Annotation of imach/src/imach.c, revision 1.204
1.204 ! brouard 1: /* $Id: imach.c,v 1.203 2015/09/30 17:45:14 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.204 ! brouard 4: Revision 1.203 2015/09/30 17:45:14 brouard
! 5: Summary: looking at better estimation of the hessian
! 6:
! 7: Also a better criteria for convergence to the period prevalence And
! 8: therefore adding the number of years needed to converge. (The
! 9: prevalence in any alive state shold sum to one
! 10:
1.203 brouard 11: Revision 1.202 2015/09/22 19:45:16 brouard
12: Summary: Adding some overall graph on contribution to likelihood. Might change
13:
1.202 brouard 14: Revision 1.201 2015/09/15 17:34:58 brouard
15: Summary: 0.98r0
16:
17: - Some new graphs like suvival functions
18: - Some bugs fixed like model=1+age+V2.
19:
1.201 brouard 20: Revision 1.200 2015/09/09 16:53:55 brouard
21: Summary: Big bug thanks to Flavia
22:
23: Even model=1+age+V2. did not work anymore
24:
1.200 brouard 25: Revision 1.199 2015/09/07 14:09:23 brouard
26: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
27:
1.199 brouard 28: Revision 1.198 2015/09/03 07:14:39 brouard
29: Summary: 0.98q5 Flavia
30:
1.198 brouard 31: Revision 1.197 2015/09/01 18:24:39 brouard
32: *** empty log message ***
33:
1.197 brouard 34: Revision 1.196 2015/08/18 23:17:52 brouard
35: Summary: 0.98q5
36:
1.196 brouard 37: Revision 1.195 2015/08/18 16:28:39 brouard
38: Summary: Adding a hack for testing purpose
39:
40: After reading the title, ftol and model lines, if the comment line has
41: a q, starting with #q, the answer at the end of the run is quit. It
42: permits to run test files in batch with ctest. The former workaround was
43: $ echo q | imach foo.imach
44:
1.195 brouard 45: Revision 1.194 2015/08/18 13:32:00 brouard
46: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
47:
1.194 brouard 48: Revision 1.193 2015/08/04 07:17:42 brouard
49: Summary: 0.98q4
50:
1.193 brouard 51: Revision 1.192 2015/07/16 16:49:02 brouard
52: Summary: Fixing some outputs
53:
1.192 brouard 54: Revision 1.191 2015/07/14 10:00:33 brouard
55: Summary: Some fixes
56:
1.191 brouard 57: Revision 1.190 2015/05/05 08:51:13 brouard
58: Summary: Adding digits in output parameters (7 digits instead of 6)
59:
60: Fix 1+age+.
61:
1.190 brouard 62: Revision 1.189 2015/04/30 14:45:16 brouard
63: Summary: 0.98q2
64:
1.189 brouard 65: Revision 1.188 2015/04/30 08:27:53 brouard
66: *** empty log message ***
67:
1.188 brouard 68: Revision 1.187 2015/04/29 09:11:15 brouard
69: *** empty log message ***
70:
1.187 brouard 71: Revision 1.186 2015/04/23 12:01:52 brouard
72: Summary: V1*age is working now, version 0.98q1
73:
74: Some codes had been disabled in order to simplify and Vn*age was
75: working in the optimization phase, ie, giving correct MLE parameters,
76: but, as usual, outputs were not correct and program core dumped.
77:
1.186 brouard 78: Revision 1.185 2015/03/11 13:26:42 brouard
79: Summary: Inclusion of compile and links command line for Intel Compiler
80:
1.185 brouard 81: Revision 1.184 2015/03/11 11:52:39 brouard
82: Summary: Back from Windows 8. Intel Compiler
83:
1.184 brouard 84: Revision 1.183 2015/03/10 20:34:32 brouard
85: Summary: 0.98q0, trying with directest, mnbrak fixed
86:
87: We use directest instead of original Powell test; probably no
88: incidence on the results, but better justifications;
89: We fixed Numerical Recipes mnbrak routine which was wrong and gave
90: wrong results.
91:
1.183 brouard 92: Revision 1.182 2015/02/12 08:19:57 brouard
93: Summary: Trying to keep directest which seems simpler and more general
94: Author: Nicolas Brouard
95:
1.182 brouard 96: Revision 1.181 2015/02/11 23:22:24 brouard
97: Summary: Comments on Powell added
98:
99: Author:
100:
1.181 brouard 101: Revision 1.180 2015/02/11 17:33:45 brouard
102: Summary: Finishing move from main to function (hpijx and prevalence_limit)
103:
1.180 brouard 104: Revision 1.179 2015/01/04 09:57:06 brouard
105: Summary: back to OS/X
106:
1.179 brouard 107: Revision 1.178 2015/01/04 09:35:48 brouard
108: *** empty log message ***
109:
1.178 brouard 110: Revision 1.177 2015/01/03 18:40:56 brouard
111: Summary: Still testing ilc32 on OSX
112:
1.177 brouard 113: Revision 1.176 2015/01/03 16:45:04 brouard
114: *** empty log message ***
115:
1.176 brouard 116: Revision 1.175 2015/01/03 16:33:42 brouard
117: *** empty log message ***
118:
1.175 brouard 119: Revision 1.174 2015/01/03 16:15:49 brouard
120: Summary: Still in cross-compilation
121:
1.174 brouard 122: Revision 1.173 2015/01/03 12:06:26 brouard
123: Summary: trying to detect cross-compilation
124:
1.173 brouard 125: Revision 1.172 2014/12/27 12:07:47 brouard
126: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
127:
1.172 brouard 128: Revision 1.171 2014/12/23 13:26:59 brouard
129: Summary: Back from Visual C
130:
131: Still problem with utsname.h on Windows
132:
1.171 brouard 133: Revision 1.170 2014/12/23 11:17:12 brouard
134: Summary: Cleaning some \%% back to %%
135:
136: The escape was mandatory for a specific compiler (which one?), but too many warnings.
137:
1.170 brouard 138: Revision 1.169 2014/12/22 23:08:31 brouard
139: Summary: 0.98p
140:
141: Outputs some informations on compiler used, OS etc. Testing on different platforms.
142:
1.169 brouard 143: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 144: Summary: update
1.169 brouard 145:
1.168 brouard 146: Revision 1.167 2014/12/22 13:50:56 brouard
147: Summary: Testing uname and compiler version and if compiled 32 or 64
148:
149: Testing on Linux 64
150:
1.167 brouard 151: Revision 1.166 2014/12/22 11:40:47 brouard
152: *** empty log message ***
153:
1.166 brouard 154: Revision 1.165 2014/12/16 11:20:36 brouard
155: Summary: After compiling on Visual C
156:
157: * imach.c (Module): Merging 1.61 to 1.162
158:
1.165 brouard 159: Revision 1.164 2014/12/16 10:52:11 brouard
160: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
161:
162: * imach.c (Module): Merging 1.61 to 1.162
163:
1.164 brouard 164: Revision 1.163 2014/12/16 10:30:11 brouard
165: * imach.c (Module): Merging 1.61 to 1.162
166:
1.163 brouard 167: Revision 1.162 2014/09/25 11:43:39 brouard
168: Summary: temporary backup 0.99!
169:
1.162 brouard 170: Revision 1.1 2014/09/16 11:06:58 brouard
171: Summary: With some code (wrong) for nlopt
172:
173: Author:
174:
175: Revision 1.161 2014/09/15 20:41:41 brouard
176: Summary: Problem with macro SQR on Intel compiler
177:
1.161 brouard 178: Revision 1.160 2014/09/02 09:24:05 brouard
179: *** empty log message ***
180:
1.160 brouard 181: Revision 1.159 2014/09/01 10:34:10 brouard
182: Summary: WIN32
183: Author: Brouard
184:
1.159 brouard 185: Revision 1.158 2014/08/27 17:11:51 brouard
186: *** empty log message ***
187:
1.158 brouard 188: Revision 1.157 2014/08/27 16:26:55 brouard
189: Summary: Preparing windows Visual studio version
190: Author: Brouard
191:
192: In order to compile on Visual studio, time.h is now correct and time_t
193: and tm struct should be used. difftime should be used but sometimes I
194: just make the differences in raw time format (time(&now).
195: Trying to suppress #ifdef LINUX
196: Add xdg-open for __linux in order to open default browser.
197:
1.157 brouard 198: Revision 1.156 2014/08/25 20:10:10 brouard
199: *** empty log message ***
200:
1.156 brouard 201: Revision 1.155 2014/08/25 18:32:34 brouard
202: Summary: New compile, minor changes
203: Author: Brouard
204:
1.155 brouard 205: Revision 1.154 2014/06/20 17:32:08 brouard
206: Summary: Outputs now all graphs of convergence to period prevalence
207:
1.154 brouard 208: Revision 1.153 2014/06/20 16:45:46 brouard
209: Summary: If 3 live state, convergence to period prevalence on same graph
210: Author: Brouard
211:
1.153 brouard 212: Revision 1.152 2014/06/18 17:54:09 brouard
213: Summary: open browser, use gnuplot on same dir than imach if not found in the path
214:
1.152 brouard 215: Revision 1.151 2014/06/18 16:43:30 brouard
216: *** empty log message ***
217:
1.151 brouard 218: Revision 1.150 2014/06/18 16:42:35 brouard
219: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
220: Author: brouard
221:
1.150 brouard 222: Revision 1.149 2014/06/18 15:51:14 brouard
223: Summary: Some fixes in parameter files errors
224: Author: Nicolas Brouard
225:
1.149 brouard 226: Revision 1.148 2014/06/17 17:38:48 brouard
227: Summary: Nothing new
228: Author: Brouard
229:
230: Just a new packaging for OS/X version 0.98nS
231:
1.148 brouard 232: Revision 1.147 2014/06/16 10:33:11 brouard
233: *** empty log message ***
234:
1.147 brouard 235: Revision 1.146 2014/06/16 10:20:28 brouard
236: Summary: Merge
237: Author: Brouard
238:
239: Merge, before building revised version.
240:
1.146 brouard 241: Revision 1.145 2014/06/10 21:23:15 brouard
242: Summary: Debugging with valgrind
243: Author: Nicolas Brouard
244:
245: Lot of changes in order to output the results with some covariates
246: After the Edimburgh REVES conference 2014, it seems mandatory to
247: improve the code.
248: No more memory valgrind error but a lot has to be done in order to
249: continue the work of splitting the code into subroutines.
250: Also, decodemodel has been improved. Tricode is still not
251: optimal. nbcode should be improved. Documentation has been added in
252: the source code.
253:
1.144 brouard 254: Revision 1.143 2014/01/26 09:45:38 brouard
255: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
256:
257: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
258: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
259:
1.143 brouard 260: Revision 1.142 2014/01/26 03:57:36 brouard
261: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
262:
263: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
264:
1.142 brouard 265: Revision 1.141 2014/01/26 02:42:01 brouard
266: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
267:
1.141 brouard 268: Revision 1.140 2011/09/02 10:37:54 brouard
269: Summary: times.h is ok with mingw32 now.
270:
1.140 brouard 271: Revision 1.139 2010/06/14 07:50:17 brouard
272: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
273: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
274:
1.139 brouard 275: Revision 1.138 2010/04/30 18:19:40 brouard
276: *** empty log message ***
277:
1.138 brouard 278: Revision 1.137 2010/04/29 18:11:38 brouard
279: (Module): Checking covariates for more complex models
280: than V1+V2. A lot of change to be done. Unstable.
281:
1.137 brouard 282: Revision 1.136 2010/04/26 20:30:53 brouard
283: (Module): merging some libgsl code. Fixing computation
284: of likelione (using inter/intrapolation if mle = 0) in order to
285: get same likelihood as if mle=1.
286: Some cleaning of code and comments added.
287:
1.136 brouard 288: Revision 1.135 2009/10/29 15:33:14 brouard
289: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
290:
1.135 brouard 291: Revision 1.134 2009/10/29 13:18:53 brouard
292: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
293:
1.134 brouard 294: Revision 1.133 2009/07/06 10:21:25 brouard
295: just nforces
296:
1.133 brouard 297: Revision 1.132 2009/07/06 08:22:05 brouard
298: Many tings
299:
1.132 brouard 300: Revision 1.131 2009/06/20 16:22:47 brouard
301: Some dimensions resccaled
302:
1.131 brouard 303: Revision 1.130 2009/05/26 06:44:34 brouard
304: (Module): Max Covariate is now set to 20 instead of 8. A
305: lot of cleaning with variables initialized to 0. Trying to make
306: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
307:
1.130 brouard 308: Revision 1.129 2007/08/31 13:49:27 lievre
309: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
310:
1.129 lievre 311: Revision 1.128 2006/06/30 13:02:05 brouard
312: (Module): Clarifications on computing e.j
313:
1.128 brouard 314: Revision 1.127 2006/04/28 18:11:50 brouard
315: (Module): Yes the sum of survivors was wrong since
316: imach-114 because nhstepm was no more computed in the age
317: loop. Now we define nhstepma in the age loop.
318: (Module): In order to speed up (in case of numerous covariates) we
319: compute health expectancies (without variances) in a first step
320: and then all the health expectancies with variances or standard
321: deviation (needs data from the Hessian matrices) which slows the
322: computation.
323: In the future we should be able to stop the program is only health
324: expectancies and graph are needed without standard deviations.
325:
1.127 brouard 326: Revision 1.126 2006/04/28 17:23:28 brouard
327: (Module): Yes the sum of survivors was wrong since
328: imach-114 because nhstepm was no more computed in the age
329: loop. Now we define nhstepma in the age loop.
330: Version 0.98h
331:
1.126 brouard 332: Revision 1.125 2006/04/04 15:20:31 lievre
333: Errors in calculation of health expectancies. Age was not initialized.
334: Forecasting file added.
335:
336: Revision 1.124 2006/03/22 17:13:53 lievre
337: Parameters are printed with %lf instead of %f (more numbers after the comma).
338: The log-likelihood is printed in the log file
339:
340: Revision 1.123 2006/03/20 10:52:43 brouard
341: * imach.c (Module): <title> changed, corresponds to .htm file
342: name. <head> headers where missing.
343:
344: * imach.c (Module): Weights can have a decimal point as for
345: English (a comma might work with a correct LC_NUMERIC environment,
346: otherwise the weight is truncated).
347: Modification of warning when the covariates values are not 0 or
348: 1.
349: Version 0.98g
350:
351: Revision 1.122 2006/03/20 09:45:41 brouard
352: (Module): Weights can have a decimal point as for
353: English (a comma might work with a correct LC_NUMERIC environment,
354: otherwise the weight is truncated).
355: Modification of warning when the covariates values are not 0 or
356: 1.
357: Version 0.98g
358:
359: Revision 1.121 2006/03/16 17:45:01 lievre
360: * imach.c (Module): Comments concerning covariates added
361:
362: * imach.c (Module): refinements in the computation of lli if
363: status=-2 in order to have more reliable computation if stepm is
364: not 1 month. Version 0.98f
365:
366: Revision 1.120 2006/03/16 15:10:38 lievre
367: (Module): refinements in the computation of lli if
368: status=-2 in order to have more reliable computation if stepm is
369: not 1 month. Version 0.98f
370:
371: Revision 1.119 2006/03/15 17:42:26 brouard
372: (Module): Bug if status = -2, the loglikelihood was
373: computed as likelihood omitting the logarithm. Version O.98e
374:
375: Revision 1.118 2006/03/14 18:20:07 brouard
376: (Module): varevsij Comments added explaining the second
377: table of variances if popbased=1 .
378: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
379: (Module): Function pstamp added
380: (Module): Version 0.98d
381:
382: Revision 1.117 2006/03/14 17:16:22 brouard
383: (Module): varevsij Comments added explaining the second
384: table of variances if popbased=1 .
385: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
386: (Module): Function pstamp added
387: (Module): Version 0.98d
388:
389: Revision 1.116 2006/03/06 10:29:27 brouard
390: (Module): Variance-covariance wrong links and
391: varian-covariance of ej. is needed (Saito).
392:
393: Revision 1.115 2006/02/27 12:17:45 brouard
394: (Module): One freematrix added in mlikeli! 0.98c
395:
396: Revision 1.114 2006/02/26 12:57:58 brouard
397: (Module): Some improvements in processing parameter
398: filename with strsep.
399:
400: Revision 1.113 2006/02/24 14:20:24 brouard
401: (Module): Memory leaks checks with valgrind and:
402: datafile was not closed, some imatrix were not freed and on matrix
403: allocation too.
404:
405: Revision 1.112 2006/01/30 09:55:26 brouard
406: (Module): Back to gnuplot.exe instead of wgnuplot.exe
407:
408: Revision 1.111 2006/01/25 20:38:18 brouard
409: (Module): Lots of cleaning and bugs added (Gompertz)
410: (Module): Comments can be added in data file. Missing date values
411: can be a simple dot '.'.
412:
413: Revision 1.110 2006/01/25 00:51:50 brouard
414: (Module): Lots of cleaning and bugs added (Gompertz)
415:
416: Revision 1.109 2006/01/24 19:37:15 brouard
417: (Module): Comments (lines starting with a #) are allowed in data.
418:
419: Revision 1.108 2006/01/19 18:05:42 lievre
420: Gnuplot problem appeared...
421: To be fixed
422:
423: Revision 1.107 2006/01/19 16:20:37 brouard
424: Test existence of gnuplot in imach path
425:
426: Revision 1.106 2006/01/19 13:24:36 brouard
427: Some cleaning and links added in html output
428:
429: Revision 1.105 2006/01/05 20:23:19 lievre
430: *** empty log message ***
431:
432: Revision 1.104 2005/09/30 16:11:43 lievre
433: (Module): sump fixed, loop imx fixed, and simplifications.
434: (Module): If the status is missing at the last wave but we know
435: that the person is alive, then we can code his/her status as -2
436: (instead of missing=-1 in earlier versions) and his/her
437: contributions to the likelihood is 1 - Prob of dying from last
438: health status (= 1-p13= p11+p12 in the easiest case of somebody in
439: the healthy state at last known wave). Version is 0.98
440:
441: Revision 1.103 2005/09/30 15:54:49 lievre
442: (Module): sump fixed, loop imx fixed, and simplifications.
443:
444: Revision 1.102 2004/09/15 17:31:30 brouard
445: Add the possibility to read data file including tab characters.
