilefiname);
1375: strcat(tmpout,"/");
1376: strcat(tmpout,preop);
1377: strcat(tmpout,preop2);
1378: strcat(tmpout,fileres);
1379: return tmpout;
1380: }
1381:
1.162 brouard 1382: char *asc_diff_time(long time_sec, char ascdiff[])
1383: {
1384: long sec_left, days, hours, minutes;
1385: days = (time_sec) / (60*60*24);
1386: sec_left = (time_sec) % (60*60*24);
1387: hours = (sec_left) / (60*60) ;
1388: sec_left = (sec_left) %(60*60);
1389: minutes = (sec_left) /60;
1390: sec_left = (sec_left) % (60);
1391: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1392: return ascdiff;
1393: }
1394:
1.126 brouard 1395: /***************** f1dim *************************/
1396: extern int ncom;
1397: extern double *pcom,*xicom;
1398: extern double (*nrfunc)(double []);
1399:
1400: double f1dim(double x)
1401: {
1402: int j;
1403: double f;
1404: double *xt;
1405:
1406: xt=vector(1,ncom);
1407: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1408: f=(*nrfunc)(xt);
1409: free_vector(xt,1,ncom);
1410: return f;
1411: }
1412:
1413: /*****************brent *************************/
1414: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1415: {
1416: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1417: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1418: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1419: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1420: * returned function value.
1421: */
1.126 brouard 1422: int iter;
1423: double a,b,d,etemp;
1.159 brouard 1424: double fu=0,fv,fw,fx;
1.164 brouard 1425: double ftemp=0.;
1.126 brouard 1426: double p,q,r,tol1,tol2,u,v,w,x,xm;
1427: double e=0.0;
1428:
1429: a=(ax < cx ? ax : cx);
1430: b=(ax > cx ? ax : cx);
1431: x=w=v=bx;
1432: fw=fv=fx=(*f)(x);
1433: for (iter=1;iter<=ITMAX;iter++) {
1434: xm=0.5*(a+b);
1435: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1436: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1437: printf(".");fflush(stdout);
1438: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1439: #ifdef DEBUGBRENT
1.126 brouard 1440: 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);
1441: 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);
1442: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1443: #endif
1444: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1445: *xmin=x;
1446: return fx;
1447: }
1448: ftemp=fu;
1449: if (fabs(e) > tol1) {
1450: r=(x-w)*(fx-fv);
1451: q=(x-v)*(fx-fw);
1452: p=(x-v)*q-(x-w)*r;
1453: q=2.0*(q-r);
1454: if (q > 0.0) p = -p;
1455: q=fabs(q);
1456: etemp=e;
1457: e=d;
1458: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1459: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1460: else {
1461: d=p/q;
1462: u=x+d;
1463: if (u-a < tol2 || b-u < tol2)
1464: d=SIGN(tol1,xm-x);
1465: }
1466: } else {
1467: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1468: }
1469: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1470: fu=(*f)(u);
1471: if (fu <= fx) {
1472: if (u >= x) a=x; else b=x;
1473: SHFT(v,w,x,u)
1.183 brouard 1474: SHFT(fv,fw,fx,fu)
1475: } else {
1476: if (u < x) a=u; else b=u;
1477: if (fu <= fw || w == x) {
1478: v=w;
1479: w=u;
1480: fv=fw;
1481: fw=fu;
1482: } else if (fu <= fv || v == x || v == w) {
1483: v=u;
1484: fv=fu;
1485: }
1486: }
1.126 brouard 1487: }
1488: nrerror("Too many iterations in brent");
1489: *xmin=x;
1490: return fx;
1491: }
1492:
1493: /****************** mnbrak ***********************/
1494:
1495: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1496: double (*func)(double))
1.183 brouard 1497: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1498: the downhill direction (defined by the function as evaluated at the initial points) and returns
1499: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1500: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1501: */
1.126 brouard 1502: double ulim,u,r,q, dum;
1503: double fu;
1.187 brouard 1504:
1505: double scale=10.;
1506: int iterscale=0;
1507:
1508: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1509: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1510:
1511:
1512: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1513: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1514: /* *bx = *ax - (*ax - *bx)/scale; */
1515: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1516: /* } */
1517:
1.126 brouard 1518: if (*fb > *fa) {
1519: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1520: SHFT(dum,*fb,*fa,dum)
1521: }
1.126 brouard 1522: *cx=(*bx)+GOLD*(*bx-*ax);
1523: *fc=(*func)(*cx);
1.183 brouard 1524: #ifdef DEBUG
1525: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1526: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1527: #endif
1528: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1529: r=(*bx-*ax)*(*fb-*fc);
1530: q=(*bx-*cx)*(*fb-*fa);
1531: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1532: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1533: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1534: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1535: fu=(*func)(u);
1.163 brouard 1536: #ifdef DEBUG
1537: /* f(x)=A(x-u)**2+f(u) */
1538: double A, fparabu;
1539: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1540: fparabu= *fa - A*(*ax-u)*(*ax-u);
1541: 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);
1542: 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 1543: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1544: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1545: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1546: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1547: #endif
1.184 brouard 1548: #ifdef MNBRAKORIGINAL
1.183 brouard 1549: #else
1.191 brouard 1550: /* if (fu > *fc) { */
1551: /* #ifdef DEBUG */
1552: /* printf("mnbrak4 fu > fc \n"); */
1553: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1554: /* #endif */
1555: /* /\* 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 *\\/ *\/ */
1556: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1557: /* dum=u; /\* Shifting c and u *\/ */
1558: /* u = *cx; */
1559: /* *cx = dum; */
1560: /* dum = fu; */
1561: /* fu = *fc; */
1562: /* *fc =dum; */
1563: /* } else { /\* end *\/ */
1564: /* #ifdef DEBUG */
1565: /* printf("mnbrak3 fu < fc \n"); */
1566: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1567: /* #endif */
1568: /* dum=u; /\* Shifting c and u *\/ */
1569: /* u = *cx; */
1570: /* *cx = dum; */
1571: /* dum = fu; */
1572: /* fu = *fc; */
1573: /* *fc =dum; */
1574: /* } */
1.183 brouard 1575: #ifdef DEBUG
1.191 brouard 1576: printf("mnbrak34 fu < or >= fc \n");
1577: fprintf(ficlog, "mnbrak34 fu < fc\n");
1.183 brouard 1578: #endif
1.191 brouard 1579: dum=u; /* Shifting c and u */
1580: u = *cx;
1581: *cx = dum;
1582: dum = fu;
1583: fu = *fc;
1584: *fc =dum;
1.183 brouard 1585: #endif
1.162 brouard 1586: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1587: #ifdef DEBUG
1588: printf("mnbrak2 u after c but before ulim\n");
1589: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1590: #endif
1.126 brouard 1591: fu=(*func)(u);
1592: if (fu < *fc) {
1.183 brouard 1593: #ifdef DEBUG
1594: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1595: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1596: #endif
1.126 brouard 1597: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1598: SHFT(*fb,*fc,fu,(*func)(u))
1599: }
1.162 brouard 1600: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1601: #ifdef DEBUG
1602: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1603: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1604: #endif
1.126 brouard 1605: u=ulim;
1606: fu=(*func)(u);
1.183 brouard 1607: } else { /* u could be left to b (if r > q parabola has a maximum) */
1608: #ifdef DEBUG
1609: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1610: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1611: #endif
1.126 brouard 1612: u=(*cx)+GOLD*(*cx-*bx);
1613: fu=(*func)(u);
1.183 brouard 1614: } /* end tests */
1.126 brouard 1615: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1616: SHFT(*fa,*fb,*fc,fu)
1617: #ifdef DEBUG
1618: 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);
1619: 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);
1620: #endif
1621: } /* 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 1622: }
1623:
1624: /*************** linmin ************************/
1.162 brouard 1625: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1626: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1627: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1628: the value of func at the returned location p . This is actually all accomplished by calling the
1629: routines mnbrak and brent .*/
1.126 brouard 1630: int ncom;
1631: double *pcom,*xicom;
1632: double (*nrfunc)(double []);
1633:
1634: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1635: {
1636: double brent(double ax, double bx, double cx,
1637: double (*f)(double), double tol, double *xmin);
1638: double f1dim(double x);
1639: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1640: double *fc, double (*func)(double));
1641: int j;
1642: double xx,xmin,bx,ax;
1643: double fx,fb,fa;
1.187 brouard 1644:
1.203 brouard 1645: #ifdef LINMINORIGINAL
1646: #else
1647: double scale=10., axs, xxs; /* Scale added for infinity */
1648: #endif
1649:
1.126 brouard 1650: ncom=n;
1651: pcom=vector(1,n);
1652: xicom=vector(1,n);
1653: nrfunc=func;
1654: for (j=1;j<=n;j++) {
1655: pcom[j]=p[j];
1.202 brouard 1656: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1657: }
1.187 brouard 1658:
1.203 brouard 1659: #ifdef LINMINORIGINAL
1660: xx=1.;
1661: #else
1662: axs=0.0;
1663: xxs=1.;
1664: do{
1665: xx= xxs;
1666: #endif
1.187 brouard 1667: ax=0.;
1668: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1669: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1670: /* 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)) */
1671: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1672: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1673: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1674: /* 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 1675: #ifdef LINMINORIGINAL
1676: #else
1677: if (fx != fx){
1678: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1679: printf("|");
1680: fprintf(ficlog,"|");
1681: #ifdef DEBUGLINMIN
1682: 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);
1683: #endif
1684: }
1685: }while(fx != fx);
1686: #endif
1687:
1.191 brouard 1688: #ifdef DEBUGLINMIN
1689: 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 1690: 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 1691: #endif
1.187 brouard 1692: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1693: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1694: /* fmin = f(p[j] + xmin * xi[j]) */
1695: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1696: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1697: #ifdef DEBUG
1698: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1699: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1700: #endif
1.191 brouard 1701: #ifdef DEBUGLINMIN
1702: printf("linmin end ");
1.202 brouard 1703: fprintf(ficlog,"linmin end ");
1.191 brouard 1704: #endif
1.126 brouard 1705: for (j=1;j<=n;j++) {
1.203 brouard 1706: #ifdef LINMINORIGINAL
1707: xi[j] *= xmin;
1708: #else
1709: #ifdef DEBUGLINMIN
1710: if(xxs <1.0)
1711: printf(" before xi[%d]=%12.8f", j,xi[j]);
1712: #endif
1713: 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) */
1714: #ifdef DEBUGLINMIN
1715: if(xxs <1.0)
1716: 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 );
1717: #endif
1718: #endif
1.187 brouard 1719: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1720: }
1.191 brouard 1721: #ifdef DEBUGLINMIN
1.203 brouard 1722: printf("\n");
1.191 brouard 1723: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 1724: 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 1725: for (j=1;j<=n;j++) {
1.202 brouard 1726: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1727: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1728: if(j % ncovmodel == 0){
1.191 brouard 1729: printf("\n");
1.202 brouard 1730: fprintf(ficlog,"\n");
1731: }
1.191 brouard 1732: }
1.203 brouard 1733: #else
1.191 brouard 1734: #endif
1.126 brouard 1735: free_vector(xicom,1,n);
1736: free_vector(pcom,1,n);
1737: }
1738:
1739:
1740: /*************** powell ************************/
1.162 brouard 1741: /*
1742: Minimization of a function func of n variables. Input consists of an initial starting point
1743: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1744: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1745: such that failure to decrease by more than this amount on one iteration signals doneness. On
1746: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1747: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1748: */
1.126 brouard 1749: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1750: double (*func)(double []))
1751: {
1752: void linmin(double p[], double xi[], int n, double *fret,
1753: double (*func)(double []));
1754: int i,ibig,j;
1755: double del,t,*pt,*ptt,*xit;
1.181 brouard 1756: double directest;
1.126 brouard 1757: double fp,fptt;
1758: double *xits;
1759: int niterf, itmp;
1760:
1761: pt=vector(1,n);
1762: ptt=vector(1,n);
1763: xit=vector(1,n);
1764: xits=vector(1,n);
1765: *fret=(*func)(p);
1766: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 1767: rcurr_time = time(NULL);
1.126 brouard 1768: for (*iter=1;;++(*iter)) {
1.187 brouard 1769: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1770: ibig=0;
1771: del=0.0;
1.157 brouard 1772: rlast_time=rcurr_time;
1773: /* (void) gettimeofday(&curr_time,&tzp); */
1774: rcurr_time = time(NULL);
1775: curr_time = *localtime(&rcurr_time);
1776: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1777: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1778: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1779: for (i=1;i<=n;i++) {
1.126 brouard 1780: printf(" %d %.12f",i, p[i]);
1781: fprintf(ficlog," %d %.12lf",i, p[i]);
1782: fprintf(ficrespow," %.12lf", p[i]);
1783: }
1784: printf("\n");
1785: fprintf(ficlog,"\n");
1786: fprintf(ficrespow,"\n");fflush(ficrespow);
1787: if(*iter <=3){
1.157 brouard 1788: tml = *localtime(&rcurr_time);
1789: strcpy(strcurr,asctime(&tml));
1790: rforecast_time=rcurr_time;
1.126 brouard 1791: itmp = strlen(strcurr);
1792: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1793: strcurr[itmp-1]='\0';
1.162 brouard 1794: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1795: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1796: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1797: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1798: forecast_time = *localtime(&rforecast_time);
1799: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1800: itmp = strlen(strfor);
1801: if(strfor[itmp-1]=='\n')
1802: strfor[itmp-1]='\0';
1.157 brouard 1803: 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);
1804: 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 1805: }
1806: }
1.187 brouard 1807: for (i=1;i<=n;i++) { /* For each direction i */
1808: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1809: fptt=(*fret);
1810: #ifdef DEBUG
1.203 brouard 1811: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1812: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1813: #endif
1.203 brouard 1814: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1815: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 brouard 1816: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1817: /* Outputs are fret(new point p) p is updated and xit rescaled */
1818: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1819: /* because that direction will be replaced unless the gain del is small */
1820: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1821: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1822: /* with the new direction. */
1.126 brouard 1823: del=fabs(fptt-(*fret));
1824: ibig=i;
1825: }
1826: #ifdef DEBUG
1827: printf("%d %.12e",i,(*fret));
1828: fprintf(ficlog,"%d %.12e",i,(*fret));
1829: for (j=1;j<=n;j++) {
1830: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1831: printf(" x(%d)=%.12e",j,xit[j]);
1832: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1833: }
1834: for(j=1;j<=n;j++) {
1.162 brouard 1835: printf(" p(%d)=%.12e",j,p[j]);
1836: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1837: }
1838: printf("\n");
1839: fprintf(ficlog,"\n");
1840: #endif
1.187 brouard 1841: } /* end loop on each direction i */
1842: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1843: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1844: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1845: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1846: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1847: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1848: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1849: /* decreased of more than 3.84 */
1850: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1851: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1852: /* By adding 10 parameters more the gain should be 18.31 */
1853:
1854: /* Starting the program with initial values given by a former maximization will simply change */
1855: /* the scales of the directions and the directions, because the are reset to canonical directions */
1856: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1857: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1858: #ifdef DEBUG
1859: int k[2],l;
1860: k[0]=1;
1861: k[1]=-1;
1862: printf("Max: %.12e",(*func)(p));
1863: fprintf(ficlog,"Max: %.12e",(*func)(p));
1864: for (j=1;j<=n;j++) {
1865: printf(" %.12e",p[j]);
1866: fprintf(ficlog," %.12e",p[j]);
1867: }
1868: printf("\n");
1869: fprintf(ficlog,"\n");
1870: for(l=0;l<=1;l++) {
1871: for (j=1;j<=n;j++) {
1872: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1873: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1874: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1875: }
1876: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1877: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1878: }
1879: #endif
1880:
1881:
1882: free_vector(xit,1,n);
1883: free_vector(xits,1,n);
1884: free_vector(ptt,1,n);
1885: free_vector(pt,1,n);
1886: return;
1.192 brouard 1887: } /* enough precision */
1.126 brouard 1888: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1889: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1890: ptt[j]=2.0*p[j]-pt[j];
1891: xit[j]=p[j]-pt[j];
1892: pt[j]=p[j];
1893: }
1.181 brouard 1894: fptt=(*func)(ptt); /* f_3 */
1.192 brouard 1895: #ifdef POWELLF1F3
1896: #else
1.161 brouard 1897: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 1898: #endif
1.162 brouard 1899: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1900: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1901: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1902: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1903: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1904: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1905: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1906: #ifdef NRCORIGINAL
1907: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1908: #else
1909: 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 1910: t= t- del*SQR(fp-fptt);
1.183 brouard 1911: #endif
1.202 brouard 1912: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 1913: #ifdef DEBUG
1.181 brouard 1914: 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);
1915: 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 1916: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1917: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1918: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1919: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1920: 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);
1921: 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);
1922: #endif
1.183 brouard 1923: #ifdef POWELLORIGINAL
1924: if (t < 0.0) { /* Then we use it for new direction */
1925: #else
1.182 brouard 1926: if (directest*t < 0.0) { /* Contradiction between both tests */
1.202 brouard 1927: 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 1928: 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 1929: 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 1930: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1931: }
1.181 brouard 1932: if (directest < 0.0) { /* Then we use it for new direction */
1933: #endif
1.191 brouard 1934: #ifdef DEBUGLINMIN
1935: printf("Before linmin in direction P%d-P0\n",n);
1936: for (j=1;j<=n;j++) {
1.202 brouard 1937: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1938: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1939: if(j % ncovmodel == 0){
1.191 brouard 1940: printf("\n");
1.202 brouard 1941: fprintf(ficlog,"\n");
1942: }
1.191 brouard 1943: }
1944: #endif
1.187 brouard 1945: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.191 brouard 1946: #ifdef DEBUGLINMIN
1947: for (j=1;j<=n;j++) {
1948: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1.202 brouard 1949: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1950: if(j % ncovmodel == 0){
1.191 brouard 1951: printf("\n");
1.202 brouard 1952: fprintf(ficlog,"\n");
1953: }
1.191 brouard 1954: }
1955: #endif
1.126 brouard 1956: for (j=1;j<=n;j++) {
1.181 brouard 1957: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1958: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 1959: }
1.181 brouard 1960: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1961: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1962:
1.126 brouard 1963: #ifdef DEBUG
1.164 brouard 1964: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1965: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 1966: for(j=1;j<=n;j++){
1967: printf(" %.12e",xit[j]);
1968: fprintf(ficlog," %.12e",xit[j]);
1969: }
1970: printf("\n");
1971: fprintf(ficlog,"\n");
1972: #endif
1.192 brouard 1973: } /* end of t or directest negative */
1974: #ifdef POWELLF1F3
1975: #else
1.162 brouard 1976: } /* end if (fptt < fp) */
1.192 brouard 1977: #endif
1978: } /* loop iteration */
1.126 brouard 1979: }
1980:
1981: /**** Prevalence limit (stable or period prevalence) ****************/
1982:
1.203 brouard 1983: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
1.126 brouard 1984: {
1985: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1.203 brouard 1986: matrix by transitions matrix until convergence is reached with precision ftolpl */
1.206 brouard 1987: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
1988: /* Wx is row vector: population in state 1, population in state 2, population dead */
1989: /* or prevalence in state 1, prevalence in state 2, 0 */
1990: /* newm is the matrix after multiplications, its rows are identical at a factor */
1991: /* Initial matrix pimij */
1992: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
1993: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
1994: /* 0, 0 , 1} */
1995: /*
1996: * and after some iteration: */
1997: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
1998: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
1999: /* 0, 0 , 1} */
2000: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2001: /* {0.51571254859325999, 0.4842874514067399, */
2002: /* 0.51326036147820708, 0.48673963852179264} */
2003: /* If we start from prlim again, prlim tends to a constant matrix */
2004:
1.126 brouard 2005: int i, ii,j,k;
1.209 brouard 2006: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2007: /* double **matprod2(); */ /* test */
1.131 brouard 2008: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 2009: double **newm;
1.209 brouard 2010: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2011: int ncvloop=0;
1.169 brouard 2012:
1.209 brouard 2013: min=vector(1,nlstate);
2014: max=vector(1,nlstate);
2015: meandiff=vector(1,nlstate);
2016:
1.126 brouard 2017: for (ii=1;ii<=nlstate+ndeath;ii++)
2018: for (j=1;j<=nlstate+ndeath;j++){
2019: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2020: }
1.169 brouard 2021:
2022: cov[1]=1.;
2023:
2024: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2025: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2026: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2027: ncvloop++;
1.126 brouard 2028: newm=savm;
2029: /* Covariates have to be included here again */
1.138 brouard 2030: cov[2]=agefin;
1.187 brouard 2031: if(nagesqr==1)
2032: cov[3]= agefin*agefin;;
1.138 brouard 2033: for (k=1; k<=cptcovn;k++) {
1.200 brouard 2034: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
2035: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
1.198 brouard 2036: /* 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 2037: }
1.186 brouard 2038: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2039: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2040: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
1.186 brouard 2041: for (k=1; k<=cptcovprod;k++) /* Useless */
1.200 brouard 2042: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2043: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.138 brouard 2044:
2045: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2046: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2047: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2048: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2049: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 2050: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2051:
1.126 brouard 2052: savm=oldm;
2053: oldm=newm;
1.209 brouard 2054:
2055: for(j=1; j<=nlstate; j++){
2056: max[j]=0.;
2057: min[j]=1.;
2058: }
2059: for(i=1;i<=nlstate;i++){
2060: sumnew=0;
2061: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2062: for(j=1; j<=nlstate; j++){
2063: prlim[i][j]= newm[i][j]/(1-sumnew);
2064: max[j]=FMAX(max[j],prlim[i][j]);
2065: min[j]=FMIN(min[j],prlim[i][j]);
2066: }
2067: }
2068:
1.126 brouard 2069: maxmax=0.;
1.209 brouard 2070: for(j=1; j<=nlstate; j++){
2071: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2072: maxmax=FMAX(maxmax,meandiff[j]);
2073: /* 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 2074: } /* j loop */
1.203 brouard 2075: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2076: /* 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 2077: if(maxmax < ftolpl){
1.209 brouard 2078: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2079: free_vector(min,1,nlstate);
2080: free_vector(max,1,nlstate);
2081: free_vector(meandiff,1,nlstate);
1.126 brouard 2082: return prlim;
2083: }
1.169 brouard 2084: } /* age loop */
1.208 brouard 2085: /* After some age loop it doesn't converge */
1.209 brouard 2086: 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 2087: 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 2088: /* 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); */
2089: free_vector(min,1,nlstate);
2090: free_vector(max,1,nlstate);
2091: free_vector(meandiff,1,nlstate);
1.208 brouard 2092:
1.169 brouard 2093: return prlim; /* should not reach here */
1.126 brouard 2094: }
2095:
2096: /*************** transition probabilities ***************/
2097:
2098: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2099: {
1.138 brouard 2100: /* According to parameters values stored in x and the covariate's values stored in cov,
2101: computes the probability to be observed in state j being in state i by appying the
2102: model to the ncovmodel covariates (including constant and age).
2103: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2104: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2105: ncth covariate in the global vector x is given by the formula:
2106: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2107: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2108: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2109: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2110: Outputs ps[i][j] the probability to be observed in j being in j according to
2111: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2112: */
2113: double s1, lnpijopii;
1.126 brouard 2114: /*double t34;*/
1.164 brouard 2115: int i,j, nc, ii, jj;
1.126 brouard 2116:
2117: for(i=1; i<= nlstate; i++){
2118: for(j=1; j<i;j++){
1.138 brouard 2119: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2120: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2121: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2122: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2123: }
1.138 brouard 2124: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2125: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2126: }
2127: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 2128: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2129: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2130: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2131: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 2132: }
1.138 brouard 2133: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 2134: }
2135: }
2136:
2137: for(i=1; i<= nlstate; i++){
2138: s1=0;
1.131 brouard 2139: for(j=1; j<i; j++){
1.138 brouard 2140: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2141: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2142: }
2143: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 2144: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2145: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2146: }
1.138 brouard 2147: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 2148: ps[i][i]=1./(s1+1.);
1.138 brouard 2149: /* Computing other pijs */
1.126 brouard 2150: for(j=1; j<i; j++)
2151: ps[i][j]= exp(ps[i][j])*ps[i][i];
2152: for(j=i+1; j<=nlstate+ndeath; j++)
2153: ps[i][j]= exp(ps[i][j])*ps[i][i];
2154: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2155: } /* end i */
2156:
2157: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2158: for(jj=1; jj<= nlstate+ndeath; jj++){
2159: ps[ii][jj]=0;
2160: ps[ii][ii]=1;
2161: }
2162: }
2163:
1.145 brouard 2164:
2165: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2166: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2167: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2168: /* } */
2169: /* printf("\n "); */
2170: /* } */
2171: /* printf("\n ");printf("%lf ",cov[2]);*/
2172: /*
1.126 brouard 2173: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2174: goto end;*/
2175: return ps;
2176: }
2177:
2178: /**************** Product of 2 matrices ******************/
2179:
1.145 brouard 2180: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2181: {
2182: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2183: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2184: /* in, b, out are matrice of pointers which should have been initialized
2185: before: only the contents of out is modified. The function returns
2186: a pointer to pointers identical to out */
1.145 brouard 2187: int i, j, k;
1.126 brouard 2188: for(i=nrl; i<= nrh; i++)
1.145 brouard 2189: for(k=ncolol; k<=ncoloh; k++){
2190: out[i][k]=0.;
2191: for(j=ncl; j<=nch; j++)
2192: out[i][k] +=in[i][j]*b[j][k];
2193: }
1.126 brouard 2194: return out;
2195: }
2196:
2197:
2198: /************* Higher Matrix Product ***************/
2199:
2200: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2201: {
2202: /* Computes the transition matrix starting at age 'age' over
2203: 'nhstepm*hstepm*stepm' months (i.e. until
2204: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2205: nhstepm*hstepm matrices.
2206: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2207: (typically every 2 years instead of every month which is too big
2208: for the memory).
2209: Model is determined by parameters x and covariates have to be
2210: included manually here.
2211:
2212: */
2213:
2214: int i, j, d, h, k;
1.131 brouard 2215: double **out, cov[NCOVMAX+1];
1.126 brouard 2216: double **newm;
1.187 brouard 2217: double agexact;
1.126 brouard 2218:
2219: /* Hstepm could be zero and should return the unit matrix */
2220: for (i=1;i<=nlstate+ndeath;i++)
2221: for (j=1;j<=nlstate+ndeath;j++){
2222: oldm[i][j]=(i==j ? 1.0 : 0.0);
2223: po[i][j][0]=(i==j ? 1.0 : 0.0);
2224: }
2225: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2226: for(h=1; h <=nhstepm; h++){
2227: for(d=1; d <=hstepm; d++){
2228: newm=savm;
2229: /* Covariates have to be included here again */
2230: cov[1]=1.;
1.187 brouard 2231: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
2232: cov[2]=agexact;
2233: if(nagesqr==1)
2234: cov[3]= agexact*agexact;
1.131 brouard 2235: for (k=1; k<=cptcovn;k++)
1.200 brouard 2236: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2237: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.186 brouard 2238: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
2239: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2240: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2241: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.145 brouard 2242: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.200 brouard 2243: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2244: /* 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 2245:
2246:
2247: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2248: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2249: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2250: pmij(pmmij,cov,ncovmodel,x,nlstate));
2251: savm=oldm;
2252: oldm=newm;
2253: }
2254: for(i=1; i<=nlstate+ndeath; i++)
2255: for(j=1;j<=nlstate+ndeath;j++) {
2256: po[i][j][h]=newm[i][j];
1.128 brouard 2257: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2258: }
1.128 brouard 2259: /*printf("h=%d ",h);*/
1.126 brouard 2260: } /* end h */
1.128 brouard 2261: /* printf("\n H=%d \n",h); */
1.126 brouard 2262: return po;
2263: }
2264:
1.162 brouard 2265: #ifdef NLOPT
2266: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2267: double fret;
2268: double *xt;
2269: int j;
2270: myfunc_data *d2 = (myfunc_data *) pd;
2271: /* xt = (p1-1); */
2272: xt=vector(1,n);
2273: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2274:
2275: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2276: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2277: printf("Function = %.12lf ",fret);
2278: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2279: printf("\n");
2280: free_vector(xt,1,n);
2281: return fret;
2282: }
2283: #endif
1.126 brouard 2284:
2285: /*************** log-likelihood *************/
2286: double func( double *x)
2287: {
2288: int i, ii, j, k, mi, d, kk;
1.131 brouard 2289: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2290: double **out;
2291: double sw; /* Sum of weights */
2292: double lli; /* Individual log likelihood */
2293: int s1, s2;
2294: double bbh, survp;
2295: long ipmx;
1.187 brouard 2296: double agexact;
1.126 brouard 2297: /*extern weight */
2298: /* We are differentiating ll according to initial status */
2299: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2300: /*for(i=1;i<imx;i++)
2301: printf(" %d\n",s[4][i]);
2302: */
1.162 brouard 2303:
2304: ++countcallfunc;
2305:
1.126 brouard 2306: cov[1]=1.;
2307:
2308: for(k=1; k<=nlstate; k++) ll[k]=0.;
2309:
2310: if(mle==1){
2311: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2312: /* Computes the values of the ncovmodel covariates of the model
2313: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2314: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2315: to be observed in j being in i according to the model.