446:
447: Revision 1.101 2004/09/15 10:38:38 brouard
448: Fix on curr_time
449:
450: Revision 1.100 2004/07/12 18:29:06 brouard
451: Add version for Mac OS X. Just define UNIX in Makefile
452:
453: Revision 1.99 2004/06/05 08:57:40 brouard
454: *** empty log message ***
455:
456: Revision 1.98 2004/05/16 15:05:56 brouard
457: New version 0.97 . First attempt to estimate force of mortality
458: directly from the data i.e. without the need of knowing the health
459: state at each age, but using a Gompertz model: log u =a + b*age .
460: This is the basic analysis of mortality and should be done before any
461: other analysis, in order to test if the mortality estimated from the
462: cross-longitudinal survey is different from the mortality estimated
463: from other sources like vital statistic data.
464:
465: The same imach parameter file can be used but the option for mle should be -3.
466:
1.133 brouard 467: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 468: former routines in order to include the new code within the former code.
469:
470: The output is very simple: only an estimate of the intercept and of
471: the slope with 95% confident intervals.
472:
473: Current limitations:
474: A) Even if you enter covariates, i.e. with the
475: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
476: B) There is no computation of Life Expectancy nor Life Table.
477:
478: Revision 1.97 2004/02/20 13:25:42 lievre
479: Version 0.96d. Population forecasting command line is (temporarily)
480: suppressed.
481:
482: Revision 1.96 2003/07/15 15:38:55 brouard
483: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
484: rewritten within the same printf. Workaround: many printfs.
485:
486: Revision 1.95 2003/07/08 07:54:34 brouard
487: * imach.c (Repository):
488: (Repository): Using imachwizard code to output a more meaningful covariance
489: matrix (cov(a12,c31) instead of numbers.
490:
491: Revision 1.94 2003/06/27 13:00:02 brouard
492: Just cleaning
493:
494: Revision 1.93 2003/06/25 16:33:55 brouard
495: (Module): On windows (cygwin) function asctime_r doesn't
496: exist so I changed back to asctime which exists.
497: (Module): Version 0.96b
498:
499: Revision 1.92 2003/06/25 16:30:45 brouard
500: (Module): On windows (cygwin) function asctime_r doesn't
501: exist so I changed back to asctime which exists.
502:
503: Revision 1.91 2003/06/25 15:30:29 brouard
504: * imach.c (Repository): Duplicated warning errors corrected.
505: (Repository): Elapsed time after each iteration is now output. It
506: helps to forecast when convergence will be reached. Elapsed time
507: is stamped in powell. We created a new html file for the graphs
508: concerning matrix of covariance. It has extension -cov.htm.
509:
510: Revision 1.90 2003/06/24 12:34:15 brouard
511: (Module): Some bugs corrected for windows. Also, when
512: mle=-1 a template is output in file "or"mypar.txt with the design
513: of the covariance matrix to be input.
514:
515: Revision 1.89 2003/06/24 12:30:52 brouard
516: (Module): Some bugs corrected for windows. Also, when
517: mle=-1 a template is output in file "or"mypar.txt with the design
518: of the covariance matrix to be input.
519:
520: Revision 1.88 2003/06/23 17:54:56 brouard
521: * 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.
522:
523: Revision 1.87 2003/06/18 12:26:01 brouard
524: Version 0.96
525:
526: Revision 1.86 2003/06/17 20:04:08 brouard
527: (Module): Change position of html and gnuplot routines and added
528: routine fileappend.
529:
530: Revision 1.85 2003/06/17 13:12:43 brouard
531: * imach.c (Repository): Check when date of death was earlier that
532: current date of interview. It may happen when the death was just
533: prior to the death. In this case, dh was negative and likelihood
534: was wrong (infinity). We still send an "Error" but patch by
535: assuming that the date of death was just one stepm after the
536: interview.
537: (Repository): Because some people have very long ID (first column)
538: we changed int to long in num[] and we added a new lvector for
539: memory allocation. But we also truncated to 8 characters (left
540: truncation)
541: (Repository): No more line truncation errors.
542:
543: Revision 1.84 2003/06/13 21:44:43 brouard
544: * imach.c (Repository): Replace "freqsummary" at a correct
545: place. It differs from routine "prevalence" which may be called
546: many times. Probs is memory consuming and must be used with
547: parcimony.
548: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
549:
550: Revision 1.83 2003/06/10 13:39:11 lievre
551: *** empty log message ***
552:
553: Revision 1.82 2003/06/05 15:57:20 brouard
554: Add log in imach.c and fullversion number is now printed.
555:
556: */
557: /*
558: Interpolated Markov Chain
559:
560: Short summary of the programme:
561:
562: This program computes Healthy Life Expectancies from
563: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
564: first survey ("cross") where individuals from different ages are
565: interviewed on their health status or degree of disability (in the
566: case of a health survey which is our main interest) -2- at least a
567: second wave of interviews ("longitudinal") which measure each change
568: (if any) in individual health status. Health expectancies are
569: computed from the time spent in each health state according to a
570: model. More health states you consider, more time is necessary to reach the
571: Maximum Likelihood of the parameters involved in the model. The
572: simplest model is the multinomial logistic model where pij is the
573: probability to be observed in state j at the second wave
574: conditional to be observed in state i at the first wave. Therefore
575: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
576: 'age' is age and 'sex' is a covariate. If you want to have a more
577: complex model than "constant and age", you should modify the program
578: where the markup *Covariates have to be included here again* invites
579: you to do it. More covariates you add, slower the
580: convergence.
581:
582: The advantage of this computer programme, compared to a simple
583: multinomial logistic model, is clear when the delay between waves is not
584: identical for each individual. Also, if a individual missed an
585: intermediate interview, the information is lost, but taken into
586: account using an interpolation or extrapolation.
587:
588: hPijx is the probability to be observed in state i at age x+h
589: conditional to the observed state i at age x. The delay 'h' can be
590: split into an exact number (nh*stepm) of unobserved intermediate
591: states. This elementary transition (by month, quarter,
592: semester or year) is modelled as a multinomial logistic. The hPx
593: matrix is simply the matrix product of nh*stepm elementary matrices
594: and the contribution of each individual to the likelihood is simply
595: hPijx.
596:
597: Also this programme outputs the covariance matrix of the parameters but also
598: of the life expectancies. It also computes the period (stable) prevalence.
599:
1.133 brouard 600: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
601: Institut national d'études démographiques, Paris.
1.126 brouard 602: This software have been partly granted by Euro-REVES, a concerted action
603: from the European Union.
604: It is copyrighted identically to a GNU software product, ie programme and
605: software can be distributed freely for non commercial use. Latest version
606: can be accessed at http://euroreves.ined.fr/imach .
607:
608: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
609: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
610:
611: **********************************************************************/
612: /*
613: main
614: read parameterfile
615: read datafile
616: concatwav
617: freqsummary
618: if (mle >= 1)
619: mlikeli
620: print results files
621: if mle==1
622: computes hessian
623: read end of parameter file: agemin, agemax, bage, fage, estepm
624: begin-prev-date,...
625: open gnuplot file
626: open html file
1.145 brouard 627: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
628: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
629: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
630: freexexit2 possible for memory heap.
631:
632: h Pij x | pij_nom ficrestpij
633: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
634: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
635: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
636:
637: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
638: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
639: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
640: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
641: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
642:
1.126 brouard 643: forecasting if prevfcast==1 prevforecast call prevalence()
644: health expectancies
645: Variance-covariance of DFLE
646: prevalence()
647: movingaverage()
648: varevsij()
649: if popbased==1 varevsij(,popbased)
650: total life expectancies
651: Variance of period (stable) prevalence
652: end
653: */
654:
1.187 brouard 655: /* #define DEBUG */
656: /* #define DEBUGBRENT */
1.203 brouard 657: /* #define DEBUGLINMIN */
658: /* #define DEBUGHESS */
659: #define DEBUGHESSIJ
660: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan)*\/ */
1.165 brouard 661: #define POWELL /* Instead of NLOPT */
1.192 brouard 662: #define POWELLF1F3 /* Skip test */
1.186 brouard 663: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
664: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 665:
666: #include <math.h>
667: #include <stdio.h>
668: #include <stdlib.h>
669: #include <string.h>
1.159 brouard 670:
671: #ifdef _WIN32
672: #include <io.h>
1.172 brouard 673: #include <windows.h>
674: #include <tchar.h>
1.159 brouard 675: #else
1.126 brouard 676: #include <unistd.h>
1.159 brouard 677: #endif
1.126 brouard 678:
679: #include <limits.h>
680: #include <sys/types.h>
1.171 brouard 681:
682: #if defined(__GNUC__)
683: #include <sys/utsname.h> /* Doesn't work on Windows */
684: #endif
685:
1.126 brouard 686: #include <sys/stat.h>
687: #include <errno.h>
1.159 brouard 688: /* extern int errno; */
1.126 brouard 689:
1.157 brouard 690: /* #ifdef LINUX */
691: /* #include <time.h> */
692: /* #include "timeval.h" */
693: /* #else */
694: /* #include <sys/time.h> */
695: /* #endif */
696:
1.126 brouard 697: #include <time.h>
698:
1.136 brouard 699: #ifdef GSL
700: #include <gsl/gsl_errno.h>
701: #include <gsl/gsl_multimin.h>
702: #endif
703:
1.167 brouard 704:
1.162 brouard 705: #ifdef NLOPT
706: #include <nlopt.h>
707: typedef struct {
708: double (* function)(double [] );
709: } myfunc_data ;
710: #endif
711:
1.126 brouard 712: /* #include <libintl.h> */
713: /* #define _(String) gettext (String) */
714:
1.141 brouard 715: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 716:
717: #define GNUPLOTPROGRAM "gnuplot"
718: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
719: #define FILENAMELENGTH 132
720:
721: #define GLOCK_ERROR_NOPATH -1 /* empty path */
722: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
723:
1.144 brouard 724: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
725: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 726:
727: #define NINTERVMAX 8
1.144 brouard 728: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
729: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
730: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 731: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.126 brouard 732: #define MAXN 20000
1.144 brouard 733: #define YEARM 12. /**< Number of months per year */
1.126 brouard 734: #define AGESUP 130
735: #define AGEBASE 40
1.194 brouard 736: #define AGEOVERFLOW 1.e20
1.164 brouard 737: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 738: #ifdef _WIN32
739: #define DIRSEPARATOR '\\'
740: #define CHARSEPARATOR "\\"
741: #define ODIRSEPARATOR '/'
742: #else
1.126 brouard 743: #define DIRSEPARATOR '/'
744: #define CHARSEPARATOR "/"
745: #define ODIRSEPARATOR '\\'
746: #endif
747:
1.204 ! brouard 748: /* $Id: imach.c,v 1.203 2015/09/30 17:45:14 brouard Exp $ */
1.126 brouard 749: /* $State: Exp $ */
1.196 brouard 750: #include "version.h"
751: char version[]=__IMACH_VERSION__;
1.204 ! brouard 752: 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";
! 753: char fullversion[]="$Revision: 1.203 $ $Date: 2015/09/30 17:45:14 $";
1.126 brouard 754: char strstart[80];
755: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 756: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 757: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 758: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
759: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
760: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
761: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
762: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
763: int cptcovprodnoage=0; /**< Number of covariate products without age */
764: int cptcoveff=0; /* Total number of covariates to vary for printing results */
765: int cptcov=0; /* Working variable */
1.126 brouard 766: int npar=NPARMAX;
767: int nlstate=2; /* Number of live states */
768: int ndeath=1; /* Number of dead states */
1.130 brouard 769: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 770: int popbased=0;
771:
772: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 773: int maxwav=0; /* Maxim number of waves */
774: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
775: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
776: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 777: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 778: int mle=1, weightopt=0;
1.126 brouard 779: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
780: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
781: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
782: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 783: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 784: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 785: double **matprod2(); /* test */
1.126 brouard 786: double **oldm, **newm, **savm; /* Working pointers to matrices */
787: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 788: /*FILE *fic ; */ /* Used in readdata only */
789: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 790: FILE *ficlog, *ficrespow;
1.130 brouard 791: int globpr=0; /* Global variable for printing or not */
1.126 brouard 792: double fretone; /* Only one call to likelihood */
1.130 brouard 793: long ipmx=0; /* Number of contributions */
1.126 brouard 794: double sw; /* Sum of weights */
795: char filerespow[FILENAMELENGTH];
796: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
797: FILE *ficresilk;
798: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
799: FILE *ficresprobmorprev;
800: FILE *fichtm, *fichtmcov; /* Html File */
801: FILE *ficreseij;
802: char filerese[FILENAMELENGTH];
803: FILE *ficresstdeij;
804: char fileresstde[FILENAMELENGTH];
805: FILE *ficrescveij;
806: char filerescve[FILENAMELENGTH];
807: FILE *ficresvij;
808: char fileresv[FILENAMELENGTH];
809: FILE *ficresvpl;
810: char fileresvpl[FILENAMELENGTH];
811: char title[MAXLINE];
812: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
813: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
814: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
815: char command[FILENAMELENGTH];
816: int outcmd=0;
817:
818: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 819: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 820: char filelog[FILENAMELENGTH]; /* Log file */
821: char filerest[FILENAMELENGTH];
822: char fileregp[FILENAMELENGTH];
823: char popfile[FILENAMELENGTH];
824:
825: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
826:
1.157 brouard 827: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
828: /* struct timezone tzp; */
829: /* extern int gettimeofday(); */
830: struct tm tml, *gmtime(), *localtime();
831:
832: extern time_t time();
833:
834: struct tm start_time, end_time, curr_time, last_time, forecast_time;
835: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
836: struct tm tm;
837:
1.126 brouard 838: char strcurr[80], strfor[80];
839:
840: char *endptr;
841: long lval;
842: double dval;
843:
844: #define NR_END 1
845: #define FREE_ARG char*
846: #define FTOL 1.0e-10
847:
848: #define NRANSI
849: #define ITMAX 200
850:
851: #define TOL 2.0e-4
852:
853: #define CGOLD 0.3819660
854: #define ZEPS 1.0e-10
855: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
856:
857: #define GOLD 1.618034
858: #define GLIMIT 100.0
859: #define TINY 1.0e-20
860:
861: static double maxarg1,maxarg2;
862: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
863: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
864:
865: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
866: #define rint(a) floor(a+0.5)
1.166 brouard 867: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 868: #define mytinydouble 1.0e-16
1.166 brouard 869: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
870: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
871: /* static double dsqrarg; */
872: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 873: static double sqrarg;
874: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
875: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
876: int agegomp= AGEGOMP;
877:
878: int imx;
879: int stepm=1;
880: /* Stepm, step in month: minimum step interpolation*/
881:
882: int estepm;
883: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
884:
885: int m,nb;
886: long *num;
1.197 brouard 887: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 888: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
889: covariate for which somebody answered excluding
890: undefined. Usually 2: 0 and 1. */
891: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
892: covariate for which somebody answered including
893: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 894: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
895: double **pmmij, ***probs;
896: double *ageexmed,*agecens;
897: double dateintmean=0;
898:
899: double *weight;
900: int **s; /* Status */
1.141 brouard 901: double *agedc;
1.145 brouard 902: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 903: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 904: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 905: double idx;
906: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.197 brouard 907: int *Tage;
1.145 brouard 908: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 909: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.141 brouard 910: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 911: double *lsurv, *lpop, *tpop;
912:
1.143 brouard 913: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
914: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 915:
916: /**************** split *************************/
917: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
918: {
919: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
920: the name of the file (name), its extension only (ext) and its first part of the name (finame)
921: */
922: char *ss; /* pointer */
1.186 brouard 923: int l1=0, l2=0; /* length counters */
1.126 brouard 924:
925: l1 = strlen(path ); /* length of path */
926: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
927: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
928: if ( ss == NULL ) { /* no directory, so determine current directory */
929: strcpy( name, path ); /* we got the fullname name because no directory */
930: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
931: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
932: /* get current working directory */
933: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 934: #ifdef WIN32
935: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
936: #else
937: if (getcwd(dirc, FILENAME_MAX) == NULL) {
938: #endif
1.126 brouard 939: return( GLOCK_ERROR_GETCWD );
940: }
941: /* got dirc from getcwd*/
942: printf(" DIRC = %s \n",dirc);
943: } else { /* strip direcotry from path */
944: ss++; /* after this, the filename */
945: l2 = strlen( ss ); /* length of filename */
946: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
947: strcpy( name, ss ); /* save file name */
948: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 949: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 950: printf(" DIRC2 = %s \n",dirc);
951: }
952: /* We add a separator at the end of dirc if not exists */
953: l1 = strlen( dirc ); /* length of directory */
954: if( dirc[l1-1] != DIRSEPARATOR ){
955: dirc[l1] = DIRSEPARATOR;
956: dirc[l1+1] = 0;
957: printf(" DIRC3 = %s \n",dirc);
958: }
959: ss = strrchr( name, '.' ); /* find last / */
960: if (ss >0){
961: ss++;
962: strcpy(ext,ss); /* save extension */
963: l1= strlen( name);
964: l2= strlen(ss)+1;
965: strncpy( finame, name, l1-l2);
966: finame[l1-l2]= 0;
967: }
968:
969: return( 0 ); /* we're done */
970: }
971:
972:
973: /******************************************/
974:
975: void replace_back_to_slash(char *s, char*t)
976: {
977: int i;
978: int lg=0;
979: i=0;
980: lg=strlen(t);
981: for(i=0; i<= lg; i++) {
982: (s[i] = t[i]);
983: if (t[i]== '\\') s[i]='/';
984: }
985: }
986:
1.132 brouard 987: char *trimbb(char *out, char *in)
1.137 brouard 988: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 989: char *s;
990: s=out;
991: while (*in != '\0'){
1.137 brouard 992: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 993: in++;
994: }
995: *out++ = *in++;
996: }
997: *out='\0';
998: return s;
999: }
1000:
1.187 brouard 1001: /* char *substrchaine(char *out, char *in, char *chain) */
1002: /* { */
1003: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1004: /* char *s, *t; */
1005: /* t=in;s=out; */
1006: /* while ((*in != *chain) && (*in != '\0')){ */
1007: /* *out++ = *in++; */
1008: /* } */
1009:
1010: /* /\* *in matches *chain *\/ */
1011: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1012: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1013: /* } */
1014: /* in--; chain--; */
1015: /* while ( (*in != '\0')){ */
1016: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1017: /* *out++ = *in++; */
1018: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1019: /* } */
1020: /* *out='\0'; */
1021: /* out=s; */
1022: /* return out; */
1023: /* } */
1024: char *substrchaine(char *out, char *in, char *chain)
1025: {
1026: /* Substract chain 'chain' from 'in', return and output 'out' */
1027: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1028:
1029: char *strloc;
1030:
1031: strcpy (out, in);
1032: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1033: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1034: if(strloc != NULL){
1035: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1036: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1037: /* strcpy (strloc, strloc +strlen(chain));*/
1038: }
1039: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1040: return out;
1041: }
1042:
1043:
1.145 brouard 1044: char *cutl(char *blocc, char *alocc, char *in, char occ)
1045: {
1.187 brouard 1046: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1047: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1048: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1049: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1050: */
1.160 brouard 1051: char *s, *t;
1.145 brouard 1052: t=in;s=in;
1053: while ((*in != occ) && (*in != '\0')){
1054: *alocc++ = *in++;
1055: }
1056: if( *in == occ){
1057: *(alocc)='\0';
1058: s=++in;
1059: }
1060:
1061: if (s == t) {/* occ not found */
1062: *(alocc-(in-s))='\0';
1063: in=s;
1064: }
1065: while ( *in != '\0'){
1066: *blocc++ = *in++;
1067: }
1068:
1069: *blocc='\0';
1070: return t;
1071: }
1.137 brouard 1072: char *cutv(char *blocc, char *alocc, char *in, char occ)
1073: {
1.187 brouard 1074: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1075: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1076: gives blocc="abcdef2ghi" and alocc="j".
1077: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1078: */
1079: char *s, *t;
1080: t=in;s=in;
1081: while (*in != '\0'){
1082: while( *in == occ){
1083: *blocc++ = *in++;
1084: s=in;
1085: }
1086: *blocc++ = *in++;
1087: }
1088: if (s == t) /* occ not found */
1089: *(blocc-(in-s))='\0';
1090: else
1091: *(blocc-(in-s)-1)='\0';
1092: in=s;
1093: while ( *in != '\0'){
1094: *alocc++ = *in++;
1095: }
1096:
1097: *alocc='\0';
1098: return s;
1099: }
1100:
1.126 brouard 1101: int nbocc(char *s, char occ)
1102: {
1103: int i,j=0;
1104: int lg=20;
1105: i=0;
1106: lg=strlen(s);
1107: for(i=0; i<= lg; i++) {
1108: if (s[i] == occ ) j++;
1109: }
1110: return j;
1111: }
1112:
1.137 brouard 1113: /* void cutv(char *u,char *v, char*t, char occ) */
1114: /* { */
1115: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1116: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1117: /* gives u="abcdef2ghi" and v="j" *\/ */
1118: /* int i,lg,j,p=0; */
1119: /* i=0; */
1120: /* lg=strlen(t); */
1121: /* for(j=0; j<=lg-1; j++) { */
1122: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1123: /* } */
1.126 brouard 1124:
1.137 brouard 1125: /* for(j=0; j<p; j++) { */
1126: /* (u[j] = t[j]); */
1127: /* } */
1128: /* u[p]='\0'; */
1.126 brouard 1129:
1.137 brouard 1130: /* for(j=0; j<= lg; j++) { */
1131: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1132: /* } */
1133: /* } */
1.126 brouard 1134:
1.160 brouard 1135: #ifdef _WIN32
1136: char * strsep(char **pp, const char *delim)
1137: {
1138: char *p, *q;
1139:
1140: if ((p = *pp) == NULL)
1141: return 0;
1142: if ((q = strpbrk (p, delim)) != NULL)
1143: {
1144: *pp = q + 1;
1145: *q = '\0';
1146: }
1147: else
1148: *pp = 0;
1149: return p;
1150: }
1151: #endif
1152:
1.126 brouard 1153: /********************** nrerror ********************/
1154:
1155: void nrerror(char error_text[])
1156: {
1157: fprintf(stderr,"ERREUR ...\n");
1158: fprintf(stderr,"%s\n",error_text);
1159: exit(EXIT_FAILURE);
1160: }
1161: /*********************** vector *******************/
1162: double *vector(int nl, int nh)
1163: {
1164: double *v;
1165: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1166: if (!v) nrerror("allocation failure in vector");
1167: return v-nl+NR_END;
1168: }
1169:
1170: /************************ free vector ******************/
1171: void free_vector(double*v, int nl, int nh)
1172: {
1173: free((FREE_ARG)(v+nl-NR_END));
1174: }
1175:
1176: /************************ivector *******************************/
1177: int *ivector(long nl,long nh)
1178: {
1179: int *v;
1180: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1181: if (!v) nrerror("allocation failure in ivector");
1182: return v-nl+NR_END;
1183: }
1184:
1185: /******************free ivector **************************/
1186: void free_ivector(int *v, long nl, long nh)
1187: {
1188: free((FREE_ARG)(v+nl-NR_END));
1189: }
1190:
1191: /************************lvector *******************************/
1192: long *lvector(long nl,long nh)
1193: {
1194: long *v;
1195: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1196: if (!v) nrerror("allocation failure in ivector");
1197: return v-nl+NR_END;
1198: }
1199:
1200: /******************free lvector **************************/
1201: void free_lvector(long *v, long nl, long nh)
1202: {
1203: free((FREE_ARG)(v+nl-NR_END));
1204: }
1205:
1206: /******************* imatrix *******************************/
1207: int **imatrix(long nrl, long nrh, long ncl, long nch)
1208: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1209: {
1210: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1211: int **m;
1212:
1213: /* allocate pointers to rows */
1214: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1215: if (!m) nrerror("allocation failure 1 in matrix()");
1216: m += NR_END;
1217: m -= nrl;
1218:
1219:
1220: /* allocate rows and set pointers to them */
1221: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1222: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1223: m[nrl] += NR_END;
1224: m[nrl] -= ncl;
1225:
1226: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1227:
1228: /* return pointer to array of pointers to rows */
1229: return m;
1230: }
1231:
1232: /****************** free_imatrix *************************/
1233: void free_imatrix(m,nrl,nrh,ncl,nch)
1234: int **m;
1235: long nch,ncl,nrh,nrl;
1236: /* free an int matrix allocated by imatrix() */
1237: {
1238: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1239: free((FREE_ARG) (m+nrl-NR_END));
1240: }
1241:
1242: /******************* matrix *******************************/
1243: double **matrix(long nrl, long nrh, long ncl, long nch)
1244: {
1245: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1246: double **m;
1247:
1248: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1249: if (!m) nrerror("allocation failure 1 in matrix()");
1250: m += NR_END;
1251: m -= nrl;
1252:
1253: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1254: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1255: m[nrl] += NR_END;
1256: m[nrl] -= ncl;
1257:
1258: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1259: return m;
1.145 brouard 1260: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1261: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1262: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1263: */
1264: }
1265:
1266: /*************************free matrix ************************/
1267: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1268: {
1269: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1270: free((FREE_ARG)(m+nrl-NR_END));
1271: }
1272:
1273: /******************* ma3x *******************************/
1274: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1275: {
1276: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1277: double ***m;
1278:
1279: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1280: if (!m) nrerror("allocation failure 1 in matrix()");
1281: m += NR_END;
1282: m -= nrl;
1283:
1284: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1285: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1286: m[nrl] += NR_END;
1287: m[nrl] -= ncl;
1288:
1289: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1290:
1291: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1292: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1293: m[nrl][ncl] += NR_END;
1294: m[nrl][ncl] -= nll;
1295: for (j=ncl+1; j<=nch; j++)
1296: m[nrl][j]=m[nrl][j-1]+nlay;
1297:
1298: for (i=nrl+1; i<=nrh; i++) {
1299: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1300: for (j=ncl+1; j<=nch; j++)
1301: m[i][j]=m[i][j-1]+nlay;
1302: }
1303: return m;
1304: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1305: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1306: */
1307: }
1308:
1309: /*************************free ma3x ************************/
1310: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1311: {
1312: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1313: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1314: free((FREE_ARG)(m+nrl-NR_END));
1315: }
1316:
1317: /*************** function subdirf ***********/
1318: char *subdirf(char fileres[])
1319: {
1320: /* Caution optionfilefiname is hidden */
1321: strcpy(tmpout,optionfilefiname);
1322: strcat(tmpout,"/"); /* Add to the right */
1323: strcat(tmpout,fileres);
1324: return tmpout;
1325: }
1326:
1327: /*************** function subdirf2 ***********/
1328: char *subdirf2(char fileres[], char *preop)
1329: {
1330:
1331: /* Caution optionfilefiname is hidden */
1332: strcpy(tmpout,optionfilefiname);
1333: strcat(tmpout,"/");
1334: strcat(tmpout,preop);
1335: strcat(tmpout,fileres);
1336: return tmpout;
1337: }
1338:
1339: /*************** function subdirf3 ***********/
1340: char *subdirf3(char fileres[], char *preop, char *preop2)
1341: {
1342:
1343: /* Caution optionfilefiname is hidden */
1344: strcpy(tmpout,optionfilefiname);
1345: strcat(tmpout,"/");
1346: strcat(tmpout,preop);
1347: strcat(tmpout,preop2);
1348: strcat(tmpout,fileres);
1349: return tmpout;
1350: }
1351:
1.162 brouard 1352: char *asc_diff_time(long time_sec, char ascdiff[])
1353: {
1354: long sec_left, days, hours, minutes;
1355: days = (time_sec) / (60*60*24);
1356: sec_left = (time_sec) % (60*60*24);
1357: hours = (sec_left) / (60*60) ;
1358: sec_left = (sec_left) %(60*60);
1359: minutes = (sec_left) /60;
1360: sec_left = (sec_left) % (60);
1361: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1362: return ascdiff;
1363: }
1364:
1.126 brouard 1365: /***************** f1dim *************************/
1366: extern int ncom;
1367: extern double *pcom,*xicom;
1368: extern double (*nrfunc)(double []);
1369:
1370: double f1dim(double x)
1371: {
1372: int j;
1373: double f;
1374: double *xt;
1375:
1376: xt=vector(1,ncom);
1377: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1378: f=(*nrfunc)(xt);
1379: free_vector(xt,1,ncom);
1380: return f;
1381: }
1382:
1383: /*****************brent *************************/
1384: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1385: {
1386: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1387: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1388: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1389: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1390: * returned function value.
1391: */
1.126 brouard 1392: int iter;
1393: double a,b,d,etemp;
1.159 brouard 1394: double fu=0,fv,fw,fx;
1.164 brouard 1395: double ftemp=0.;
1.126 brouard 1396: double p,q,r,tol1,tol2,u,v,w,x,xm;
1397: double e=0.0;
1398:
1399: a=(ax < cx ? ax : cx);
1400: b=(ax > cx ? ax : cx);
1401: x=w=v=bx;
1402: fw=fv=fx=(*f)(x);
1403: for (iter=1;iter<=ITMAX;iter++) {
1404: xm=0.5*(a+b);
1405: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1406: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1407: printf(".");fflush(stdout);
1408: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1409: #ifdef DEBUGBRENT
1.126 brouard 1410: 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);
1411: 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);
1412: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1413: #endif
1414: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1415: *xmin=x;
1416: return fx;
1417: }
1418: ftemp=fu;
1419: if (fabs(e) > tol1) {
1420: r=(x-w)*(fx-fv);
1421: q=(x-v)*(fx-fw);
1422: p=(x-v)*q-(x-w)*r;
1423: q=2.0*(q-r);
1424: if (q > 0.0) p = -p;
1425: q=fabs(q);
1426: etemp=e;
1427: e=d;
1428: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1429: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1430: else {
1431: d=p/q;
1432: u=x+d;
1433: if (u-a < tol2 || b-u < tol2)
1434: d=SIGN(tol1,xm-x);
1435: }
1436: } else {
1437: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1438: }
1439: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1440: fu=(*f)(u);
1441: if (fu <= fx) {
1442: if (u >= x) a=x; else b=x;
1443: SHFT(v,w,x,u)
1.183 brouard 1444: SHFT(fv,fw,fx,fu)
1445: } else {
1446: if (u < x) a=u; else b=u;
1447: if (fu <= fw || w == x) {
1448: v=w;
1449: w=u;
1450: fv=fw;
1451: fw=fu;
1452: } else if (fu <= fv || v == x || v == w) {
1453: v=u;
1454: fv=fu;
1455: }
1456: }
1.126 brouard 1457: }
1458: nrerror("Too many iterations in brent");
1459: *xmin=x;
1460: return fx;
1461: }
1462:
1463: /****************** mnbrak ***********************/
1464:
1465: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1466: double (*func)(double))
1.183 brouard 1467: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1468: the downhill direction (defined by the function as evaluated at the initial points) and returns
1469: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1470: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1471: */
1.126 brouard 1472: double ulim,u,r,q, dum;
1473: double fu;
1.187 brouard 1474:
1475: double scale=10.;
1476: int iterscale=0;
1477:
1478: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1479: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1480:
1481:
1482: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1483: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1484: /* *bx = *ax - (*ax - *bx)/scale; */
1485: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1486: /* } */
1487:
1.126 brouard 1488: if (*fb > *fa) {
1489: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1490: SHFT(dum,*fb,*fa,dum)
1491: }
1.126 brouard 1492: *cx=(*bx)+GOLD*(*bx-*ax);
1493: *fc=(*func)(*cx);
1.183 brouard 1494: #ifdef DEBUG
1495: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1496: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1497: #endif
1498: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1499: r=(*bx-*ax)*(*fb-*fc);
1500: q=(*bx-*cx)*(*fb-*fa);
1501: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1502: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1503: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1504: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1505: fu=(*func)(u);
1.163 brouard 1506: #ifdef DEBUG
1507: /* f(x)=A(x-u)**2+f(u) */
1508: double A, fparabu;
1509: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1510: fparabu= *fa - A*(*ax-u)*(*ax-u);
1511: 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);
1512: 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 1513: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1514: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1515: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1516: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1517: #endif
1.184 brouard 1518: #ifdef MNBRAKORIGINAL
1.183 brouard 1519: #else
1.191 brouard 1520: /* if (fu > *fc) { */
1521: /* #ifdef DEBUG */
1522: /* printf("mnbrak4 fu > fc \n"); */
1523: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1524: /* #endif */
1525: /* /\* 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 *\\/ *\/ */
1526: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1527: /* dum=u; /\* Shifting c and u *\/ */
1528: /* u = *cx; */
1529: /* *cx = dum; */
1530: /* dum = fu; */
1531: /* fu = *fc; */
1532: /* *fc =dum; */
1533: /* } else { /\* end *\/ */
1534: /* #ifdef DEBUG */
1535: /* printf("mnbrak3 fu < fc \n"); */
1536: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1537: /* #endif */
1538: /* dum=u; /\* Shifting c and u *\/ */
1539: /* u = *cx; */
1540: /* *cx = dum; */
1541: /* dum = fu; */
1542: /* fu = *fc; */
1543: /* *fc =dum; */
1544: /* } */
1.183 brouard 1545: #ifdef DEBUG
1.191 brouard 1546: printf("mnbrak34 fu < or >= fc \n");
1547: fprintf(ficlog, "mnbrak34 fu < fc\n");
1.183 brouard 1548: #endif
1.191 brouard 1549: dum=u; /* Shifting c and u */
1550: u = *cx;
1551: *cx = dum;
1552: dum = fu;
1553: fu = *fc;
1554: *fc =dum;
1.183 brouard 1555: #endif
1.162 brouard 1556: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1557: #ifdef DEBUG
1558: printf("mnbrak2 u after c but before ulim\n");
1559: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1560: #endif
1.126 brouard 1561: fu=(*func)(u);
1562: if (fu < *fc) {
1.183 brouard 1563: #ifdef DEBUG
1564: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1565: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1566: #endif
1.126 brouard 1567: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1568: SHFT(*fb,*fc,fu,(*func)(u))
1569: }
1.162 brouard 1570: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1571: #ifdef DEBUG
1572: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1573: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1574: #endif
1.126 brouard 1575: u=ulim;
1576: fu=(*func)(u);
1.183 brouard 1577: } else { /* u could be left to b (if r > q parabola has a maximum) */
1578: #ifdef DEBUG
1579: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1580: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1581: #endif
1.126 brouard 1582: u=(*cx)+GOLD*(*cx-*bx);
1583: fu=(*func)(u);
1.183 brouard 1584: } /* end tests */
1.126 brouard 1585: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1586: SHFT(*fa,*fb,*fc,fu)
1587: #ifdef DEBUG
1588: 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);
1589: 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);
1590: #endif
1591: } /* 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 1592: }
1593:
1594: /*************** linmin ************************/
1.162 brouard 1595: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1596: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1597: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1598: the value of func at the returned location p . This is actually all accomplished by calling the
1599: routines mnbrak and brent .*/
1.126 brouard 1600: int ncom;
1601: double *pcom,*xicom;
1602: double (*nrfunc)(double []);
1603:
1604: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1605: {
1606: double brent(double ax, double bx, double cx,
1607: double (*f)(double), double tol, double *xmin);
1608: double f1dim(double x);
1609: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1610: double *fc, double (*func)(double));
1611: int j;
1612: double xx,xmin,bx,ax;
1613: double fx,fb,fa;
1.187 brouard 1614:
1.203 brouard 1615: #ifdef LINMINORIGINAL
1616: #else
1617: double scale=10., axs, xxs; /* Scale added for infinity */
1618: #endif
1619:
1.126 brouard 1620: ncom=n;
1621: pcom=vector(1,n);
1622: xicom=vector(1,n);
1623: nrfunc=func;
1624: for (j=1;j<=n;j++) {
1625: pcom[j]=p[j];
1.202 brouard 1626: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1627: }
1.187 brouard 1628:
1.203 brouard 1629: #ifdef LINMINORIGINAL
1630: xx=1.;
1631: #else
1632: axs=0.0;
1633: xxs=1.;
1634: do{
1635: xx= xxs;
1636: #endif
1.187 brouard 1637: ax=0.;
1638: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1639: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1640: /* 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)) */
1641: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1642: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1643: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1644: /* 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 1645: #ifdef LINMINORIGINAL
1646: #else
1647: if (fx != fx){
1648: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1649: printf("|");
1650: fprintf(ficlog,"|");
1651: #ifdef DEBUGLINMIN
1652: 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);
1653: #endif
1654: }
1655: }while(fx != fx);
1656: #endif
1657:
1.191 brouard 1658: #ifdef DEBUGLINMIN
1659: 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 1660: 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 1661: #endif
1.187 brouard 1662: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1663: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1664: /* fmin = f(p[j] + xmin * xi[j]) */
1665: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1666: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1667: #ifdef DEBUG
1668: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1669: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1670: #endif
1.191 brouard 1671: #ifdef DEBUGLINMIN
1672: printf("linmin end ");
1.202 brouard 1673: fprintf(ficlog,"linmin end ");
1.191 brouard 1674: #endif
1.126 brouard 1675: for (j=1;j<=n;j++) {
1.203 brouard 1676: #ifdef LINMINORIGINAL
1677: xi[j] *= xmin;
1678: #else
1679: #ifdef DEBUGLINMIN
1680: if(xxs <1.0)
1681: printf(" before xi[%d]=%12.8f", j,xi[j]);
1682: #endif
1683: 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) */
1684: #ifdef DEBUGLINMIN
1685: if(xxs <1.0)
1686: 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 );
1687: #endif
1688: #endif
1.187 brouard 1689: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1690: }
1.191 brouard 1691: #ifdef DEBUGLINMIN
1.203 brouard 1692: printf("\n");
1.191 brouard 1693: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 1694: 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 1695: for (j=1;j<=n;j++) {
1.202 brouard 1696: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1697: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1698: if(j % ncovmodel == 0){
1.191 brouard 1699: printf("\n");
1.202 brouard 1700: fprintf(ficlog,"\n");
1701: }
1.191 brouard 1702: }
1.203 brouard 1703: #else
1.191 brouard 1704: #endif
1.126 brouard 1705: free_vector(xicom,1,n);
1706: free_vector(pcom,1,n);
1707: }
1708:
1709:
1710: /*************** powell ************************/
1.162 brouard 1711: /*
1712: Minimization of a function func of n variables. Input consists of an initial starting point
1713: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1714: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1715: such that failure to decrease by more than this amount on one iteration signals doneness. On
1716: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1717: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1718: */
1.126 brouard 1719: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1720: double (*func)(double []))
1721: {
1722: void linmin(double p[], double xi[], int n, double *fret,
1723: double (*func)(double []));
1724: int i,ibig,j;
1725: double del,t,*pt,*ptt,*xit;
1.181 brouard 1726: double directest;
1.126 brouard 1727: double fp,fptt;
1728: double *xits;
1729: int niterf, itmp;