2316: */
1.145 brouard 2317: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 brouard 2318: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2319: }
1.137 brouard 2320: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2321: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2322: has been calculated etc */
1.126 brouard 2323: for(mi=1; mi<= wav[i]-1; mi++){
2324: for (ii=1;ii<=nlstate+ndeath;ii++)
2325: for (j=1;j<=nlstate+ndeath;j++){
2326: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2327: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2328: }
2329: for(d=0; d<dh[mi][i]; d++){
2330: newm=savm;
1.187 brouard 2331: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2332: cov[2]=agexact;
2333: if(nagesqr==1)
2334: cov[3]= agexact*agexact;
1.126 brouard 2335: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2336: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2337: }
2338: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2339: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2340: savm=oldm;
2341: oldm=newm;
2342: } /* end mult */
2343:
2344: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2345: /* But now since version 0.9 we anticipate for bias at large stepm.
2346: * If stepm is larger than one month (smallest stepm) and if the exact delay
2347: * (in months) between two waves is not a multiple of stepm, we rounded to
2348: * the nearest (and in case of equal distance, to the lowest) interval but now
2349: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2350: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2351: * probability in order to take into account the bias as a fraction of the way
2352: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2353: * -stepm/2 to stepm/2 .
2354: * For stepm=1 the results are the same as for previous versions of Imach.
2355: * For stepm > 1 the results are less biased than in previous versions.
2356: */
2357: s1=s[mw[mi][i]][i];
2358: s2=s[mw[mi+1][i]][i];
2359: bbh=(double)bh[mi][i]/(double)stepm;
2360: /* bias bh is positive if real duration
2361: * is higher than the multiple of stepm and negative otherwise.
2362: */
2363: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2364: if( s2 > nlstate){
2365: /* i.e. if s2 is a death state and if the date of death is known
2366: then the contribution to the likelihood is the probability to
2367: die between last step unit time and current step unit time,
2368: which is also equal to probability to die before dh
2369: minus probability to die before dh-stepm .
2370: In version up to 0.92 likelihood was computed
2371: as if date of death was unknown. Death was treated as any other
2372: health state: the date of the interview describes the actual state
2373: and not the date of a change in health state. The former idea was
2374: to consider that at each interview the state was recorded
2375: (healthy, disable or death) and IMaCh was corrected; but when we
2376: introduced the exact date of death then we should have modified
2377: the contribution of an exact death to the likelihood. This new
2378: contribution is smaller and very dependent of the step unit
2379: stepm. It is no more the probability to die between last interview
2380: and month of death but the probability to survive from last
2381: interview up to one month before death multiplied by the
2382: probability to die within a month. Thanks to Chris
2383: Jackson for correcting this bug. Former versions increased
2384: mortality artificially. The bad side is that we add another loop
2385: which slows down the processing. The difference can be up to 10%
2386: lower mortality.
2387: */
1.183 brouard 2388: /* If, at the beginning of the maximization mostly, the
2389: cumulative probability or probability to be dead is
2390: constant (ie = 1) over time d, the difference is equal to
2391: 0. out[s1][3] = savm[s1][3]: probability, being at state
2392: s1 at precedent wave, to be dead a month before current
2393: wave is equal to probability, being at state s1 at
2394: precedent wave, to be dead at mont of the current
2395: wave. Then the observed probability (that this person died)
2396: is null according to current estimated parameter. In fact,
2397: it should be very low but not zero otherwise the log go to
2398: infinity.
2399: */
2400: /* #ifdef INFINITYORIGINAL */
2401: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2402: /* #else */
2403: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2404: /* lli=log(mytinydouble); */
2405: /* else */
2406: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2407: /* #endif */
2408: lli=log(out[s1][s2] - savm[s1][s2]);
1.126 brouard 2409:
2410: } else if (s2==-2) {
2411: for (j=1,survp=0. ; j<=nlstate; j++)
2412: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2413: /*survp += out[s1][j]; */
2414: lli= log(survp);
2415: }
2416:
2417: else if (s2==-4) {
2418: for (j=3,survp=0. ; j<=nlstate; j++)
2419: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2420: lli= log(survp);
2421: }
2422:
2423: else if (s2==-5) {
2424: for (j=1,survp=0. ; j<=2; j++)
2425: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2426: lli= log(survp);
2427: }
2428:
2429: else{
2430: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2431: /* 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 */
2432: }
2433: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2434: /*if(lli ==000.0)*/
2435: /*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); */
2436: ipmx +=1;
2437: sw += weight[i];
2438: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2439: /* if (lli < log(mytinydouble)){ */
2440: /* 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); */
2441: /* 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]); */
2442: /* } */
1.126 brouard 2443: } /* end of wave */
2444: } /* end of individual */
2445: } else if(mle==2){
2446: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2447: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2448: for(mi=1; mi<= wav[i]-1; mi++){
2449: for (ii=1;ii<=nlstate+ndeath;ii++)
2450: for (j=1;j<=nlstate+ndeath;j++){
2451: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2452: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2453: }
2454: for(d=0; d<=dh[mi][i]; d++){
2455: newm=savm;
1.187 brouard 2456: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2457: cov[2]=agexact;
2458: if(nagesqr==1)
2459: cov[3]= agexact*agexact;
1.126 brouard 2460: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2461: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2462: }
2463: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2464: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2465: savm=oldm;
2466: oldm=newm;
2467: } /* end mult */
2468:
2469: s1=s[mw[mi][i]][i];
2470: s2=s[mw[mi+1][i]][i];
2471: bbh=(double)bh[mi][i]/(double)stepm;
2472: 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 */
2473: ipmx +=1;
2474: sw += weight[i];
2475: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2476: } /* end of wave */
2477: } /* end of individual */
2478: } else if(mle==3){ /* exponential inter-extrapolation */
2479: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2480: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2481: for(mi=1; mi<= wav[i]-1; mi++){
2482: for (ii=1;ii<=nlstate+ndeath;ii++)
2483: for (j=1;j<=nlstate+ndeath;j++){
2484: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2485: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2486: }
2487: for(d=0; d<dh[mi][i]; d++){
2488: newm=savm;
1.187 brouard 2489: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2490: cov[2]=agexact;
2491: if(nagesqr==1)
2492: cov[3]= agexact*agexact;
1.126 brouard 2493: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2494: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2495: }
2496: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2497: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2498: savm=oldm;
2499: oldm=newm;
2500: } /* end mult */
2501:
2502: s1=s[mw[mi][i]][i];
2503: s2=s[mw[mi+1][i]][i];
2504: bbh=(double)bh[mi][i]/(double)stepm;
2505: 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 */
2506: ipmx +=1;
2507: sw += weight[i];
2508: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2509: } /* end of wave */
2510: } /* end of individual */
2511: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2512: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2513: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2514: for(mi=1; mi<= wav[i]-1; mi++){
2515: for (ii=1;ii<=nlstate+ndeath;ii++)
2516: for (j=1;j<=nlstate+ndeath;j++){
2517: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2518: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2519: }
2520: for(d=0; d<dh[mi][i]; d++){
2521: newm=savm;
1.187 brouard 2522: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2523: cov[2]=agexact;
2524: if(nagesqr==1)
2525: cov[3]= agexact*agexact;
1.126 brouard 2526: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2527: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2528: }
2529:
2530: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2531: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2532: savm=oldm;
2533: oldm=newm;
2534: } /* end mult */
2535:
2536: s1=s[mw[mi][i]][i];
2537: s2=s[mw[mi+1][i]][i];
2538: if( s2 > nlstate){
2539: lli=log(out[s1][s2] - savm[s1][s2]);
2540: }else{
2541: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2542: }
2543: ipmx +=1;
2544: sw += weight[i];
2545: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2546: /* 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]); */
2547: } /* end of wave */
2548: } /* end of individual */
2549: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2550: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2551: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2552: for(mi=1; mi<= wav[i]-1; mi++){
2553: for (ii=1;ii<=nlstate+ndeath;ii++)
2554: for (j=1;j<=nlstate+ndeath;j++){
2555: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2556: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2557: }
2558: for(d=0; d<dh[mi][i]; d++){
2559: newm=savm;
1.187 brouard 2560: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2561: cov[2]=agexact;
2562: if(nagesqr==1)
2563: cov[3]= agexact*agexact;
1.126 brouard 2564: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2565: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2566: }
2567:
2568: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2569: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2570: savm=oldm;
2571: oldm=newm;
2572: } /* end mult */
2573:
2574: s1=s[mw[mi][i]][i];
2575: s2=s[mw[mi+1][i]][i];
2576: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2577: ipmx +=1;
2578: sw += weight[i];
2579: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2580: /*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]);*/
2581: } /* end of wave */
2582: } /* end of individual */
2583: } /* End of if */
2584: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2585: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2586: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2587: return -l;
2588: }
2589:
2590: /*************** log-likelihood *************/
2591: double funcone( double *x)
2592: {
2593: /* Same as likeli but slower because of a lot of printf and if */
2594: int i, ii, j, k, mi, d, kk;
1.131 brouard 2595: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2596: double **out;
2597: double lli; /* Individual log likelihood */
2598: double llt;
2599: int s1, s2;
2600: double bbh, survp;
1.187 brouard 2601: double agexact;
1.126 brouard 2602: /*extern weight */
2603: /* We are differentiating ll according to initial status */
2604: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2605: /*for(i=1;i<imx;i++)
2606: printf(" %d\n",s[4][i]);
2607: */
2608: cov[1]=1.;
2609:
2610: for(k=1; k<=nlstate; k++) ll[k]=0.;
2611:
2612: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2613: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2614: for(mi=1; mi<= wav[i]-1; mi++){
2615: for (ii=1;ii<=nlstate+ndeath;ii++)
2616: for (j=1;j<=nlstate+ndeath;j++){
2617: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2618: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2619: }
2620: for(d=0; d<dh[mi][i]; d++){
2621: newm=savm;
1.187 brouard 2622: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2623: cov[2]=agexact;
2624: if(nagesqr==1)
2625: cov[3]= agexact*agexact;
1.126 brouard 2626: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2627: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2628: }
1.187 brouard 2629:
1.145 brouard 2630: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2631: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2632: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2633: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2634: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2635: savm=oldm;
2636: oldm=newm;
2637: } /* end mult */
2638:
2639: s1=s[mw[mi][i]][i];
2640: s2=s[mw[mi+1][i]][i];
2641: bbh=(double)bh[mi][i]/(double)stepm;
2642: /* bias is positive if real duration
2643: * is higher than the multiple of stepm and negative otherwise.
2644: */
2645: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2646: lli=log(out[s1][s2] - savm[s1][s2]);
2647: } else if (s2==-2) {
2648: for (j=1,survp=0. ; j<=nlstate; j++)
2649: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2650: lli= log(survp);
2651: }else if (mle==1){
2652: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2653: } else if(mle==2){
2654: 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 */
2655: } else if(mle==3){ /* exponential inter-extrapolation */
2656: 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 */
2657: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2658: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2659: } else{ /* mle=0 back to 1 */
2660: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2661: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2662: } /* End of if */
2663: ipmx +=1;
2664: sw += weight[i];
2665: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2666: /*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 2667: if(globpr){
1.205 brouard 2668: fprintf(ficresilk,"%9ld %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\
1.126 brouard 2669: %11.6f %11.6f %11.6f ", \
1.205 brouard 2670: num[i], agexact, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
1.126 brouard 2671: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2672: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2673: llt +=ll[k]*gipmx/gsw;
2674: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2675: }
2676: fprintf(ficresilk," %10.6f\n", -llt);
2677: }
2678: } /* end of wave */
2679: } /* end of individual */
2680: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2681: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2682: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2683: if(globpr==0){ /* First time we count the contributions and weights */
2684: gipmx=ipmx;
2685: gsw=sw;
2686: }
2687: return -l;
2688: }
2689:
2690:
2691: /*************** function likelione ***********/
2692: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2693: {
2694: /* This routine should help understanding what is done with
2695: the selection of individuals/waves and
2696: to check the exact contribution to the likelihood.
2697: Plotting could be done.
2698: */
2699: int k;
2700:
2701: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 2702: strcpy(fileresilk,"ILK_");
1.202 brouard 2703: strcat(fileresilk,fileresu);
1.126 brouard 2704: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2705: printf("Problem with resultfile: %s\n", fileresilk);
2706: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2707: }
1.205 brouard 2708: fprintf(ficresilk, "#individual(line's_record) count age 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");
1.207 brouard 2709: fprintf(ficresilk, "#num_i age i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 2710: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2711: for(k=1; k<=nlstate; k++)
2712: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2713: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2714: }
2715:
2716: *fretone=(*funcone)(p);
2717: if(*globpri !=0){
2718: fclose(ficresilk);
1.205 brouard 2719: if (mle ==0)
2720: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
2721: else if(mle >=1)
2722: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
2723: 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 2724:
1.208 brouard 2725:
2726: for (k=1; k<= nlstate ; k++) {
1.211 ! brouard 2727: 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 2728: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
2729: }
1.207 brouard 2730: 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 2731: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 2732: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 2733: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 2734: fflush(fichtm);
1.205 brouard 2735: }
1.126 brouard 2736: return;
2737: }
2738:
2739:
2740: /*********** Maximum Likelihood Estimation ***************/
2741:
2742: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2743: {
1.165 brouard 2744: int i,j, iter=0;
1.126 brouard 2745: double **xi;
2746: double fret;
2747: double fretone; /* Only one call to likelihood */
2748: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2749:
2750: #ifdef NLOPT
2751: int creturn;
2752: nlopt_opt opt;
2753: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2754: double *lb;
2755: double minf; /* the minimum objective value, upon return */
2756: double * p1; /* Shifted parameters from 0 instead of 1 */
2757: myfunc_data dinst, *d = &dinst;
2758: #endif
2759:
2760:
1.126 brouard 2761: xi=matrix(1,npar,1,npar);
2762: for (i=1;i<=npar;i++)
2763: for (j=1;j<=npar;j++)
2764: xi[i][j]=(i==j ? 1.0 : 0.0);
2765: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 2766: strcpy(filerespow,"POW_");
1.126 brouard 2767: strcat(filerespow,fileres);
2768: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2769: printf("Problem with resultfile: %s\n", filerespow);
2770: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2771: }
2772: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2773: for (i=1;i<=nlstate;i++)
2774: for(j=1;j<=nlstate+ndeath;j++)
2775: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2776: fprintf(ficrespow,"\n");
1.162 brouard 2777: #ifdef POWELL
1.126 brouard 2778: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2779: #endif
1.126 brouard 2780:
1.162 brouard 2781: #ifdef NLOPT
2782: #ifdef NEWUOA
2783: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2784: #else
2785: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2786: #endif
2787: lb=vector(0,npar-1);
2788: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2789: nlopt_set_lower_bounds(opt, lb);
2790: nlopt_set_initial_step1(opt, 0.1);
2791:
2792: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2793: d->function = func;
2794: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2795: nlopt_set_min_objective(opt, myfunc, d);
2796: nlopt_set_xtol_rel(opt, ftol);
2797: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2798: printf("nlopt failed! %d\n",creturn);
2799: }
2800: else {
2801: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2802: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2803: iter=1; /* not equal */
2804: }
2805: nlopt_destroy(opt);
2806: #endif
1.126 brouard 2807: free_matrix(xi,1,npar,1,npar);
2808: fclose(ficrespow);
1.203 brouard 2809: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2810: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 2811: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2812:
2813: }
2814:
2815: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 2816: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 2817: {
2818: double **a,**y,*x,pd;
1.203 brouard 2819: /* double **hess; */
1.164 brouard 2820: int i, j;
1.126 brouard 2821: int *indx;
2822:
2823: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 2824: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 2825: void lubksb(double **a, int npar, int *indx, double b[]) ;
2826: void ludcmp(double **a, int npar, int *indx, double *d) ;
2827: double gompertz(double p[]);
1.203 brouard 2828: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 2829:
2830: printf("\nCalculation of the hessian matrix. Wait...\n");
2831: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2832: for (i=1;i<=npar;i++){
1.203 brouard 2833: printf("%d-",i);fflush(stdout);
2834: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 2835:
2836: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2837:
2838: /* printf(" %f ",p[i]);
2839: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2840: }
2841:
2842: for (i=1;i<=npar;i++) {
2843: for (j=1;j<=npar;j++) {
2844: if (j>i) {
1.203 brouard 2845: printf(".%d-%d",i,j);fflush(stdout);
2846: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
2847: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 2848:
2849: hess[j][i]=hess[i][j];
2850: /*printf(" %lf ",hess[i][j]);*/
2851: }
2852: }
2853: }
2854: printf("\n");
2855: fprintf(ficlog,"\n");
2856:
2857: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2858: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2859:
2860: a=matrix(1,npar,1,npar);
2861: y=matrix(1,npar,1,npar);
2862: x=vector(1,npar);
2863: indx=ivector(1,npar);
2864: for (i=1;i<=npar;i++)
2865: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2866: ludcmp(a,npar,indx,&pd);
2867:
2868: for (j=1;j<=npar;j++) {
2869: for (i=1;i<=npar;i++) x[i]=0;
2870: x[j]=1;
2871: lubksb(a,npar,indx,x);
2872: for (i=1;i<=npar;i++){
2873: matcov[i][j]=x[i];
2874: }
2875: }
2876:
2877: printf("\n#Hessian matrix#\n");
2878: fprintf(ficlog,"\n#Hessian matrix#\n");
2879: for (i=1;i<=npar;i++) {
2880: for (j=1;j<=npar;j++) {
1.203 brouard 2881: printf("%.6e ",hess[i][j]);
2882: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 2883: }
2884: printf("\n");
2885: fprintf(ficlog,"\n");
2886: }
2887:
1.203 brouard 2888: /* printf("\n#Covariance matrix#\n"); */
2889: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
2890: /* for (i=1;i<=npar;i++) { */
2891: /* for (j=1;j<=npar;j++) { */
2892: /* printf("%.6e ",matcov[i][j]); */
2893: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
2894: /* } */
2895: /* printf("\n"); */
2896: /* fprintf(ficlog,"\n"); */
2897: /* } */
2898:
1.126 brouard 2899: /* Recompute Inverse */
1.203 brouard 2900: /* for (i=1;i<=npar;i++) */
2901: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
2902: /* ludcmp(a,npar,indx,&pd); */
2903:
2904: /* printf("\n#Hessian matrix recomputed#\n"); */
2905:
2906: /* for (j=1;j<=npar;j++) { */
2907: /* for (i=1;i<=npar;i++) x[i]=0; */
2908: /* x[j]=1; */
2909: /* lubksb(a,npar,indx,x); */
2910: /* for (i=1;i<=npar;i++){ */
2911: /* y[i][j]=x[i]; */
2912: /* printf("%.3e ",y[i][j]); */
2913: /* fprintf(ficlog,"%.3e ",y[i][j]); */
2914: /* } */
2915: /* printf("\n"); */
2916: /* fprintf(ficlog,"\n"); */
2917: /* } */
2918:
2919: /* Verifying the inverse matrix */
2920: #ifdef DEBUGHESS
2921: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 2922:
1.203 brouard 2923: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
2924: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 2925:
2926: for (j=1;j<=npar;j++) {
2927: for (i=1;i<=npar;i++){
1.203 brouard 2928: printf("%.2f ",y[i][j]);
2929: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 2930: }
2931: printf("\n");
2932: fprintf(ficlog,"\n");
2933: }
1.203 brouard 2934: #endif
1.126 brouard 2935:
2936: free_matrix(a,1,npar,1,npar);
2937: free_matrix(y,1,npar,1,npar);
2938: free_vector(x,1,npar);
2939: free_ivector(indx,1,npar);
1.203 brouard 2940: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 2941:
2942:
2943: }
2944:
2945: /*************** hessian matrix ****************/
2946: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 2947: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 2948: int i;
2949: int l=1, lmax=20;
1.203 brouard 2950: double k1,k2, res, fx;
1.132 brouard 2951: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2952: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2953: int k=0,kmax=10;
2954: double l1;
2955:
2956: fx=func(x);
2957: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2958: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2959: l1=pow(10,l);
2960: delts=delt;
2961: for(k=1 ; k <kmax; k=k+1){
2962: delt = delta*(l1*k);
2963: p2[theta]=x[theta] +delt;
1.145 brouard 2964: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2965: p2[theta]=x[theta]-delt;
2966: k2=func(p2)-fx;
2967: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 2968: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 2969:
1.203 brouard 2970: #ifdef DEBUGHESSII
1.126 brouard 2971: 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);
2972: 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);
2973: #endif
2974: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2975: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2976: k=kmax;
2977: }
2978: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 2979: k=kmax; l=lmax*10;
1.126 brouard 2980: }
2981: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2982: delts=delt;
2983: }
1.203 brouard 2984: } /* End loop k */
1.126 brouard 2985: }
2986: delti[theta]=delts;
2987: return res;
2988:
2989: }
2990:
1.203 brouard 2991: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 2992: {
2993: int i;
1.164 brouard 2994: int l=1, lmax=20;
1.126 brouard 2995: double k1,k2,k3,k4,res,fx;
1.132 brouard 2996: double p2[MAXPARM+1];
1.203 brouard 2997: int k, kmax=1;
2998: double v1, v2, cv12, lc1, lc2;
1.208 brouard 2999:
3000: int firstime=0;
1.203 brouard 3001:
1.126 brouard 3002: fx=func(x);
1.203 brouard 3003: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 3004: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 3005: p2[thetai]=x[thetai]+delti[thetai]*k;
3006: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3007: k1=func(p2)-fx;
3008:
1.203 brouard 3009: p2[thetai]=x[thetai]+delti[thetai]*k;
3010: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3011: k2=func(p2)-fx;
3012:
1.203 brouard 3013: p2[thetai]=x[thetai]-delti[thetai]*k;
3014: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3015: k3=func(p2)-fx;
3016:
1.203 brouard 3017: p2[thetai]=x[thetai]-delti[thetai]*k;
3018: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3019: k4=func(p2)-fx;
1.203 brouard 3020: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
3021: if(k1*k2*k3*k4 <0.){
1.208 brouard 3022: firstime=1;
1.203 brouard 3023: kmax=kmax+10;
1.208 brouard 3024: }
3025: if(kmax >=10 || firstime ==1){
1.203 brouard 3026: printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
3027: fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
3028: 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);
3029: 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);
3030: }
3031: #ifdef DEBUGHESSIJ
3032: v1=hess[thetai][thetai];
3033: v2=hess[thetaj][thetaj];
3034: cv12=res;
3035: /* Computing eigen value of Hessian matrix */
3036: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3037: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3038: if ((lc2 <0) || (lc1 <0) ){
3039: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3040: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3041: 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);
3042: 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);
3043: }
1.126 brouard 3044: #endif
3045: }
3046: return res;
3047: }
3048:
1.203 brouard 3049: /* Not done yet: Was supposed to fix if not exactly at the maximum */
3050: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
3051: /* { */
3052: /* int i; */
3053: /* int l=1, lmax=20; */
3054: /* double k1,k2,k3,k4,res,fx; */
3055: /* double p2[MAXPARM+1]; */
3056: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
3057: /* int k=0,kmax=10; */
3058: /* double l1; */
3059:
3060: /* fx=func(x); */
3061: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
3062: /* l1=pow(10,l); */
3063: /* delts=delt; */
3064: /* for(k=1 ; k <kmax; k=k+1){ */
3065: /* delt = delti*(l1*k); */
3066: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
3067: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3068: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3069: /* k1=func(p2)-fx; */
3070:
3071: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3072: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3073: /* k2=func(p2)-fx; */
3074:
3075: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3076: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3077: /* k3=func(p2)-fx; */
3078:
3079: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3080: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3081: /* k4=func(p2)-fx; */
3082: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
3083: /* #ifdef DEBUGHESSIJ */
3084: /* 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); */
3085: /* 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); */
3086: /* #endif */
3087: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
3088: /* k=kmax; */
3089: /* } */
3090: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
3091: /* k=kmax; l=lmax*10; */
3092: /* } */
3093: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
3094: /* delts=delt; */
3095: /* } */
3096: /* } /\* End loop k *\/ */
3097: /* } */
3098: /* delti[theta]=delts; */
3099: /* return res; */
3100: /* } */
3101:
3102:
1.126 brouard 3103: /************** Inverse of matrix **************/
3104: void ludcmp(double **a, int n, int *indx, double *d)
3105: {
3106: int i,imax,j,k;
3107: double big,dum,sum,temp;
3108: double *vv;
3109:
3110: vv=vector(1,n);
3111: *d=1.0;
3112: for (i=1;i<=n;i++) {
3113: big=0.0;
3114: for (j=1;j<=n;j++)
3115: if ((temp=fabs(a[i][j])) > big) big=temp;
3116: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
3117: vv[i]=1.0/big;
3118: }
3119: for (j=1;j<=n;j++) {
3120: for (i=1;i<j;i++) {
3121: sum=a[i][j];
3122: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
3123: a[i][j]=sum;
3124: }
3125: big=0.0;
3126: for (i=j;i<=n;i++) {
3127: sum=a[i][j];
3128: for (k=1;k<j;k++)
3129: sum -= a[i][k]*a[k][j];
3130: a[i][j]=sum;
3131: if ( (dum=vv[i]*fabs(sum)) >= big) {
3132: big=dum;
3133: imax=i;
3134: }
3135: }
3136: if (j != imax) {
3137: for (k=1;k<=n;k++) {
3138: dum=a[imax][k];
3139: a[imax][k]=a[j][k];
3140: a[j][k]=dum;
3141: }
3142: *d = -(*d);
3143: vv[imax]=vv[j];
3144: }
3145: indx[j]=imax;
3146: if (a[j][j] == 0.0) a[j][j]=TINY;
3147: if (j != n) {
3148: dum=1.0/(a[j][j]);
3149: for (i=j+1;i<=n;i++) a[i][j] *= dum;
3150: }
3151: }
3152: free_vector(vv,1,n); /* Doesn't work */
3153: ;
3154: }
3155:
3156: void lubksb(double **a, int n, int *indx, double b[])
3157: {
3158: int i,ii=0,ip,j;
3159: double sum;
3160:
3161: for (i=1;i<=n;i++) {
3162: ip=indx[i];
3163: sum=b[ip];
3164: b[ip]=b[i];
3165: if (ii)
3166: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
3167: else if (sum) ii=i;
3168: b[i]=sum;
3169: }
3170: for (i=n;i>=1;i--) {
3171: sum=b[i];
3172: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
3173: b[i]=sum/a[i][i];
3174: }
3175: }
3176:
3177: void pstamp(FILE *fichier)
3178: {
1.196 brouard 3179: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 3180: }
3181:
3182: /************ Frequencies ********************/
3183: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
3184: { /* Some frequencies */
3185:
1.164 brouard 3186: int i, m, jk, j1, bool, z1,j;
1.126 brouard 3187: int first;
3188: double ***freq; /* Frequencies */
3189: double *pp, **prop;
3190: double pos,posprop, k2, dateintsum=0,k2cpt=0;
3191: char fileresp[FILENAMELENGTH];
3192:
3193: pp=vector(1,nlstate);
3194: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.201 brouard 3195: strcpy(fileresp,"P_");
3196: strcat(fileresp,fileresu);
1.126 brouard 3197: if((ficresp=fopen(fileresp,"w"))==NULL) {
3198: printf("Problem with prevalence resultfile: %s\n", fileresp);
3199: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
3200: exit(0);
3201: }
3202: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
3203: j1=0;
3204:
3205: j=cptcoveff;
3206: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3207:
3208: first=1;
3209:
1.169 brouard 3210: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
3211: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
3212: /* j1++; */
1.145 brouard 3213: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 3214: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
3215: scanf("%d", i);*/
3216: for (i=-5; i<=nlstate+ndeath; i++)
3217: for (jk=-5; jk<=nlstate+ndeath; jk++)
3218: for(m=iagemin; m <= iagemax+3; m++)
3219: freq[i][jk][m]=0;
1.143 brouard 3220:
3221: for (i=1; i<=nlstate; i++)
3222: for(m=iagemin; m <= iagemax+3; m++)
3223: prop[i][m]=0;
1.126 brouard 3224:
3225: dateintsum=0;
3226: k2cpt=0;
3227: for (i=1; i<=imx; i++) {
3228: bool=1;
1.210 brouard 3229: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
1.144 brouard 3230: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 3231: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
1.145 brouard 3232: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 3233: bool=0;
1.198 brouard 3234: /* 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",
3235: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
3236: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
3237: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
1.144 brouard 3238: }
1.210 brouard 3239: } /* cptcovn > 0 */
1.144 brouard 3240:
1.126 brouard 3241: if (bool==1){
3242: for(m=firstpass; m<=lastpass; m++){
3243: k2=anint[m][i]+(mint[m][i]/12.);
3244: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
3245: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3246: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3247: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
3248: if (m<lastpass) {
3249: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
3250: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
3251: }
3252:
1.210 brouard 3253: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3)) && (anint[m][i]!=9999) && (mint[m][i]!=99)) {
1.126 brouard 3254: dateintsum=dateintsum+k2;
3255: k2cpt++;
1.210 brouard 3256: /* printf("i=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",i, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
1.126 brouard 3257: }
3258: /*}*/
1.210 brouard 3259: } /* end m */
3260: } /* end bool */
3261: } /* end i = 1 to imx */
1.126 brouard 3262:
3263: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
3264: pstamp(ficresp);
3265: if (cptcovn>0) {
3266: fprintf(ficresp, "\n#********** Variable ");
1.198 brouard 3267: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 3268: fprintf(ficresp, "**********\n#");
1.143 brouard 3269: fprintf(ficlog, "\n#********** Variable ");
1.198 brouard 3270: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.143 brouard 3271: fprintf(ficlog, "**********\n#");
1.126 brouard 3272: }
3273: for(i=1; i<=nlstate;i++)
3274: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
3275: fprintf(ficresp, "\n");
3276:
3277: for(i=iagemin; i <= iagemax+3; i++){
3278: if(i==iagemax+3){
3279: fprintf(ficlog,"Total");
3280: }else{
3281: if(first==1){
3282: first=0;
3283: printf("See log file for details...\n");
3284: }
3285: fprintf(ficlog,"Age %d", i);
3286: }
3287: for(jk=1; jk <=nlstate ; jk++){
3288: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
3289: pp[jk] += freq[jk][m][i];
3290: }
3291: for(jk=1; jk <=nlstate ; jk++){
3292: for(m=-1, pos=0; m <=0 ; m++)
3293: pos += freq[jk][m][i];
3294: if(pp[jk]>=1.e-10){
3295: if(first==1){
1.132 brouard 3296: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 3297: }
3298: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3299: }else{
3300: if(first==1)
3301: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3302: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3303: }
3304: }
3305:
3306: for(jk=1; jk <=nlstate ; jk++){
3307: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
3308: pp[jk] += freq[jk][m][i];
3309: }
3310: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
3311: pos += pp[jk];
3312: posprop += prop[jk][i];
3313: }
3314: for(jk=1; jk <=nlstate ; jk++){
3315: if(pos>=1.e-5){
3316: if(first==1)
3317: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3318: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3319: }else{
3320: if(first==1)
3321: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3322: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3323: }
3324: if( i <= iagemax){
3325: if(pos>=1.e-5){
3326: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
3327: /*probs[i][jk][j1]= pp[jk]/pos;*/
3328: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
3329: }
3330: else
3331: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
3332: }
3333: }
3334:
3335: for(jk=-1; jk <=nlstate+ndeath; jk++)
3336: for(m=-1; m <=nlstate+ndeath; m++)
3337: if(freq[jk][m][i] !=0 ) {
3338: if(first==1)
3339: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
3340: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
3341: }
3342: if(i <= iagemax)
3343: fprintf(ficresp,"\n");
3344: if(first==1)
3345: printf("Others in log...\n");
3346: fprintf(ficlog,"\n");
1.210 brouard 3347: } /* end loop i */
1.145 brouard 3348: /*}*/
1.210 brouard 3349: } /* end j1 */
1.126 brouard 3350: dateintmean=dateintsum/k2cpt;
3351:
3352: fclose(ficresp);
3353: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
3354: free_vector(pp,1,nlstate);
3355: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
3356: /* End of Freq */
3357: }
3358:
3359: /************ Prevalence ********************/
3360: 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)
3361: {
3362: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3363: in each health status at the date of interview (if between dateprev1 and dateprev2).