1730:
1731: pt=vector(1,n);
1732: ptt=vector(1,n);
1733: xit=vector(1,n);
1734: xits=vector(1,n);
1735: *fret=(*func)(p);
1736: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 1737: rcurr_time = time(NULL);
1.126 brouard 1738: for (*iter=1;;++(*iter)) {
1.187 brouard 1739: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1740: ibig=0;
1741: del=0.0;
1.157 brouard 1742: rlast_time=rcurr_time;
1743: /* (void) gettimeofday(&curr_time,&tzp); */
1744: rcurr_time = time(NULL);
1745: curr_time = *localtime(&rcurr_time);
1746: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1747: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1748: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1749: for (i=1;i<=n;i++) {
1.126 brouard 1750: printf(" %d %.12f",i, p[i]);
1751: fprintf(ficlog," %d %.12lf",i, p[i]);
1752: fprintf(ficrespow," %.12lf", p[i]);
1753: }
1754: printf("\n");
1755: fprintf(ficlog,"\n");
1756: fprintf(ficrespow,"\n");fflush(ficrespow);
1757: if(*iter <=3){
1.157 brouard 1758: tml = *localtime(&rcurr_time);
1759: strcpy(strcurr,asctime(&tml));
1760: rforecast_time=rcurr_time;
1.126 brouard 1761: itmp = strlen(strcurr);
1762: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1763: strcurr[itmp-1]='\0';
1.162 brouard 1764: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1765: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1766: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1767: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1768: forecast_time = *localtime(&rforecast_time);
1769: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1770: itmp = strlen(strfor);
1771: if(strfor[itmp-1]=='\n')
1772: strfor[itmp-1]='\0';
1.157 brouard 1773: 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);
1774: 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 1775: }
1776: }
1.187 brouard 1777: for (i=1;i<=n;i++) { /* For each direction i */
1778: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1779: fptt=(*fret);
1780: #ifdef DEBUG
1.203 brouard 1781: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1782: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1783: #endif
1.203 brouard 1784: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1785: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 brouard 1786: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1787: /* Outputs are fret(new point p) p is updated and xit rescaled */
1788: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1789: /* because that direction will be replaced unless the gain del is small */
1790: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1791: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1792: /* with the new direction. */
1.126 brouard 1793: del=fabs(fptt-(*fret));
1794: ibig=i;
1795: }
1796: #ifdef DEBUG
1797: printf("%d %.12e",i,(*fret));
1798: fprintf(ficlog,"%d %.12e",i,(*fret));
1799: for (j=1;j<=n;j++) {
1800: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1801: printf(" x(%d)=%.12e",j,xit[j]);
1802: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1803: }
1804: for(j=1;j<=n;j++) {
1.162 brouard 1805: printf(" p(%d)=%.12e",j,p[j]);
1806: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1807: }
1808: printf("\n");
1809: fprintf(ficlog,"\n");
1810: #endif
1.187 brouard 1811: } /* end loop on each direction i */
1812: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1813: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1814: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1815: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1816: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1817: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1818: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1819: /* decreased of more than 3.84 */
1820: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1821: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1822: /* By adding 10 parameters more the gain should be 18.31 */
1823:
1824: /* Starting the program with initial values given by a former maximization will simply change */
1825: /* the scales of the directions and the directions, because the are reset to canonical directions */
1826: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1827: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1828: #ifdef DEBUG
1829: int k[2],l;
1830: k[0]=1;
1831: k[1]=-1;
1832: printf("Max: %.12e",(*func)(p));
1833: fprintf(ficlog,"Max: %.12e",(*func)(p));
1834: for (j=1;j<=n;j++) {
1835: printf(" %.12e",p[j]);
1836: fprintf(ficlog," %.12e",p[j]);
1837: }
1838: printf("\n");
1839: fprintf(ficlog,"\n");
1840: for(l=0;l<=1;l++) {
1841: for (j=1;j<=n;j++) {
1842: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1843: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1844: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1845: }
1846: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1847: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1848: }
1849: #endif
1850:
1851:
1852: free_vector(xit,1,n);
1853: free_vector(xits,1,n);
1854: free_vector(ptt,1,n);
1855: free_vector(pt,1,n);
1856: return;
1.192 brouard 1857: } /* enough precision */
1.126 brouard 1858: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1859: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1860: ptt[j]=2.0*p[j]-pt[j];
1861: xit[j]=p[j]-pt[j];
1862: pt[j]=p[j];
1863: }
1.181 brouard 1864: fptt=(*func)(ptt); /* f_3 */
1.192 brouard 1865: #ifdef POWELLF1F3
1866: #else
1.161 brouard 1867: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 1868: #endif
1.162 brouard 1869: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1870: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1871: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1872: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1873: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1874: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1875: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1876: #ifdef NRCORIGINAL
1877: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1878: #else
1879: 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 1880: t= t- del*SQR(fp-fptt);
1.183 brouard 1881: #endif
1.202 brouard 1882: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 1883: #ifdef DEBUG
1.181 brouard 1884: 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);
1885: 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 1886: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1887: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1888: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1889: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1890: 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);
1891: 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);
1892: #endif
1.183 brouard 1893: #ifdef POWELLORIGINAL
1894: if (t < 0.0) { /* Then we use it for new direction */
1895: #else
1.182 brouard 1896: if (directest*t < 0.0) { /* Contradiction between both tests */
1.202 brouard 1897: 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 1898: 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 1899: 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 1900: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1901: }
1.181 brouard 1902: if (directest < 0.0) { /* Then we use it for new direction */
1903: #endif
1.191 brouard 1904: #ifdef DEBUGLINMIN
1905: printf("Before linmin in direction P%d-P0\n",n);
1906: for (j=1;j<=n;j++) {
1.202 brouard 1907: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1908: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1909: if(j % ncovmodel == 0){
1.191 brouard 1910: printf("\n");
1.202 brouard 1911: fprintf(ficlog,"\n");
1912: }
1.191 brouard 1913: }
1914: #endif
1.187 brouard 1915: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.191 brouard 1916: #ifdef DEBUGLINMIN
1917: for (j=1;j<=n;j++) {
1918: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1.202 brouard 1919: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1920: if(j % ncovmodel == 0){
1.191 brouard 1921: printf("\n");
1.202 brouard 1922: fprintf(ficlog,"\n");
1923: }
1.191 brouard 1924: }
1925: #endif
1.126 brouard 1926: for (j=1;j<=n;j++) {
1.181 brouard 1927: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1928: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 1929: }
1.181 brouard 1930: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1931: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1932:
1.126 brouard 1933: #ifdef DEBUG
1.164 brouard 1934: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1935: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 1936: for(j=1;j<=n;j++){
1937: printf(" %.12e",xit[j]);
1938: fprintf(ficlog," %.12e",xit[j]);
1939: }
1940: printf("\n");
1941: fprintf(ficlog,"\n");
1942: #endif
1.192 brouard 1943: } /* end of t or directest negative */
1944: #ifdef POWELLF1F3
1945: #else
1.162 brouard 1946: } /* end if (fptt < fp) */
1.192 brouard 1947: #endif
1948: } /* loop iteration */
1.126 brouard 1949: }
1950:
1951: /**** Prevalence limit (stable or period prevalence) ****************/
1952:
1.203 brouard 1953: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
1.126 brouard 1954: {
1955: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1.203 brouard 1956: matrix by transitions matrix until convergence is reached with precision ftolpl */
1.169 brouard 1957:
1.126 brouard 1958: int i, ii,j,k;
1959: double min, max, maxmin, maxmax,sumnew=0.;
1.145 brouard 1960: /* double **matprod2(); */ /* test */
1.131 brouard 1961: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1962: double **newm;
1.202 brouard 1963: double agefin, delaymax=100 ; /* Max number of years to converge */
1.203 brouard 1964: int ncvloop=0;
1.169 brouard 1965:
1.126 brouard 1966: for (ii=1;ii<=nlstate+ndeath;ii++)
1967: for (j=1;j<=nlstate+ndeath;j++){
1968: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1969: }
1.169 brouard 1970:
1971: cov[1]=1.;
1972:
1973: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 1974: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 1975: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 1976: ncvloop++;
1.126 brouard 1977: newm=savm;
1978: /* Covariates have to be included here again */
1.138 brouard 1979: cov[2]=agefin;
1.187 brouard 1980: if(nagesqr==1)
1981: cov[3]= agefin*agefin;;
1.138 brouard 1982: for (k=1; k<=cptcovn;k++) {
1.200 brouard 1983: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1984: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
1.198 brouard 1985: /* 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 1986: }
1.186 brouard 1987: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 1988: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
1989: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
1.186 brouard 1990: for (k=1; k<=cptcovprod;k++) /* Useless */
1.200 brouard 1991: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
1992: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.138 brouard 1993:
1994: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1995: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1996: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 1997: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1998: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 1999: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2000:
1.126 brouard 2001: savm=oldm;
2002: oldm=newm;
2003: maxmax=0.;
2004: for(j=1;j<=nlstate;j++){
2005: min=1.;
2006: max=0.;
2007: for(i=1; i<=nlstate; i++) {
2008: sumnew=0;
2009: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2010: prlim[i][j]= newm[i][j]/(1-sumnew);
2011: max=FMAX(max,prlim[i][j]);
2012: min=FMIN(min,prlim[i][j]);
1.202 brouard 2013: /* printf(" age= %d prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d max=%f min=%f\n", (int)age, i, j, i, j, prlim[i][j],(int)agefin, max, min); */
1.126 brouard 2014: }
1.203 brouard 2015: maxmin=(max-min)/(max+min)*2;
1.126 brouard 2016: maxmax=FMAX(maxmax,maxmin);
1.169 brouard 2017: } /* j loop */
1.203 brouard 2018: *ncvyear= (int)age- (int)agefin;
2019: /* printf("maxmax=%lf maxmin=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.126 brouard 2020: if(maxmax < ftolpl){
1.203 brouard 2021: /* printf("maxmax=%lf maxmin=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.126 brouard 2022: return prlim;
2023: }
1.169 brouard 2024: } /* age loop */
1.203 brouard 2025: printf("Warning: the stable prevalence at age %d did not converge with the required precision %g > ftolpl=%g. \n\
2026: Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
2027: /* 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); */
1.169 brouard 2028: return prlim; /* should not reach here */
1.126 brouard 2029: }
2030:
2031: /*************** transition probabilities ***************/
2032:
2033: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2034: {
1.138 brouard 2035: /* According to parameters values stored in x and the covariate's values stored in cov,
2036: computes the probability to be observed in state j being in state i by appying the
2037: model to the ncovmodel covariates (including constant and age).
2038: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2039: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2040: ncth covariate in the global vector x is given by the formula:
2041: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2042: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2043: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2044: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2045: Outputs ps[i][j] the probability to be observed in j being in j according to
2046: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2047: */
2048: double s1, lnpijopii;
1.126 brouard 2049: /*double t34;*/
1.164 brouard 2050: int i,j, nc, ii, jj;
1.126 brouard 2051:
2052: for(i=1; i<= nlstate; i++){
2053: for(j=1; j<i;j++){
1.138 brouard 2054: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2055: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2056: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2057: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2058: }
1.138 brouard 2059: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2060: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2061: }
2062: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 2063: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2064: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2065: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2066: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 2067: }
1.138 brouard 2068: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 2069: }
2070: }
2071:
2072: for(i=1; i<= nlstate; i++){
2073: s1=0;
1.131 brouard 2074: for(j=1; j<i; j++){
1.138 brouard 2075: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2076: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2077: }
2078: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 2079: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2080: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2081: }
1.138 brouard 2082: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 2083: ps[i][i]=1./(s1+1.);
1.138 brouard 2084: /* Computing other pijs */
1.126 brouard 2085: for(j=1; j<i; j++)
2086: ps[i][j]= exp(ps[i][j])*ps[i][i];
2087: for(j=i+1; j<=nlstate+ndeath; j++)
2088: ps[i][j]= exp(ps[i][j])*ps[i][i];
2089: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2090: } /* end i */
2091:
2092: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2093: for(jj=1; jj<= nlstate+ndeath; jj++){
2094: ps[ii][jj]=0;
2095: ps[ii][ii]=1;
2096: }
2097: }
2098:
1.145 brouard 2099:
2100: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2101: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2102: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2103: /* } */
2104: /* printf("\n "); */
2105: /* } */
2106: /* printf("\n ");printf("%lf ",cov[2]);*/
2107: /*
1.126 brouard 2108: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2109: goto end;*/
2110: return ps;
2111: }
2112:
2113: /**************** Product of 2 matrices ******************/
2114:
1.145 brouard 2115: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2116: {
2117: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2118: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2119: /* in, b, out are matrice of pointers which should have been initialized
2120: before: only the contents of out is modified. The function returns
2121: a pointer to pointers identical to out */
1.145 brouard 2122: int i, j, k;
1.126 brouard 2123: for(i=nrl; i<= nrh; i++)
1.145 brouard 2124: for(k=ncolol; k<=ncoloh; k++){
2125: out[i][k]=0.;
2126: for(j=ncl; j<=nch; j++)
2127: out[i][k] +=in[i][j]*b[j][k];
2128: }
1.126 brouard 2129: return out;
2130: }
2131:
2132:
2133: /************* Higher Matrix Product ***************/
2134:
2135: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2136: {
2137: /* Computes the transition matrix starting at age 'age' over
2138: 'nhstepm*hstepm*stepm' months (i.e. until
2139: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2140: nhstepm*hstepm matrices.
2141: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2142: (typically every 2 years instead of every month which is too big
2143: for the memory).
2144: Model is determined by parameters x and covariates have to be
2145: included manually here.
2146:
2147: */
2148:
2149: int i, j, d, h, k;
1.131 brouard 2150: double **out, cov[NCOVMAX+1];
1.126 brouard 2151: double **newm;
1.187 brouard 2152: double agexact;
1.126 brouard 2153:
2154: /* Hstepm could be zero and should return the unit matrix */
2155: for (i=1;i<=nlstate+ndeath;i++)
2156: for (j=1;j<=nlstate+ndeath;j++){
2157: oldm[i][j]=(i==j ? 1.0 : 0.0);
2158: po[i][j][0]=(i==j ? 1.0 : 0.0);
2159: }
2160: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2161: for(h=1; h <=nhstepm; h++){
2162: for(d=1; d <=hstepm; d++){
2163: newm=savm;
2164: /* Covariates have to be included here again */
2165: cov[1]=1.;
1.187 brouard 2166: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
2167: cov[2]=agexact;
2168: if(nagesqr==1)
2169: cov[3]= agexact*agexact;
1.131 brouard 2170: for (k=1; k<=cptcovn;k++)
1.200 brouard 2171: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2172: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.186 brouard 2173: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
2174: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2175: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2176: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.145 brouard 2177: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.200 brouard 2178: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2179: /* 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 2180:
2181:
2182: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2183: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2184: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2185: pmij(pmmij,cov,ncovmodel,x,nlstate));
2186: savm=oldm;
2187: oldm=newm;
2188: }
2189: for(i=1; i<=nlstate+ndeath; i++)
2190: for(j=1;j<=nlstate+ndeath;j++) {
2191: po[i][j][h]=newm[i][j];
1.128 brouard 2192: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2193: }
1.128 brouard 2194: /*printf("h=%d ",h);*/
1.126 brouard 2195: } /* end h */
1.128 brouard 2196: /* printf("\n H=%d \n",h); */
1.126 brouard 2197: return po;
2198: }
2199:
1.162 brouard 2200: #ifdef NLOPT
2201: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2202: double fret;
2203: double *xt;
2204: int j;
2205: myfunc_data *d2 = (myfunc_data *) pd;
2206: /* xt = (p1-1); */
2207: xt=vector(1,n);
2208: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2209:
2210: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2211: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2212: printf("Function = %.12lf ",fret);
2213: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2214: printf("\n");
2215: free_vector(xt,1,n);
2216: return fret;
2217: }
2218: #endif
1.126 brouard 2219:
2220: /*************** log-likelihood *************/
2221: double func( double *x)
2222: {
2223: int i, ii, j, k, mi, d, kk;
1.131 brouard 2224: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2225: double **out;
2226: double sw; /* Sum of weights */
2227: double lli; /* Individual log likelihood */
2228: int s1, s2;
2229: double bbh, survp;
2230: long ipmx;
1.187 brouard 2231: double agexact;
1.126 brouard 2232: /*extern weight */
2233: /* We are differentiating ll according to initial status */
2234: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2235: /*for(i=1;i<imx;i++)
2236: printf(" %d\n",s[4][i]);
2237: */
1.162 brouard 2238:
2239: ++countcallfunc;
2240:
1.126 brouard 2241: cov[1]=1.;
2242:
2243: for(k=1; k<=nlstate; k++) ll[k]=0.;
2244:
2245: if(mle==1){
2246: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2247: /* Computes the values of the ncovmodel covariates of the model
2248: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2249: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2250: to be observed in j being in i according to the model.
2251: */
1.145 brouard 2252: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 brouard 2253: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2254: }
1.137 brouard 2255: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2256: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2257: has been calculated etc */
1.126 brouard 2258: for(mi=1; mi<= wav[i]-1; mi++){
2259: for (ii=1;ii<=nlstate+ndeath;ii++)
2260: for (j=1;j<=nlstate+ndeath;j++){
2261: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2262: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2263: }
2264: for(d=0; d<dh[mi][i]; d++){
2265: newm=savm;
1.187 brouard 2266: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2267: cov[2]=agexact;
2268: if(nagesqr==1)
2269: cov[3]= agexact*agexact;
1.126 brouard 2270: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2271: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2272: }
2273: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2274: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2275: savm=oldm;
2276: oldm=newm;
2277: } /* end mult */
2278:
2279: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2280: /* But now since version 0.9 we anticipate for bias at large stepm.
2281: * If stepm is larger than one month (smallest stepm) and if the exact delay
2282: * (in months) between two waves is not a multiple of stepm, we rounded to
2283: * the nearest (and in case of equal distance, to the lowest) interval but now
2284: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2285: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2286: * probability in order to take into account the bias as a fraction of the way
2287: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2288: * -stepm/2 to stepm/2 .
2289: * For stepm=1 the results are the same as for previous versions of Imach.
2290: * For stepm > 1 the results are less biased than in previous versions.
2291: */
2292: s1=s[mw[mi][i]][i];
2293: s2=s[mw[mi+1][i]][i];
2294: bbh=(double)bh[mi][i]/(double)stepm;
2295: /* bias bh is positive if real duration
2296: * is higher than the multiple of stepm and negative otherwise.
2297: */
2298: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2299: if( s2 > nlstate){
2300: /* i.e. if s2 is a death state and if the date of death is known
2301: then the contribution to the likelihood is the probability to
2302: die between last step unit time and current step unit time,
2303: which is also equal to probability to die before dh
2304: minus probability to die before dh-stepm .
2305: In version up to 0.92 likelihood was computed
2306: as if date of death was unknown. Death was treated as any other
2307: health state: the date of the interview describes the actual state
2308: and not the date of a change in health state. The former idea was
2309: to consider that at each interview the state was recorded
2310: (healthy, disable or death) and IMaCh was corrected; but when we
2311: introduced the exact date of death then we should have modified
2312: the contribution of an exact death to the likelihood. This new
2313: contribution is smaller and very dependent of the step unit
2314: stepm. It is no more the probability to die between last interview
2315: and month of death but the probability to survive from last
2316: interview up to one month before death multiplied by the
2317: probability to die within a month. Thanks to Chris
2318: Jackson for correcting this bug. Former versions increased
2319: mortality artificially. The bad side is that we add another loop
2320: which slows down the processing. The difference can be up to 10%
2321: lower mortality.
2322: */
1.183 brouard 2323: /* If, at the beginning of the maximization mostly, the
2324: cumulative probability or probability to be dead is
2325: constant (ie = 1) over time d, the difference is equal to
2326: 0. out[s1][3] = savm[s1][3]: probability, being at state
2327: s1 at precedent wave, to be dead a month before current
2328: wave is equal to probability, being at state s1 at
2329: precedent wave, to be dead at mont of the current
2330: wave. Then the observed probability (that this person died)
2331: is null according to current estimated parameter. In fact,
2332: it should be very low but not zero otherwise the log go to
2333: infinity.
2334: */
2335: /* #ifdef INFINITYORIGINAL */
2336: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2337: /* #else */
2338: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2339: /* lli=log(mytinydouble); */
2340: /* else */
2341: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2342: /* #endif */
2343: lli=log(out[s1][s2] - savm[s1][s2]);
1.126 brouard 2344:
2345: } else if (s2==-2) {
2346: for (j=1,survp=0. ; j<=nlstate; j++)
2347: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2348: /*survp += out[s1][j]; */
2349: lli= log(survp);
2350: }
2351:
2352: else if (s2==-4) {
2353: for (j=3,survp=0. ; j<=nlstate; j++)
2354: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2355: lli= log(survp);
2356: }
2357:
2358: else if (s2==-5) {
2359: for (j=1,survp=0. ; j<=2; j++)
2360: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2361: lli= log(survp);
2362: }
2363:
2364: else{
2365: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2366: /* 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 */
2367: }
2368: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2369: /*if(lli ==000.0)*/
2370: /*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); */
2371: ipmx +=1;
2372: sw += weight[i];
2373: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2374: /* if (lli < log(mytinydouble)){ */
2375: /* 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); */
2376: /* 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]); */
2377: /* } */
1.126 brouard 2378: } /* end of wave */
2379: } /* end of individual */
2380: } else if(mle==2){
2381: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2382: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2383: for(mi=1; mi<= wav[i]-1; mi++){
2384: for (ii=1;ii<=nlstate+ndeath;ii++)
2385: for (j=1;j<=nlstate+ndeath;j++){
2386: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2387: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2388: }
2389: for(d=0; d<=dh[mi][i]; d++){
2390: newm=savm;
1.187 brouard 2391: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2392: cov[2]=agexact;
2393: if(nagesqr==1)
2394: cov[3]= agexact*agexact;
1.126 brouard 2395: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2396: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2397: }
2398: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2399: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2400: savm=oldm;
2401: oldm=newm;
2402: } /* end mult */
2403:
2404: s1=s[mw[mi][i]][i];
2405: s2=s[mw[mi+1][i]][i];
2406: bbh=(double)bh[mi][i]/(double)stepm;
2407: 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 */
2408: ipmx +=1;
2409: sw += weight[i];
2410: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2411: } /* end of wave */
2412: } /* end of individual */
2413: } else if(mle==3){ /* exponential inter-extrapolation */
2414: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2415: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2416: for(mi=1; mi<= wav[i]-1; mi++){
2417: for (ii=1;ii<=nlstate+ndeath;ii++)
2418: for (j=1;j<=nlstate+ndeath;j++){
2419: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2420: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2421: }
2422: for(d=0; d<dh[mi][i]; d++){
2423: newm=savm;
1.187 brouard 2424: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2425: cov[2]=agexact;
2426: if(nagesqr==1)
2427: cov[3]= agexact*agexact;
1.126 brouard 2428: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2429: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2430: }
2431: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2432: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2433: savm=oldm;
2434: oldm=newm;
2435: } /* end mult */
2436:
2437: s1=s[mw[mi][i]][i];
2438: s2=s[mw[mi+1][i]][i];
2439: bbh=(double)bh[mi][i]/(double)stepm;
2440: 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 */
2441: ipmx +=1;
2442: sw += weight[i];
2443: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2444: } /* end of wave */
2445: } /* end of individual */
2446: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2447: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2448: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2449: for(mi=1; mi<= wav[i]-1; mi++){
2450: for (ii=1;ii<=nlstate+ndeath;ii++)
2451: for (j=1;j<=nlstate+ndeath;j++){
2452: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2453: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2454: }
2455: for(d=0; d<dh[mi][i]; d++){
2456: newm=savm;
1.187 brouard 2457: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2458: cov[2]=agexact;
2459: if(nagesqr==1)
2460: cov[3]= agexact*agexact;
1.126 brouard 2461: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2462: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2463: }
2464:
2465: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2466: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2467: savm=oldm;
2468: oldm=newm;
2469: } /* end mult */
2470:
2471: s1=s[mw[mi][i]][i];
2472: s2=s[mw[mi+1][i]][i];
2473: if( s2 > nlstate){
2474: lli=log(out[s1][s2] - savm[s1][s2]);
2475: }else{
2476: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2477: }
2478: ipmx +=1;
2479: sw += weight[i];
2480: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2481: /* 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]); */
2482: } /* end of wave */
2483: } /* end of individual */
2484: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2485: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2486: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2487: for(mi=1; mi<= wav[i]-1; mi++){
2488: for (ii=1;ii<=nlstate+ndeath;ii++)
2489: for (j=1;j<=nlstate+ndeath;j++){
2490: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2491: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2492: }
2493: for(d=0; d<dh[mi][i]; d++){
2494: newm=savm;
1.187 brouard 2495: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2496: cov[2]=agexact;
2497: if(nagesqr==1)
2498: cov[3]= agexact*agexact;
1.126 brouard 2499: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2500: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2501: }
2502:
2503: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2504: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2505: savm=oldm;
2506: oldm=newm;
2507: } /* end mult */
2508:
2509: s1=s[mw[mi][i]][i];
2510: s2=s[mw[mi+1][i]][i];
2511: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2512: ipmx +=1;
2513: sw += weight[i];
2514: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2515: /*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]);*/
2516: } /* end of wave */
2517: } /* end of individual */
2518: } /* End of if */
2519: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2520: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2521: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2522: return -l;
2523: }
2524:
2525: /*************** log-likelihood *************/
2526: double funcone( double *x)
2527: {
2528: /* Same as likeli but slower because of a lot of printf and if */
2529: int i, ii, j, k, mi, d, kk;
1.131 brouard 2530: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2531: double **out;
2532: double lli; /* Individual log likelihood */
2533: double llt;
2534: int s1, s2;
2535: double bbh, survp;
1.187 brouard 2536: double agexact;
1.126 brouard 2537: /*extern weight */
2538: /* We are differentiating ll according to initial status */
2539: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2540: /*for(i=1;i<imx;i++)
2541: printf(" %d\n",s[4][i]);
2542: */
2543: cov[1]=1.;
2544:
2545: for(k=1; k<=nlstate; k++) ll[k]=0.;
2546:
2547: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2548: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2549: for(mi=1; mi<= wav[i]-1; mi++){
2550: for (ii=1;ii<=nlstate+ndeath;ii++)
2551: for (j=1;j<=nlstate+ndeath;j++){
2552: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2553: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2554: }
2555: for(d=0; d<dh[mi][i]; d++){
2556: newm=savm;
1.187 brouard 2557: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2558: cov[2]=agexact;
2559: if(nagesqr==1)
2560: cov[3]= agexact*agexact;
1.126 brouard 2561: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2562: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2563: }
1.187 brouard 2564:
1.145 brouard 2565: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2566: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2567: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2568: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2569: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 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: bbh=(double)bh[mi][i]/(double)stepm;
2577: /* bias is positive if real duration
2578: * is higher than the multiple of stepm and negative otherwise.
2579: */
2580: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2581: lli=log(out[s1][s2] - savm[s1][s2]);
2582: } else if (s2==-2) {
2583: for (j=1,survp=0. ; j<=nlstate; j++)
2584: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2585: lli= log(survp);
2586: }else if (mle==1){
2587: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2588: } else if(mle==2){
2589: 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 */
2590: } else if(mle==3){ /* exponential inter-extrapolation */
2591: 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 */
2592: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2593: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2594: } else{ /* mle=0 back to 1 */
2595: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2596: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2597: } /* End of if */
2598: ipmx +=1;
2599: sw += weight[i];
2600: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2601: /*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 2602: if(globpr){
1.202 brouard 2603: fprintf(ficresilk,"%9ld %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f\
1.126 brouard 2604: %11.6f %11.6f %11.6f ", \
1.202 brouard 2605: num[i], agexact, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1.126 brouard 2606: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2607: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2608: llt +=ll[k]*gipmx/gsw;
2609: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2610: }
2611: fprintf(ficresilk," %10.6f\n", -llt);
2612: }
2613: } /* end of wave */
2614: } /* end of individual */
2615: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2616: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2617: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2618: if(globpr==0){ /* First time we count the contributions and weights */
2619: gipmx=ipmx;
2620: gsw=sw;
2621: }
2622: return -l;
2623: }
2624:
2625:
2626: /*************** function likelione ***********/
2627: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2628: {
2629: /* This routine should help understanding what is done with
2630: the selection of individuals/waves and
2631: to check the exact contribution to the likelihood.
2632: Plotting could be done.
2633: */
2634: int k;
2635:
2636: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 2637: strcpy(fileresilk,"ILK_");
1.202 brouard 2638: strcat(fileresilk,fileresu);
1.126 brouard 2639: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2640: printf("Problem with resultfile: %s\n", fileresilk);
2641: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2642: }
2643: fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
1.202 brouard 2644: fprintf(ficresilk, "#num_i age i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1.126 brouard 2645: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2646: for(k=1; k<=nlstate; k++)
2647: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2648: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2649: }
2650:
2651: *fretone=(*funcone)(p);
2652: if(*globpri !=0){
2653: fclose(ficresilk);
1.202 brouard 2654: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle >= 1. You should at least run with mle >= 1 and 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));
1.204 ! brouard 2655: 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> \
! 2656: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
! 2657: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
! 2658: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.202 brouard 2659: fflush(fichtm);
1.204 ! brouard 2660:
! 2661: for (k=1; k<= nlstate ; k++) {
! 2662: fprintf(fichtm,"<br>- Probability p%dj by origin %d and destination j <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
! 2663: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
! 2664:
! 2665: }
1.126 brouard 2666: }
2667: return;
2668: }
2669:
2670:
2671: /*********** Maximum Likelihood Estimation ***************/
2672:
2673: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2674: {
1.165 brouard 2675: int i,j, iter=0;
1.126 brouard 2676: double **xi;
2677: double fret;
2678: double fretone; /* Only one call to likelihood */
2679: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2680:
2681: #ifdef NLOPT
2682: int creturn;
2683: nlopt_opt opt;
2684: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2685: double *lb;
2686: double minf; /* the minimum objective value, upon return */
2687: double * p1; /* Shifted parameters from 0 instead of 1 */
2688: myfunc_data dinst, *d = &dinst;
2689: #endif
2690:
2691:
1.126 brouard 2692: xi=matrix(1,npar,1,npar);
2693: for (i=1;i<=npar;i++)
2694: for (j=1;j<=npar;j++)
2695: xi[i][j]=(i==j ? 1.0 : 0.0);
2696: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 2697: strcpy(filerespow,"POW_");
1.126 brouard 2698: strcat(filerespow,fileres);
2699: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2700: printf("Problem with resultfile: %s\n", filerespow);
2701: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2702: }
2703: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2704: for (i=1;i<=nlstate;i++)
2705: for(j=1;j<=nlstate+ndeath;j++)
2706: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2707: fprintf(ficrespow,"\n");
1.162 brouard 2708: #ifdef POWELL
1.126 brouard 2709: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2710: #endif
1.126 brouard 2711:
1.162 brouard 2712: #ifdef NLOPT
2713: #ifdef NEWUOA
2714: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2715: #else
2716: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2717: #endif
2718: lb=vector(0,npar-1);
2719: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2720: nlopt_set_lower_bounds(opt, lb);
2721: nlopt_set_initial_step1(opt, 0.1);
2722:
2723: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2724: d->function = func;
2725: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2726: nlopt_set_min_objective(opt, myfunc, d);
2727: nlopt_set_xtol_rel(opt, ftol);
2728: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2729: printf("nlopt failed! %d\n",creturn);
2730: }
2731: else {
2732: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2733: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2734: iter=1; /* not equal */
2735: }
2736: nlopt_destroy(opt);
2737: #endif
1.126 brouard 2738: free_matrix(xi,1,npar,1,npar);
2739: fclose(ficrespow);
1.203 brouard 2740: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2741: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 2742: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2743:
2744: }
2745:
2746: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 2747: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 2748: {
2749: double **a,**y,*x,pd;
1.203 brouard 2750: /* double **hess; */
1.164 brouard 2751: int i, j;
1.126 brouard 2752: int *indx;
2753:
2754: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 2755: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 2756: void lubksb(double **a, int npar, int *indx, double b[]) ;
2757: void ludcmp(double **a, int npar, int *indx, double *d) ;
2758: double gompertz(double p[]);
1.203 brouard 2759: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 2760:
2761: printf("\nCalculation of the hessian matrix. Wait...\n");
2762: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2763: for (i=1;i<=npar;i++){
1.203 brouard 2764: printf("%d-",i);fflush(stdout);
2765: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 2766:
2767: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2768:
2769: /* printf(" %f ",p[i]);
2770: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2771: }
2772:
2773: for (i=1;i<=npar;i++) {
2774: for (j=1;j<=npar;j++) {
2775: if (j>i) {
1.203 brouard 2776: printf(".%d-%d",i,j);fflush(stdout);
2777: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
2778: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 2779:
2780: hess[j][i]=hess[i][j];
2781: /*printf(" %lf ",hess[i][j]);*/
2782: }
2783: }
2784: }
2785: printf("\n");
2786: fprintf(ficlog,"\n");
2787:
2788: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2789: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2790:
2791: a=matrix(1,npar,1,npar);
2792: y=matrix(1,npar,1,npar);
2793: x=vector(1,npar);
2794: indx=ivector(1,npar);
2795: for (i=1;i<=npar;i++)
2796: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2797: ludcmp(a,npar,indx,&pd);
2798:
2799: for (j=1;j<=npar;j++) {
2800: for (i=1;i<=npar;i++) x[i]=0;
2801: x[j]=1;
2802: lubksb(a,npar,indx,x);
2803: for (i=1;i<=npar;i++){
2804: matcov[i][j]=x[i];
2805: }
2806: }
2807:
2808: printf("\n#Hessian matrix#\n");
2809: fprintf(ficlog,"\n#Hessian matrix#\n");