3364: We still use firstpass and lastpass as another selection.
3365: */
3366:
1.164 brouard 3367: int i, m, jk, j1, bool, z1,j;
3368:
3369: double **prop;
3370: double posprop;
1.126 brouard 3371: double y2; /* in fractional years */
3372: int iagemin, iagemax;
1.145 brouard 3373: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 3374:
3375: iagemin= (int) agemin;
3376: iagemax= (int) agemax;
3377: /*pp=vector(1,nlstate);*/
3378: prop=matrix(1,nlstate,iagemin,iagemax+3);
3379: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3380: j1=0;
3381:
1.145 brouard 3382: /*j=cptcoveff;*/
1.126 brouard 3383: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3384:
1.145 brouard 3385: first=1;
3386: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
3387: /*for(i1=1; i1<=ncodemax[k1];i1++){
3388: j1++;*/
1.126 brouard 3389:
3390: for (i=1; i<=nlstate; i++)
3391: for(m=iagemin; m <= iagemax+3; m++)
3392: prop[i][m]=0.0;
3393:
3394: for (i=1; i<=imx; i++) { /* Each individual */
3395: bool=1;
3396: if (cptcovn>0) {
3397: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 3398: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
1.126 brouard 3399: bool=0;
3400: }
3401: if (bool==1) {
3402: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
3403: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3404: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3405: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3406: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3407: if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
3408: if (s[m][i]>0 && s[m][i]<=nlstate) {
3409: /*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]]);*/
3410: prop[s[m][i]][(int)agev[m][i]] += weight[i];
3411: prop[s[m][i]][iagemax+3] += weight[i];
3412: }
3413: }
3414: } /* end selection of waves */
3415: }
3416: }
3417: for(i=iagemin; i <= iagemax+3; i++){
3418: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3419: posprop += prop[jk][i];
3420: }
1.145 brouard 3421:
1.126 brouard 3422: for(jk=1; jk <=nlstate ; jk++){
3423: if( i <= iagemax){
3424: if(posprop>=1.e-5){
3425: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 3426: } else{
3427: if(first==1){
3428: first=0;
3429: 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]);
3430: }
3431: }
1.126 brouard 3432: }
3433: }/* end jk */
3434: }/* end i */
1.145 brouard 3435: /*} *//* end i1 */
3436: } /* end j1 */
1.126 brouard 3437:
3438: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3439: /*free_vector(pp,1,nlstate);*/
3440: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3441: } /* End of prevalence */
3442:
3443: /************* Waves Concatenation ***************/
3444:
3445: 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)
3446: {
3447: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3448: Death is a valid wave (if date is known).
3449: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3450: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3451: and mw[mi+1][i]. dh depends on stepm.
3452: */
3453:
3454: int i, mi, m;
3455: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3456: double sum=0., jmean=0.;*/
3457: int first;
3458: int j, k=0,jk, ju, jl;
3459: double sum=0.;
3460: first=0;
1.164 brouard 3461: jmin=100000;
1.126 brouard 3462: jmax=-1;
3463: jmean=0.;
3464: for(i=1; i<=imx; i++){
3465: mi=0;
3466: m=firstpass;
3467: while(s[m][i] <= nlstate){
3468: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
3469: mw[++mi][i]=m;
3470: if(m >=lastpass)
3471: break;
3472: else
3473: m++;
3474: }/* end while */
3475: if (s[m][i] > nlstate){
3476: mi++; /* Death is another wave */
3477: /* if(mi==0) never been interviewed correctly before death */
3478: /* Only death is a correct wave */
3479: mw[mi][i]=m;
3480: }
3481:
3482: wav[i]=mi;
3483: if(mi==0){
3484: nbwarn++;
3485: if(first==0){
3486: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3487: first=1;
3488: }
3489: if(first==1){
3490: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3491: }
3492: } /* end mi==0 */
3493: } /* End individuals */
3494:
3495: for(i=1; i<=imx; i++){
3496: for(mi=1; mi<wav[i];mi++){
3497: if (stepm <=0)
3498: dh[mi][i]=1;
3499: else{
3500: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3501: if (agedc[i] < 2*AGESUP) {
3502: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3503: if(j==0) j=1; /* Survives at least one month after exam */
3504: else if(j<0){
3505: nberr++;
3506: 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]);
3507: j=1; /* Temporary Dangerous patch */
3508: 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);
3509: 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]);
3510: 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);
3511: }
3512: k=k+1;
3513: if (j >= jmax){
3514: jmax=j;
3515: ijmax=i;
3516: }
3517: if (j <= jmin){
3518: jmin=j;
3519: ijmin=i;
3520: }
3521: sum=sum+j;
3522: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3523: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3524: }
3525: }
3526: else{
3527: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3528: /* 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]); */
3529:
3530: k=k+1;
3531: if (j >= jmax) {
3532: jmax=j;
3533: ijmax=i;
3534: }
3535: else if (j <= jmin){
3536: jmin=j;
3537: ijmin=i;
3538: }
3539: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3540: /*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]);*/
3541: if(j<0){
3542: nberr++;
3543: 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]);
3544: 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]);
3545: }
3546: sum=sum+j;
3547: }
3548: jk= j/stepm;
3549: jl= j -jk*stepm;
3550: ju= j -(jk+1)*stepm;
3551: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3552: if(jl==0){
3553: dh[mi][i]=jk;
3554: bh[mi][i]=0;
3555: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 3556: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 3557: dh[mi][i]=jk+1;
3558: bh[mi][i]=ju;
3559: }
3560: }else{
3561: if(jl <= -ju){
3562: dh[mi][i]=jk;
3563: bh[mi][i]=jl; /* bias is positive if real duration
3564: * is higher than the multiple of stepm and negative otherwise.
3565: */
3566: }
3567: else{
3568: dh[mi][i]=jk+1;
3569: bh[mi][i]=ju;
3570: }
3571: if(dh[mi][i]==0){
3572: dh[mi][i]=1; /* At least one step */
3573: bh[mi][i]=ju; /* At least one step */
3574: /* 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);*/
3575: }
3576: } /* end if mle */
3577: }
3578: } /* end wave */
3579: }
3580: jmean=sum/k;
3581: 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 3582: 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 3583: }
3584:
3585: /*********** Tricode ****************************/
1.145 brouard 3586: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 3587: {
1.144 brouard 3588: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3589: /* 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 3590: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 3591: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 3592: * nbcode[Tvar[j]][1]=
1.144 brouard 3593: */
1.130 brouard 3594:
1.145 brouard 3595: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 3596: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 3597: int cptcode=0; /* Modality max of covariates j */
3598: int modmincovj=0; /* Modality min of covariates j */
3599:
3600:
1.126 brouard 3601: cptcoveff=0;
3602:
1.144 brouard 3603: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 3604:
1.145 brouard 3605: /* Loop on covariates without age and products */
1.186 brouard 3606: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
1.192 brouard 3607: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.186 brouard 3608: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.136 brouard 3609: modality of this covariate Vj*/
1.145 brouard 3610: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3611: * If product of Vn*Vm, still boolean *:
3612: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3613: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3614: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 3615: modality of the nth covariate of individual i. */
1.145 brouard 3616: if (ij > modmaxcovj)
3617: modmaxcovj=ij;
3618: else if (ij < modmincovj)
3619: modmincovj=ij;
3620: if ((ij < -1) && (ij > NCOVMAX)){
3621: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3622: exit(1);
3623: }else
1.136 brouard 3624: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 3625: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 3626: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 3627: /* getting the maximum value of the modality of the covariate
3628: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3629: female is 1, then modmaxcovj=1.*/
1.192 brouard 3630: } /* end for loop on individuals i */
1.145 brouard 3631: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.192 brouard 3632: 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 3633: cptcode=modmaxcovj;
1.137 brouard 3634: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 3635: /*for (i=0; i<=cptcode; i++) {*/
1.192 brouard 3636: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
3637: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3638: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3639: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
3640: if( k != -1){
3641: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
3642: covariate for which somebody answered excluding
3643: undefined. Usually 2: 0 and 1. */
3644: }
3645: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
3646: covariate for which somebody answered including
3647: undefined. Usually 3: -1, 0 and 1. */
1.145 brouard 3648: }
3649: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3650: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3651: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3652:
1.136 brouard 3653: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 3654: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3655: 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 3656: modmincovj=3; modmaxcovj = 7;
1.186 brouard 3657: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3658: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3659: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 3660: nbcode[Tvar[j]][ij]=k;
3661: nbcode[Tvar[j]][1]=0;
3662: nbcode[Tvar[j]][2]=1;
3663: nbcode[Tvar[j]][3]=2;
1.197 brouard 3664: To be continued (not working yet).
1.145 brouard 3665: */
1.197 brouard 3666: ij=0; /* ij is similar to i but can jump over null modalities */
3667: 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*/
3668: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
1.192 brouard 3669: break;
3670: }
3671: ij++;
1.197 brouard 3672: 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 3673: cptcode = ij; /* New max modality for covar j */
3674: } /* end of loop on modality i=-1 to 1 or more */
3675:
3676: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
3677: /* /\*recode from 0 *\/ */
3678: /* k is a modality. If we have model=V1+V1*sex */
3679: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3680: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
3681: /* } */
3682: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
3683: /* if (ij > ncodemax[j]) { */
3684: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3685: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3686: /* break; */
3687: /* } */
3688: /* } /\* end of loop on modality k *\/ */
1.137 brouard 3689: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3690:
1.145 brouard 3691: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3692:
1.187 brouard 3693: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.145 brouard 3694: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3695: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.187 brouard 3696: Ndum[ij]++; /* Might be supersed V1 + V1*age */
1.145 brouard 3697: }
1.126 brouard 3698:
1.192 brouard 3699: ij=0;
1.145 brouard 3700: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3701: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3702: if((Ndum[i]!=0) && (i<=ncovcol)){
1.192 brouard 3703: ij++;
1.145 brouard 3704: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3705: Tvaraff[ij]=i; /*For printing (unclear) */
1.192 brouard 3706: }else{
3707: /* Tvaraff[ij]=0; */
3708: }
1.126 brouard 3709: }
1.192 brouard 3710: /* ij--; */
1.144 brouard 3711: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3712:
1.126 brouard 3713: }
3714:
1.145 brouard 3715:
1.126 brouard 3716: /*********** Health Expectancies ****************/
3717:
1.127 brouard 3718: 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 3719:
3720: {
3721: /* Health expectancies, no variances */
1.164 brouard 3722: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3723: int nhstepma, nstepma; /* Decreasing with age */
3724: double age, agelim, hf;
3725: double ***p3mat;
3726: double eip;
3727:
3728: pstamp(ficreseij);
3729: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3730: fprintf(ficreseij,"# Age");
3731: for(i=1; i<=nlstate;i++){
3732: for(j=1; j<=nlstate;j++){
3733: fprintf(ficreseij," e%1d%1d ",i,j);
3734: }
3735: fprintf(ficreseij," e%1d. ",i);
3736: }
3737: fprintf(ficreseij,"\n");
3738:
3739:
3740: if(estepm < stepm){
3741: printf ("Problem %d lower than %d\n",estepm, stepm);
3742: }
3743: else hstepm=estepm;
3744: /* We compute the life expectancy from trapezoids spaced every estepm months
3745: * This is mainly to measure the difference between two models: for example
3746: * if stepm=24 months pijx are given only every 2 years and by summing them
3747: * we are calculating an estimate of the Life Expectancy assuming a linear
3748: * progression in between and thus overestimating or underestimating according
3749: * to the curvature of the survival function. If, for the same date, we
3750: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3751: * to compare the new estimate of Life expectancy with the same linear
3752: * hypothesis. A more precise result, taking into account a more precise
3753: * curvature will be obtained if estepm is as small as stepm. */
3754:
3755: /* For example we decided to compute the life expectancy with the smallest unit */
3756: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3757: nhstepm is the number of hstepm from age to agelim
3758: nstepm is the number of stepm from age to agelin.
3759: Look at hpijx to understand the reason of that which relies in memory size
3760: and note for a fixed period like estepm months */
3761: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3762: survival function given by stepm (the optimization length). Unfortunately it
3763: means that if the survival funtion is printed only each two years of age and if
3764: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3765: results. So we changed our mind and took the option of the best precision.
3766: */
3767: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3768:
3769: agelim=AGESUP;
3770: /* If stepm=6 months */
3771: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3772: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3773:
3774: /* nhstepm age range expressed in number of stepm */
3775: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3776: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3777: /* if (stepm >= YEARM) hstepm=1;*/
3778: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3779: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3780:
3781: for (age=bage; age<=fage; age ++){
3782: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3783: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3784: /* if (stepm >= YEARM) hstepm=1;*/
3785: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3786:
3787: /* If stepm=6 months */
3788: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3789: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3790:
3791: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3792:
3793: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3794:
3795: printf("%d|",(int)age);fflush(stdout);
3796: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3797:
3798: /* Computing expectancies */
3799: for(i=1; i<=nlstate;i++)
3800: for(j=1; j<=nlstate;j++)
3801: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3802: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3803:
3804: /* 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]);*/
3805:
3806: }
3807:
3808: fprintf(ficreseij,"%3.0f",age );
3809: for(i=1; i<=nlstate;i++){
3810: eip=0;
3811: for(j=1; j<=nlstate;j++){
3812: eip +=eij[i][j][(int)age];
3813: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3814: }
3815: fprintf(ficreseij,"%9.4f", eip );
3816: }
3817: fprintf(ficreseij,"\n");
3818:
3819: }
3820: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3821: printf("\n");
3822: fprintf(ficlog,"\n");
3823:
3824: }
3825:
1.127 brouard 3826: 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 3827:
3828: {
3829: /* Covariances of health expectancies eij and of total life expectancies according
3830: to initial status i, ei. .
3831: */
3832: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3833: int nhstepma, nstepma; /* Decreasing with age */
3834: double age, agelim, hf;
3835: double ***p3matp, ***p3matm, ***varhe;
3836: double **dnewm,**doldm;
3837: double *xp, *xm;
3838: double **gp, **gm;
3839: double ***gradg, ***trgradg;
3840: int theta;
3841:
3842: double eip, vip;
3843:
3844: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3845: xp=vector(1,npar);
3846: xm=vector(1,npar);
3847: dnewm=matrix(1,nlstate*nlstate,1,npar);
3848: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3849:
3850: pstamp(ficresstdeij);
3851: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3852: fprintf(ficresstdeij,"# Age");
3853: for(i=1; i<=nlstate;i++){
3854: for(j=1; j<=nlstate;j++)
3855: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3856: fprintf(ficresstdeij," e%1d. ",i);
3857: }
3858: fprintf(ficresstdeij,"\n");
3859:
3860: pstamp(ficrescveij);
3861: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3862: fprintf(ficrescveij,"# Age");
3863: for(i=1; i<=nlstate;i++)
3864: for(j=1; j<=nlstate;j++){
3865: cptj= (j-1)*nlstate+i;
3866: for(i2=1; i2<=nlstate;i2++)
3867: for(j2=1; j2<=nlstate;j2++){
3868: cptj2= (j2-1)*nlstate+i2;
3869: if(cptj2 <= cptj)
3870: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3871: }
3872: }
3873: fprintf(ficrescveij,"\n");
3874:
3875: if(estepm < stepm){
3876: printf ("Problem %d lower than %d\n",estepm, stepm);
3877: }
3878: else hstepm=estepm;
3879: /* We compute the life expectancy from trapezoids spaced every estepm months
3880: * This is mainly to measure the difference between two models: for example
3881: * if stepm=24 months pijx are given only every 2 years and by summing them
3882: * we are calculating an estimate of the Life Expectancy assuming a linear
3883: * progression in between and thus overestimating or underestimating according
3884: * to the curvature of the survival function. If, for the same date, we
3885: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3886: * to compare the new estimate of Life expectancy with the same linear
3887: * hypothesis. A more precise result, taking into account a more precise
3888: * curvature will be obtained if estepm is as small as stepm. */
3889:
3890: /* For example we decided to compute the life expectancy with the smallest unit */
3891: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3892: nhstepm is the number of hstepm from age to agelim
3893: nstepm is the number of stepm from age to agelin.
3894: Look at hpijx to understand the reason of that which relies in memory size
3895: and note for a fixed period like estepm months */
3896: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3897: survival function given by stepm (the optimization length). Unfortunately it
3898: means that if the survival funtion is printed only each two years of age and if
3899: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3900: results. So we changed our mind and took the option of the best precision.
3901: */
3902: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3903:
3904: /* If stepm=6 months */
3905: /* nhstepm age range expressed in number of stepm */
3906: agelim=AGESUP;
3907: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3908: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3909: /* if (stepm >= YEARM) hstepm=1;*/
3910: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3911:
3912: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3913: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3914: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3915: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3916: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3917: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3918:
3919: for (age=bage; age<=fage; age ++){
3920: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3921: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3922: /* if (stepm >= YEARM) hstepm=1;*/
3923: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3924:
3925: /* If stepm=6 months */
3926: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3927: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3928:
3929: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3930:
3931: /* Computing Variances of health expectancies */
3932: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3933: decrease memory allocation */
3934: for(theta=1; theta <=npar; theta++){
3935: for(i=1; i<=npar; i++){
3936: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3937: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3938: }
3939: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3940: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3941:
3942: for(j=1; j<= nlstate; j++){
3943: for(i=1; i<=nlstate; i++){
3944: for(h=0; h<=nhstepm-1; h++){
3945: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3946: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3947: }
3948: }
3949: }
3950:
3951: for(ij=1; ij<= nlstate*nlstate; ij++)
3952: for(h=0; h<=nhstepm-1; h++){
3953: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3954: }
3955: }/* End theta */
3956:
3957:
3958: for(h=0; h<=nhstepm-1; h++)
3959: for(j=1; j<=nlstate*nlstate;j++)
3960: for(theta=1; theta <=npar; theta++)
3961: trgradg[h][j][theta]=gradg[h][theta][j];
3962:
3963:
3964: for(ij=1;ij<=nlstate*nlstate;ij++)
3965: for(ji=1;ji<=nlstate*nlstate;ji++)
3966: varhe[ij][ji][(int)age] =0.;
3967:
3968: printf("%d|",(int)age);fflush(stdout);
3969: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3970: for(h=0;h<=nhstepm-1;h++){
3971: for(k=0;k<=nhstepm-1;k++){
3972: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3973: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3974: for(ij=1;ij<=nlstate*nlstate;ij++)
3975: for(ji=1;ji<=nlstate*nlstate;ji++)
3976: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3977: }
3978: }
3979:
3980: /* Computing expectancies */
3981: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3982: for(i=1; i<=nlstate;i++)
3983: for(j=1; j<=nlstate;j++)
3984: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3985: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3986:
3987: /* 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]);*/
3988:
3989: }
3990:
3991: fprintf(ficresstdeij,"%3.0f",age );
3992: for(i=1; i<=nlstate;i++){
3993: eip=0.;
3994: vip=0.;
3995: for(j=1; j<=nlstate;j++){
3996: eip += eij[i][j][(int)age];
3997: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3998: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3999: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
4000: }
4001: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
4002: }
4003: fprintf(ficresstdeij,"\n");
4004:
4005: fprintf(ficrescveij,"%3.0f",age );
4006: for(i=1; i<=nlstate;i++)
4007: for(j=1; j<=nlstate;j++){
4008: cptj= (j-1)*nlstate+i;
4009: for(i2=1; i2<=nlstate;i2++)
4010: for(j2=1; j2<=nlstate;j2++){
4011: cptj2= (j2-1)*nlstate+i2;
4012: if(cptj2 <= cptj)
4013: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
4014: }
4015: }
4016: fprintf(ficrescveij,"\n");
4017:
4018: }
4019: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
4020: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
4021: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
4022: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
4023: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4024: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4025: printf("\n");
4026: fprintf(ficlog,"\n");
4027:
4028: free_vector(xm,1,npar);
4029: free_vector(xp,1,npar);
4030: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
4031: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
4032: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
4033: }
4034:
4035: /************ Variance ******************/
1.209 brouard 4036: void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
1.126 brouard 4037: {
4038: /* Variance of health expectancies */
4039: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
4040: /* double **newm;*/
1.169 brouard 4041: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
4042:
4043: int movingaverage();
1.126 brouard 4044: double **dnewm,**doldm;
4045: double **dnewmp,**doldmp;
4046: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 4047: int k;
1.126 brouard 4048: double *xp;
4049: double **gp, **gm; /* for var eij */
4050: double ***gradg, ***trgradg; /*for var eij */
4051: double **gradgp, **trgradgp; /* for var p point j */
4052: double *gpp, *gmp; /* for var p point j */
4053: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
4054: double ***p3mat;
4055: double age,agelim, hf;
4056: double ***mobaverage;
4057: int theta;
4058: char digit[4];
4059: char digitp[25];
4060:
4061: char fileresprobmorprev[FILENAMELENGTH];
4062:
4063: if(popbased==1){
4064: if(mobilav!=0)
1.201 brouard 4065: strcpy(digitp,"-POPULBASED-MOBILAV_");
4066: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
1.126 brouard 4067: }
4068: else
1.201 brouard 4069: strcpy(digitp,"-STABLBASED_");
1.126 brouard 4070:
4071: if (mobilav!=0) {
4072: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4073: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4074: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4075: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4076: }
4077: }
4078:
1.201 brouard 4079: strcpy(fileresprobmorprev,"PRMORPREV-");
1.126 brouard 4080: sprintf(digit,"%-d",ij);
4081: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
4082: strcat(fileresprobmorprev,digit); /* Tvar to be done */
4083: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
1.202 brouard 4084: strcat(fileresprobmorprev,fileresu);
1.126 brouard 4085: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
4086: printf("Problem with resultfile: %s\n", fileresprobmorprev);
4087: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
4088: }
4089: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4090: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4091: pstamp(ficresprobmorprev);
4092: 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);
4093: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
4094: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4095: fprintf(ficresprobmorprev," p.%-d SE",j);
4096: for(i=1; i<=nlstate;i++)
4097: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
4098: }
4099: fprintf(ficresprobmorprev,"\n");
1.208 brouard 4100:
1.126 brouard 4101: fprintf(ficgp,"\n# Routine varevsij");
1.200 brouard 4102: fprintf(ficgp,"\nunset title \n");
4103: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
1.126 brouard 4104: 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");
4105: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
4106: /* } */
4107: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4108: pstamp(ficresvij);
4109: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
4110: if(popbased==1)
1.128 brouard 4111: fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
1.126 brouard 4112: else
4113: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
4114: fprintf(ficresvij,"# Age");
4115: for(i=1; i<=nlstate;i++)
4116: for(j=1; j<=nlstate;j++)
4117: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
4118: fprintf(ficresvij,"\n");
4119:
4120: xp=vector(1,npar);
4121: dnewm=matrix(1,nlstate,1,npar);
4122: doldm=matrix(1,nlstate,1,nlstate);
4123: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
4124: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4125:
4126: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
4127: gpp=vector(nlstate+1,nlstate+ndeath);
4128: gmp=vector(nlstate+1,nlstate+ndeath);
4129: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
4130:
4131: if(estepm < stepm){
4132: printf ("Problem %d lower than %d\n",estepm, stepm);
4133: }
4134: else hstepm=estepm;
4135: /* For example we decided to compute the life expectancy with the smallest unit */
4136: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4137: nhstepm is the number of hstepm from age to agelim
1.208 brouard 4138: nstepm is the number of stepm from age to agelim.
1.209 brouard 4139: Look at function hpijx to understand why because of memory size limitations,
1.208 brouard 4140: we decided (b) to get a life expectancy respecting the most precise curvature of the
1.126 brouard 4141: survival function given by stepm (the optimization length). Unfortunately it
4142: means that if the survival funtion is printed every two years of age and if
4143: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4144: results. So we changed our mind and took the option of the best precision.