2810: for (i=1;i<=npar;i++) {
2811: for (j=1;j<=npar;j++) {
1.203 brouard 2812: printf("%.6e ",hess[i][j]);
2813: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 2814: }
2815: printf("\n");
2816: fprintf(ficlog,"\n");
2817: }
2818:
1.203 brouard 2819: /* printf("\n#Covariance matrix#\n"); */
2820: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
2821: /* for (i=1;i<=npar;i++) { */
2822: /* for (j=1;j<=npar;j++) { */
2823: /* printf("%.6e ",matcov[i][j]); */
2824: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
2825: /* } */
2826: /* printf("\n"); */
2827: /* fprintf(ficlog,"\n"); */
2828: /* } */
2829:
1.126 brouard 2830: /* Recompute Inverse */
1.203 brouard 2831: /* for (i=1;i<=npar;i++) */
2832: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
2833: /* ludcmp(a,npar,indx,&pd); */
2834:
2835: /* printf("\n#Hessian matrix recomputed#\n"); */
2836:
2837: /* for (j=1;j<=npar;j++) { */
2838: /* for (i=1;i<=npar;i++) x[i]=0; */
2839: /* x[j]=1; */
2840: /* lubksb(a,npar,indx,x); */
2841: /* for (i=1;i<=npar;i++){ */
2842: /* y[i][j]=x[i]; */
2843: /* printf("%.3e ",y[i][j]); */
2844: /* fprintf(ficlog,"%.3e ",y[i][j]); */
2845: /* } */
2846: /* printf("\n"); */
2847: /* fprintf(ficlog,"\n"); */
2848: /* } */
2849:
2850: /* Verifying the inverse matrix */
2851: #ifdef DEBUGHESS
2852: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 2853:
1.203 brouard 2854: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
2855: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 2856:
2857: for (j=1;j<=npar;j++) {
2858: for (i=1;i<=npar;i++){
1.203 brouard 2859: printf("%.2f ",y[i][j]);
2860: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 2861: }
2862: printf("\n");
2863: fprintf(ficlog,"\n");
2864: }
1.203 brouard 2865: #endif
1.126 brouard 2866:
2867: free_matrix(a,1,npar,1,npar);
2868: free_matrix(y,1,npar,1,npar);
2869: free_vector(x,1,npar);
2870: free_ivector(indx,1,npar);
1.203 brouard 2871: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 2872:
2873:
2874: }
2875:
2876: /*************** hessian matrix ****************/
2877: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 2878: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 2879: int i;
2880: int l=1, lmax=20;
1.203 brouard 2881: double k1,k2, res, fx;
1.132 brouard 2882: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2883: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2884: int k=0,kmax=10;
2885: double l1;
2886:
2887: fx=func(x);
2888: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2889: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2890: l1=pow(10,l);
2891: delts=delt;
2892: for(k=1 ; k <kmax; k=k+1){
2893: delt = delta*(l1*k);
2894: p2[theta]=x[theta] +delt;
1.145 brouard 2895: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2896: p2[theta]=x[theta]-delt;
2897: k2=func(p2)-fx;
2898: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 2899: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 2900:
1.203 brouard 2901: #ifdef DEBUGHESSII
1.126 brouard 2902: 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);
2903: 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);
2904: #endif
2905: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2906: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2907: k=kmax;
2908: }
2909: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 2910: k=kmax; l=lmax*10;
1.126 brouard 2911: }
2912: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2913: delts=delt;
2914: }
1.203 brouard 2915: } /* End loop k */
1.126 brouard 2916: }
2917: delti[theta]=delts;
2918: return res;
2919:
2920: }
2921:
1.203 brouard 2922: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 2923: {
2924: int i;
1.164 brouard 2925: int l=1, lmax=20;
1.126 brouard 2926: double k1,k2,k3,k4,res,fx;
1.132 brouard 2927: double p2[MAXPARM+1];
1.203 brouard 2928: int k, kmax=1;
2929: double v1, v2, cv12, lc1, lc2;
2930:
1.126 brouard 2931: fx=func(x);
1.203 brouard 2932: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 2933: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 2934: p2[thetai]=x[thetai]+delti[thetai]*k;
2935: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 2936: k1=func(p2)-fx;
2937:
1.203 brouard 2938: p2[thetai]=x[thetai]+delti[thetai]*k;
2939: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 2940: k2=func(p2)-fx;
2941:
1.203 brouard 2942: p2[thetai]=x[thetai]-delti[thetai]*k;
2943: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 2944: k3=func(p2)-fx;
2945:
1.203 brouard 2946: p2[thetai]=x[thetai]-delti[thetai]*k;
2947: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 2948: k4=func(p2)-fx;
1.203 brouard 2949: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
2950: if(k1*k2*k3*k4 <0.){
2951: kmax=kmax+10;
2952: if(kmax >=10){
2953: printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
2954: fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
2955: 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);
2956: 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);
2957: }
2958: }
2959: #ifdef DEBUGHESSIJ
2960: v1=hess[thetai][thetai];
2961: v2=hess[thetaj][thetaj];
2962: cv12=res;
2963: /* Computing eigen value of Hessian matrix */
2964: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2965: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2966: if ((lc2 <0) || (lc1 <0) ){
2967: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
2968: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
2969: 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);
2970: 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);
2971: }
1.126 brouard 2972: #endif
2973: }
2974: return res;
2975: }
2976:
1.203 brouard 2977: /* Not done yet: Was supposed to fix if not exactly at the maximum */
2978: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
2979: /* { */
2980: /* int i; */
2981: /* int l=1, lmax=20; */
2982: /* double k1,k2,k3,k4,res,fx; */
2983: /* double p2[MAXPARM+1]; */
2984: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
2985: /* int k=0,kmax=10; */
2986: /* double l1; */
2987:
2988: /* fx=func(x); */
2989: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
2990: /* l1=pow(10,l); */
2991: /* delts=delt; */
2992: /* for(k=1 ; k <kmax; k=k+1){ */
2993: /* delt = delti*(l1*k); */
2994: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
2995: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
2996: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
2997: /* k1=func(p2)-fx; */
2998:
2999: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3000: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3001: /* k2=func(p2)-fx; */
3002:
3003: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3004: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3005: /* k3=func(p2)-fx; */
3006:
3007: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3008: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3009: /* k4=func(p2)-fx; */
3010: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
3011: /* #ifdef DEBUGHESSIJ */
3012: /* 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); */
3013: /* 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); */
3014: /* #endif */
3015: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
3016: /* k=kmax; */
3017: /* } */
3018: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
3019: /* k=kmax; l=lmax*10; */
3020: /* } */
3021: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
3022: /* delts=delt; */
3023: /* } */
3024: /* } /\* End loop k *\/ */
3025: /* } */
3026: /* delti[theta]=delts; */
3027: /* return res; */
3028: /* } */
3029:
3030:
1.126 brouard 3031: /************** Inverse of matrix **************/
3032: void ludcmp(double **a, int n, int *indx, double *d)
3033: {
3034: int i,imax,j,k;
3035: double big,dum,sum,temp;
3036: double *vv;
3037:
3038: vv=vector(1,n);
3039: *d=1.0;
3040: for (i=1;i<=n;i++) {
3041: big=0.0;
3042: for (j=1;j<=n;j++)
3043: if ((temp=fabs(a[i][j])) > big) big=temp;
3044: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
3045: vv[i]=1.0/big;
3046: }
3047: for (j=1;j<=n;j++) {
3048: for (i=1;i<j;i++) {
3049: sum=a[i][j];
3050: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
3051: a[i][j]=sum;
3052: }
3053: big=0.0;
3054: for (i=j;i<=n;i++) {
3055: sum=a[i][j];
3056: for (k=1;k<j;k++)
3057: sum -= a[i][k]*a[k][j];
3058: a[i][j]=sum;
3059: if ( (dum=vv[i]*fabs(sum)) >= big) {
3060: big=dum;
3061: imax=i;
3062: }
3063: }
3064: if (j != imax) {
3065: for (k=1;k<=n;k++) {
3066: dum=a[imax][k];
3067: a[imax][k]=a[j][k];
3068: a[j][k]=dum;
3069: }
3070: *d = -(*d);
3071: vv[imax]=vv[j];
3072: }
3073: indx[j]=imax;
3074: if (a[j][j] == 0.0) a[j][j]=TINY;
3075: if (j != n) {
3076: dum=1.0/(a[j][j]);
3077: for (i=j+1;i<=n;i++) a[i][j] *= dum;
3078: }
3079: }
3080: free_vector(vv,1,n); /* Doesn't work */
3081: ;
3082: }
3083:
3084: void lubksb(double **a, int n, int *indx, double b[])
3085: {
3086: int i,ii=0,ip,j;
3087: double sum;
3088:
3089: for (i=1;i<=n;i++) {
3090: ip=indx[i];
3091: sum=b[ip];
3092: b[ip]=b[i];
3093: if (ii)
3094: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
3095: else if (sum) ii=i;
3096: b[i]=sum;
3097: }
3098: for (i=n;i>=1;i--) {
3099: sum=b[i];
3100: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
3101: b[i]=sum/a[i][i];
3102: }
3103: }
3104:
3105: void pstamp(FILE *fichier)
3106: {
1.196 brouard 3107: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 3108: }
3109:
3110: /************ Frequencies ********************/
3111: 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[])
3112: { /* Some frequencies */
3113:
1.164 brouard 3114: int i, m, jk, j1, bool, z1,j;
1.126 brouard 3115: int first;
3116: double ***freq; /* Frequencies */
3117: double *pp, **prop;
3118: double pos,posprop, k2, dateintsum=0,k2cpt=0;
3119: char fileresp[FILENAMELENGTH];
3120:
3121: pp=vector(1,nlstate);
3122: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.201 brouard 3123: strcpy(fileresp,"P_");
3124: strcat(fileresp,fileresu);
1.126 brouard 3125: if((ficresp=fopen(fileresp,"w"))==NULL) {
3126: printf("Problem with prevalence resultfile: %s\n", fileresp);
3127: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
3128: exit(0);
3129: }
3130: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
3131: j1=0;
3132:
3133: j=cptcoveff;
3134: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3135:
3136: first=1;
3137:
1.169 brouard 3138: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
3139: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
3140: /* j1++; */
1.145 brouard 3141: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 3142: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
3143: scanf("%d", i);*/
3144: for (i=-5; i<=nlstate+ndeath; i++)
3145: for (jk=-5; jk<=nlstate+ndeath; jk++)
3146: for(m=iagemin; m <= iagemax+3; m++)
3147: freq[i][jk][m]=0;
1.143 brouard 3148:
3149: for (i=1; i<=nlstate; i++)
3150: for(m=iagemin; m <= iagemax+3; m++)
3151: prop[i][m]=0;
1.126 brouard 3152:
3153: dateintsum=0;
3154: k2cpt=0;
3155: for (i=1; i<=imx; i++) {
3156: bool=1;
1.144 brouard 3157: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
3158: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 3159: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
1.145 brouard 3160: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 3161: bool=0;
1.198 brouard 3162: /* 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",
3163: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
3164: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
3165: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
1.144 brouard 3166: }
1.126 brouard 3167: }
1.144 brouard 3168:
1.126 brouard 3169: if (bool==1){
3170: for(m=firstpass; m<=lastpass; m++){
3171: k2=anint[m][i]+(mint[m][i]/12.);
3172: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
3173: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3174: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3175: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
3176: if (m<lastpass) {
3177: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
3178: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
3179: }
3180:
3181: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
3182: dateintsum=dateintsum+k2;
3183: k2cpt++;
3184: }
3185: /*}*/
3186: }
3187: }
1.145 brouard 3188: } /* end i */
1.126 brouard 3189:
3190: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
3191: pstamp(ficresp);
3192: if (cptcovn>0) {
3193: fprintf(ficresp, "\n#********** Variable ");
1.198 brouard 3194: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 3195: fprintf(ficresp, "**********\n#");
1.143 brouard 3196: fprintf(ficlog, "\n#********** Variable ");
1.198 brouard 3197: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.143 brouard 3198: fprintf(ficlog, "**********\n#");
1.126 brouard 3199: }
3200: for(i=1; i<=nlstate;i++)
3201: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
3202: fprintf(ficresp, "\n");
3203:
3204: for(i=iagemin; i <= iagemax+3; i++){
3205: if(i==iagemax+3){
3206: fprintf(ficlog,"Total");
3207: }else{
3208: if(first==1){
3209: first=0;
3210: printf("See log file for details...\n");
3211: }
3212: fprintf(ficlog,"Age %d", i);
3213: }
3214: for(jk=1; jk <=nlstate ; jk++){
3215: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
3216: pp[jk] += freq[jk][m][i];
3217: }
3218: for(jk=1; jk <=nlstate ; jk++){
3219: for(m=-1, pos=0; m <=0 ; m++)
3220: pos += freq[jk][m][i];
3221: if(pp[jk]>=1.e-10){
3222: if(first==1){
1.132 brouard 3223: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 3224: }
3225: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3226: }else{
3227: if(first==1)
3228: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3229: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3230: }
3231: }
3232:
3233: for(jk=1; jk <=nlstate ; jk++){
3234: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
3235: pp[jk] += freq[jk][m][i];
3236: }
3237: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
3238: pos += pp[jk];
3239: posprop += prop[jk][i];
3240: }
3241: for(jk=1; jk <=nlstate ; jk++){
3242: if(pos>=1.e-5){
3243: if(first==1)
3244: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3245: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3246: }else{
3247: if(first==1)
3248: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3249: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3250: }
3251: if( i <= iagemax){
3252: if(pos>=1.e-5){
3253: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
3254: /*probs[i][jk][j1]= pp[jk]/pos;*/
3255: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
3256: }
3257: else
3258: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
3259: }
3260: }
3261:
3262: for(jk=-1; jk <=nlstate+ndeath; jk++)
3263: for(m=-1; m <=nlstate+ndeath; m++)
3264: if(freq[jk][m][i] !=0 ) {
3265: if(first==1)
3266: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
3267: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
3268: }
3269: if(i <= iagemax)
3270: fprintf(ficresp,"\n");
3271: if(first==1)
3272: printf("Others in log...\n");
3273: fprintf(ficlog,"\n");
3274: }
1.145 brouard 3275: /*}*/
1.126 brouard 3276: }
3277: dateintmean=dateintsum/k2cpt;
3278:
3279: fclose(ficresp);
3280: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
3281: free_vector(pp,1,nlstate);
3282: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
3283: /* End of Freq */
3284: }
3285:
3286: /************ Prevalence ********************/
3287: 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)
3288: {
3289: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3290: in each health status at the date of interview (if between dateprev1 and dateprev2).
3291: We still use firstpass and lastpass as another selection.
3292: */
3293:
1.164 brouard 3294: int i, m, jk, j1, bool, z1,j;
3295:
3296: double **prop;
3297: double posprop;
1.126 brouard 3298: double y2; /* in fractional years */
3299: int iagemin, iagemax;
1.145 brouard 3300: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 3301:
3302: iagemin= (int) agemin;
3303: iagemax= (int) agemax;
3304: /*pp=vector(1,nlstate);*/
3305: prop=matrix(1,nlstate,iagemin,iagemax+3);
3306: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3307: j1=0;
3308:
1.145 brouard 3309: /*j=cptcoveff;*/
1.126 brouard 3310: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3311:
1.145 brouard 3312: first=1;
3313: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
3314: /*for(i1=1; i1<=ncodemax[k1];i1++){
3315: j1++;*/
1.126 brouard 3316:
3317: for (i=1; i<=nlstate; i++)
3318: for(m=iagemin; m <= iagemax+3; m++)
3319: prop[i][m]=0.0;
3320:
3321: for (i=1; i<=imx; i++) { /* Each individual */
3322: bool=1;
3323: if (cptcovn>0) {
3324: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 3325: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
1.126 brouard 3326: bool=0;
3327: }
3328: if (bool==1) {
3329: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
3330: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3331: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3332: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3333: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3334: 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);
3335: if (s[m][i]>0 && s[m][i]<=nlstate) {
3336: /*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]]);*/
3337: prop[s[m][i]][(int)agev[m][i]] += weight[i];
3338: prop[s[m][i]][iagemax+3] += weight[i];
3339: }
3340: }
3341: } /* end selection of waves */
3342: }
3343: }
3344: for(i=iagemin; i <= iagemax+3; i++){
3345: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3346: posprop += prop[jk][i];
3347: }
1.145 brouard 3348:
1.126 brouard 3349: for(jk=1; jk <=nlstate ; jk++){
3350: if( i <= iagemax){
3351: if(posprop>=1.e-5){
3352: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 3353: } else{
3354: if(first==1){
3355: first=0;
3356: 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]);
3357: }
3358: }
1.126 brouard 3359: }
3360: }/* end jk */
3361: }/* end i */
1.145 brouard 3362: /*} *//* end i1 */
3363: } /* end j1 */
1.126 brouard 3364:
3365: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3366: /*free_vector(pp,1,nlstate);*/
3367: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3368: } /* End of prevalence */
3369:
3370: /************* Waves Concatenation ***************/
3371:
3372: 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)
3373: {
3374: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3375: Death is a valid wave (if date is known).
3376: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3377: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3378: and mw[mi+1][i]. dh depends on stepm.
3379: */
3380:
3381: int i, mi, m;
3382: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3383: double sum=0., jmean=0.;*/
3384: int first;
3385: int j, k=0,jk, ju, jl;
3386: double sum=0.;
3387: first=0;
1.164 brouard 3388: jmin=100000;
1.126 brouard 3389: jmax=-1;
3390: jmean=0.;
3391: for(i=1; i<=imx; i++){
3392: mi=0;
3393: m=firstpass;
3394: while(s[m][i] <= nlstate){
3395: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
3396: mw[++mi][i]=m;
3397: if(m >=lastpass)
3398: break;
3399: else
3400: m++;
3401: }/* end while */
3402: if (s[m][i] > nlstate){
3403: mi++; /* Death is another wave */
3404: /* if(mi==0) never been interviewed correctly before death */
3405: /* Only death is a correct wave */
3406: mw[mi][i]=m;
3407: }
3408:
3409: wav[i]=mi;
3410: if(mi==0){
3411: nbwarn++;
3412: if(first==0){
3413: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3414: first=1;
3415: }
3416: if(first==1){
3417: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3418: }
3419: } /* end mi==0 */
3420: } /* End individuals */
3421:
3422: for(i=1; i<=imx; i++){
3423: for(mi=1; mi<wav[i];mi++){
3424: if (stepm <=0)
3425: dh[mi][i]=1;
3426: else{
3427: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3428: if (agedc[i] < 2*AGESUP) {
3429: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3430: if(j==0) j=1; /* Survives at least one month after exam */
3431: else if(j<0){
3432: nberr++;
3433: 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]);
3434: j=1; /* Temporary Dangerous patch */
3435: 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);
3436: 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]);
3437: 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);
3438: }
3439: k=k+1;
3440: if (j >= jmax){
3441: jmax=j;
3442: ijmax=i;
3443: }
3444: if (j <= jmin){
3445: jmin=j;
3446: ijmin=i;
3447: }
3448: sum=sum+j;
3449: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3450: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3451: }
3452: }
3453: else{
3454: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3455: /* 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]); */
3456:
3457: k=k+1;
3458: if (j >= jmax) {
3459: jmax=j;
3460: ijmax=i;
3461: }
3462: else if (j <= jmin){
3463: jmin=j;
3464: ijmin=i;
3465: }
3466: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3467: /*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]);*/
3468: if(j<0){
3469: nberr++;
3470: 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]);
3471: 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]);
3472: }
3473: sum=sum+j;
3474: }
3475: jk= j/stepm;
3476: jl= j -jk*stepm;
3477: ju= j -(jk+1)*stepm;
3478: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3479: if(jl==0){
3480: dh[mi][i]=jk;
3481: bh[mi][i]=0;
3482: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 3483: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 3484: dh[mi][i]=jk+1;
3485: bh[mi][i]=ju;
3486: }
3487: }else{
3488: if(jl <= -ju){
3489: dh[mi][i]=jk;
3490: bh[mi][i]=jl; /* bias is positive if real duration
3491: * is higher than the multiple of stepm and negative otherwise.