4145: */
4146: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4147: agelim = AGESUP;
4148: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4149: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4150: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4151: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4152: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
4153: gp=matrix(0,nhstepm,1,nlstate);
4154: gm=matrix(0,nhstepm,1,nlstate);
4155:
4156:
4157: for(theta=1; theta <=npar; theta++){
4158: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
4159: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4160: }
1.209 brouard 4161:
4162: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.126 brouard 4163:
4164: if (popbased==1) {
4165: if(mobilav ==0){
4166: for(i=1; i<=nlstate;i++)
4167: prlim[i][i]=probs[(int)age][i][ij];
4168: }else{ /* mobilav */
4169: for(i=1; i<=nlstate;i++)
4170: prlim[i][i]=mobaverage[(int)age][i][ij];
4171: }
4172: }
4173:
1.209 brouard 4174: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); /* Returns p3mat[i][j][h] for h=1 to nhstepm */
1.126 brouard 4175: for(j=1; j<= nlstate; j++){
4176: for(h=0; h<=nhstepm; h++){
4177: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
4178: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
4179: }
4180: }
1.209 brouard 4181: /* Next for computing probability of death (h=1 means
1.126 brouard 4182: computed over hstepm matrices product = hstepm*stepm months)
4183: as a weighted average of prlim.
4184: */
4185: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4186: for(i=1,gpp[j]=0.; i<= nlstate; i++)
4187: gpp[j] += prlim[i][i]*p3mat[i][j][1];
4188: }
4189: /* end probability of death */
4190:
4191: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
4192: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 4193:
4194: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
1.126 brouard 4195:
4196: if (popbased==1) {
4197: if(mobilav ==0){
4198: for(i=1; i<=nlstate;i++)
4199: prlim[i][i]=probs[(int)age][i][ij];
4200: }else{ /* mobilav */
4201: for(i=1; i<=nlstate;i++)
4202: prlim[i][i]=mobaverage[(int)age][i][ij];
4203: }
4204: }
4205:
1.209 brouard 4206: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
4207:
1.128 brouard 4208: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 4209: for(h=0; h<=nhstepm; h++){
4210: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
4211: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
4212: }
4213: }
4214: /* This for computing probability of death (h=1 means
4215: computed over hstepm matrices product = hstepm*stepm months)
4216: as a weighted average of prlim.
4217: */
4218: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4219: for(i=1,gmp[j]=0.; i<= nlstate; i++)
4220: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4221: }
4222: /* end probability of death */
4223:
4224: for(j=1; j<= nlstate; j++) /* vareij */
4225: for(h=0; h<=nhstepm; h++){
4226: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
4227: }
4228:
4229: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
4230: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
4231: }
4232:
4233: } /* End theta */
4234:
4235: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
4236:
4237: for(h=0; h<=nhstepm; h++) /* veij */
4238: for(j=1; j<=nlstate;j++)
4239: for(theta=1; theta <=npar; theta++)
4240: trgradg[h][j][theta]=gradg[h][theta][j];
4241:
4242: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
4243: for(theta=1; theta <=npar; theta++)
4244: trgradgp[j][theta]=gradgp[theta][j];
4245:
4246:
4247: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4248: for(i=1;i<=nlstate;i++)
4249: for(j=1;j<=nlstate;j++)
4250: vareij[i][j][(int)age] =0.;
4251:
4252: for(h=0;h<=nhstepm;h++){
4253: for(k=0;k<=nhstepm;k++){
4254: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
4255: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
4256: for(i=1;i<=nlstate;i++)
4257: for(j=1;j<=nlstate;j++)
4258: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
4259: }
4260: }
4261:
4262: /* pptj */
4263: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
4264: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
4265: for(j=nlstate+1;j<=nlstate+ndeath;j++)
4266: for(i=nlstate+1;i<=nlstate+ndeath;i++)
4267: varppt[j][i]=doldmp[j][i];
4268: /* end ppptj */
4269: /* x centered again */
1.209 brouard 4270:
4271: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
1.126 brouard 4272:
4273: if (popbased==1) {
4274: if(mobilav ==0){
4275: for(i=1; i<=nlstate;i++)
4276: prlim[i][i]=probs[(int)age][i][ij];
4277: }else{ /* mobilav */
4278: for(i=1; i<=nlstate;i++)
4279: prlim[i][i]=mobaverage[(int)age][i][ij];
4280: }
4281: }
4282:
4283: /* This for computing probability of death (h=1 means
4284: computed over hstepm (estepm) matrices product = hstepm*stepm months)
4285: as a weighted average of prlim.
4286: */
1.209 brouard 4287: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
1.126 brouard 4288: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4289: for(i=1,gmp[j]=0.;i<= nlstate; i++)
4290: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4291: }
4292: /* end probability of death */
4293:
4294: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
4295: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4296: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
4297: for(i=1; i<=nlstate;i++){
4298: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
4299: }
4300: }
4301: fprintf(ficresprobmorprev,"\n");
4302:
4303: fprintf(ficresvij,"%.0f ",age );
4304: for(i=1; i<=nlstate;i++)
4305: for(j=1; j<=nlstate;j++){
4306: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
4307: }
4308: fprintf(ficresvij,"\n");
4309: free_matrix(gp,0,nhstepm,1,nlstate);
4310: free_matrix(gm,0,nhstepm,1,nlstate);
4311: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
4312: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
4313: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4314: } /* End age */
4315: free_vector(gpp,nlstate+1,nlstate+ndeath);
4316: free_vector(gmp,nlstate+1,nlstate+ndeath);
4317: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
4318: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.199 brouard 4319: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
4320: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
1.126 brouard 4321: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 4322: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.201 brouard 4323: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4324: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
4325: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
4326: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 4327: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 4328: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 4329: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 4330: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
1.201 brouard 4331: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.svg\"> <br>\n", estepm,subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.199 brouard 4332: /* 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 4333: */
1.199 brouard 4334: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
1.201 brouard 4335: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4336:
4337: free_vector(xp,1,npar);
4338: free_matrix(doldm,1,nlstate,1,nlstate);
4339: free_matrix(dnewm,1,nlstate,1,npar);
4340: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4341: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
4342: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4343: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4344: fclose(ficresprobmorprev);
4345: fflush(ficgp);
4346: fflush(fichtm);
4347: } /* end varevsij */
4348:
4349: /************ Variance of prevlim ******************/
1.209 brouard 4350: 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 4351: {
1.205 brouard 4352: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 4353: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 4354:
1.126 brouard 4355: double **dnewm,**doldm;
4356: int i, j, nhstepm, hstepm;
4357: double *xp;
4358: double *gp, *gm;
4359: double **gradg, **trgradg;
1.208 brouard 4360: double **mgm, **mgp;
1.126 brouard 4361: double age,agelim;
4362: int theta;
4363:
4364: pstamp(ficresvpl);
4365: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
4366: fprintf(ficresvpl,"# Age");
4367: for(i=1; i<=nlstate;i++)
4368: fprintf(ficresvpl," %1d-%1d",i,i);
4369: fprintf(ficresvpl,"\n");
4370:
4371: xp=vector(1,npar);
4372: dnewm=matrix(1,nlstate,1,npar);
4373: doldm=matrix(1,nlstate,1,nlstate);
4374:
4375: hstepm=1*YEARM; /* Every year of age */
4376: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
4377: agelim = AGESUP;
4378: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4379: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4380: if (stepm >= YEARM) hstepm=1;
4381: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4382: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 4383: mgp=matrix(1,npar,1,nlstate);
4384: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 4385: gp=vector(1,nlstate);
4386: gm=vector(1,nlstate);
4387:
4388: for(theta=1; theta <=npar; theta++){
4389: for(i=1; i<=npar; i++){ /* Computes gradient */
4390: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4391: }
1.209 brouard 4392: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
4393: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
4394: else
4395: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 4396: for(i=1;i<=nlstate;i++){
1.126 brouard 4397: gp[i] = prlim[i][i];
1.208 brouard 4398: mgp[theta][i] = prlim[i][i];
4399: }
1.126 brouard 4400: for(i=1; i<=npar; i++) /* Computes gradient */
4401: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 4402: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
4403: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
4404: else
4405: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 4406: for(i=1;i<=nlstate;i++){
1.126 brouard 4407: gm[i] = prlim[i][i];
1.208 brouard 4408: mgm[theta][i] = prlim[i][i];
4409: }
1.126 brouard 4410: for(i=1;i<=nlstate;i++)
4411: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 4412: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 4413: } /* End theta */
4414:
4415: trgradg =matrix(1,nlstate,1,npar);
4416:
4417: for(j=1; j<=nlstate;j++)
4418: for(theta=1; theta <=npar; theta++)
4419: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 4420: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
4421: /* printf("\nmgm mgp %d ",(int)age); */
4422: /* for(j=1; j<=nlstate;j++){ */
4423: /* printf(" %d ",j); */
4424: /* for(theta=1; theta <=npar; theta++) */
4425: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
4426: /* printf("\n "); */
4427: /* } */
4428: /* } */
4429: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
4430: /* printf("\n gradg %d ",(int)age); */
4431: /* for(j=1; j<=nlstate;j++){ */
4432: /* printf("%d ",j); */
4433: /* for(theta=1; theta <=npar; theta++) */
4434: /* printf("%d %lf ",theta,gradg[theta][j]); */
4435: /* printf("\n "); */
4436: /* } */
4437: /* } */
1.126 brouard 4438:
4439: for(i=1;i<=nlstate;i++)
4440: varpl[i][(int)age] =0.;
1.209 brouard 4441: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.205 brouard 4442: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4443: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4444: }else{
1.126 brouard 4445: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4446: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 4447: }
1.126 brouard 4448: for(i=1;i<=nlstate;i++)
4449: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4450:
4451: fprintf(ficresvpl,"%.0f ",age );
4452: for(i=1; i<=nlstate;i++)
4453: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4454: fprintf(ficresvpl,"\n");
4455: free_vector(gp,1,nlstate);
4456: free_vector(gm,1,nlstate);
1.208 brouard 4457: free_matrix(mgm,1,npar,1,nlstate);
4458: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 4459: free_matrix(gradg,1,npar,1,nlstate);
4460: free_matrix(trgradg,1,nlstate,1,npar);
4461: } /* End age */
4462:
4463: free_vector(xp,1,npar);
4464: free_matrix(doldm,1,nlstate,1,npar);
4465: free_matrix(dnewm,1,nlstate,1,nlstate);
4466:
4467: }
4468:
4469: /************ Variance of one-step probabilities ******************/
4470: 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[])
4471: {
1.164 brouard 4472: int i, j=0, k1, l1, tj;
1.126 brouard 4473: int k2, l2, j1, z1;
1.164 brouard 4474: int k=0, l;
1.145 brouard 4475: int first=1, first1, first2;
1.126 brouard 4476: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4477: double **dnewm,**doldm;
4478: double *xp;
4479: double *gp, *gm;
4480: double **gradg, **trgradg;
4481: double **mu;
1.164 brouard 4482: double age, cov[NCOVMAX+1];
1.126 brouard 4483: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4484: int theta;
4485: char fileresprob[FILENAMELENGTH];
4486: char fileresprobcov[FILENAMELENGTH];
4487: char fileresprobcor[FILENAMELENGTH];
4488: double ***varpij;
4489:
1.201 brouard 4490: strcpy(fileresprob,"PROB_");
1.126 brouard 4491: strcat(fileresprob,fileres);
4492: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4493: printf("Problem with resultfile: %s\n", fileresprob);
4494: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4495: }
1.201 brouard 4496: strcpy(fileresprobcov,"PROBCOV_");
1.202 brouard 4497: strcat(fileresprobcov,fileresu);
1.126 brouard 4498: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4499: printf("Problem with resultfile: %s\n", fileresprobcov);
4500: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4501: }
1.201 brouard 4502: strcpy(fileresprobcor,"PROBCOR_");
1.202 brouard 4503: strcat(fileresprobcor,fileresu);
1.126 brouard 4504: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4505: printf("Problem with resultfile: %s\n", fileresprobcor);
4506: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4507: }
4508: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4509: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4510: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4511: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4512: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4513: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4514: pstamp(ficresprob);
4515: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4516: fprintf(ficresprob,"# Age");
4517: pstamp(ficresprobcov);
4518: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4519: fprintf(ficresprobcov,"# Age");
4520: pstamp(ficresprobcor);
4521: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4522: fprintf(ficresprobcor,"# Age");
4523:
4524:
4525: for(i=1; i<=nlstate;i++)
4526: for(j=1; j<=(nlstate+ndeath);j++){
4527: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4528: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4529: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4530: }
4531: /* fprintf(ficresprob,"\n");
4532: fprintf(ficresprobcov,"\n");
4533: fprintf(ficresprobcor,"\n");
4534: */
1.131 brouard 4535: xp=vector(1,npar);
1.126 brouard 4536: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4537: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4538: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4539: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4540: first=1;
4541: fprintf(ficgp,"\n# Routine varprob");
4542: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4543: fprintf(fichtm,"\n");
4544:
1.200 brouard 4545: 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 4546: 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);
4547: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 4548: and drawn. It helps understanding how is the covariance between two incidences.\
4549: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4550: 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. \
4551: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4552: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4553: standard deviations wide on each axis. <br>\
4554: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4555: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4556: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4557:
4558: cov[1]=1;
1.145 brouard 4559: /* tj=cptcoveff; */
4560: tj = (int) pow(2,cptcoveff);
1.126 brouard 4561: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4562: j1=0;
1.145 brouard 4563: for(j1=1; j1<=tj;j1++){
4564: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4565: /*j1++;*/
1.126 brouard 4566: if (cptcovn>0) {
4567: fprintf(ficresprob, "\n#********** Variable ");
1.198 brouard 4568: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4569: fprintf(ficresprob, "**********\n#\n");
4570: fprintf(ficresprobcov, "\n#********** Variable ");
1.198 brouard 4571: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4572: fprintf(ficresprobcov, "**********\n#\n");
4573:
4574: fprintf(ficgp, "\n#********** Variable ");
1.198 brouard 4575: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4576: fprintf(ficgp, "**********\n#\n");
4577:
4578:
4579: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.198 brouard 4580: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4581: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4582:
4583: fprintf(ficresprobcor, "\n#********** Variable ");
1.198 brouard 4584: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4585: fprintf(ficresprobcor, "**********\n#");
4586: }
4587:
1.145 brouard 4588: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4589: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4590: gp=vector(1,(nlstate)*(nlstate+ndeath));
4591: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 4592: for (age=bage; age<=fage; age ++){
4593: cov[2]=age;
1.187 brouard 4594: if(nagesqr==1)
4595: cov[3]= age*age;
1.126 brouard 4596: for (k=1; k<=cptcovn;k++) {
1.200 brouard 4597: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
4598: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
1.145 brouard 4599: * 1 1 1 1 1
4600: * 2 2 1 1 1
4601: * 3 1 2 1 1
4602: */
4603: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 4604: }
1.186 brouard 4605: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 4606: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
1.126 brouard 4607: for (k=1; k<=cptcovprod;k++)
1.200 brouard 4608: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.126 brouard 4609:
4610:
4611: for(theta=1; theta <=npar; theta++){
4612: for(i=1; i<=npar; i++)
4613: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4614:
4615: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4616:
4617: k=0;
4618: for(i=1; i<= (nlstate); i++){
4619: for(j=1; j<=(nlstate+ndeath);j++){
4620: k=k+1;
4621: gp[k]=pmmij[i][j];
4622: }
4623: }
4624:
4625: for(i=1; i<=npar; i++)
4626: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4627:
4628: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4629: k=0;
4630: for(i=1; i<=(nlstate); i++){
4631: for(j=1; j<=(nlstate+ndeath);j++){
4632: k=k+1;
4633: gm[k]=pmmij[i][j];
4634: }
4635: }
4636:
4637: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4638: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4639: }
4640:
4641: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4642: for(theta=1; theta <=npar; theta++)
4643: trgradg[j][theta]=gradg[theta][j];
4644:
4645: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4646: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4647:
4648: pmij(pmmij,cov,ncovmodel,x,nlstate);
4649:
4650: k=0;
4651: for(i=1; i<=(nlstate); i++){
4652: for(j=1; j<=(nlstate+ndeath);j++){
4653: k=k+1;
4654: mu[k][(int) age]=pmmij[i][j];
4655: }
4656: }
4657: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4658: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4659: varpij[i][j][(int)age] = doldm[i][j];
4660:
4661: /*printf("\n%d ",(int)age);
4662: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4663: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4664: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4665: }*/
4666:
4667: fprintf(ficresprob,"\n%d ",(int)age);
4668: fprintf(ficresprobcov,"\n%d ",(int)age);
4669: fprintf(ficresprobcor,"\n%d ",(int)age);
4670:
4671: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4672: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4673: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4674: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4675: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4676: }
4677: i=0;
4678: for (k=1; k<=(nlstate);k++){
4679: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 4680: i++;
1.126 brouard 4681: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4682: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4683: for (j=1; j<=i;j++){
1.145 brouard 4684: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 4685: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4686: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4687: }
4688: }
4689: }/* end of loop for state */
4690: } /* end of loop for age */
1.145 brouard 4691: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4692: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4693: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4694: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4695:
1.126 brouard 4696: /* Confidence intervalle of pij */
4697: /*
1.131 brouard 4698: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 4699: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4700: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4701: 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);
4702: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4703: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4704: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4705: */
4706:
4707: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 4708: first1=1;first2=2;
1.126 brouard 4709: for (k2=1; k2<=(nlstate);k2++){
4710: for (l2=1; l2<=(nlstate+ndeath);l2++){
4711: if(l2==k2) continue;
4712: j=(k2-1)*(nlstate+ndeath)+l2;
4713: for (k1=1; k1<=(nlstate);k1++){
4714: for (l1=1; l1<=(nlstate+ndeath);l1++){
4715: if(l1==k1) continue;
4716: i=(k1-1)*(nlstate+ndeath)+l1;
4717: if(i<=j) continue;
4718: for (age=bage; age<=fage; age ++){
4719: if ((int)age %5==0){
4720: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4721: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4722: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4723: mu1=mu[i][(int) age]/stepm*YEARM ;
4724: mu2=mu[j][(int) age]/stepm*YEARM;
4725: c12=cv12/sqrt(v1*v2);
4726: /* Computing eigen value of matrix of covariance */
4727: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4728: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4729: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4730: if(first2==1){
4731: first1=0;
4732: 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);
4733: }
4734: 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);
4735: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4736: /* lc2=fabs(lc2); */
1.135 brouard 4737: }
4738:
1.126 brouard 4739: /* Eigen vectors */
4740: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4741: /*v21=sqrt(1.-v11*v11); *//* error */
4742: v21=(lc1-v1)/cv12*v11;
4743: v12=-v21;
4744: v22=v11;
4745: tnalp=v21/v11;
4746: if(first1==1){
4747: first1=0;
4748: 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);
4749: }
4750: 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);
4751: /*printf(fignu*/
4752: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4753: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4754: if(first==1){
4755: first=0;
1.200 brouard 4756: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
1.126 brouard 4757: fprintf(ficgp,"\nset parametric;unset label");
4758: 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 4759: fprintf(ficgp,"\nset ter svg size 640, 480");
1.126 brouard 4760: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.201 brouard 4761: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">\
4762: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
4763: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\
4764: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
4765: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4766: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.201 brouard 4767: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4768: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4769: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4770: 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",\
4771: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4772: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4773: }else{
4774: first=0;
4775: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4776: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4777: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4778: 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",\
4779: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4780: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4781: }/* if first */
4782: } /* age mod 5 */
4783: } /* end loop age */
1.201 brouard 4784: 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 4785: first=1;
4786: } /*l12 */
4787: } /* k12 */
4788: } /*l1 */
4789: }/* k1 */
1.169 brouard 4790: /* } */ /* loop covariates */
1.126 brouard 4791: }
4792: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4793: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4794: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4795: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4796: free_vector(xp,1,npar);
4797: fclose(ficresprob);
4798: fclose(ficresprobcov);
4799: fclose(ficresprobcor);
4800: fflush(ficgp);
4801: fflush(fichtmcov);
4802: }
4803:
4804:
4805: /******************* Printing html file ***********/
1.201 brouard 4806: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 4807: int lastpass, int stepm, int weightopt, char model[],\
4808: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.211 ! brouard 4809: int popforecast, int prevfcast, int estepm , \
1.126 brouard 4810: double jprev1, double mprev1,double anprev1, \
4811: double jprev2, double mprev2,double anprev2){
4812: int jj1, k1, i1, cpt;
4813:
4814: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4815: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4816: </ul>");
4817: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4818: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
1.201 brouard 4819: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 4820: fprintf(fichtm,"\
4821: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 4822: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 4823: fprintf(fichtm,"\
4824: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4825: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 4826: fprintf(fichtm,"\
1.211 ! brouard 4827: - (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 4828: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4829: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 ! brouard 4830: if(prevfcast==1){
! 4831: fprintf(fichtm,"\
! 4832: - Prevalence projections by age and states: \
1.201 brouard 4833: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 ! brouard 4834: }
1.126 brouard 4835:
4836: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4837:
1.145 brouard 4838: m=pow(2,cptcoveff);
1.126 brouard 4839: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4840:
4841: jj1=0;
4842: for(k1=1; k1<=m;k1++){
1.192 brouard 4843: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4844: jj1++;
4845: if (cptcovn > 0) {
4846: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.192 brouard 4847: for (cpt=1; cpt<=cptcoveff;cpt++){
1.198 brouard 4848: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
4849: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
1.192 brouard 4850: }
1.126 brouard 4851: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4852: }
1.201 brouard 4853: /* aij, bij */
1.211 ! brouard 4854: 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> \
! 4855: <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 4856: /* Pij */
1.211 ! brouard 4857: 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 4858: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 4859: /* Quasi-incidences */
1.211 ! brouard 4860: 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 4861: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\
1.211 ! brouard 4862: incidence (rates) are the limit when h tends to zero of the ratio of the probability <sub>h</sub>P<sub>ij</sub> \
! 4863: 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 4864: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
4865: /* Survival functions (period) in state j */
4866: for(cpt=1; cpt<=nlstate;cpt++){
4867: 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> \
4868: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
4869: }
4870: /* State specific survival functions (period) */
4871: for(cpt=1; cpt<=nlstate;cpt++){
1.208 brouard 4872: fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
1.201 brouard 4873: Or probability to survive in various states (1 to %d) being in state %d at different ages.\
4874: <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);
4875: }
4876: /* Period (stable) prevalence in each health state */
4877: for(cpt=1; cpt<=nlstate;cpt++){
4878: 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> \
4879: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
4880: }
1.211 ! brouard 4881: if(prevfcast==1){
! 4882: /* Projection of prevalence up to period (stable) prevalence in each health state */
! 4883: for(cpt=1; cpt<=nlstate;cpt++){
! 4884: fprintf(fichtm,"<br>\n- Projection of prevalece 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> \
! 4885: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);
! 4886: }
! 4887: }
! 4888:
1.126 brouard 4889: for(cpt=1; cpt<=nlstate;cpt++) {
1.205 brouard 4890: 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 4891: <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 4892: }
1.192 brouard 4893: /* } /\* end i1 *\/ */
1.126 brouard 4894: }/* End k1 */
4895: fprintf(fichtm,"</ul>");
4896:
4897: fprintf(fichtm,"\
4898: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 4899: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 4900: - 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 4901: But because parameters are usually highly correlated (a higher incidence of disability \
4902: and a higher incidence of recovery can give very close observed transition) it might \
4903: be very useful to look not only at linear confidence intervals estimated from the \
4904: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
4905: (parameters) of the logistic regression, it might be more meaningful to visualize the \
4906: covariance matrix of the one-step probabilities. \
4907: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 4908:
1.193 brouard 4909: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4910: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
1.126 brouard 4911: fprintf(fichtm,"\
4912: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4913: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 4914:
4915: fprintf(fichtm,"\
4916: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4917: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
1.126 brouard 4918: fprintf(fichtm,"\
4919: - 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): \
4920: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 4921: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.126 brouard 4922: fprintf(fichtm,"\
4923: - (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): \
4924: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 4925: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.126 brouard 4926: fprintf(fichtm,"\
1.128 brouard 4927: - 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 4928: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
1.126 brouard 4929: fprintf(fichtm,"\
1.128 brouard 4930: - 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 4931: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
1.126 brouard 4932: fprintf(fichtm,"\
4933: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.201 brouard 4934: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 4935:
4936: /* if(popforecast==1) fprintf(fichtm,"\n */
4937: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4938: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4939: /* <br>",fileres,fileres,fileres,fileres); */
4940: /* else */
4941: /* 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); */
4942: fflush(fichtm);
4943: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4944:
1.145 brouard 4945: m=pow(2,cptcoveff);
1.126 brouard 4946: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4947:
4948: jj1=0;
4949: for(k1=1; k1<=m;k1++){
1.192 brouard 4950: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4951: jj1++;
4952: if (cptcovn > 0) {
4953: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4954: for (cpt=1; cpt<=cptcoveff;cpt++)
1.198 brouard 4955: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 4956: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4957: }
4958: for(cpt=1; cpt<=nlstate;cpt++) {
4959: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.205 brouard 4960: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d%d.svg\"> %s_%d-%d.svg <br>\
4961: <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 4962: }
4963: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4964: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4965: true period expectancies (those weighted with period prevalences are also\
4966: drawn in addition to the population based expectancies computed using\
1.205 brouard 4967: observed and cahotic prevalences: <a href=\"%s_%d.svg\">%s_%d.svg<br>\
4968: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.192 brouard 4969: /* } /\* end i1 *\/ */
1.126 brouard 4970: }/* End k1 */
4971: fprintf(fichtm,"</ul>");
4972: fflush(fichtm);
4973: }
4974:
4975: /******************* Gnuplot file **************/
1.211 ! brouard 4976: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, char pathc[], double p[]){
1.126 brouard 4977:
4978: char dirfileres[132],optfileres[132];
1.164 brouard 4979: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.211 ! brouard 4980: int lv=0, vlv=0, kl=0;
1.130 brouard 4981: int ng=0;
1.201 brouard 4982: int vpopbased;
1.126 brouard 4983: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4984: /* printf("Problem with file %s",optionfilegnuplot); */
4985: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4986: /* } */
4987:
4988: /*#ifdef windows */
4989: fprintf(ficgp,"cd \"%s\" \n",pathc);
4990: /*#endif */
4991: m=pow(2,cptcoveff);
4992:
1.202 brouard 4993: /* Contribution to likelihood */
4994: /* Plot the probability implied in the likelihood */
4995: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
4996: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
4997: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
1.205 brouard 4998: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 4999: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 5000: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
5001: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
5002: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
1.204 brouard 5003: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
1.205 brouard 5004: fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$12):5 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
1.204 brouard 5005: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
1.205 brouard 5006: fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$12):4 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
1.204 brouard 5007: for (i=1; i<= nlstate ; i ++) {
5008: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
1.205 brouard 5009: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
5010: fprintf(ficgp," u 2:($4 == %d && $5==%d ? $9 : 1/0):($11/4.):5 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
1.204 brouard 5011: for (j=2; j<= nlstate+ndeath ; j ++) {
1.205 brouard 5012: fprintf(ficgp,",\\\n \"\" u 2:($4 == %d && $5==%d ? $9 : 1/0):($11/4.):5 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
1.204 brouard 5013: }
5014: fprintf(ficgp,";\nset out; unset ylabel;\n");
5015: }
5016: /* 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 */
5017: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
5018: /* 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 5019: fprintf(ficgp,"\nset out;unset log\n");
1.202 brouard 5020: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
5021:
1.126 brouard 5022: strcpy(dirfileres,optionfilefiname);
5023: strcpy(optfileres,"vpl");
5024: /* 1eme*/
1.211 ! brouard 5025: for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
! 5026: for (k1=1; k1<= m ; k1 ++) { /* For each combination of covariate */
! 5027: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
! 5028: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
! 5029: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
! 5030: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
! 5031: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
! 5032: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
! 5033: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
! 5034: vlv= nbcode[Tvaraff[lv]][lv];
! 5035: fprintf(ficgp," V%d=%d ",k,vlv);
! 5036: }
! 5037: fprintf(ficgp,"\n#\n");
! 5038:
1.201 brouard 5039: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
5040: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
1.126 brouard 5041: fprintf(ficgp,"set xlabel \"Age\" \n\
5042: set ylabel \"Probability\" \n\
1.199 brouard 5043: set ter svg size 640, 480\n\
1.201 brouard 5044: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 5045:
5046: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 5047: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5048: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 5049: }
1.201 brouard 5050: fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 5051: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 5052: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5053: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 5054: }
1.201 brouard 5055: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 5056: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 5057: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5058: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 5059: }
1.201 brouard 5060: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
5061: fprintf(ficgp,"\nset out \n");
5062: } /* k1 */
5063: } /* cpt */
1.126 brouard 5064: /*2 eme*/
5065: for (k1=1; k1<= m ; k1 ++) {
1.211 ! brouard 5066: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
! 5067: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
! 5068: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
! 5069: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
! 5070: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
! 5071: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
! 5072: vlv= nbcode[Tvaraff[lv]][lv];
! 5073: fprintf(ficgp," V%d=%d ",k,vlv);
! 5074: }
! 5075: fprintf(ficgp,"\n#\n");
! 5076:
1.201 brouard 5077: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
5078: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
5079: if(vpopbased==0)
5080: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
5081: else
5082: fprintf(ficgp,"\nreplot ");
5083: for (i=1; i<= nlstate+1 ; i ++) {
5084: k=2*i;
5085: 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);
5086: for (j=1; j<= nlstate+1 ; j ++) {
5087: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5088: else fprintf(ficgp," %%*lf (%%*lf)");
5089: }
5090: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
5091: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
5092: 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);
5093: for (j=1; j<= nlstate+1 ; j ++) {
5094: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5095: else fprintf(ficgp," %%*lf (%%*lf)");
5096: }
5097: fprintf(ficgp,"\" t\"\" w l lt 0,");
5098: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
5099: for (j=1; j<= nlstate+1 ; j ++) {
5100: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5101: else fprintf(ficgp," %%*lf (%%*lf)");
5102: }
5103: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
5104: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
5105: } /* state */
5106: } /* vpopbased */
5107: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
5108: } /* k1 */
1.211 ! brouard 5109:
! 5110:
1.126 brouard 5111: /*3eme*/
5112: for (k1=1; k1<= m ; k1 ++) {
5113: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.211 ! brouard 5114: fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt);
! 5115: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
! 5116: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
! 5117: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
! 5118: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
! 5119: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
! 5120: vlv= nbcode[Tvaraff[lv]][lv];
! 5121: fprintf(ficgp," V%d=%d ",k,vlv);
! 5122: }
! 5123: fprintf(ficgp,"\n#\n");
! 5124:
1.126 brouard 5125: /* k=2+nlstate*(2*cpt-2); */
5126: k=2+(nlstate+1)*(cpt-1);
1.201 brouard 5127: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
1.199 brouard 5128: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 5129: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.126 brouard 5130: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
5131: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
5132: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
5133: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
5134: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
5135: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
5136:
5137: */
5138: for (i=1; i< nlstate ; i ++) {
1.201 brouard 5139: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);
1.126 brouard 5140: /* 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);*/
5141:
5142: }
1.201 brouard 5143: 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 5144: }
5145: }
5146:
1.201 brouard 5147: /* Survival functions (period) from state i in state j by initial state i */
5148: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
5149: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.211 ! brouard 5150: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
! 5151: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
! 5152: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
! 5153: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
! 5154: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
! 5155: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
! 5156: vlv= nbcode[Tvaraff[lv]][lv];
! 5157: fprintf(ficgp," V%d=%d ",k,vlv);
! 5158: }
! 5159: fprintf(ficgp,"\n#\n");
! 5160:
1.201 brouard 5161: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
5162: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
5163: set ter svg size 640, 480\n\
5164: unset log y\n\
5165: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 ! brouard 5166: k=3;
1.201 brouard 5167: for (i=1; i<= nlstate ; i ++){
5168: if(i==1)
5169: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5170: else
5171: fprintf(ficgp,", '' ");
5172: l=(nlstate+ndeath)*(i-1)+1;
5173: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
5174: for (j=2; j<= nlstate+ndeath ; j ++)
5175: fprintf(ficgp,"+$%d",k+l+j-1);
5176: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
5177: } /* nlstate */
5178: fprintf(ficgp,"\nset out\n");
5179: } /* end cpt state*/
5180: } /* end covariate */
5181:
5182: /* Survival functions (period) from state i in state j by final state j */
1.202 brouard 5183: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.201 brouard 5184: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
5185: 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 5186: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
! 5187: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
! 5188: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
! 5189: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
! 5190: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
! 5191: vlv= nbcode[Tvaraff[lv]][lv];
! 5192: fprintf(ficgp," V%d=%d ",k,vlv);
! 5193: }
! 5194: fprintf(ficgp,"\n#\n");
! 5195:
1.201 brouard 5196: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
5197: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
5198: set ter svg size 640, 480\n\
5199: unset log y\n\
5200: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 ! brouard 5201: k=3;
1.201 brouard 5202: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
5203: if(j==1)
5204: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5205: else
5206: fprintf(ficgp,", '' ");
5207: l=(nlstate+ndeath)*(cpt-1) +j;
5208: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
5209: /* for (i=2; i<= nlstate+ndeath ; i ++) */
5210: /* fprintf(ficgp,"+$%d",k+l+i-1); */
5211: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
5212: } /* nlstate */
5213: fprintf(ficgp,", '' ");
5214: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
5215: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
5216: l=(nlstate+ndeath)*(cpt-1) +j;
5217: if(j < nlstate)
5218: fprintf(ficgp,"$%d +",k+l);
5219: else
5220: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
5221: }
5222: fprintf(ficgp,"\nset out\n");
5223: } /* end cpt state*/
5224: } /* end covariate */
5225:
1.202 brouard 5226: /* CV preval stable (period) for each covariate */
1.211 ! brouard 5227: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.153 brouard 5228: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.211 ! brouard 5229: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
! 5230: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
! 5231: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
! 5232: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
! 5233: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
! 5234: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
! 5235: vlv= nbcode[Tvaraff[lv]][lv];
! 5236: fprintf(ficgp," V%d=%d ",k,vlv);
! 5237: }
! 5238: fprintf(ficgp,"\n#\n");
! 5239:
1.201 brouard 5240: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 5241: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.199 brouard 5242: set ter svg size 640, 480\n\
1.126 brouard 5243: unset log y\n\
1.153 brouard 5244: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 ! brouard 5245: k=3; /* Offset */
1.153 brouard 5246: for (i=1; i<= nlstate ; i ++){
5247: if(i==1)
1.201 brouard 5248: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
1.153 brouard 5249: else
5250: fprintf(ficgp,", '' ");
1.154 brouard 5251: l=(nlstate+ndeath)*(i-1)+1;
5252: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.201 brouard 5253: for (j=2; j<= nlstate ; j ++)
5254: fprintf(ficgp,"+$%d",k+l+j-1);
1.153 brouard 5255: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
5256: } /* nlstate */
1.201 brouard 5257: fprintf(ficgp,"\nset out\n");
1.153 brouard 5258: } /* end cpt state*/
5259: } /* end covariate */
1.201 brouard 5260:
1.211 ! brouard 5261: if(prevfcast==1){
! 5262: /* Projection from cross-sectional to stable (period) for each covariate */
! 5263:
! 5264: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
! 5265: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
! 5266: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
! 5267: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
! 5268: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
! 5269: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
! 5270: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
! 5271: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
! 5272: vlv= nbcode[Tvaraff[lv]][lv];
! 5273: fprintf(ficgp," V%d=%d ",k,vlv);
! 5274: }
! 5275: fprintf(ficgp,"\n#\n");
! 5276:
! 5277: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
! 5278: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
! 5279: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
! 5280: set ter svg size 640, 480\n\
! 5281: unset log y\n\
! 5282: plot [%.f:%.f] ", ageminpar, agemaxpar);
! 5283: for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
! 5284: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
! 5285: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
! 5286: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
! 5287: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
! 5288: if(i==1){
! 5289: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
! 5290: }else{
! 5291: fprintf(ficgp,",\\\n '' ");
! 5292: }
! 5293: if(cptcoveff ==0){ /* No covariate */
! 5294: fprintf(ficgp," u 2:("); /* Age is in 2 */
! 5295: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
! 5296: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
! 5297: if(i==nlstate+1)
! 5298: fprintf(ficgp," $%d/(1.-$%d)) t 'p.%d' with line ", \
! 5299: 2+(cpt-1)*(nlstate+1)+1+(i-1), 2+1+(i-1)+(nlstate+1)*nlstate,cpt );
! 5300: else
! 5301: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
! 5302: 2+(cpt-1)*(nlstate+1)+1+(i-1), 2+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
! 5303: }else{
! 5304: fprintf(ficgp,"u 6:(("); /* Age is in 6 */
! 5305: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
! 5306: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
! 5307: kl=0;
! 5308: for (k=1; k<=cptcoveff; k++){ /* For each covariate */
! 5309: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
! 5310: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
! 5311: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
! 5312: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
! 5313: vlv= nbcode[Tvaraff[lv]][lv];
! 5314: kl++;
! 5315: /* 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 *\/ */
! 5316: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
! 5317: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
! 5318: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
! 5319: if(k==cptcoveff)
! 5320: if(i==nlstate+1)
! 5321: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv], \
! 5322: 6+(cpt-1)*(nlstate+1)+1+(i-1), 6+1+(i-1)+(nlstate+1)*nlstate,cpt );
! 5323: else
! 5324: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv], \
! 5325: 6+(cpt-1)*(nlstate+1)+1+(i-1), 6+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
! 5326: else{
! 5327: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv]);
! 5328: kl++;
! 5329: }
! 5330: } /* end covariate */
! 5331: } /* end if covariate */
! 5332: } /* nlstate */
! 5333: fprintf(ficgp,"\nset out\n");
! 5334: } /* end cpt state*/
! 5335: } /* end covariate */
! 5336: } /* End if prevfcast */
! 5337:
! 5338:
1.126 brouard 5339: /* proba elementaires */
1.187 brouard 5340: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 5341: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 5342: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 5343: for(k=1; k <=(nlstate+ndeath); k++){
5344: if (k != i) {
1.187 brouard 5345: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 5346: for(j=1; j <=ncovmodel; j++){
1.187 brouard 5347: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 5348: jk++;
5349: }
1.187 brouard 5350: fprintf(ficgp,"\n");
1.126 brouard 5351: }
5352: }
5353: }
1.187 brouard 5354: fprintf(ficgp,"##############\n#\n");
5355:
1.145 brouard 5356: /*goto avoid;*/
1.200 brouard 5357: fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
1.187 brouard 5358: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
5359: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
5360: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
5361: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
5362: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5363: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
5364: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5365: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
5366: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
5367: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5368: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
5369: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
5370: fprintf(ficgp,"#\n");
1.201 brouard 5371: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.187 brouard 5372: fprintf(ficgp,"# ng=%d\n",ng);
5373: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 5374: for(jk=1; jk <=m; jk++) {
1.187 brouard 5375: fprintf(ficgp,"# jk=%d\n",jk);
1.201 brouard 5376: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
5377: fprintf(ficgp,"\nset ter svg size 640, 480 ");
5378: if (ng==1){
5379: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
5380: fprintf(ficgp,"\nunset log y");
5381: }else if (ng==2){
5382: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
5383: fprintf(ficgp,"\nset log y");
5384: }else if (ng==3){
1.126 brouard 5385: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
1.201 brouard 5386: fprintf(ficgp,"\nset log y");
5387: }else
5388: fprintf(ficgp,"\nunset title ");
5389: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 5390: i=1;
5391: for(k2=1; k2<=nlstate; k2++) {
5392: k3=i;
5393: for(k=1; k<=(nlstate+ndeath); k++) {
5394: if (k != k2){
1.201 brouard 5395: switch( ng) {
5396: case 1:
1.187 brouard 5397: if(nagesqr==0)
1.201 brouard 5398: fprintf(ficgp," p%d+p%d*x",i,i+1);
1.187 brouard 5399: else /* nagesqr =1 */
1.201 brouard 5400: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
5401: break;
5402: case 2: /* ng=2 */
1.187 brouard 5403: if(nagesqr==0)
5404: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
5405: else /* nagesqr =1 */
1.201 brouard 5406: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
5407: break;
5408: case 3:
5409: if(nagesqr==0)
5410: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
5411: else /* nagesqr =1 */
5412: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
5413: break;
5414: }
1.141 brouard 5415: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 brouard 5416: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.197 brouard 5417: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
5418: if(ij <=cptcovage) { /* Bug valgrind */
5419: if((j-2)==Tage[ij]) { /* Bug valgrind */
1.200 brouard 5420: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
5421: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
1.197 brouard 5422: ij++;
5423: }
1.186 brouard 5424: }
5425: else
1.198 brouard 5426: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.126 brouard 5427: }
1.201 brouard 5428: if(ng != 1){
5429: fprintf(ficgp,")/(1");
1.126 brouard 5430:
1.201 brouard 5431: for(k1=1; k1 <=nlstate; k1++){
5432: if(nagesqr==0)
5433: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
5434: else /* nagesqr =1 */
5435: 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);
5436:
5437: ij=1;
5438: for(j=3; j <=ncovmodel-nagesqr; j++){
5439: if(ij <=cptcovage) { /* Bug valgrind */
5440: if((j-2)==Tage[ij]) { /* Bug valgrind */
5441: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
5442: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
5443: ij++;
5444: }
1.197 brouard 5445: }
1.201 brouard 5446: else
5447: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.186 brouard 5448: }
1.201 brouard 5449: fprintf(ficgp,")");
1.126 brouard 5450: }
5451: fprintf(ficgp,")");
1.201 brouard 5452: if(ng ==2)
5453: fprintf(ficgp," t \"p%d%d\" ", k2,k);
5454: else /* ng= 3 */
5455: fprintf(ficgp," t \"i%d%d\" ", k2,k);
5456: }else{ /* end ng <> 1 */
5457: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
1.126 brouard 5458: }
5459: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
5460: i=i+ncovmodel;
5461: }
5462: } /* end k */
5463: } /* end k2 */
1.201 brouard 5464: fprintf(ficgp,"\n set out\n");
1.126 brouard 5465: } /* end jk */
5466: } /* end ng */
1.164 brouard 5467: /* avoid: */
1.126 brouard 5468: fflush(ficgp);
5469: } /* end gnuplot */
5470:
5471:
5472: /*************** Moving average **************/
5473: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
5474:
5475: int i, cpt, cptcod;
5476: int modcovmax =1;
5477: int mobilavrange, mob;
5478: double age;
5479:
5480: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
5481: a covariate has 2 modalities */
5482: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
5483:
5484: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
5485: if(mobilav==1) mobilavrange=5; /* default */
5486: else mobilavrange=mobilav;
5487: for (age=bage; age<=fage; age++)
5488: for (i=1; i<=nlstate;i++)
5489: for (cptcod=1;cptcod<=modcovmax;cptcod++)
5490: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
5491: /* We keep the original values on the extreme ages bage, fage and for
5492: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
5493: we use a 5 terms etc. until the borders are no more concerned.
5494: */
5495: for (mob=3;mob <=mobilavrange;mob=mob+2){
5496: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
5497: for (i=1; i<=nlstate;i++){
5498: for (cptcod=1;cptcod<=modcovmax;cptcod++){
5499: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
5500: for (cpt=1;cpt<=(mob-1)/2;cpt++){
5501: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
5502: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
5503: }
5504: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
5505: }
5506: }
5507: }/* end age */
5508: }/* end mob */
5509: }else return -1;
5510: return 0;
5511: }/* End movingaverage */
5512:
5513:
5514: /************** Forecasting ******************/
1.169 brouard 5515: 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 5516: /* proj1, year, month, day of starting projection
5517: agemin, agemax range of age
5518: dateprev1 dateprev2 range of dates during which prevalence is computed
5519: anproj2 year of en of projection (same day and month as proj1).
5520: */
1.164 brouard 5521: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 5522: double agec; /* generic age */
5523: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
5524: double *popeffectif,*popcount;
5525: double ***p3mat;
5526: double ***mobaverage;
5527: char fileresf[FILENAMELENGTH];
5528:
5529: agelim=AGESUP;
1.211 ! brouard 5530: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
! 5531: in each health status at the date of interview (if between dateprev1 and dateprev2).
! 5532: We still use firstpass and lastpass as another selection.
! 5533: */
1.126 brouard 5534: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5535:
1.201 brouard 5536: strcpy(fileresf,"F_");
5537: strcat(fileresf,fileresu);
1.126 brouard 5538: if((ficresf=fopen(fileresf,"w"))==NULL) {
5539: printf("Problem with forecast resultfile: %s\n", fileresf);
5540: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
5541: }
5542: printf("Computing forecasting: result on file '%s' \n", fileresf);
5543: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
5544:
5545: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5546:
5547: if (mobilav!=0) {
5548: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5549: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5550: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5551: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5552: }
5553: }
5554:
5555: stepsize=(int) (stepm+YEARM-1)/YEARM;
5556: if (stepm<=12) stepsize=1;
5557: if(estepm < stepm){
5558: printf ("Problem %d lower than %d\n",estepm, stepm);
5559: }
5560: else hstepm=estepm;
5561:
5562: hstepm=hstepm/stepm;
5563: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
5564: fractional in yp1 */
5565: anprojmean=yp;
5566: yp2=modf((yp1*12),&yp);
5567: mprojmean=yp;
5568: yp1=modf((yp2*30.5),&yp);
5569: jprojmean=yp;
5570: if(jprojmean==0) jprojmean=1;
5571: if(mprojmean==0) jprojmean=1;
5572:
5573: i1=cptcoveff;
5574: if (cptcovn < 1){i1=1;}
5575:
5576: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
5577:
5578: fprintf(ficresf,"#****** Routine prevforecast **\n");
5579:
5580: /* if (h==(int)(YEARM*yearp)){ */
5581: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
5582: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5583: k=k+1;
1.211 ! brouard 5584: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
1.126 brouard 5585: for(j=1;j<=cptcoveff;j++) {
1.211 ! brouard 5586: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5587: }
1.211 ! brouard 5588: fprintf(ficresf," yearproj age");
1.126 brouard 5589: for(j=1; j<=nlstate+ndeath;j++){
5590: for(i=1; i<=nlstate;i++)
5591: fprintf(ficresf," p%d%d",i,j);
5592: fprintf(ficresf," p.%d",j);
5593: }
5594: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
5595: fprintf(ficresf,"\n");
5596: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
5597:
5598: for (agec=fage; agec>=(ageminpar-1); agec--){
5599: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
5600: nhstepm = nhstepm/hstepm;
5601: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5602: oldm=oldms;savm=savms;
5603: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
5604:
5605: for (h=0; h<=nhstepm; h++){
5606: if (h*hstepm/YEARM*stepm ==yearp) {
5607: fprintf(ficresf,"\n");
5608: for(j=1;j<=cptcoveff;j++)
1.198 brouard 5609: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5610: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
5611: }
5612: for(j=1; j<=nlstate+ndeath;j++) {
5613: ppij=0.;
5614: for(i=1; i<=nlstate;i++) {
5615: if (mobilav==1)
5616: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
5617: else {
5618: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
5619: }
5620: if (h*hstepm/YEARM*stepm== yearp) {
5621: fprintf(ficresf," %.3f", p3mat[i][j][h]);
5622: }
5623: } /* end i */
5624: if (h*hstepm/YEARM*stepm==yearp) {
5625: fprintf(ficresf," %.3f", ppij);
5626: }
5627: }/* end j */
5628: } /* end h */
5629: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5630: } /* end agec */
5631: } /* end yearp */
5632: } /* end cptcod */
5633: } /* end cptcov */
5634:
5635: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5636:
5637: fclose(ficresf);
5638: }
5639:
5640: /************** Forecasting *****not tested NB*************/
1.169 brouard 5641: 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 5642:
5643: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
5644: int *popage;
5645: double calagedatem, agelim, kk1, kk2;
5646: double *popeffectif,*popcount;
5647: double ***p3mat,***tabpop,***tabpopprev;
5648: double ***mobaverage;
5649: char filerespop[FILENAMELENGTH];
5650:
5651: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5652: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5653: agelim=AGESUP;
5654: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
5655:
5656: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5657:
5658:
1.201 brouard 5659: strcpy(filerespop,"POP_");
5660: strcat(filerespop,fileresu);
1.126 brouard 5661: if((ficrespop=fopen(filerespop,"w"))==NULL) {
5662: printf("Problem with forecast resultfile: %s\n", filerespop);
5663: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
5664: }
5665: printf("Computing forecasting: result on file '%s' \n", filerespop);
5666: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
5667:
5668: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5669:
5670: if (mobilav!=0) {
5671: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5672: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5673: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5674: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5675: }
5676: }
5677:
5678: stepsize=(int) (stepm+YEARM-1)/YEARM;
5679: if (stepm<=12) stepsize=1;
5680:
5681: agelim=AGESUP;
5682:
5683: hstepm=1;
5684: hstepm=hstepm/stepm;
5685:
5686: if (popforecast==1) {
5687: if((ficpop=fopen(popfile,"r"))==NULL) {
5688: printf("Problem with population file : %s\n",popfile);exit(0);
5689: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
5690: }
5691: popage=ivector(0,AGESUP);
5692: popeffectif=vector(0,AGESUP);
5693: popcount=vector(0,AGESUP);
5694:
5695: i=1;
5696: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
5697:
5698: imx=i;
5699: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
5700: }
5701:
5702: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
5703: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5704: k=k+1;
5705: fprintf(ficrespop,"\n#******");
5706: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 5707: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5708: }
5709: fprintf(ficrespop,"******\n");
5710: fprintf(ficrespop,"# Age");
5711: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
5712: if (popforecast==1) fprintf(ficrespop," [Population]");
5713:
5714: for (cpt=0; cpt<=0;cpt++) {
5715: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5716:
5717: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5718: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5719: nhstepm = nhstepm/hstepm;
5720:
5721: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5722: oldm=oldms;savm=savms;
5723: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5724:
5725: for (h=0; h<=nhstepm; h++){
5726: if (h==(int) (calagedatem+YEARM*cpt)) {
5727: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5728: }
5729: for(j=1; j<=nlstate+ndeath;j++) {
5730: kk1=0.;kk2=0;
5731: for(i=1; i<=nlstate;i++) {
5732: if (mobilav==1)
5733: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
5734: else {
5735: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
5736: }
5737: }
5738: if (h==(int)(calagedatem+12*cpt)){
5739: tabpop[(int)(agedeb)][j][cptcod]=kk1;
5740: /*fprintf(ficrespop," %.3f", kk1);
5741: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
5742: }
5743: }
5744: for(i=1; i<=nlstate;i++){
5745: kk1=0.;
5746: for(j=1; j<=nlstate;j++){
5747: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5748: }
5749: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5750: }
5751:
5752: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5753: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5754: }
5755: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5756: }
5757: }
5758:
5759: /******/
5760:
5761: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5762: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5763: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5764: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5765: nhstepm = nhstepm/hstepm;
5766:
5767: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5768: oldm=oldms;savm=savms;
5769: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5770: for (h=0; h<=nhstepm; h++){
5771: if (h==(int) (calagedatem+YEARM*cpt)) {
5772: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5773: }
5774: for(j=1; j<=nlstate+ndeath;j++) {
5775: kk1=0.;kk2=0;
5776: for(i=1; i<=nlstate;i++) {
5777: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5778: }
5779: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5780: }
5781: }
5782: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5783: }
5784: }
5785: }
5786: }
5787:
5788: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5789:
5790: if (popforecast==1) {
5791: free_ivector(popage,0,AGESUP);
5792: free_vector(popeffectif,0,AGESUP);
5793: free_vector(popcount,0,AGESUP);
5794: }
5795: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5796: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5797: fclose(ficrespop);
5798: } /* End of popforecast */
5799:
5800: int fileappend(FILE *fichier, char *optionfich)
5801: {
5802: if((fichier=fopen(optionfich,"a"))==NULL) {
5803: printf("Problem with file: %s\n", optionfich);
5804: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5805: return (0);
5806: }
5807: fflush(fichier);
5808: return (1);
5809: }
5810:
5811:
5812: /**************** function prwizard **********************/
5813: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
5814: {
5815:
5816: /* Wizard to print covariance matrix template */
5817:
1.164 brouard 5818: char ca[32], cb[32];
5819: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 5820: int numlinepar;
5821:
5822: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5823: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5824: for(i=1; i <=nlstate; i++){
5825: jj=0;
5826: for(j=1; j <=nlstate+ndeath; j++){
5827: if(j==i) continue;
5828: jj++;
5829: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5830: printf("%1d%1d",i,j);
5831: fprintf(ficparo,"%1d%1d",i,j);
5832: for(k=1; k<=ncovmodel;k++){
5833: /* printf(" %lf",param[i][j][k]); */
5834: /* fprintf(ficparo," %lf",param[i][j][k]); */
5835: printf(" 0.");
5836: fprintf(ficparo," 0.");
5837: }
5838: printf("\n");
5839: fprintf(ficparo,"\n");
5840: }
5841: }
5842: printf("# Scales (for hessian or gradient estimation)\n");
5843: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
5844: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
5845: for(i=1; i <=nlstate; i++){
5846: jj=0;
5847: for(j=1; j <=nlstate+ndeath; j++){
5848: if(j==i) continue;
5849: jj++;
5850: fprintf(ficparo,"%1d%1d",i,j);
5851: printf("%1d%1d",i,j);
5852: fflush(stdout);
5853: for(k=1; k<=ncovmodel;k++){
5854: /* printf(" %le",delti3[i][j][k]); */
5855: /* fprintf(ficparo," %le",delti3[i][j][k]); */
5856: printf(" 0.");
5857: fprintf(ficparo," 0.");
5858: }
5859: numlinepar++;
5860: printf("\n");
5861: fprintf(ficparo,"\n");
5862: }
5863: }
5864: printf("# Covariance matrix\n");
5865: /* # 121 Var(a12)\n\ */
5866: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5867: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5868: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5869: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5870: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5871: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5872: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5873: fflush(stdout);
5874: fprintf(ficparo,"# Covariance matrix\n");
5875: /* # 121 Var(a12)\n\ */
5876: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5877: /* # ...\n\ */
5878: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5879:
5880: for(itimes=1;itimes<=2;itimes++){
5881: jj=0;
5882: for(i=1; i <=nlstate; i++){
5883: for(j=1; j <=nlstate+ndeath; j++){
5884: if(j==i) continue;
5885: for(k=1; k<=ncovmodel;k++){
5886: jj++;
5887: ca[0]= k+'a'-1;ca[1]='\0';
5888: if(itimes==1){
5889: printf("#%1d%1d%d",i,j,k);
5890: fprintf(ficparo,"#%1d%1d%d",i,j,k);
5891: }else{
5892: printf("%1d%1d%d",i,j,k);
5893: fprintf(ficparo,"%1d%1d%d",i,j,k);
5894: /* printf(" %.5le",matcov[i][j]); */
5895: }
5896: ll=0;
5897: for(li=1;li <=nlstate; li++){
5898: for(lj=1;lj <=nlstate+ndeath; lj++){
5899: if(lj==li) continue;
5900: for(lk=1;lk<=ncovmodel;lk++){
5901: ll++;
5902: if(ll<=jj){
5903: cb[0]= lk +'a'-1;cb[1]='\0';
5904: if(ll<jj){
5905: if(itimes==1){
5906: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5907: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5908: }else{
5909: printf(" 0.");
5910: fprintf(ficparo," 0.");
5911: }
5912: }else{
5913: if(itimes==1){
5914: printf(" Var(%s%1d%1d)",ca,i,j);
5915: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5916: }else{
5917: printf(" 0.");
5918: fprintf(ficparo," 0.");
5919: }
5920: }
5921: }
5922: } /* end lk */
5923: } /* end lj */
5924: } /* end li */
5925: printf("\n");
5926: fprintf(ficparo,"\n");
5927: numlinepar++;
5928: } /* end k*/
5929: } /*end j */
5930: } /* end i */
5931: } /* end itimes */
5932:
5933: } /* end of prwizard */
5934: /******************* Gompertz Likelihood ******************************/
5935: double gompertz(double x[])
5936: {
5937: double A,B,L=0.0,sump=0.,num=0.;
5938: int i,n=0; /* n is the size of the sample */
5939:
5940: for (i=0;i<=imx-1 ; i++) {
5941: sump=sump+weight[i];
5942: /* sump=sump+1;*/
5943: num=num+1;
5944: }
5945:
5946:
5947: /* for (i=0; i<=imx; i++)
5948: 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]);*/
5949:
5950: for (i=1;i<=imx ; i++)
5951: {
5952: if (cens[i] == 1 && wav[i]>1)
5953: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5954:
5955: if (cens[i] == 0 && wav[i]>1)
5956: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5957: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5958:
5959: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5960: if (wav[i] > 1 ) { /* ??? */
5961: L=L+A*weight[i];
5962: /* 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]);*/
5963: }
5964: }
5965:
5966: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5967:
5968: return -2*L*num/sump;
5969: }
5970:
1.136 brouard 5971: #ifdef GSL
5972: /******************* Gompertz_f Likelihood ******************************/
5973: double gompertz_f(const gsl_vector *v, void *params)
5974: {
5975: double A,B,LL=0.0,sump=0.,num=0.;
5976: double *x= (double *) v->data;
5977: int i,n=0; /* n is the size of the sample */
5978:
5979: for (i=0;i<=imx-1 ; i++) {
5980: sump=sump+weight[i];
5981: /* sump=sump+1;*/
5982: num=num+1;
5983: }
5984:
5985:
5986: /* for (i=0; i<=imx; i++)
5987: 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]);*/
5988: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5989: for (i=1;i<=imx ; i++)
5990: {
5991: if (cens[i] == 1 && wav[i]>1)
5992: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5993:
5994: if (cens[i] == 0 && wav[i]>1)
5995: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5996: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5997:
5998: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5999: if (wav[i] > 1 ) { /* ??? */
6000: LL=LL+A*weight[i];
6001: /* 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]);*/
6002: }
6003: }
6004:
6005: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
6006: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
6007:
6008: return -2*LL*num/sump;
6009: }
6010: #endif
6011:
1.126 brouard 6012: /******************* Printing html file ***********/
1.201 brouard 6013: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 6014: int lastpass, int stepm, int weightopt, char model[],\
6015: int imx, double p[],double **matcov,double agemortsup){
6016: int i,k;
6017:
6018: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
6019: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
6020: for (i=1;i<=2;i++)
6021: 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 6022: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 6023: fprintf(fichtm,"</ul>");
6024:
6025: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
6026:
6027: 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>");
6028:
6029: for (k=agegomp;k<(agemortsup-2);k++)
6030: 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]);
6031:
6032:
6033: fflush(fichtm);
6034: }
6035:
6036: /******************* Gnuplot file **************/
1.201 brouard 6037: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 6038:
6039: char dirfileres[132],optfileres[132];
1.164 brouard 6040:
1.126 brouard 6041: int ng;
6042:
6043:
6044: /*#ifdef windows */
6045: fprintf(ficgp,"cd \"%s\" \n",pathc);
6046: /*#endif */
6047:
6048:
6049: strcpy(dirfileres,optionfilefiname);
6050: strcpy(optfileres,"vpl");
1.199 brouard 6051: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 6052: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 6053: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 6054: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 6055: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
6056:
6057: }
6058:
1.136 brouard 6059: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
6060: {
1.126 brouard 6061:
1.136 brouard 6062: /*-------- data file ----------*/
6063: FILE *fic;
6064: char dummy[]=" ";
1.164 brouard 6065: int i=0, j=0, n=0;
1.136 brouard 6066: int linei, month, year,iout;
6067: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 6068: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 6069: char *stratrunc;
6070: int lstra;
1.126 brouard 6071:
6072:
1.136 brouard 6073: if((fic=fopen(datafile,"r"))==NULL) {
1.195 brouard 6074: printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
6075: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
1.136 brouard 6076: }
1.126 brouard 6077:
1.136 brouard 6078: i=1;
6079: linei=0;
6080: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
6081: linei=linei+1;
6082: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
6083: if(line[j] == '\t')
6084: line[j] = ' ';
6085: }
6086: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
6087: ;
6088: };
6089: line[j+1]=0; /* Trims blanks at end of line */
6090: if(line[0]=='#'){
6091: fprintf(ficlog,"Comment line\n%s\n",line);
6092: printf("Comment line\n%s\n",line);
6093: continue;
6094: }
6095: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 6096: strcpy(line, linetmp);
1.136 brouard 6097:
1.126 brouard 6098:
1.136 brouard 6099: for (j=maxwav;j>=1;j--){
1.137 brouard 6100: cutv(stra, strb, line, ' ');
1.136 brouard 6101: if(strb[0]=='.') { /* Missing status */
6102: lval=-1;
6103: }else{
6104: errno=0;
6105: lval=strtol(strb,&endptr,10);
6106: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
6107: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 6108: 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);
6109: 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 6110: return 1;
6111: }
6112: }
6113: s[j][i]=lval;
6114:
6115: strcpy(line,stra);
6116: cutv(stra, strb,line,' ');
1.169 brouard 6117: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 6118: }
1.169 brouard 6119: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 6120: month=99;
6121: year=9999;
6122: }else{
1.141 brouard 6123: 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);
6124: 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 6125: return 1;
6126: }
6127: anint[j][i]= (double) year;
6128: mint[j][i]= (double)month;
6129: strcpy(line,stra);
6130: } /* ENd Waves */
6131:
6132: cutv(stra, strb,line,' ');
1.169 brouard 6133: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 6134: }
1.169 brouard 6135: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 6136: month=99;
6137: year=9999;
6138: }else{
1.141 brouard 6139: 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);
6140: 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 6141: return 1;
6142: }
6143: andc[i]=(double) year;
6144: moisdc[i]=(double) month;
6145: strcpy(line,stra);
6146:
6147: cutv(stra, strb,line,' ');
1.169 brouard 6148: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 6149: }
1.169 brouard 6150: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 6151: month=99;
6152: year=9999;
6153: }else{
1.141 brouard 6154: 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);
6155: 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 6156: return 1;
6157: }
6158: if (year==9999) {
1.141 brouard 6159: 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);
6160: 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 6161: return 1;
1.126 brouard 6162:
1.136 brouard 6163: }
6164: annais[i]=(double)(year);
6165: moisnais[i]=(double)(month);
6166: strcpy(line,stra);
6167:
6168: cutv(stra, strb,line,' ');
6169: errno=0;
6170: dval=strtod(strb,&endptr);
6171: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 6172: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
6173: 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 6174: fflush(ficlog);
6175: return 1;
6176: }
6177: weight[i]=dval;
6178: strcpy(line,stra);
6179:
6180: for (j=ncovcol;j>=1;j--){
6181: cutv(stra, strb,line,' ');
6182: if(strb[0]=='.') { /* Missing status */
6183: lval=-1;
6184: }else{
6185: errno=0;
6186: lval=strtol(strb,&endptr,10);
6187: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 6188: 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);
6189: 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 6190: return 1;
6191: }
6192: }
6193: if(lval <-1 || lval >1){
1.141 brouard 6194: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 6195: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
6196: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
6197: For example, for multinomial values like 1, 2 and 3,\n \
6198: build V1=0 V2=0 for the reference value (1),\n \
6199: V1=1 V2=0 for (2) \n \
6200: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
6201: output of IMaCh is often meaningless.\n \
6202: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 6203: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 6204: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
6205: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
6206: For example, for multinomial values like 1, 2 and 3,\n \
6207: build V1=0 V2=0 for the reference value (1),\n \
6208: V1=1 V2=0 for (2) \n \
6209: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
6210: output of IMaCh is often meaningless.\n \
6211: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
6212: return 1;
6213: }
6214: covar[j][i]=(double)(lval);
6215: strcpy(line,stra);
6216: }
6217: lstra=strlen(stra);
6218:
6219: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
6220: stratrunc = &(stra[lstra-9]);
6221: num[i]=atol(stratrunc);
6222: }
6223: else
6224: num[i]=atol(stra);
6225: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
6226: 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;}*/
6227:
6228: i=i+1;
6229: } /* End loop reading data */
1.126 brouard 6230:
1.136 brouard 6231: *imax=i-1; /* Number of individuals */
6232: fclose(fic);
6233:
6234: return (0);
1.164 brouard 6235: /* endread: */
1.136 brouard 6236: printf("Exiting readdata: ");
6237: fclose(fic);
6238: return (1);
1.126 brouard 6239:
6240:
6241:
1.136 brouard 6242: }
1.145 brouard 6243: void removespace(char *str) {
6244: char *p1 = str, *p2 = str;
6245: do
6246: while (*p2 == ' ')
6247: p2++;
1.169 brouard 6248: while (*p1++ == *p2++);
1.145 brouard 6249: }
6250:
6251: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 6252: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
6253: * - nagesqr = 1 if age*age in the model, otherwise 0.