3492: */
3493: }
3494: else{
3495: dh[mi][i]=jk+1;
3496: bh[mi][i]=ju;
3497: }
3498: if(dh[mi][i]==0){
3499: dh[mi][i]=1; /* At least one step */
3500: bh[mi][i]=ju; /* At least one step */
3501: /* 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);*/
3502: }
3503: } /* end if mle */
3504: }
3505: } /* end wave */
3506: }
3507: jmean=sum/k;
3508: 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 3509: 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 3510: }
3511:
3512: /*********** Tricode ****************************/
1.145 brouard 3513: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 3514: {
1.144 brouard 3515: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3516: /* 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 3517: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 3518: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 3519: * nbcode[Tvar[j]][1]=
1.144 brouard 3520: */
1.130 brouard 3521:
1.145 brouard 3522: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 3523: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 3524: int cptcode=0; /* Modality max of covariates j */
3525: int modmincovj=0; /* Modality min of covariates j */
3526:
3527:
1.126 brouard 3528: cptcoveff=0;
3529:
1.144 brouard 3530: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 3531:
1.145 brouard 3532: /* Loop on covariates without age and products */
1.186 brouard 3533: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
1.192 brouard 3534: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.186 brouard 3535: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.136 brouard 3536: modality of this covariate Vj*/
1.145 brouard 3537: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3538: * If product of Vn*Vm, still boolean *:
3539: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3540: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3541: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 3542: modality of the nth covariate of individual i. */
1.145 brouard 3543: if (ij > modmaxcovj)
3544: modmaxcovj=ij;
3545: else if (ij < modmincovj)
3546: modmincovj=ij;
3547: if ((ij < -1) && (ij > NCOVMAX)){
3548: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3549: exit(1);
3550: }else
1.136 brouard 3551: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 3552: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 3553: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 3554: /* getting the maximum value of the modality of the covariate
3555: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3556: female is 1, then modmaxcovj=1.*/
1.192 brouard 3557: } /* end for loop on individuals i */
1.145 brouard 3558: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.192 brouard 3559: 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 3560: cptcode=modmaxcovj;
1.137 brouard 3561: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 3562: /*for (i=0; i<=cptcode; i++) {*/
1.192 brouard 3563: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
3564: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3565: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3566: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
3567: if( k != -1){
3568: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
3569: covariate for which somebody answered excluding
3570: undefined. Usually 2: 0 and 1. */
3571: }
3572: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
3573: covariate for which somebody answered including
3574: undefined. Usually 3: -1, 0 and 1. */
1.145 brouard 3575: }
3576: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3577: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3578: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3579:
1.136 brouard 3580: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 3581: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3582: 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 3583: modmincovj=3; modmaxcovj = 7;
1.186 brouard 3584: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3585: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3586: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 3587: nbcode[Tvar[j]][ij]=k;
3588: nbcode[Tvar[j]][1]=0;
3589: nbcode[Tvar[j]][2]=1;
3590: nbcode[Tvar[j]][3]=2;
1.197 brouard 3591: To be continued (not working yet).
1.145 brouard 3592: */
1.197 brouard 3593: ij=0; /* ij is similar to i but can jump over null modalities */
3594: 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*/
3595: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
1.192 brouard 3596: break;
3597: }
3598: ij++;
1.197 brouard 3599: 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 3600: cptcode = ij; /* New max modality for covar j */
3601: } /* end of loop on modality i=-1 to 1 or more */
3602:
3603: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
3604: /* /\*recode from 0 *\/ */
3605: /* k is a modality. If we have model=V1+V1*sex */
3606: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3607: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
3608: /* } */
3609: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
3610: /* if (ij > ncodemax[j]) { */
3611: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3612: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3613: /* break; */
3614: /* } */
3615: /* } /\* end of loop on modality k *\/ */
1.137 brouard 3616: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3617:
1.145 brouard 3618: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3619:
1.187 brouard 3620: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.145 brouard 3621: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3622: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.187 brouard 3623: Ndum[ij]++; /* Might be supersed V1 + V1*age */
1.145 brouard 3624: }
1.126 brouard 3625:
1.192 brouard 3626: ij=0;
1.145 brouard 3627: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3628: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3629: if((Ndum[i]!=0) && (i<=ncovcol)){
1.192 brouard 3630: ij++;
1.145 brouard 3631: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3632: Tvaraff[ij]=i; /*For printing (unclear) */
1.192 brouard 3633: }else{
3634: /* Tvaraff[ij]=0; */
3635: }
1.126 brouard 3636: }
1.192 brouard 3637: /* ij--; */
1.144 brouard 3638: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3639:
1.126 brouard 3640: }
3641:
1.145 brouard 3642:
1.126 brouard 3643: /*********** Health Expectancies ****************/
3644:
1.127 brouard 3645: 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 3646:
3647: {
3648: /* Health expectancies, no variances */
1.164 brouard 3649: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3650: int nhstepma, nstepma; /* Decreasing with age */
3651: double age, agelim, hf;
3652: double ***p3mat;
3653: double eip;
3654:
3655: pstamp(ficreseij);
3656: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3657: fprintf(ficreseij,"# Age");
3658: for(i=1; i<=nlstate;i++){
3659: for(j=1; j<=nlstate;j++){
3660: fprintf(ficreseij," e%1d%1d ",i,j);
3661: }
3662: fprintf(ficreseij," e%1d. ",i);
3663: }
3664: fprintf(ficreseij,"\n");
3665:
3666:
3667: if(estepm < stepm){
3668: printf ("Problem %d lower than %d\n",estepm, stepm);
3669: }
3670: else hstepm=estepm;
3671: /* We compute the life expectancy from trapezoids spaced every estepm months
3672: * This is mainly to measure the difference between two models: for example
3673: * if stepm=24 months pijx are given only every 2 years and by summing them
3674: * we are calculating an estimate of the Life Expectancy assuming a linear
3675: * progression in between and thus overestimating or underestimating according
3676: * to the curvature of the survival function. If, for the same date, we
3677: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3678: * to compare the new estimate of Life expectancy with the same linear
3679: * hypothesis. A more precise result, taking into account a more precise
3680: * curvature will be obtained if estepm is as small as stepm. */
3681:
3682: /* For example we decided to compute the life expectancy with the smallest unit */
3683: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3684: nhstepm is the number of hstepm from age to agelim
3685: nstepm is the number of stepm from age to agelin.
3686: Look at hpijx to understand the reason of that which relies in memory size
3687: and note for a fixed period like estepm months */
3688: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3689: survival function given by stepm (the optimization length). Unfortunately it
3690: means that if the survival funtion is printed only each two years of age and if
3691: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3692: results. So we changed our mind and took the option of the best precision.
3693: */
3694: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3695:
3696: agelim=AGESUP;
3697: /* If stepm=6 months */
3698: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3699: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3700:
3701: /* nhstepm age range expressed in number of stepm */
3702: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3703: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3704: /* if (stepm >= YEARM) hstepm=1;*/
3705: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3706: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3707:
3708: for (age=bage; age<=fage; age ++){
3709: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3710: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3711: /* if (stepm >= YEARM) hstepm=1;*/
3712: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3713:
3714: /* If stepm=6 months */
3715: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3716: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3717:
3718: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3719:
3720: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3721:
3722: printf("%d|",(int)age);fflush(stdout);
3723: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3724:
3725: /* Computing expectancies */
3726: for(i=1; i<=nlstate;i++)
3727: for(j=1; j<=nlstate;j++)
3728: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3729: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3730:
3731: /* 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]);*/
3732:
3733: }
3734:
3735: fprintf(ficreseij,"%3.0f",age );
3736: for(i=1; i<=nlstate;i++){
3737: eip=0;
3738: for(j=1; j<=nlstate;j++){
3739: eip +=eij[i][j][(int)age];
3740: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3741: }
3742: fprintf(ficreseij,"%9.4f", eip );
3743: }
3744: fprintf(ficreseij,"\n");
3745:
3746: }
3747: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3748: printf("\n");
3749: fprintf(ficlog,"\n");
3750:
3751: }
3752:
1.127 brouard 3753: 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 3754:
3755: {
3756: /* Covariances of health expectancies eij and of total life expectancies according
3757: to initial status i, ei. .
3758: */
3759: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3760: int nhstepma, nstepma; /* Decreasing with age */
3761: double age, agelim, hf;
3762: double ***p3matp, ***p3matm, ***varhe;
3763: double **dnewm,**doldm;
3764: double *xp, *xm;
3765: double **gp, **gm;
3766: double ***gradg, ***trgradg;
3767: int theta;
3768:
3769: double eip, vip;
3770:
3771: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3772: xp=vector(1,npar);
3773: xm=vector(1,npar);
3774: dnewm=matrix(1,nlstate*nlstate,1,npar);
3775: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3776:
3777: pstamp(ficresstdeij);
3778: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3779: fprintf(ficresstdeij,"# Age");
3780: for(i=1; i<=nlstate;i++){
3781: for(j=1; j<=nlstate;j++)
3782: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3783: fprintf(ficresstdeij," e%1d. ",i);
3784: }
3785: fprintf(ficresstdeij,"\n");
3786:
3787: pstamp(ficrescveij);
3788: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3789: fprintf(ficrescveij,"# Age");
3790: for(i=1; i<=nlstate;i++)
3791: for(j=1; j<=nlstate;j++){
3792: cptj= (j-1)*nlstate+i;
3793: for(i2=1; i2<=nlstate;i2++)
3794: for(j2=1; j2<=nlstate;j2++){
3795: cptj2= (j2-1)*nlstate+i2;
3796: if(cptj2 <= cptj)
3797: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3798: }
3799: }
3800: fprintf(ficrescveij,"\n");
3801:
3802: if(estepm < stepm){
3803: printf ("Problem %d lower than %d\n",estepm, stepm);
3804: }
3805: else hstepm=estepm;
3806: /* We compute the life expectancy from trapezoids spaced every estepm months
3807: * This is mainly to measure the difference between two models: for example
3808: * if stepm=24 months pijx are given only every 2 years and by summing them
3809: * we are calculating an estimate of the Life Expectancy assuming a linear
3810: * progression in between and thus overestimating or underestimating according
3811: * to the curvature of the survival function. If, for the same date, we
3812: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3813: * to compare the new estimate of Life expectancy with the same linear
3814: * hypothesis. A more precise result, taking into account a more precise
3815: * curvature will be obtained if estepm is as small as stepm. */
3816:
3817: /* For example we decided to compute the life expectancy with the smallest unit */
3818: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3819: nhstepm is the number of hstepm from age to agelim
3820: nstepm is the number of stepm from age to agelin.
3821: Look at hpijx to understand the reason of that which relies in memory size
3822: and note for a fixed period like estepm months */
3823: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3824: survival function given by stepm (the optimization length). Unfortunately it
3825: means that if the survival funtion is printed only each two years of age and if
3826: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3827: results. So we changed our mind and took the option of the best precision.
3828: */
3829: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3830:
3831: /* If stepm=6 months */
3832: /* nhstepm age range expressed in number of stepm */
3833: agelim=AGESUP;
3834: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3835: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3836: /* if (stepm >= YEARM) hstepm=1;*/
3837: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3838:
3839: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3840: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3841: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3842: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3843: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3844: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3845:
3846: for (age=bage; age<=fage; age ++){
3847: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3848: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3849: /* if (stepm >= YEARM) hstepm=1;*/
3850: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3851:
3852: /* If stepm=6 months */
3853: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3854: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3855:
3856: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3857:
3858: /* Computing Variances of health expectancies */
3859: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3860: decrease memory allocation */
3861: for(theta=1; theta <=npar; theta++){
3862: for(i=1; i<=npar; i++){
3863: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3864: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3865: }
3866: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3867: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3868:
3869: for(j=1; j<= nlstate; j++){
3870: for(i=1; i<=nlstate; i++){
3871: for(h=0; h<=nhstepm-1; h++){
3872: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3873: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3874: }
3875: }
3876: }
3877:
3878: for(ij=1; ij<= nlstate*nlstate; ij++)
3879: for(h=0; h<=nhstepm-1; h++){
3880: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3881: }
3882: }/* End theta */
3883:
3884:
3885: for(h=0; h<=nhstepm-1; h++)
3886: for(j=1; j<=nlstate*nlstate;j++)
3887: for(theta=1; theta <=npar; theta++)
3888: trgradg[h][j][theta]=gradg[h][theta][j];
3889:
3890:
3891: for(ij=1;ij<=nlstate*nlstate;ij++)
3892: for(ji=1;ji<=nlstate*nlstate;ji++)
3893: varhe[ij][ji][(int)age] =0.;
3894:
3895: printf("%d|",(int)age);fflush(stdout);
3896: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3897: for(h=0;h<=nhstepm-1;h++){
3898: for(k=0;k<=nhstepm-1;k++){
3899: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3900: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3901: for(ij=1;ij<=nlstate*nlstate;ij++)
3902: for(ji=1;ji<=nlstate*nlstate;ji++)
3903: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3904: }
3905: }
3906:
3907: /* Computing expectancies */
3908: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3909: for(i=1; i<=nlstate;i++)
3910: for(j=1; j<=nlstate;j++)
3911: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3912: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3913:
3914: /* 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]);*/
3915:
3916: }
3917:
3918: fprintf(ficresstdeij,"%3.0f",age );
3919: for(i=1; i<=nlstate;i++){
3920: eip=0.;
3921: vip=0.;
3922: for(j=1; j<=nlstate;j++){
3923: eip += eij[i][j][(int)age];
3924: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3925: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3926: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3927: }
3928: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3929: }
3930: fprintf(ficresstdeij,"\n");
3931:
3932: fprintf(ficrescveij,"%3.0f",age );
3933: for(i=1; i<=nlstate;i++)
3934: for(j=1; j<=nlstate;j++){
3935: cptj= (j-1)*nlstate+i;
3936: for(i2=1; i2<=nlstate;i2++)
3937: for(j2=1; j2<=nlstate;j2++){
3938: cptj2= (j2-1)*nlstate+i2;
3939: if(cptj2 <= cptj)
3940: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3941: }
3942: }
3943: fprintf(ficrescveij,"\n");
3944:
3945: }
3946: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3947: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3948: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3949: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3950: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3951: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3952: printf("\n");
3953: fprintf(ficlog,"\n");
3954:
3955: free_vector(xm,1,npar);
3956: free_vector(xp,1,npar);
3957: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3958: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3959: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3960: }
3961:
3962: /************ Variance ******************/
1.203 brouard 3963: 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 *ncvyear, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
1.126 brouard 3964: {
3965: /* Variance of health expectancies */
3966: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3967: /* double **newm;*/
1.169 brouard 3968: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3969:
3970: int movingaverage();
1.126 brouard 3971: double **dnewm,**doldm;
3972: double **dnewmp,**doldmp;
3973: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 3974: int k;
1.126 brouard 3975: double *xp;
3976: double **gp, **gm; /* for var eij */
3977: double ***gradg, ***trgradg; /*for var eij */
3978: double **gradgp, **trgradgp; /* for var p point j */
3979: double *gpp, *gmp; /* for var p point j */
3980: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3981: double ***p3mat;
3982: double age,agelim, hf;
3983: double ***mobaverage;
3984: int theta;
3985: char digit[4];
3986: char digitp[25];
3987:
3988: char fileresprobmorprev[FILENAMELENGTH];
3989:
3990: if(popbased==1){
3991: if(mobilav!=0)
1.201 brouard 3992: strcpy(digitp,"-POPULBASED-MOBILAV_");
3993: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
1.126 brouard 3994: }
3995: else
1.201 brouard 3996: strcpy(digitp,"-STABLBASED_");
1.126 brouard 3997:
3998: if (mobilav!=0) {
3999: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4000: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4001: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4002: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4003: }
4004: }
4005:
1.201 brouard 4006: strcpy(fileresprobmorprev,"PRMORPREV-");
1.126 brouard 4007: sprintf(digit,"%-d",ij);
4008: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
4009: strcat(fileresprobmorprev,digit); /* Tvar to be done */
4010: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
1.202 brouard 4011: strcat(fileresprobmorprev,fileresu);
1.126 brouard 4012: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
4013: printf("Problem with resultfile: %s\n", fileresprobmorprev);
4014: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
4015: }
4016: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4017:
4018: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4019: pstamp(ficresprobmorprev);
4020: 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);
4021: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
4022: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4023: fprintf(ficresprobmorprev," p.%-d SE",j);
4024: for(i=1; i<=nlstate;i++)
4025: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
4026: }
4027: fprintf(ficresprobmorprev,"\n");
4028: fprintf(ficgp,"\n# Routine varevsij");
1.200 brouard 4029: fprintf(ficgp,"\nunset title \n");
4030: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
1.126 brouard 4031: 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");
4032: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
4033: /* } */
4034: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4035: pstamp(ficresvij);
4036: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
4037: if(popbased==1)
1.128 brouard 4038: 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 4039: else
4040: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
4041: fprintf(ficresvij,"# Age");
4042: for(i=1; i<=nlstate;i++)
4043: for(j=1; j<=nlstate;j++)
4044: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
4045: fprintf(ficresvij,"\n");
4046:
4047: xp=vector(1,npar);
4048: dnewm=matrix(1,nlstate,1,npar);
4049: doldm=matrix(1,nlstate,1,nlstate);
4050: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
4051: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4052:
4053: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
4054: gpp=vector(nlstate+1,nlstate+ndeath);
4055: gmp=vector(nlstate+1,nlstate+ndeath);
4056: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
4057:
4058: if(estepm < stepm){
4059: printf ("Problem %d lower than %d\n",estepm, stepm);
4060: }
4061: else hstepm=estepm;
4062: /* For example we decided to compute the life expectancy with the smallest unit */
4063: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4064: nhstepm is the number of hstepm from age to agelim
4065: nstepm is the number of stepm from age to agelin.
1.128 brouard 4066: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 4067: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4068: survival function given by stepm (the optimization length). Unfortunately it
4069: means that if the survival funtion is printed every two years of age and if
4070: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4071: results. So we changed our mind and took the option of the best precision.