6254: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
6255: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 6256: * - cptcovage number of covariates with age*products =2
6257: * - cptcovs number of simple covariates
6258: * - 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
6259: * which is a new column after the 9 (ncovcol) variables.
6260: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
6261: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
6262: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
6263: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
6264: */
1.136 brouard 6265: {
1.145 brouard 6266: int i, j, k, ks;
1.164 brouard 6267: int j1, k1, k2;
1.136 brouard 6268: char modelsav[80];
1.145 brouard 6269: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 6270: char *strpt;
1.136 brouard 6271:
1.145 brouard 6272: /*removespace(model);*/
1.136 brouard 6273: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 6274: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 6275: if (strstr(model,"AGE") !=0){
1.192 brouard 6276: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
6277: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 6278: return 1;
6279: }
1.141 brouard 6280: if (strstr(model,"v") !=0){
6281: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
6282: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
6283: return 1;
6284: }
1.187 brouard 6285: strcpy(modelsav,model);
6286: if ((strpt=strstr(model,"age*age")) !=0){
6287: printf(" strpt=%s, model=%s\n",strpt, model);
6288: if(strpt != model){
6289: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 6290: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 6291: corresponding column of parameters.\n",model);
6292: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 6293: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 6294: corresponding column of parameters.\n",model); fflush(ficlog);
6295: return 1;
6296: }
6297:
6298: nagesqr=1;
6299: if (strstr(model,"+age*age") !=0)
6300: substrchaine(modelsav, model, "+age*age");
6301: else if (strstr(model,"age*age+") !=0)
6302: substrchaine(modelsav, model, "age*age+");
6303: else
6304: substrchaine(modelsav, model, "age*age");
6305: }else
6306: nagesqr=0;
6307: if (strlen(modelsav) >1){
6308: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
6309: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
6310: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
6311: cptcovt= j+1; /* Number of total covariates in the model, not including
6312: * cst, age and age*age
6313: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
6314: /* including age products which are counted in cptcovage.
6315: * but the covariates which are products must be treated
6316: * separately: ncovn=4- 2=2 (V1+V3). */
6317: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
6318: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
6319:
6320:
6321: /* Design
6322: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
6323: * < ncovcol=8 >
6324: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
6325: * k= 1 2 3 4 5 6 7 8
6326: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
6327: * covar[k,i], value of kth covariate if not including age for individual i:
6328: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
6329: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
6330: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
6331: * Tage[++cptcovage]=k
6332: * if products, new covar are created after ncovcol with k1
6333: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
6334: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
6335: * 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
6336: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
6337: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
6338: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
6339: * < ncovcol=8 >
6340: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
6341: * k= 1 2 3 4 5 6 7 8 9 10 11 12
6342: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
6343: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
6344: * p Tprod[1]@2={ 6, 5}
6345: *p Tvard[1][1]@4= {7, 8, 5, 6}
6346: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
6347: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
6348: *How to reorganize?
6349: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
6350: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
6351: * {2, 1, 4, 8, 5, 6, 3, 7}
6352: * Struct []
6353: */
1.145 brouard 6354:
1.187 brouard 6355: /* This loop fills the array Tvar from the string 'model'.*/
6356: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
6357: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
6358: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
6359: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
6360: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
6361: /* k=1 Tvar[1]=2 (from V2) */
6362: /* k=5 Tvar[5] */
6363: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 6364: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 6365: /* } */
1.198 brouard 6366: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 6367: /*
6368: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
6369: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 6370: Tvar[k]=0;
1.187 brouard 6371: cptcovage=0;
6372: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
6373: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
6374: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
6375: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
6376: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
6377: /*scanf("%d",i);*/
6378: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
6379: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
6380: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
6381: /* covar is not filled and then is empty */
6382: cptcovprod--;
6383: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
6384: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
6385: cptcovage++; /* Sums the number of covariates which include age as a product */
6386: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
6387: /*printf("stre=%s ", stre);*/
6388: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
6389: cptcovprod--;
6390: cutl(stre,strb,strc,'V');
6391: Tvar[k]=atoi(stre);
6392: cptcovage++;
6393: Tage[cptcovage]=k;
6394: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
6395: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
6396: cptcovn++;
6397: cptcovprodnoage++;k1++;
6398: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
6399: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
6400: because this model-covariate is a construction we invent a new column
6401: ncovcol + k1
6402: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
6403: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
6404: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
6405: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
6406: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
6407: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
6408: k2=k2+2;
6409: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
6410: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
6411: for (i=1; i<=lastobs;i++){
6412: /* Computes the new covariate which is a product of
6413: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
6414: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
6415: }
6416: } /* End age is not in the model */
6417: } /* End if model includes a product */
6418: else { /* no more sum */
6419: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
6420: /* scanf("%d",i);*/
6421: cutl(strd,strc,strb,'V');
6422: ks++; /**< Number of simple covariates */
1.145 brouard 6423: cptcovn++;
1.187 brouard 6424: Tvar[k]=atoi(strd);
6425: }
6426: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
6427: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
6428: scanf("%d",i);*/
6429: } /* end of loop + on total covariates */
6430: } /* end if strlen(modelsave == 0) age*age might exist */
6431: } /* end if strlen(model == 0) */
1.136 brouard 6432:
6433: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
6434: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
6435:
6436: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
6437: printf("cptcovprod=%d ", cptcovprod);
6438: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
6439:
6440: scanf("%d ",i);*/
6441:
6442:
1.137 brouard 6443: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 6444: /*endread:*/
1.136 brouard 6445: printf("Exiting decodemodel: ");
6446: return (1);
6447: }
6448:
1.169 brouard 6449: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 6450: {
6451: int i, m;
6452:
6453: for (i=1; i<=imx; i++) {
6454: for(m=2; (m<= maxwav); m++) {
6455: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
6456: anint[m][i]=9999;
6457: s[m][i]=-1;
6458: }
6459: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 6460: *nberr = *nberr + 1;
6461: printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
6462: fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
1.136 brouard 6463: s[m][i]=-1;
6464: }
6465: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 6466: (*nberr)++;
1.136 brouard 6467: 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]);
6468: 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]);
6469: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
6470: }
6471: }
6472: }
6473:
6474: for (i=1; i<=imx; i++) {
6475: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
6476: for(m=firstpass; (m<= lastpass); m++){
6477: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
6478: if (s[m][i] >= nlstate+1) {
1.169 brouard 6479: if(agedc[i]>0){
6480: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 6481: agev[m][i]=agedc[i];
6482: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 6483: }else {
1.136 brouard 6484: if ((int)andc[i]!=9999){
6485: nbwarn++;
6486: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
6487: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
6488: agev[m][i]=-1;
6489: }
6490: }
1.169 brouard 6491: } /* agedc > 0 */
1.136 brouard 6492: }
6493: else if(s[m][i] !=9){ /* Standard case, age in fractional
6494: years but with the precision of a month */
6495: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
6496: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
6497: agev[m][i]=1;
6498: else if(agev[m][i] < *agemin){
6499: *agemin=agev[m][i];
6500: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
6501: }
6502: else if(agev[m][i] >*agemax){
6503: *agemax=agev[m][i];
1.156 brouard 6504: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 6505: }
6506: /*agev[m][i]=anint[m][i]-annais[i];*/
6507: /* agev[m][i] = age[i]+2*m;*/
6508: }
6509: else { /* =9 */
6510: agev[m][i]=1;
6511: s[m][i]=-1;
6512: }
6513: }
6514: else /*= 0 Unknown */
6515: agev[m][i]=1;
6516: }
6517:
6518: }
6519: for (i=1; i<=imx; i++) {
6520: for(m=firstpass; (m<=lastpass); m++){
6521: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 6522: (*nberr)++;
1.136 brouard 6523: 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);
6524: 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);
6525: return 1;
6526: }
6527: }
6528: }
6529:
6530: /*for (i=1; i<=imx; i++){
6531: for (m=firstpass; (m<lastpass); m++){
6532: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
6533: }
6534:
6535: }*/
6536:
6537:
1.139 brouard 6538: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
6539: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 6540:
6541: return (0);
1.164 brouard 6542: /* endread:*/
1.136 brouard 6543: printf("Exiting calandcheckages: ");
6544: return (1);
6545: }
6546:
1.172 brouard 6547: #if defined(_MSC_VER)
6548: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6549: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6550: //#include "stdafx.h"
6551: //#include <stdio.h>
6552: //#include <tchar.h>
6553: //#include <windows.h>
6554: //#include <iostream>
6555: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
6556:
6557: LPFN_ISWOW64PROCESS fnIsWow64Process;
6558:
6559: BOOL IsWow64()
6560: {
6561: BOOL bIsWow64 = FALSE;
6562:
6563: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
6564: // (HANDLE, PBOOL);
6565:
6566: //LPFN_ISWOW64PROCESS fnIsWow64Process;
6567:
6568: HMODULE module = GetModuleHandle(_T("kernel32"));
6569: const char funcName[] = "IsWow64Process";
6570: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
6571: GetProcAddress(module, funcName);
6572:
6573: if (NULL != fnIsWow64Process)
6574: {
6575: if (!fnIsWow64Process(GetCurrentProcess(),
6576: &bIsWow64))
6577: //throw std::exception("Unknown error");
6578: printf("Unknown error\n");
6579: }
6580: return bIsWow64 != FALSE;
6581: }
6582: #endif
1.177 brouard 6583:
1.191 brouard 6584: void syscompilerinfo(int logged)
1.167 brouard 6585: {
6586: /* #include "syscompilerinfo.h"*/
1.185 brouard 6587: /* command line Intel compiler 32bit windows, XP compatible:*/
6588: /* /GS /W3 /Gy
6589: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
6590: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
6591: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 6592: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
6593: */
6594: /* 64 bits */
1.185 brouard 6595: /*
6596: /GS /W3 /Gy
6597: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
6598: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
6599: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
6600: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
6601: /* Optimization are useless and O3 is slower than O2 */
6602: /*
6603: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
6604: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
6605: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
6606: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
6607: */
1.186 brouard 6608: /* Link is */ /* /OUT:"visual studio
1.185 brouard 6609: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
6610: /PDB:"visual studio
6611: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
6612: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
6613: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
6614: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
6615: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
6616: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
6617: uiAccess='false'"
6618: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
6619: /NOLOGO /TLBID:1
6620: */
1.177 brouard 6621: #if defined __INTEL_COMPILER
1.178 brouard 6622: #if defined(__GNUC__)
6623: struct utsname sysInfo; /* For Intel on Linux and OS/X */
6624: #endif
1.177 brouard 6625: #elif defined(__GNUC__)
1.179 brouard 6626: #ifndef __APPLE__
1.174 brouard 6627: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 6628: #endif
1.177 brouard 6629: struct utsname sysInfo;
1.178 brouard 6630: int cross = CROSS;
6631: if (cross){
6632: printf("Cross-");
1.191 brouard 6633: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 6634: }
1.174 brouard 6635: #endif
6636:
1.171 brouard 6637: #include <stdint.h>
1.178 brouard 6638:
1.191 brouard 6639: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 6640: #if defined(__clang__)
1.191 brouard 6641: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 6642: #endif
6643: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 6644: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 6645: #endif
6646: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 6647: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 6648: #endif
6649: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 6650: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 6651: #endif
6652: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 6653: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 6654: #endif
6655: #if defined(_MSC_VER)
1.191 brouard 6656: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 6657: #endif
6658: #if defined(__PGI)
1.191 brouard 6659: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 6660: #endif
6661: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 6662: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 6663: #endif
1.191 brouard 6664: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 6665:
1.167 brouard 6666: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
6667: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
6668: // Windows (x64 and x86)
1.191 brouard 6669: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 6670: #elif __unix__ // all unices, not all compilers
6671: // Unix
1.191 brouard 6672: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 6673: #elif __linux__
6674: // linux
1.191 brouard 6675: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 6676: #elif __APPLE__
1.174 brouard 6677: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 6678: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 6679: #endif
6680:
6681: /* __MINGW32__ */
6682: /* __CYGWIN__ */
6683: /* __MINGW64__ */
6684: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
6685: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
6686: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
6687: /* _WIN64 // Defined for applications for Win64. */
6688: /* _M_X64 // Defined for compilations that target x64 processors. */
6689: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 6690:
1.167 brouard 6691: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 6692: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 6693: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 6694: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 6695: #else
1.191 brouard 6696: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 6697: #endif
6698:
1.169 brouard 6699: #if defined(__GNUC__)
6700: # if defined(__GNUC_PATCHLEVEL__)
6701: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6702: + __GNUC_MINOR__ * 100 \
6703: + __GNUC_PATCHLEVEL__)
6704: # else
6705: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6706: + __GNUC_MINOR__ * 100)
6707: # endif
1.174 brouard 6708: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 6709: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 6710:
6711: if (uname(&sysInfo) != -1) {
6712: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 6713: 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 6714: }
6715: else
6716: perror("uname() error");
1.179 brouard 6717: //#ifndef __INTEL_COMPILER
6718: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 6719: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 6720: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 6721: #endif
1.169 brouard 6722: #endif
1.172 brouard 6723:
6724: // void main()
6725: // {
1.169 brouard 6726: #if defined(_MSC_VER)
1.174 brouard 6727: if (IsWow64()){
1.191 brouard 6728: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6729: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 6730: }
6731: else{
1.191 brouard 6732: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
6733: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 6734: }
1.172 brouard 6735: // printf("\nPress Enter to continue...");
6736: // getchar();
6737: // }
6738:
1.169 brouard 6739: #endif
6740:
1.167 brouard 6741:
6742: }
1.136 brouard 6743:
1.209 brouard 6744: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.180 brouard 6745: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6746: int i, j, k, i1 ;
1.202 brouard 6747: /* double ftolpl = 1.e-10; */
1.180 brouard 6748: double age, agebase, agelim;
1.203 brouard 6749: double tot;
1.180 brouard 6750:
1.202 brouard 6751: strcpy(filerespl,"PL_");
6752: strcat(filerespl,fileresu);
6753: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6754: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6755: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6756: }
6757: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6758: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6759: pstamp(ficrespl);
1.203 brouard 6760: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 6761: fprintf(ficrespl,"#Age ");
6762: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6763: fprintf(ficrespl,"\n");
1.180 brouard 6764:
6765: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6766:
6767: agebase=ageminpar;
6768: agelim=agemaxpar;
6769:
6770: i1=pow(2,cptcoveff);
6771: if (cptcovn < 1){i1=1;}
6772:
6773: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6774: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6775: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6776: k=k+1;
6777: /* to clean */
1.198 brouard 6778: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
1.200 brouard 6779: fprintf(ficrespl,"#******");
6780: printf("#******");
6781: fprintf(ficlog,"#******");
1.180 brouard 6782: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 6783: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6784: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6785: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6786: }
6787: fprintf(ficrespl,"******\n");
6788: printf("******\n");
6789: fprintf(ficlog,"******\n");
6790:
6791: fprintf(ficrespl,"#Age ");
6792: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 6793: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6794: }
1.203 brouard 6795: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
6796: fprintf(ficrespl,"Total Years_to_converge\n");
1.180 brouard 6797:
6798: for (age=agebase; age<=agelim; age++){
6799: /* for (age=agebase; age<=agebase; age++){ */
1.209 brouard 6800: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
1.180 brouard 6801: fprintf(ficrespl,"%.0f ",age );
6802: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6803: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.203 brouard 6804: tot=0.;
6805: for(i=1; i<=nlstate;i++){
6806: tot += prlim[i][i];
1.180 brouard 6807: fprintf(ficrespl," %.5f", prlim[i][i]);
1.203 brouard 6808: }
1.209 brouard 6809: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
1.180 brouard 6810: } /* Age */
6811: /* was end of cptcod */
6812: } /* cptcov */
1.184 brouard 6813: return 0;
1.180 brouard 6814: }
6815:
6816: int hPijx(double *p, int bage, int fage){
6817: /*------------- h Pij x at various ages ------------*/
6818:
6819: int stepsize;
6820: int agelim;
6821: int hstepm;
6822: int nhstepm;
6823: int h, i, i1, j, k;
6824:
6825: double agedeb;
6826: double ***p3mat;
6827:
1.201 brouard 6828: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 6829: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6830: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
6831: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
6832: }
6833: printf("Computing pij: result on file '%s' \n", filerespij);
6834: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6835:
6836: stepsize=(int) (stepm+YEARM-1)/YEARM;
6837: /*if (stepm<=24) stepsize=2;*/
6838:
6839: agelim=AGESUP;
6840: hstepm=stepsize*YEARM; /* Every year of age */
6841: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6842:
6843: /* hstepm=1; aff par mois*/
6844: pstamp(ficrespij);
6845: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6846: i1= pow(2,cptcoveff);
1.183 brouard 6847: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
6848: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
6849: /* k=k+1; */
6850: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6851: fprintf(ficrespij,"\n#****** ");
6852: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6853: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.183 brouard 6854: fprintf(ficrespij,"******\n");
6855:
6856: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6857: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6858: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6859:
6860: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 6861:
1.183 brouard 6862: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6863: oldm=oldms;savm=savms;
6864: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6865: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6866: for(i=1; i<=nlstate;i++)
6867: for(j=1; j<=nlstate+ndeath;j++)
6868: fprintf(ficrespij," %1d-%1d",i,j);
6869: fprintf(ficrespij,"\n");
6870: for (h=0; h<=nhstepm; h++){
6871: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
6872: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 6873: for(i=1; i<=nlstate;i++)
6874: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 6875: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 6876: fprintf(ficrespij,"\n");
6877: }
1.183 brouard 6878: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6879: fprintf(ficrespij,"\n");
6880: }
1.180 brouard 6881: /*}*/
6882: }
1.184 brouard 6883: return 0;
1.180 brouard 6884: }
6885:
6886:
1.136 brouard 6887: /***********************************************/
6888: /**************** Main Program *****************/
6889: /***********************************************/
6890:
6891: int main(int argc, char *argv[])
6892: {
6893: #ifdef GSL
6894: const gsl_multimin_fminimizer_type *T;
6895: size_t iteri = 0, it;
6896: int rval = GSL_CONTINUE;
6897: int status = GSL_SUCCESS;
6898: double ssval;
6899: #endif
6900: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 6901: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.209 brouard 6902: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 6903: int jj, ll, li, lj, lk;
1.136 brouard 6904: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 6905: int num_filled;
1.136 brouard 6906: int itimes;
6907: int NDIM=2;
6908: int vpopbased=0;
6909:
1.164 brouard 6910: char ca[32], cb[32];
1.136 brouard 6911: /* FILE *fichtm; *//* Html File */
6912: /* FILE *ficgp;*/ /*Gnuplot File */
6913: struct stat info;
1.191 brouard 6914: double agedeb=0.;
1.194 brouard 6915:
6916: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.136 brouard 6917:
1.165 brouard 6918: double fret;
1.191 brouard 6919: double dum=0.; /* Dummy variable */
1.136 brouard 6920: double ***p3mat;
6921: double ***mobaverage;
1.164 brouard 6922:
6923: char line[MAXLINE];
1.197 brouard 6924: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
6925:
6926: char model[MAXLINE], modeltemp[MAXLINE];
1.136 brouard 6927: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 6928: char *tok, *val; /* pathtot */
1.136 brouard 6929: int firstobs=1, lastobs=10;
1.195 brouard 6930: int c, h , cpt, c2;
1.191 brouard 6931: int jl=0;
6932: int i1, j1, jk, stepsize=0;
1.194 brouard 6933: int count=0;
6934:
1.164 brouard 6935: int *tab;
1.136 brouard 6936: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
6937: int mobilav=0,popforecast=0;
1.191 brouard 6938: int hstepm=0, nhstepm=0;
1.136 brouard 6939: int agemortsup;
6940: float sumlpop=0.;
6941: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
6942: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
6943:
1.191 brouard 6944: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 6945: double ftolpl=FTOL;
6946: double **prlim;
6947: double ***param; /* Matrix of parameters */
6948: double *p;
6949: double **matcov; /* Matrix of covariance */
1.203 brouard 6950: double **hess; /* Hessian matrix */
1.136 brouard 6951: double ***delti3; /* Scale */
6952: double *delti; /* Scale */
6953: double ***eij, ***vareij;
6954: double **varpl; /* Variances of prevalence limits by age */
6955: double *epj, vepp;
1.164 brouard 6956:
1.136 brouard 6957: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6958: double **ximort;
1.145 brouard 6959: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 6960: int *dcwave;
6961:
1.164 brouard 6962: char z[1]="c";
1.136 brouard 6963:
6964: /*char *strt;*/
6965: char strtend[80];
1.126 brouard 6966:
1.164 brouard 6967:
1.126 brouard 6968: /* setlocale (LC_ALL, ""); */
6969: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6970: /* textdomain (PACKAGE); */
6971: /* setlocale (LC_CTYPE, ""); */
6972: /* setlocale (LC_MESSAGES, ""); */
6973:
6974: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 6975: rstart_time = time(NULL);
6976: /* (void) gettimeofday(&start_time,&tzp);*/
6977: start_time = *localtime(&rstart_time);
1.126 brouard 6978: curr_time=start_time;
1.157 brouard 6979: /*tml = *localtime(&start_time.tm_sec);*/
6980: /* strcpy(strstart,asctime(&tml)); */
6981: strcpy(strstart,asctime(&start_time));
1.126 brouard 6982:
6983: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 6984: /* tp.tm_sec = tp.tm_sec +86400; */
6985: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 6986: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6987: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6988: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 6989: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 6990: /* strt=asctime(&tmg); */
6991: /* printf("Time(after) =%s",strstart); */
6992: /* (void) time (&time_value);
6993: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6994: * tm = *localtime(&time_value);
6995: * strstart=asctime(&tm);
6996: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6997: */
6998:
6999: nberr=0; /* Number of errors and warnings */
7000: nbwarn=0;
1.184 brouard 7001: #ifdef WIN32
7002: _getcwd(pathcd, size);
7003: #else
1.126 brouard 7004: getcwd(pathcd, size);
1.184 brouard 7005: #endif
1.191 brouard 7006: syscompilerinfo(0);
1.196 brouard 7007: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 7008: if(argc <=1){
7009: printf("\nEnter the parameter file name: ");
1.205 brouard 7010: if(!fgets(pathr,FILENAMELENGTH,stdin)){
7011: printf("ERROR Empty parameter file name\n");
7012: goto end;
7013: }
1.126 brouard 7014: i=strlen(pathr);
7015: if(pathr[i-1]=='\n')
7016: pathr[i-1]='\0';
1.156 brouard 7017: i=strlen(pathr);
1.205 brouard 7018: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 7019: pathr[i-1]='\0';
1.205 brouard 7020: }
7021: i=strlen(pathr);
7022: if( i==0 ){
7023: printf("ERROR Empty parameter file name\n");
7024: goto end;
7025: }
7026: for (tok = pathr; tok != NULL; ){
1.126 brouard 7027: printf("Pathr |%s|\n",pathr);
7028: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
7029: printf("val= |%s| pathr=%s\n",val,pathr);
7030: strcpy (pathtot, val);
7031: if(pathr[0] == '\0') break; /* Dirty */
7032: }
7033: }
7034: else{
7035: strcpy(pathtot,argv[1]);
7036: }
7037: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
7038: /*cygwin_split_path(pathtot,path,optionfile);
7039: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
7040: /* cutv(path,optionfile,pathtot,'\\');*/
7041:
7042: /* Split argv[0], imach program to get pathimach */
7043: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
7044: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
7045: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
7046: /* strcpy(pathimach,argv[0]); */
7047: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
7048: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
7049: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 7050: #ifdef WIN32
7051: _chdir(path); /* Can be a relative path */
7052: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
7053: #else
1.126 brouard 7054: chdir(path); /* Can be a relative path */
1.184 brouard 7055: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
7056: #endif
7057: printf("Current directory %s!\n",pathcd);
1.126 brouard 7058: strcpy(command,"mkdir ");
7059: strcat(command,optionfilefiname);
7060: if((outcmd=system(command)) != 0){
1.169 brouard 7061: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 7062: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
7063: /* fclose(ficlog); */
7064: /* exit(1); */
7065: }
7066: /* if((imk=mkdir(optionfilefiname))<0){ */
7067: /* perror("mkdir"); */
7068: /* } */
7069:
7070: /*-------- arguments in the command line --------*/
7071:
1.186 brouard 7072: /* Main Log file */
1.126 brouard 7073: strcat(filelog, optionfilefiname);
7074: strcat(filelog,".log"); /* */
7075: if((ficlog=fopen(filelog,"w"))==NULL) {
7076: printf("Problem with logfile %s\n",filelog);
7077: goto end;
7078: }
7079: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 7080: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 7081: fprintf(ficlog,"\nEnter the parameter file name: \n");
7082: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
7083: path=%s \n\
7084: optionfile=%s\n\
7085: optionfilext=%s\n\
1.156 brouard 7086: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 7087:
1.197 brouard 7088: syscompilerinfo(1);
1.167 brouard 7089:
1.126 brouard 7090: printf("Local time (at start):%s",strstart);
7091: fprintf(ficlog,"Local time (at start): %s",strstart);
7092: fflush(ficlog);
7093: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 7094: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 7095:
7096: /* */
7097: strcpy(fileres,"r");
7098: strcat(fileres, optionfilefiname);
1.201 brouard 7099: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 7100: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 7101: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 7102:
1.186 brouard 7103: /* Main ---------arguments file --------*/
1.126 brouard 7104:
7105: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 7106: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
7107: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 7108: fflush(ficlog);
1.149 brouard 7109: /* goto end; */
7110: exit(70);
1.126 brouard 7111: }
7112:
7113:
7114:
7115: strcpy(filereso,"o");
1.201 brouard 7116: strcat(filereso,fileresu);
1.126 brouard 7117: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
7118: printf("Problem with Output resultfile: %s\n", filereso);
7119: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
7120: fflush(ficlog);
7121: goto end;
7122: }
7123:
7124: /* Reads comments: lines beginning with '#' */
7125: numlinepar=0;
1.197 brouard 7126:
7127: /* First parameter line */
7128: while(fgets(line, MAXLINE, ficpar)) {
7129: /* If line starts with a # it is a comment */
7130: if (line[0] == '#') {
7131: numlinepar++;
7132: fputs(line,stdout);
7133: fputs(line,ficparo);
7134: fputs(line,ficlog);
7135: continue;
7136: }else
7137: break;
7138: }
7139: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
7140: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
7141: if (num_filled != 5) {
7142: printf("Should be 5 parameters\n");
7143: }
1.126 brouard 7144: numlinepar++;
1.197 brouard 7145: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
7146: }
7147: /* Second parameter line */
7148: while(fgets(line, MAXLINE, ficpar)) {
7149: /* If line starts with a # it is a comment */
7150: if (line[0] == '#') {
7151: numlinepar++;
7152: fputs(line,stdout);
7153: fputs(line,ficparo);
7154: fputs(line,ficlog);
7155: continue;
7156: }else
7157: break;
7158: }
7159: if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
7160: &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
7161: if (num_filled != 8) {
1.209 brouard 7162: 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");
7163: printf("but line=%s\n",line);
1.197 brouard 7164: }
7165: 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 7166: }
1.203 brouard 7167: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 7168: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 7169: /* Third parameter line */
7170: while(fgets(line, MAXLINE, ficpar)) {
7171: /* If line starts with a # it is a comment */
7172: if (line[0] == '#') {
7173: numlinepar++;
7174: fputs(line,stdout);
7175: fputs(line,ficparo);
7176: fputs(line,ficlog);
7177: continue;
7178: }else
7179: break;
7180: }
1.201 brouard 7181: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
7182: if (num_filled == 0)
7183: model[0]='\0';
7184: else if (num_filled != 1){
1.197 brouard 7185: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
7186: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
7187: model[0]='\0';
7188: goto end;
7189: }
7190: else{
7191: if (model[0]=='+'){
7192: for(i=1; i<=strlen(model);i++)
7193: modeltemp[i-1]=model[i];
1.201 brouard 7194: strcpy(model,modeltemp);
1.197 brouard 7195: }
7196: }
1.199 brouard 7197: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 7198: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 7199: }
7200: /* 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); */
7201: /* numlinepar=numlinepar+3; /\* In general *\/ */
7202: /* 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 7203: 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);
7204: 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 7205: fflush(ficlog);
1.190 brouard 7206: /* if(model[0]=='#'|| model[0]== '\0'){ */
7207: if(model[0]=='#'){
1.187 brouard 7208: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
7209: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
7210: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
7211: if(mle != -1){
7212: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
7213: exit(1);
7214: }
7215: }
1.126 brouard 7216: while((c=getc(ficpar))=='#' && c!= EOF){
7217: ungetc(c,ficpar);
7218: fgets(line, MAXLINE, ficpar);
7219: numlinepar++;
1.195 brouard 7220: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
7221: z[0]=line[1];
7222: }
7223: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 7224: fputs(line, stdout);
7225: //puts(line);
1.126 brouard 7226: fputs(line,ficparo);
7227: fputs(line,ficlog);
7228: }
7229: ungetc(c,ficpar);
7230:
7231:
1.145 brouard 7232: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 7233: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
7234: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
7235: v1+v2*age+v2*v3 makes cptcovn = 3
7236: */
7237: if (strlen(model)>1)
1.187 brouard 7238: 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 7239: else
1.187 brouard 7240: ncovmodel=2; /* Constant and age */
1.133 brouard 7241: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
7242: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 7243: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
7244: 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);
7245: 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);
7246: fflush(stdout);
7247: fclose (ficlog);
7248: goto end;
7249: }
1.126 brouard 7250: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7251: delti=delti3[1][1];
7252: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
7253: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
7254: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 7255: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
7256: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 7257: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7258: fclose (ficparo);
7259: fclose (ficlog);
7260: goto end;
7261: exit(0);
7262: }
1.186 brouard 7263: else if(mle==-3) { /* Main Wizard */
1.126 brouard 7264: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 7265: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
7266: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 7267: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7268: matcov=matrix(1,npar,1,npar);
1.203 brouard 7269: hess=matrix(1,npar,1,npar);
1.126 brouard 7270: }
7271: else{
1.145 brouard 7272: /* Read guessed parameters */
1.126 brouard 7273: /* Reads comments: lines beginning with '#' */
7274: while((c=getc(ficpar))=='#' && c!= EOF){
7275: ungetc(c,ficpar);
7276: fgets(line, MAXLINE, ficpar);
7277: numlinepar++;
1.141 brouard 7278: fputs(line,stdout);
1.126 brouard 7279: fputs(line,ficparo);
7280: fputs(line,ficlog);
7281: }
7282: ungetc(c,ficpar);
7283:
7284: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7285: for(i=1; i <=nlstate; i++){
7286: j=0;
7287: for(jj=1; jj <=nlstate+ndeath; jj++){
7288: if(jj==i) continue;
7289: j++;
7290: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.193 brouard 7291: if ((i1 != i) || (j1 != jj)){
1.126 brouard 7292: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
7293: It might be a problem of design; if ncovcol and the model are correct\n \
7294: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
7295: exit(1);
7296: }
7297: fprintf(ficparo,"%1d%1d",i1,j1);
7298: if(mle==1)
1.193 brouard 7299: printf("%1d%1d",i,jj);
7300: fprintf(ficlog,"%1d%1d",i,jj);
1.126 brouard 7301: for(k=1; k<=ncovmodel;k++){
7302: fscanf(ficpar," %lf",¶m[i][j][k]);
7303: if(mle==1){
7304: printf(" %lf",param[i][j][k]);
7305: fprintf(ficlog," %lf",param[i][j][k]);
7306: }
7307: else
7308: fprintf(ficlog," %lf",param[i][j][k]);
7309: fprintf(ficparo," %lf",param[i][j][k]);
7310: }
7311: fscanf(ficpar,"\n");
7312: numlinepar++;
7313: if(mle==1)
7314: printf("\n");
7315: fprintf(ficlog,"\n");
7316: fprintf(ficparo,"\n");
7317: }
7318: }
7319: fflush(ficlog);
7320:
1.145 brouard 7321: /* Reads scales values */
1.126 brouard 7322: p=param[1][1];
7323:
7324: /* Reads comments: lines beginning with '#' */
7325: while((c=getc(ficpar))=='#' && c!= EOF){
7326: ungetc(c,ficpar);
7327: fgets(line, MAXLINE, ficpar);
7328: numlinepar++;
1.141 brouard 7329: fputs(line,stdout);
1.126 brouard 7330: fputs(line,ficparo);
7331: fputs(line,ficlog);
7332: }
7333: ungetc(c,ficpar);
7334:
7335: for(i=1; i <=nlstate; i++){
7336: for(j=1; j <=nlstate+ndeath-1; j++){
7337: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 7338: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 7339: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
7340: exit(1);
7341: }
7342: printf("%1d%1d",i,j);
7343: fprintf(ficparo,"%1d%1d",i1,j1);
7344: fprintf(ficlog,"%1d%1d",i1,j1);
7345: for(k=1; k<=ncovmodel;k++){
7346: fscanf(ficpar,"%le",&delti3[i][j][k]);
7347: printf(" %le",delti3[i][j][k]);
7348: fprintf(ficparo," %le",delti3[i][j][k]);
7349: fprintf(ficlog," %le",delti3[i][j][k]);
7350: }
7351: fscanf(ficpar,"\n");
7352: numlinepar++;
7353: printf("\n");
7354: fprintf(ficparo,"\n");
7355: fprintf(ficlog,"\n");
7356: }
7357: }
7358: fflush(ficlog);
7359:
1.145 brouard 7360: /* Reads covariance matrix */
1.126 brouard 7361: delti=delti3[1][1];
7362:
7363:
7364: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
7365:
7366: /* Reads comments: lines beginning with '#' */
7367: while((c=getc(ficpar))=='#' && c!= EOF){
7368: ungetc(c,ficpar);
7369: fgets(line, MAXLINE, ficpar);
7370: numlinepar++;
1.141 brouard 7371: fputs(line,stdout);
1.126 brouard 7372: fputs(line,ficparo);
7373: fputs(line,ficlog);
7374: }
7375: ungetc(c,ficpar);
7376:
7377: matcov=matrix(1,npar,1,npar);
1.203 brouard 7378: hess=matrix(1,npar,1,npar);
1.131 brouard 7379: for(i=1; i <=npar; i++)
7380: for(j=1; j <=npar; j++) matcov[i][j]=0.;
7381:
1.194 brouard 7382: /* Scans npar lines */
1.126 brouard 7383: for(i=1; i <=npar; i++){
1.194 brouard 7384: count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
7385: if(count != 3){
7386: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
7387: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
7388: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
7389: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
7390: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
7391: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
7392: exit(1);
7393: }else
1.126 brouard 7394: if(mle==1)
1.194 brouard 7395: printf("%1d%1d%1d",i1,j1,jk);
7396: fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
7397: fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
1.126 brouard 7398: for(j=1; j <=i; j++){
7399: fscanf(ficpar," %le",&matcov[i][j]);
7400: if(mle==1){
7401: printf(" %.5le",matcov[i][j]);
7402: }
7403: fprintf(ficlog," %.5le",matcov[i][j]);
7404: fprintf(ficparo," %.5le",matcov[i][j]);
7405: }
7406: fscanf(ficpar,"\n");
7407: numlinepar++;
7408: if(mle==1)
7409: printf("\n");
7410: fprintf(ficlog,"\n");
7411: fprintf(ficparo,"\n");
7412: }
1.194 brouard 7413: /* End of read covariance matrix npar lines */
1.126 brouard 7414: for(i=1; i <=npar; i++)
7415: for(j=i+1;j<=npar;j++)
7416: matcov[i][j]=matcov[j][i];
7417:
7418: if(mle==1)
7419: printf("\n");
7420: fprintf(ficlog,"\n");
7421:
7422: fflush(ficlog);
7423:
7424: /*-------- Rewriting parameter file ----------*/
7425: strcpy(rfileres,"r"); /* "Rparameterfile */
7426: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
7427: strcat(rfileres,"."); /* */
7428: strcat(rfileres,optionfilext); /* Other files have txt extension */
7429: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 7430: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
7431: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 7432: }
7433: fprintf(ficres,"#%s\n",version);
7434: } /* End of mle != -3 */
7435:
1.186 brouard 7436: /* Main data
7437: */
1.126 brouard 7438: n= lastobs;
7439: num=lvector(1,n);
7440: moisnais=vector(1,n);
7441: annais=vector(1,n);
7442: moisdc=vector(1,n);
7443: andc=vector(1,n);
7444: agedc=vector(1,n);
7445: cod=ivector(1,n);
7446: weight=vector(1,n);
7447: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
7448: mint=matrix(1,maxwav,1,n);
7449: anint=matrix(1,maxwav,1,n);
1.131 brouard 7450: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 7451: tab=ivector(1,NCOVMAX);
1.144 brouard 7452: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 7453: 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 7454:
1.136 brouard 7455: /* Reads data from file datafile */
7456: if (readdata(datafile, firstobs, lastobs, &imx)==1)
7457: goto end;
7458:
7459: /* Calculation of the number of parameters from char model */
1.137 brouard 7460: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
7461: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
7462: k=3 V4 Tvar[k=3]= 4 (from V4)
7463: k=2 V1 Tvar[k=2]= 1 (from V1)
7464: k=1 Tvar[1]=2 (from V2)
7465: */
7466: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
7467: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
7468: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
7469: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
7470: */
7471: /* For model-covariate k tells which data-covariate to use but
7472: because this model-covariate is a construction we invent a new column
7473: ncovcol + k1
7474: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
7475: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 7476: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 7477: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
7478: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
7479: */
1.145 brouard 7480: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
7481: 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 7482: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
7483: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 7484: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 7485: 4 covariates (3 plus signs)
7486: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
7487: */
1.136 brouard 7488:
1.186 brouard 7489: /* Main decodemodel */
7490:
1.187 brouard 7491:
1.136 brouard 7492: if(decodemodel(model, lastobs) == 1)
7493: goto end;
7494:
1.137 brouard 7495: if((double)(lastobs-imx)/(double)imx > 1.10){
7496: nbwarn++;
7497: 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);
7498: 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);
7499: }
1.136 brouard 7500: /* if(mle==1){*/
1.137 brouard 7501: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
7502: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 7503: }
7504:
7505: /*-calculation of age at interview from date of interview and age at death -*/
7506: agev=matrix(1,maxwav,1,imx);
7507:
7508: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
7509: goto end;
7510:
1.126 brouard 7511:
1.136 brouard 7512: agegomp=(int)agemin;
7513: free_vector(moisnais,1,n);
7514: free_vector(annais,1,n);
1.126 brouard 7515: /* free_matrix(mint,1,maxwav,1,n);
7516: free_matrix(anint,1,maxwav,1,n);*/
7517: free_vector(moisdc,1,n);
7518: free_vector(andc,1,n);
1.145 brouard 7519: /* */
7520:
1.126 brouard 7521: wav=ivector(1,imx);
7522: dh=imatrix(1,lastpass-firstpass+1,1,imx);
7523: bh=imatrix(1,lastpass-firstpass+1,1,imx);
7524: mw=imatrix(1,lastpass-firstpass+1,1,imx);
7525:
7526: /* Concatenates waves */
7527: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 7528: /* */
7529:
1.126 brouard 7530: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
7531:
7532: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
7533: ncodemax[1]=1;
1.145 brouard 7534: Ndum =ivector(-1,NCOVMAX);
1.187 brouard 7535: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
1.145 brouard 7536: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.211 ! brouard 7537: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 7538: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 ! brouard 7539: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.145 brouard 7540:
1.200 brouard 7541: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 7542: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 7543: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 ! brouard 7544: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
! 7545: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
! 7546: * (currently 0 or 1) in the data.
! 7547: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
! 7548: * corresponding modality (h,j).
! 7549: */
! 7550:
1.145 brouard 7551: h=0;
7552:
7553:
7554: /*if (cptcovn > 0) */
1.126 brouard 7555:
1.145 brouard 7556:
1.126 brouard 7557: m=pow(2,cptcoveff);
7558:
1.144 brouard 7559: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 ! brouard 7560: * For k=4 covariates, h goes from 1 to m=2**k
! 7561: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
! 7562: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 7563: * h\k 1 2 3 4
1.143 brouard 7564: *______________________________
7565: * 1 i=1 1 i=1 1 i=1 1 i=1 1
7566: * 2 2 1 1 1
7567: * 3 i=2 1 2 1 1
7568: * 4 2 2 1 1
7569: * 5 i=3 1 i=2 1 2 1
7570: * 6 2 1 2 1
7571: * 7 i=4 1 2 2 1
7572: * 8 2 2 2 1
1.197 brouard 7573: * 9 i=5 1 i=3 1 i=2 1 2
7574: * 10 2 1 1 2
7575: * 11 i=6 1 2 1 2
7576: * 12 2 2 1 2
7577: * 13 i=7 1 i=4 1 2 2
7578: * 14 2 1 2 2
7579: * 15 i=8 1 2 2 2
7580: * 16 2 2 2 2
1.143 brouard 7581: */
1.211 ! brouard 7582: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates?
! 7583: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
! 7584: * and the value of each covariate?
! 7585: * V1=1, V2=1, V3=2, V4=1 ?
! 7586: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
! 7587: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
! 7588: * In order to get the real value in the data, we use nbcode
! 7589: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
! 7590: * We are keeping this crazy system in order to be able (in the future?)
! 7591: * to have more than 2 values (0 or 1) for a covariate.
! 7592: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
! 7593: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
! 7594: * bbbbbbbb
! 7595: * 76543210
! 7596: * h-1 00000101 (6-1=5)
! 7597: *(h-1)>>(k-1)= 00000001 >> (2-1) = 1 right shift
! 7598: * &
! 7599: * 1 00000001 (1)
! 7600: * 00000001 = 1 & ((h-1) >> (k-1))
! 7601: * +1= 00000010 =2
! 7602: *
! 7603: * h=14, k=3 => h'=h-1=13, k'=k-1=2
! 7604: * h' 1101 =2^3+2^2+0x2^1+2^0
! 7605: * >>k' 11
! 7606: * & 00000001
! 7607: * = 00000001
! 7608: * +1 = 00000010=2 = codtabm(14,3)
! 7609: * Reverse h=6 and m=16?
! 7610: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
! 7611: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
! 7612: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
! 7613: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
! 7614: * V3=decodtabm(14,3,2**4)=2
! 7615: * h'=13 1101 =2^3+2^2+0x2^1+2^0
! 7616: *(h-1) >> (j-1) 0011 =13 >> 2
! 7617: * &1 000000001
! 7618: * = 000000001
! 7619: * +1= 000000010 =2
! 7620: * 2211
! 7621: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
! 7622: * V3=2
! 7623: */
! 7624:
1.202 brouard 7625: /* /\* for(h=1; h <=100 ;h++){ *\/ */
7626: /* /\* printf("h=%2d ", h); *\/ */
7627: /* /\* for(k=1; k <=10; k++){ *\/ */
7628: /* /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */
7629: /* /\* codtab[h][k]=codtabm(h,k); *\/ */
7630: /* /\* } *\/ */
7631: /* /\* printf("\n"); *\/ */
7632: /* } */
1.197 brouard 7633: /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
7634: /* 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 *\/ */
7635: /* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
7636: /* for(cpt=1; cpt <=pow(2,k-1); cpt++){ /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/ */
7637: /* h++; */
7638: /* if (h>m) */
7639: /* h=1; */
7640: /* codtab[h][k]=j; */
7641: /* /\* codtab[12][3]=1; *\/ */
7642: /* /\*codtab[h][Tvar[k]]=j;*\/ */
7643: /* /\* 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]]); *\/ */
7644: /* } */
7645: /* } */
7646: /* } */
7647: /* } */
1.126 brouard 7648: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
7649: codtab[1][2]=1;codtab[2][2]=2; */
1.197 brouard 7650: /* for(i=1; i <=m ;i++){ */
7651: /* for(k=1; k <=cptcovn; k++){ */
7652: /* printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
7653: /* } */
7654: /* printf("\n"); */
7655: /* } */
7656: /* scanf("%d",i);*/
1.145 brouard 7657:
7658: free_ivector(Ndum,-1,NCOVMAX);
7659:
7660:
1.126 brouard 7661:
1.186 brouard 7662: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 7663: strcpy(optionfilegnuplot,optionfilefiname);
7664: if(mle==-3)
1.201 brouard 7665: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 7666: strcat(optionfilegnuplot,".gp");
7667:
7668: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
7669: printf("Problem with file %s",optionfilegnuplot);
7670: }
7671: else{
1.204 brouard 7672: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 7673: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 7674: //fprintf(ficgp,"set missing 'NaNq'\n");
7675: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 7676: }
7677: /* fclose(ficgp);*/
1.186 brouard 7678:
7679:
7680: /* Initialisation of --------- index.htm --------*/
1.126 brouard 7681:
7682: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
7683: if(mle==-3)
1.201 brouard 7684: strcat(optionfilehtm,"-MORT_");
1.126 brouard 7685: strcat(optionfilehtm,".htm");
7686: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 7687: printf("Problem with %s \n",optionfilehtm);
7688: exit(0);
1.126 brouard 7689: }
7690:
7691: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
7692: strcat(optionfilehtmcov,"-cov.htm");
7693: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
7694: printf("Problem with %s \n",optionfilehtmcov), exit(0);
7695: }
7696: else{
7697: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
7698: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 7699: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 7700: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
7701: }
7702:
1.204 brouard 7703: 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-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</a></font><br> \
7704: <hr size=\"2\" color=\"#EC5E5E\"> \n\
7705: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 7706: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 7707: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 7708: \n\
7709: <hr size=\"2\" color=\"#EC5E5E\">\
7710: <ul><li><h4>Parameter files</h4>\n\
7711: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
7712: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
7713: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
7714: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
7715: - Date and time at start: %s</ul>\n",\
7716: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
7717: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
7718: fileres,fileres,\
7719: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
7720: fflush(fichtm);
7721:
7722: strcpy(pathr,path);
7723: strcat(pathr,optionfilefiname);
1.184 brouard 7724: #ifdef WIN32
7725: _chdir(optionfilefiname); /* Move to directory named optionfile */
7726: #else
1.126 brouard 7727: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 7728: #endif
7729:
1.126 brouard 7730:
7731: /* Calculates basic frequencies. Computes observed prevalence at single age
7732: and prints on file fileres'p'. */
7733: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
7734:
7735: fprintf(fichtm,"\n");
7736: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
7737: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
7738: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
7739: imx,agemin,agemax,jmin,jmax,jmean);
7740: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7741: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7742: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7743: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7744: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
7745:
7746:
7747: /* For Powell, parameters are in a vector p[] starting at p[1]
7748: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
7749: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
7750:
7751: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 7752: /* For mortality only */
1.126 brouard 7753: if (mle==-3){
1.136 brouard 7754: ximort=matrix(1,NDIM,1,NDIM);
1.186 brouard 7755: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 7756: cens=ivector(1,n);
7757: ageexmed=vector(1,n);
7758: agecens=vector(1,n);
7759: dcwave=ivector(1,n);
7760:
7761: for (i=1; i<=imx; i++){
7762: dcwave[i]=-1;
7763: for (m=firstpass; m<=lastpass; m++)
7764: if (s[m][i]>nlstate) {
7765: dcwave[i]=m;
7766: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
7767: break;
7768: }
7769: }
7770:
7771: for (i=1; i<=imx; i++) {
7772: if (wav[i]>0){
7773: ageexmed[i]=agev[mw[1][i]][i];
7774: j=wav[i];
7775: agecens[i]=1.;
7776:
7777: if (ageexmed[i]> 1 && wav[i] > 0){
7778: agecens[i]=agev[mw[j][i]][i];
7779: cens[i]= 1;
7780: }else if (ageexmed[i]< 1)
7781: cens[i]= -1;
7782: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
7783: cens[i]=0 ;
7784: }
7785: else cens[i]=-1;
7786: }
7787:
7788: for (i=1;i<=NDIM;i++) {
7789: for (j=1;j<=NDIM;j++)
7790: ximort[i][j]=(i == j ? 1.0 : 0.0);
7791: }
7792:
1.145 brouard 7793: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 7794: /*printf("%lf %lf", p[1], p[2]);*/
7795:
7796:
1.136 brouard 7797: #ifdef GSL
7798: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 7799: #else
1.126 brouard 7800: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 7801: #endif
1.201 brouard 7802: strcpy(filerespow,"POW-MORT_");
7803: strcat(filerespow,fileresu);
1.126 brouard 7804: if((ficrespow=fopen(filerespow,"w"))==NULL) {
7805: printf("Problem with resultfile: %s\n", filerespow);
7806: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
7807: }
1.136 brouard 7808: #ifdef GSL
7809: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 7810: #else
1.126 brouard 7811: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 7812: #endif
1.126 brouard 7813: /* for (i=1;i<=nlstate;i++)
7814: for(j=1;j<=nlstate+ndeath;j++)
7815: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
7816: */
7817: fprintf(ficrespow,"\n");
1.136 brouard 7818: #ifdef GSL
7819: /* gsl starts here */
7820: T = gsl_multimin_fminimizer_nmsimplex;
7821: gsl_multimin_fminimizer *sfm = NULL;
7822: gsl_vector *ss, *x;
7823: gsl_multimin_function minex_func;
7824:
7825: /* Initial vertex size vector */
7826: ss = gsl_vector_alloc (NDIM);
7827:
7828: if (ss == NULL){
7829: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
7830: }
7831: /* Set all step sizes to 1 */
7832: gsl_vector_set_all (ss, 0.001);
7833:
7834: /* Starting point */
1.126 brouard 7835:
1.136 brouard 7836: x = gsl_vector_alloc (NDIM);
7837:
7838: if (x == NULL){
7839: gsl_vector_free(ss);
7840: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
7841: }
7842:
7843: /* Initialize method and iterate */
7844: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 7845: /* gsl_vector_set(x, 0, 0.0268); */
7846: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 7847: gsl_vector_set(x, 0, p[1]);
7848: gsl_vector_set(x, 1, p[2]);
7849:
7850: minex_func.f = &gompertz_f;
7851: minex_func.n = NDIM;
7852: minex_func.params = (void *)&p; /* ??? */
7853:
7854: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
7855: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
7856:
7857: printf("Iterations beginning .....\n\n");
7858: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
7859:
7860: iteri=0;
7861: while (rval == GSL_CONTINUE){
7862: iteri++;
7863: status = gsl_multimin_fminimizer_iterate(sfm);
7864:
7865: if (status) printf("error: %s\n", gsl_strerror (status));
7866: fflush(0);
7867:
7868: if (status)
7869: break;
7870:
7871: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
7872: ssval = gsl_multimin_fminimizer_size (sfm);
7873:
7874: if (rval == GSL_SUCCESS)
7875: printf ("converged to a local maximum at\n");
7876:
7877: printf("%5d ", iteri);
7878: for (it = 0; it < NDIM; it++){
7879: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
7880: }
7881: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
7882: }
7883:
7884: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
7885:
7886: gsl_vector_free(x); /* initial values */
7887: gsl_vector_free(ss); /* inital step size */
7888: for (it=0; it<NDIM; it++){
7889: p[it+1]=gsl_vector_get(sfm->x,it);
7890: fprintf(ficrespow," %.12lf", p[it]);
7891: }
7892: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
7893: #endif
7894: #ifdef POWELL
7895: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
7896: #endif
1.126 brouard 7897: fclose(ficrespow);
7898:
1.203 brouard 7899: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 7900:
7901: for(i=1; i <=NDIM; i++)
7902: for(j=i+1;j<=NDIM;j++)
7903: matcov[i][j]=matcov[j][i];
7904:
7905: printf("\nCovariance matrix\n ");
1.203 brouard 7906: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 7907: for(i=1; i <=NDIM; i++) {
7908: for(j=1;j<=NDIM;j++){
7909: printf("%f ",matcov[i][j]);
1.203 brouard 7910: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 7911: }
1.203 brouard 7912: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 7913: }
7914:
7915: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 7916: for (i=1;i<=NDIM;i++) {
1.126 brouard 7917: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 7918: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
7919: }
1.126 brouard 7920: lsurv=vector(1,AGESUP);
7921: lpop=vector(1,AGESUP);
7922: tpop=vector(1,AGESUP);
7923: lsurv[agegomp]=100000;
7924:
7925: for (k=agegomp;k<=AGESUP;k++) {
7926: agemortsup=k;
7927: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
7928: }
7929:
7930: for (k=agegomp;k<agemortsup;k++)
7931: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
7932:
7933: for (k=agegomp;k<agemortsup;k++){
7934: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
7935: sumlpop=sumlpop+lpop[k];
7936: }
7937:
7938: tpop[agegomp]=sumlpop;
7939: for (k=agegomp;k<(agemortsup-3);k++){
7940: /* tpop[k+1]=2;*/
7941: tpop[k+1]=tpop[k]-lpop[k];
7942: }
7943:
7944:
7945: printf("\nAge lx qx dx Lx Tx e(x)\n");
7946: for (k=agegomp;k<(agemortsup-2);k++)
7947: 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]);
7948:
7949:
7950: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 7951: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
7952: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7953: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7954: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7955: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7956: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7957: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7958: }else
1.201 brouard 7959: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7960: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 7961: stepm, weightopt,\
7962: model,imx,p,matcov,agemortsup);
7963:
7964: free_vector(lsurv,1,AGESUP);
7965: free_vector(lpop,1,AGESUP);
7966: free_vector(tpop,1,AGESUP);
1.136 brouard 7967: #ifdef GSL
7968: free_ivector(cens,1,n);
7969: free_vector(agecens,1,n);
7970: free_ivector(dcwave,1,n);
7971: free_matrix(ximort,1,NDIM,1,NDIM);
7972: #endif
1.186 brouard 7973: } /* Endof if mle==-3 mortality only */
1.205 brouard 7974: /* Standard */
7975: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
7976: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
7977: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 7978: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 7979: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7980: for (k=1; k<=npar;k++)
7981: printf(" %d %8.5f",k,p[k]);
7982: printf("\n");
1.205 brouard 7983: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
7984: /* mlikeli uses func not funcone */
7985: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
7986: }
7987: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
7988: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
7989: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
7990: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7991: }
7992: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 7993: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7994: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7995: for (k=1; k<=npar;k++)
7996: printf(" %d %8.5f",k,p[k]);
7997: printf("\n");
7998:
7999: /*--------- results files --------------*/
1.192 brouard 8000: 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 8001:
8002:
8003: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8004: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8005: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8006: for(i=1,jk=1; i <=nlstate; i++){
8007: for(k=1; k <=(nlstate+ndeath); k++){
8008: if (k != i) {
8009: printf("%d%d ",i,k);
8010: fprintf(ficlog,"%d%d ",i,k);
8011: fprintf(ficres,"%1d%1d ",i,k);
8012: for(j=1; j <=ncovmodel; j++){
1.190 brouard 8013: printf("%12.7f ",p[jk]);
8014: fprintf(ficlog,"%12.7f ",p[jk]);
8015: fprintf(ficres,"%12.7f ",p[jk]);
1.126 brouard 8016: jk++;
8017: }
8018: printf("\n");
8019: fprintf(ficlog,"\n");
8020: fprintf(ficres,"\n");
8021: }
8022: }
8023: }
1.203 brouard 8024: if(mle != 0){
8025: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 8026: ftolhess=ftol; /* Usually correct */
1.203 brouard 8027: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
8028: 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");
8029: 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");
8030: for(i=1,jk=1; i <=nlstate; i++){
8031: for(k=1; k <=(nlstate+ndeath); k++){
8032: if (k != i) {
8033: printf("%d%d ",i,k);
8034: fprintf(ficlog,"%d%d ",i,k);
8035: for(j=1; j <=ncovmodel; j++){
8036: 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]));
8037: 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]));
8038: jk++;
8039: }
8040: printf("\n");
8041: fprintf(ficlog,"\n");
1.193 brouard 8042: }
8043: }
8044: }
1.203 brouard 8045: } /* end of hesscov and Wald tests */
1.193 brouard 8046:
1.203 brouard 8047: /* */
1.126 brouard 8048: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
8049: printf("# Scales (for hessian or gradient estimation)\n");
8050: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
8051: for(i=1,jk=1; i <=nlstate; i++){
8052: for(j=1; j <=nlstate+ndeath; j++){
8053: if (j!=i) {
8054: fprintf(ficres,"%1d%1d",i,j);
8055: printf("%1d%1d",i,j);
8056: fprintf(ficlog,"%1d%1d",i,j);
8057: for(k=1; k<=ncovmodel;k++){
8058: printf(" %.5e",delti[jk]);
8059: fprintf(ficlog," %.5e",delti[jk]);
8060: fprintf(ficres," %.5e",delti[jk]);
8061: jk++;
8062: }
8063: printf("\n");
8064: fprintf(ficlog,"\n");
8065: fprintf(ficres,"\n");
8066: }
8067: }
8068: }
8069:
8070: 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 8071: if(mle >= 1) /* To big for the screen */
1.126 brouard 8072: 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");
8073: 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");
8074: /* # 121 Var(a12)\n\ */
8075: /* # 122 Cov(b12,a12) Var(b12)\n\ */
8076: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
8077: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
8078: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
8079: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
8080: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
8081: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
8082:
8083:
8084: /* Just to have a covariance matrix which will be more understandable
8085: even is we still don't want to manage dictionary of variables
8086: */
8087: for(itimes=1;itimes<=2;itimes++){
8088: jj=0;
8089: for(i=1; i <=nlstate; i++){
8090: for(j=1; j <=nlstate+ndeath; j++){
8091: if(j==i) continue;
8092: for(k=1; k<=ncovmodel;k++){
8093: jj++;
8094: ca[0]= k+'a'-1;ca[1]='\0';
8095: if(itimes==1){
8096: if(mle>=1)
8097: printf("#%1d%1d%d",i,j,k);
8098: fprintf(ficlog,"#%1d%1d%d",i,j,k);
8099: fprintf(ficres,"#%1d%1d%d",i,j,k);
8100: }else{
8101: if(mle>=1)
8102: printf("%1d%1d%d",i,j,k);
8103: fprintf(ficlog,"%1d%1d%d",i,j,k);
8104: fprintf(ficres,"%1d%1d%d",i,j,k);
8105: }
8106: ll=0;
8107: for(li=1;li <=nlstate; li++){
8108: for(lj=1;lj <=nlstate+ndeath; lj++){
8109: if(lj==li) continue;
8110: for(lk=1;lk<=ncovmodel;lk++){
8111: ll++;
8112: if(ll<=jj){
8113: cb[0]= lk +'a'-1;cb[1]='\0';
8114: if(ll<jj){
8115: if(itimes==1){
8116: if(mle>=1)
8117: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
8118: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
8119: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
8120: }else{
8121: if(mle>=1)
8122: printf(" %.5e",matcov[jj][ll]);
8123: fprintf(ficlog," %.5e",matcov[jj][ll]);
8124: fprintf(ficres," %.5e",matcov[jj][ll]);
8125: }
8126: }else{
8127: if(itimes==1){
8128: if(mle>=1)
8129: printf(" Var(%s%1d%1d)",ca,i,j);
8130: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
8131: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
8132: }else{
8133: if(mle>=1)
1.203 brouard 8134: printf(" %.7e",matcov[jj][ll]);
8135: fprintf(ficlog," %.7e",matcov[jj][ll]);
8136: fprintf(ficres," %.7e",matcov[jj][ll]);
1.126 brouard 8137: }
8138: }
8139: }
8140: } /* end lk */
8141: } /* end lj */
8142: } /* end li */
8143: if(mle>=1)
8144: printf("\n");
8145: fprintf(ficlog,"\n");
8146: fprintf(ficres,"\n");
8147: numlinepar++;
8148: } /* end k*/
8149: } /*end j */
8150: } /* end i */
8151: } /* end itimes */
8152:
8153: fflush(ficlog);
8154: fflush(ficres);
1.209 brouard 8155: while(fgets(line, MAXLINE, ficpar)) {
8156: /* If line starts with a # it is a comment */
8157: if (line[0] == '#') {
8158: numlinepar++;
1.141 brouard 8159: fputs(line,stdout);
1.126 brouard 8160: fputs(line,ficparo);
1.209 brouard 8161: fputs(line,ficlog);
8162: continue;
8163: }else
8164: break;
8165: }
8166:
8167: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
8168: /* ungetc(c,ficpar); */
8169: /* fgets(line, MAXLINE, ficpar); */
8170: /* fputs(line,stdout); */
8171: /* fputs(line,ficparo); */
8172: /* } */
8173: /* ungetc(c,ficpar); */
1.126 brouard 8174:
8175: estepm=0;
1.209 brouard 8176: 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){
8177:
8178: if (num_filled != 6) {
8179: printf("Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n");
8180: printf("but line=%s\n",line);
8181: goto end;
8182: }
8183: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
8184: }
8185: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
8186: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
8187:
8188: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 8189: if (estepm==0 || estepm < stepm) estepm=stepm;
8190: if (fage <= 2) {
8191: bage = ageminpar;
8192: fage = agemaxpar;
8193: }
8194:
8195: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 ! brouard 8196: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
! 8197: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.186 brouard 8198:
8199: /* Other stuffs, more or less useful */
1.126 brouard 8200: while((c=getc(ficpar))=='#' && c!= EOF){
8201: ungetc(c,ficpar);
8202: fgets(line, MAXLINE, ficpar);
1.141 brouard 8203: fputs(line,stdout);
1.126 brouard 8204: fputs(line,ficparo);
8205: }
8206: ungetc(c,ficpar);
8207:
8208: 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);
8209: 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);
8210: 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);
8211: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
8212: 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);
8213:
8214: while((c=getc(ficpar))=='#' && c!= EOF){
8215: ungetc(c,ficpar);
8216: fgets(line, MAXLINE, ficpar);
1.141 brouard 8217: fputs(line,stdout);
1.126 brouard 8218: fputs(line,ficparo);
8219: }
8220: ungetc(c,ficpar);
8221:
8222:
8223: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
8224: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
8225:
8226: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 8227: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 8228: fprintf(ficparo,"pop_based=%d\n",popbased);
8229: fprintf(ficres,"pop_based=%d\n",popbased);
8230:
8231: while((c=getc(ficpar))=='#' && c!= EOF){
8232: ungetc(c,ficpar);
8233: fgets(line, MAXLINE, ficpar);
1.141 brouard 8234: fputs(line,stdout);
1.126 brouard 8235: fputs(line,ficparo);
8236: }
8237: ungetc(c,ficpar);
8238:
8239: 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);
8240: 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);
8241: 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);
8242: 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);
8243: 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);
8244: /* day and month of proj2 are not used but only year anproj2.*/
8245:
8246:
8247:
1.145 brouard 8248: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
8249: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 8250:
8251: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 8252: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
8253: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
8254: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
8255: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
8256: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
8257: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
8258: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
8259: }else
1.211 ! brouard 8260: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, pathc,p);
1.126 brouard 8261:
1.201 brouard 8262: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\
1.211 ! brouard 8263: model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,estepm, \
1.126 brouard 8264: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
8265:
8266: /*------------ free_vector -------------*/
8267: /* chdir(path); */
8268:
8269: free_ivector(wav,1,imx);
8270: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
8271: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
8272: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
8273: free_lvector(num,1,n);
8274: free_vector(agedc,1,n);
8275: /*free_matrix(covar,0,NCOVMAX,1,n);*/
8276: /*free_matrix(covar,1,NCOVMAX,1,n);*/
8277: fclose(ficparo);
8278: fclose(ficres);
8279:
8280:
1.186 brouard 8281: /* Other results (useful)*/
8282:
8283:
1.126 brouard 8284: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 8285: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
8286: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 8287: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 8288: fclose(ficrespl);
8289:
1.145 brouard 8290: #ifdef FREEEXIT2
8291: #include "freeexit2.h"
8292: #endif
8293:
1.126 brouard 8294: /*------------- h Pij x at various ages ------------*/
1.180 brouard 8295: /*#include "hpijx.h"*/
8296: hPijx(p, bage, fage);
1.145 brouard 8297: fclose(ficrespij);
1.126 brouard 8298:
1.145 brouard 8299: /*-------------- Variance of one-step probabilities---*/
8300: k=1;
1.126 brouard 8301: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
8302:
8303:
8304: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
8305: for(i=1;i<=AGESUP;i++)
8306: for(j=1;j<=NCOVMAX;j++)
8307: for(k=1;k<=NCOVMAX;k++)
8308: probs[i][j][k]=0.;
8309:
8310: /*---------- Forecasting ------------------*/
8311: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
8312: if(prevfcast==1){
8313: /* if(stepm ==1){*/
1.201 brouard 8314: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 8315: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
8316: /* } */
8317: /* else{ */
8318: /* erreur=108; */
8319: /* printf("Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
8320: /* fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
8321: /* } */
8322: }
1.186 brouard 8323:
8324: /* ------ Other prevalence ratios------------ */
1.126 brouard 8325:
1.127 brouard 8326: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
8327:
8328: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
8329: /* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
8330: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
8331: */
1.126 brouard 8332:
1.127 brouard 8333: if (mobilav!=0) {
8334: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
8335: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
8336: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
8337: printf(" Error in movingaverage mobilav=%d\n",mobilav);
8338: }
1.126 brouard 8339: }
8340:
8341:
1.127 brouard 8342: /*---------- Health expectancies, no variances ------------*/
8343:
1.201 brouard 8344: strcpy(filerese,"E_");
8345: strcat(filerese,fileresu);
1.126 brouard 8346: if((ficreseij=fopen(filerese,"w"))==NULL) {
8347: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
8348: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
8349: }
1.208 brouard 8350: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
8351: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.145 brouard 8352: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8353: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8354:
8355: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 8356: fprintf(ficreseij,"\n#****** ");
8357: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 8358: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.127 brouard 8359: }
8360: fprintf(ficreseij,"******\n");
8361:
8362: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8363: oldm=oldms;savm=savms;
8364: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
8365:
8366: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 8367: /*}*/
1.127 brouard 8368: }
8369: fclose(ficreseij);
1.208 brouard 8370: printf("done evsij\n");fflush(stdout);
8371: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.127 brouard 8372:
8373: /*---------- Health expectancies and variances ------------*/
8374:
8375:
1.201 brouard 8376: strcpy(filerest,"T_");
8377: strcat(filerest,fileresu);
1.127 brouard 8378: if((ficrest=fopen(filerest,"w"))==NULL) {
8379: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
8380: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
8381: }
1.208 brouard 8382: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
8383: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.127 brouard 8384:
1.126 brouard 8385:
1.201 brouard 8386: strcpy(fileresstde,"STDE_");
8387: strcat(fileresstde,fileresu);
1.126 brouard 8388: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
8389: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
8390: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
8391: }
1.208 brouard 8392: printf(" Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
8393: fprintf(ficlog," Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 8394:
1.201 brouard 8395: strcpy(filerescve,"CVE_");
8396: strcat(filerescve,fileresu);
1.126 brouard 8397: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
8398: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
8399: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
8400: }
1.208 brouard 8401: printf(" Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
8402: fprintf(ficlog," Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 8403:
1.201 brouard 8404: strcpy(fileresv,"V_");
8405: strcat(fileresv,fileresu);
1.126 brouard 8406: if((ficresvij=fopen(fileresv,"w"))==NULL) {
8407: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
8408: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
8409: }
1.208 brouard 8410: printf(" Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(stdout);
8411: fprintf(ficlog," Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 8412:
1.145 brouard 8413: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8414: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8415:
8416: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.208 brouard 8417: fprintf(ficrest,"\n#****** ");
8418: for(j=1;j<=cptcoveff;j++)
8419: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8420: fprintf(ficrest,"******\n");
8421:
8422: fprintf(ficresstdeij,"\n#****** ");
8423: fprintf(ficrescveij,"\n#****** ");
8424: for(j=1;j<=cptcoveff;j++) {
8425: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8426: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8427: }
8428: fprintf(ficresstdeij,"******\n");
8429: fprintf(ficrescveij,"******\n");
8430:
8431: fprintf(ficresvij,"\n#****** ");
8432: for(j=1;j<=cptcoveff;j++)
8433: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8434: fprintf(ficresvij,"******\n");
8435:
8436: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8437: oldm=oldms;savm=savms;
8438: printf(" cvevsij %d, ",k);
8439: fprintf(ficlog, " cvevsij %d, ",k);
8440: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
8441: printf(" end cvevsij \n ");
8442: fprintf(ficlog, " end cvevsij \n ");
8443:
8444: /*
8445: */
8446: /* goto endfree; */
8447:
8448: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8449: pstamp(ficrest);
8450:
8451:
8452: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
8453: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
8454: cptcod= 0; /* To be deleted */
8455: printf("varevsij %d \n",vpopbased);
8456: fprintf(ficlog, "varevsij %d \n",vpopbased);
1.209 brouard 8457: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
1.208 brouard 8458: 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 ");
8459: if(vpopbased==1)
8460: 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);
8461: else
8462: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
8463: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
8464: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
8465: fprintf(ficrest,"\n");
8466: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
8467: epj=vector(1,nlstate+1);
8468: printf("Computing age specific period (stable) prevalences in each health state \n");
8469: fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
8470: for(age=bage; age <=fage ;age++){
1.209 brouard 8471: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
1.208 brouard 8472: if (vpopbased==1) {
8473: if(mobilav ==0){
8474: for(i=1; i<=nlstate;i++)
8475: prlim[i][i]=probs[(int)age][i][k];
8476: }else{ /* mobilav */
8477: for(i=1; i<=nlstate;i++)
8478: prlim[i][i]=mobaverage[(int)age][i][k];
1.126 brouard 8479: }
1.208 brouard 8480: }
8481:
8482: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
8483: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
8484: /* printf(" age %4.0f ",age); */
8485: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
8486: for(i=1, epj[j]=0.;i <=nlstate;i++) {
8487: epj[j] += prlim[i][i]*eij[i][j][(int)age];
8488: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
8489: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
1.126 brouard 8490: }
1.208 brouard 8491: epj[nlstate+1] +=epj[j];
8492: }
8493: /* printf(" age %4.0f \n",age); */
8494:
8495: for(i=1, vepp=0.;i <=nlstate;i++)
8496: for(j=1;j <=nlstate;j++)
8497: vepp += vareij[i][j][(int)age];
8498: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
8499: for(j=1;j <=nlstate;j++){
8500: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
1.126 brouard 8501: }
1.208 brouard 8502: fprintf(ficrest,"\n");
1.126 brouard 8503: }
1.208 brouard 8504: } /* End vpopbased */
8505: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
8506: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
8507: free_vector(epj,1,nlstate+1);
8508: printf("done \n");fflush(stdout);
8509: fprintf(ficlog,"done\n");fflush(ficlog);
8510:
1.145 brouard 8511: /*}*/
1.208 brouard 8512: } /* End k */
1.126 brouard 8513: free_vector(weight,1,n);
1.145 brouard 8514: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 8515: free_imatrix(s,1,maxwav+1,1,n);
8516: free_matrix(anint,1,maxwav,1,n);
8517: free_matrix(mint,1,maxwav,1,n);
8518: free_ivector(cod,1,n);
8519: free_ivector(tab,1,NCOVMAX);
8520: fclose(ficresstdeij);
8521: fclose(ficrescveij);
8522: fclose(ficresvij);
8523: fclose(ficrest);
1.208 brouard 8524: printf("done Health expectancies\n");fflush(stdout);
8525: fprintf(ficlog,"done Health expectancies\n");fflush(ficlog);
1.126 brouard 8526: fclose(ficpar);
8527:
8528: /*------- Variance of period (stable) prevalence------*/
8529:
1.201 brouard 8530: strcpy(fileresvpl,"VPL_");
8531: strcat(fileresvpl,fileresu);
1.126 brouard 8532: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
8533: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
8534: exit(0);
8535: }
1.208 brouard 8536: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
8537: fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.126 brouard 8538:
1.145 brouard 8539: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8540: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8541:
8542: for (k=1; k <= (int) pow(2,cptcoveff); k++){
8543: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 8544: for(j=1;j<=cptcoveff;j++)
1.200 brouard 8545: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 8546: fprintf(ficresvpl,"******\n");
8547:
8548: varpl=matrix(1,nlstate,(int) bage, (int) fage);
8549: oldm=oldms;savm=savms;
1.209 brouard 8550: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
1.126 brouard 8551: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 8552: /*}*/
1.126 brouard 8553: }
8554:
8555: fclose(ficresvpl);
1.208 brouard 8556: printf("done variance-covariance of period prevalence\n");fflush(stdout);
8557: fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
1.126 brouard 8558:
8559: /*---------- End : free ----------------*/
8560: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
8561: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
8562: } /* mle==-3 arrives here for freeing */
1.164 brouard 8563: /* endfree:*/
1.141 brouard 8564: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 8565: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
8566: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
8567: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
8568: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
8569: free_matrix(covar,0,NCOVMAX,1,n);
8570: free_matrix(matcov,1,npar,1,npar);
1.203 brouard 8571: free_matrix(hess,1,npar,1,npar);
1.126 brouard 8572: /*free_vector(delti,1,npar);*/
8573: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8574: free_matrix(agev,1,maxwav,1,imx);
8575: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8576:
1.145 brouard 8577: free_ivector(ncodemax,1,NCOVMAX);
1.192 brouard 8578: free_ivector(ncodemaxwundef,1,NCOVMAX);
1.145 brouard 8579: free_ivector(Tvar,1,NCOVMAX);
8580: free_ivector(Tprod,1,NCOVMAX);
8581: free_ivector(Tvaraff,1,NCOVMAX);
8582: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 8583:
8584: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
1.200 brouard 8585: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 8586: fflush(fichtm);
8587: fflush(ficgp);
8588:
8589:
8590: if((nberr >0) || (nbwarn>0)){
8591: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
8592: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
8593: }else{
8594: printf("End of Imach\n");
8595: fprintf(ficlog,"End of Imach\n");
8596: }
8597: printf("See log file on %s\n",filelog);
8598: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 8599: /*(void) gettimeofday(&end_time,&tzp);*/
8600: rend_time = time(NULL);
8601: end_time = *localtime(&rend_time);
8602: /* tml = *localtime(&end_time.tm_sec); */
8603: strcpy(strtend,asctime(&end_time));
1.126 brouard 8604: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
8605: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 8606: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 8607:
1.157 brouard 8608: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
8609: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
8610: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 8611: /* printf("Total time was %d uSec.\n", total_usecs);*/
8612: /* if(fileappend(fichtm,optionfilehtm)){ */
8613: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8614: fclose(fichtm);
8615: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8616: fclose(fichtmcov);
8617: fclose(ficgp);
8618: fclose(ficlog);
8619: /*------ End -----------*/
8620:
8621:
8622: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 8623: #ifdef WIN32
8624: if (_chdir(pathcd) != 0)
8625: printf("Can't move to directory %s!\n",path);
8626: if(_getcwd(pathcd,MAXLINE) > 0)
8627: #else
1.126 brouard 8628: if(chdir(pathcd) != 0)
1.184 brouard 8629: printf("Can't move to directory %s!\n", path);
8630: if (getcwd(pathcd, MAXLINE) > 0)
8631: #endif
1.126 brouard 8632: printf("Current directory %s!\n",pathcd);
8633: /*strcat(plotcmd,CHARSEPARATOR);*/
8634: sprintf(plotcmd,"gnuplot");
1.157 brouard 8635: #ifdef _WIN32
1.126 brouard 8636: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
8637: #endif
8638: if(!stat(plotcmd,&info)){
1.158 brouard 8639: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8640: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 8641: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 8642: }else
8643: strcpy(pplotcmd,plotcmd);
1.157 brouard 8644: #ifdef __unix
1.126 brouard 8645: strcpy(plotcmd,GNUPLOTPROGRAM);
8646: if(!stat(plotcmd,&info)){
1.158 brouard 8647: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8648: }else
8649: strcpy(pplotcmd,plotcmd);
8650: #endif
8651: }else
8652: strcpy(pplotcmd,plotcmd);
8653:
8654: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 8655: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8656:
8657: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 8658: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 8659: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 8660: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 8661: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 8662: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 8663: }
1.158 brouard 8664: printf(" Successful, please wait...");
1.126 brouard 8665: while (z[0] != 'q') {
8666: /* chdir(path); */
1.154 brouard 8667: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 8668: scanf("%s",z);
8669: /* if (z[0] == 'c') system("./imach"); */
8670: if (z[0] == 'e') {
1.158 brouard 8671: #ifdef __APPLE__
1.152 brouard 8672: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 8673: #elif __linux
8674: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 8675: #else
1.152 brouard 8676: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 8677: #endif
8678: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
8679: system(pplotcmd);
1.126 brouard 8680: }
8681: else if (z[0] == 'g') system(plotcmd);
8682: else if (z[0] == 'q') exit(0);
8683: }
8684: end:
8685: while (z[0] != 'q') {
1.195 brouard 8686: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 8687: scanf("%s",z);
8688: }
8689: }
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