4072: */
4073: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4074: agelim = AGESUP;
4075: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4076: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4077: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4078: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4079: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
4080: gp=matrix(0,nhstepm,1,nlstate);
4081: gm=matrix(0,nhstepm,1,nlstate);
4082:
4083:
4084: for(theta=1; theta <=npar; theta++){
4085: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
4086: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4087: }
4088: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1.203 brouard 4089: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);
1.126 brouard 4090:
4091: if (popbased==1) {
4092: if(mobilav ==0){
4093: for(i=1; i<=nlstate;i++)
4094: prlim[i][i]=probs[(int)age][i][ij];
4095: }else{ /* mobilav */
4096: for(i=1; i<=nlstate;i++)
4097: prlim[i][i]=mobaverage[(int)age][i][ij];
4098: }
4099: }
4100:
4101: for(j=1; j<= nlstate; j++){
4102: for(h=0; h<=nhstepm; h++){
4103: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
4104: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
4105: }
4106: }
4107: /* This for computing probability of death (h=1 means
4108: computed over hstepm matrices product = hstepm*stepm months)
4109: as a weighted average of prlim.
4110: */
4111: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4112: for(i=1,gpp[j]=0.; i<= nlstate; i++)
4113: gpp[j] += prlim[i][i]*p3mat[i][j][1];
4114: }
4115: /* end probability of death */
4116:
4117: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
4118: xp[i] = x[i] - (i==theta ?delti[theta]:0);
4119: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1.203 brouard 4120: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear, ij);
1.126 brouard 4121:
4122: if (popbased==1) {
4123: if(mobilav ==0){
4124: for(i=1; i<=nlstate;i++)
4125: prlim[i][i]=probs[(int)age][i][ij];
4126: }else{ /* mobilav */
4127: for(i=1; i<=nlstate;i++)
4128: prlim[i][i]=mobaverage[(int)age][i][ij];
4129: }
4130: }
4131:
1.128 brouard 4132: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 4133: for(h=0; h<=nhstepm; h++){
4134: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
4135: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
4136: }
4137: }
4138: /* This for computing probability of death (h=1 means
4139: computed over hstepm matrices product = hstepm*stepm months)
4140: as a weighted average of prlim.
4141: */
4142: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4143: for(i=1,gmp[j]=0.; i<= nlstate; i++)
4144: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4145: }
4146: /* end probability of death */
4147:
4148: for(j=1; j<= nlstate; j++) /* vareij */
4149: for(h=0; h<=nhstepm; h++){
4150: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
4151: }
4152:
4153: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
4154: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
4155: }
4156:
4157: } /* End theta */
4158:
4159: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
4160:
4161: for(h=0; h<=nhstepm; h++) /* veij */
4162: for(j=1; j<=nlstate;j++)
4163: for(theta=1; theta <=npar; theta++)
4164: trgradg[h][j][theta]=gradg[h][theta][j];
4165:
4166: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
4167: for(theta=1; theta <=npar; theta++)
4168: trgradgp[j][theta]=gradgp[theta][j];
4169:
4170:
4171: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4172: for(i=1;i<=nlstate;i++)
4173: for(j=1;j<=nlstate;j++)
4174: vareij[i][j][(int)age] =0.;
4175:
4176: for(h=0;h<=nhstepm;h++){
4177: for(k=0;k<=nhstepm;k++){
4178: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
4179: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
4180: for(i=1;i<=nlstate;i++)
4181: for(j=1;j<=nlstate;j++)
4182: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
4183: }
4184: }
4185:
4186: /* pptj */
4187: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
4188: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
4189: for(j=nlstate+1;j<=nlstate+ndeath;j++)
4190: for(i=nlstate+1;i<=nlstate+ndeath;i++)
4191: varppt[j][i]=doldmp[j][i];
4192: /* end ppptj */
4193: /* x centered again */
4194: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
1.203 brouard 4195: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyear,ij);
1.126 brouard 4196:
4197: if (popbased==1) {
4198: if(mobilav ==0){
4199: for(i=1; i<=nlstate;i++)
4200: prlim[i][i]=probs[(int)age][i][ij];
4201: }else{ /* mobilav */
4202: for(i=1; i<=nlstate;i++)
4203: prlim[i][i]=mobaverage[(int)age][i][ij];
4204: }
4205: }
4206:
4207: /* This for computing probability of death (h=1 means
4208: computed over hstepm (estepm) matrices product = hstepm*stepm months)
4209: as a weighted average of prlim.
4210: */
4211: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4212: for(i=1,gmp[j]=0.;i<= nlstate; i++)
4213: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4214: }
4215: /* end probability of death */
4216:
4217: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
4218: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4219: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
4220: for(i=1; i<=nlstate;i++){
4221: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
4222: }
4223: }
4224: fprintf(ficresprobmorprev,"\n");
4225:
4226: fprintf(ficresvij,"%.0f ",age );
4227: for(i=1; i<=nlstate;i++)
4228: for(j=1; j<=nlstate;j++){
4229: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
4230: }
4231: fprintf(ficresvij,"\n");
4232: free_matrix(gp,0,nhstepm,1,nlstate);
4233: free_matrix(gm,0,nhstepm,1,nlstate);
4234: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
4235: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
4236: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4237: } /* End age */
4238: free_vector(gpp,nlstate+1,nlstate+ndeath);
4239: free_vector(gmp,nlstate+1,nlstate+ndeath);
4240: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
4241: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.199 brouard 4242: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
4243: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
1.126 brouard 4244: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 4245: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.201 brouard 4246: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4247: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
4248: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
4249: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 4250: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 4251: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 4252: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 4253: 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 4254: 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 4255: /* 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 4256: */
1.199 brouard 4257: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
1.201 brouard 4258: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4259:
4260: free_vector(xp,1,npar);
4261: free_matrix(doldm,1,nlstate,1,nlstate);
4262: free_matrix(dnewm,1,nlstate,1,npar);
4263: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4264: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
4265: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4266: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4267: fclose(ficresprobmorprev);
4268: fflush(ficgp);
4269: fflush(fichtm);
4270: } /* end varevsij */
4271:
4272: /************ Variance of prevlim ******************/
1.203 brouard 4273: 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 *ncvyear, int ij, char strstart[])
1.126 brouard 4274: {
4275: /* Variance of prevalence limit */
4276: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 4277:
1.126 brouard 4278: double **dnewm,**doldm;
4279: int i, j, nhstepm, hstepm;
4280: double *xp;
4281: double *gp, *gm;
4282: double **gradg, **trgradg;
4283: double age,agelim;
4284: int theta;
4285:
4286: pstamp(ficresvpl);
4287: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
4288: fprintf(ficresvpl,"# Age");
4289: for(i=1; i<=nlstate;i++)
4290: fprintf(ficresvpl," %1d-%1d",i,i);
4291: fprintf(ficresvpl,"\n");
4292:
4293: xp=vector(1,npar);
4294: dnewm=matrix(1,nlstate,1,npar);
4295: doldm=matrix(1,nlstate,1,nlstate);
4296:
4297: hstepm=1*YEARM; /* Every year of age */
4298: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
4299: agelim = AGESUP;
4300: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4301: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4302: if (stepm >= YEARM) hstepm=1;
4303: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4304: gradg=matrix(1,npar,1,nlstate);
4305: gp=vector(1,nlstate);
4306: gm=vector(1,nlstate);
4307:
4308: for(theta=1; theta <=npar; theta++){
4309: for(i=1; i<=npar; i++){ /* Computes gradient */
4310: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4311: }
1.203 brouard 4312: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);
1.126 brouard 4313: for(i=1;i<=nlstate;i++)
4314: gp[i] = prlim[i][i];
4315:
4316: for(i=1; i<=npar; i++) /* Computes gradient */
4317: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.203 brouard 4318: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);
1.126 brouard 4319: for(i=1;i<=nlstate;i++)
4320: gm[i] = prlim[i][i];
4321:
4322: for(i=1;i<=nlstate;i++)
4323: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
4324: } /* End theta */
4325:
4326: trgradg =matrix(1,nlstate,1,npar);
4327:
4328: for(j=1; j<=nlstate;j++)
4329: for(theta=1; theta <=npar; theta++)
4330: trgradg[j][theta]=gradg[theta][j];
4331:
4332: for(i=1;i<=nlstate;i++)
4333: varpl[i][(int)age] =0.;
4334: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4335: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4336: for(i=1;i<=nlstate;i++)
4337: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4338:
4339: fprintf(ficresvpl,"%.0f ",age );
4340: for(i=1; i<=nlstate;i++)
4341: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4342: fprintf(ficresvpl,"\n");
4343: free_vector(gp,1,nlstate);
4344: free_vector(gm,1,nlstate);
4345: free_matrix(gradg,1,npar,1,nlstate);
4346: free_matrix(trgradg,1,nlstate,1,npar);
4347: } /* End age */
4348:
4349: free_vector(xp,1,npar);
4350: free_matrix(doldm,1,nlstate,1,npar);
4351: free_matrix(dnewm,1,nlstate,1,nlstate);
4352:
4353: }
4354:
4355: /************ Variance of one-step probabilities ******************/
4356: 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[])
4357: {
1.164 brouard 4358: int i, j=0, k1, l1, tj;
1.126 brouard 4359: int k2, l2, j1, z1;
1.164 brouard 4360: int k=0, l;
1.145 brouard 4361: int first=1, first1, first2;
1.126 brouard 4362: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4363: double **dnewm,**doldm;
4364: double *xp;
4365: double *gp, *gm;
4366: double **gradg, **trgradg;
4367: double **mu;
1.164 brouard 4368: double age, cov[NCOVMAX+1];
1.126 brouard 4369: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4370: int theta;
4371: char fileresprob[FILENAMELENGTH];
4372: char fileresprobcov[FILENAMELENGTH];
4373: char fileresprobcor[FILENAMELENGTH];
4374: double ***varpij;
4375:
1.201 brouard 4376: strcpy(fileresprob,"PROB_");
1.126 brouard 4377: strcat(fileresprob,fileres);
4378: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4379: printf("Problem with resultfile: %s\n", fileresprob);
4380: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4381: }
1.201 brouard 4382: strcpy(fileresprobcov,"PROBCOV_");
1.202 brouard 4383: strcat(fileresprobcov,fileresu);
1.126 brouard 4384: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4385: printf("Problem with resultfile: %s\n", fileresprobcov);
4386: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4387: }
1.201 brouard 4388: strcpy(fileresprobcor,"PROBCOR_");
1.202 brouard 4389: strcat(fileresprobcor,fileresu);
1.126 brouard 4390: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4391: printf("Problem with resultfile: %s\n", fileresprobcor);
4392: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4393: }
4394: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4395: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4396: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4397: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4398: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4399: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4400: pstamp(ficresprob);
4401: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4402: fprintf(ficresprob,"# Age");
4403: pstamp(ficresprobcov);
4404: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4405: fprintf(ficresprobcov,"# Age");
4406: pstamp(ficresprobcor);
4407: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4408: fprintf(ficresprobcor,"# Age");
4409:
4410:
4411: for(i=1; i<=nlstate;i++)
4412: for(j=1; j<=(nlstate+ndeath);j++){
4413: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4414: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4415: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4416: }
4417: /* fprintf(ficresprob,"\n");
4418: fprintf(ficresprobcov,"\n");
4419: fprintf(ficresprobcor,"\n");
4420: */
1.131 brouard 4421: xp=vector(1,npar);
1.126 brouard 4422: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4423: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4424: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4425: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4426: first=1;
4427: fprintf(ficgp,"\n# Routine varprob");
4428: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4429: fprintf(fichtm,"\n");
4430:
1.200 brouard 4431: 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 4432: 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);
4433: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 4434: and drawn. It helps understanding how is the covariance between two incidences.\
4435: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4436: 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. \
4437: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4438: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4439: standard deviations wide on each axis. <br>\
4440: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4441: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4442: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4443:
4444: cov[1]=1;
1.145 brouard 4445: /* tj=cptcoveff; */
4446: tj = (int) pow(2,cptcoveff);
1.126 brouard 4447: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4448: j1=0;
1.145 brouard 4449: for(j1=1; j1<=tj;j1++){
4450: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4451: /*j1++;*/
1.126 brouard 4452: if (cptcovn>0) {
4453: fprintf(ficresprob, "\n#********** Variable ");
1.198 brouard 4454: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4455: fprintf(ficresprob, "**********\n#\n");
4456: fprintf(ficresprobcov, "\n#********** Variable ");
1.198 brouard 4457: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4458: fprintf(ficresprobcov, "**********\n#\n");
4459:
4460: fprintf(ficgp, "\n#********** Variable ");
1.198 brouard 4461: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4462: fprintf(ficgp, "**********\n#\n");
4463:
4464:
4465: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.198 brouard 4466: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4467: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4468:
4469: fprintf(ficresprobcor, "\n#********** Variable ");
1.198 brouard 4470: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4471: fprintf(ficresprobcor, "**********\n#");
4472: }
4473:
1.145 brouard 4474: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4475: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4476: gp=vector(1,(nlstate)*(nlstate+ndeath));
4477: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 4478: for (age=bage; age<=fage; age ++){
4479: cov[2]=age;
1.187 brouard 4480: if(nagesqr==1)
4481: cov[3]= age*age;
1.126 brouard 4482: for (k=1; k<=cptcovn;k++) {
1.200 brouard 4483: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
4484: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
1.145 brouard 4485: * 1 1 1 1 1
4486: * 2 2 1 1 1
4487: * 3 1 2 1 1
4488: */
4489: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 4490: }
1.186 brouard 4491: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 4492: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
1.126 brouard 4493: for (k=1; k<=cptcovprod;k++)
1.200 brouard 4494: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.126 brouard 4495:
4496:
4497: for(theta=1; theta <=npar; theta++){
4498: for(i=1; i<=npar; i++)
4499: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4500:
4501: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4502:
4503: k=0;
4504: for(i=1; i<= (nlstate); i++){
4505: for(j=1; j<=(nlstate+ndeath);j++){
4506: k=k+1;
4507: gp[k]=pmmij[i][j];
4508: }
4509: }
4510:
4511: for(i=1; i<=npar; i++)
4512: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4513:
4514: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4515: k=0;
4516: for(i=1; i<=(nlstate); i++){
4517: for(j=1; j<=(nlstate+ndeath);j++){
4518: k=k+1;
4519: gm[k]=pmmij[i][j];
4520: }
4521: }
4522:
4523: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4524: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4525: }
4526:
4527: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4528: for(theta=1; theta <=npar; theta++)
4529: trgradg[j][theta]=gradg[theta][j];
4530:
4531: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4532: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4533:
4534: pmij(pmmij,cov,ncovmodel,x,nlstate);
4535:
4536: k=0;
4537: for(i=1; i<=(nlstate); i++){
4538: for(j=1; j<=(nlstate+ndeath);j++){
4539: k=k+1;
4540: mu[k][(int) age]=pmmij[i][j];
4541: }
4542: }
4543: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4544: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4545: varpij[i][j][(int)age] = doldm[i][j];
4546:
4547: /*printf("\n%d ",(int)age);
4548: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4549: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4550: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4551: }*/
4552:
4553: fprintf(ficresprob,"\n%d ",(int)age);
4554: fprintf(ficresprobcov,"\n%d ",(int)age);
4555: fprintf(ficresprobcor,"\n%d ",(int)age);
4556:
4557: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4558: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4559: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4560: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4561: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4562: }
4563: i=0;
4564: for (k=1; k<=(nlstate);k++){
4565: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 4566: i++;
1.126 brouard 4567: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4568: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4569: for (j=1; j<=i;j++){
1.145 brouard 4570: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 4571: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4572: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4573: }
4574: }
4575: }/* end of loop for state */
4576: } /* end of loop for age */
1.145 brouard 4577: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4578: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4579: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4580: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4581:
1.126 brouard 4582: /* Confidence intervalle of pij */
4583: /*
1.131 brouard 4584: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 4585: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4586: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4587: 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);
4588: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4589: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4590: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4591: */
4592:
4593: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 4594: first1=1;first2=2;
1.126 brouard 4595: for (k2=1; k2<=(nlstate);k2++){
4596: for (l2=1; l2<=(nlstate+ndeath);l2++){
4597: if(l2==k2) continue;
4598: j=(k2-1)*(nlstate+ndeath)+l2;
4599: for (k1=1; k1<=(nlstate);k1++){
4600: for (l1=1; l1<=(nlstate+ndeath);l1++){
4601: if(l1==k1) continue;
4602: i=(k1-1)*(nlstate+ndeath)+l1;
4603: if(i<=j) continue;
4604: for (age=bage; age<=fage; age ++){
4605: if ((int)age %5==0){
4606: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4607: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4608: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4609: mu1=mu[i][(int) age]/stepm*YEARM ;
4610: mu2=mu[j][(int) age]/stepm*YEARM;
4611: c12=cv12/sqrt(v1*v2);
4612: /* Computing eigen value of matrix of covariance */
4613: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4614: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4615: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4616: if(first2==1){
4617: first1=0;
4618: 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);
4619: }
4620: 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);
4621: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4622: /* lc2=fabs(lc2); */
1.135 brouard 4623: }
4624:
1.126 brouard 4625: /* Eigen vectors */
4626: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4627: /*v21=sqrt(1.-v11*v11); *//* error */
4628: v21=(lc1-v1)/cv12*v11;
4629: v12=-v21;
4630: v22=v11;
4631: tnalp=v21/v11;
4632: if(first1==1){
4633: first1=0;
4634: 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);
4635: }
4636: 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);
4637: /*printf(fignu*/
4638: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4639: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4640: if(first==1){
4641: first=0;
1.200 brouard 4642: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
1.126 brouard 4643: fprintf(ficgp,"\nset parametric;unset label");
4644: 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 4645: fprintf(ficgp,"\nset ter svg size 640, 480");
1.126 brouard 4646: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.201 brouard 4647: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">\
4648: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
4649: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\
4650: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
4651: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4652: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.201 brouard 4653: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4654: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4655: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4656: 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",\
4657: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4658: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4659: }else{
4660: first=0;
4661: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4662: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4663: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4664: 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",\
4665: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4666: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4667: }/* if first */
4668: } /* age mod 5 */
4669: } /* end loop age */
1.201 brouard 4670: 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 4671: first=1;
4672: } /*l12 */
4673: } /* k12 */
4674: } /*l1 */
4675: }/* k1 */
1.169 brouard 4676: /* } */ /* loop covariates */
1.126 brouard 4677: }
4678: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4679: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4680: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4681: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4682: free_vector(xp,1,npar);
4683: fclose(ficresprob);
4684: fclose(ficresprobcov);
4685: fclose(ficresprobcor);
4686: fflush(ficgp);
4687: fflush(fichtmcov);
4688: }
4689:
4690:
4691: /******************* Printing html file ***********/
1.201 brouard 4692: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 4693: int lastpass, int stepm, int weightopt, char model[],\
4694: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4695: int popforecast, int estepm ,\
4696: double jprev1, double mprev1,double anprev1, \
4697: double jprev2, double mprev2,double anprev2){
4698: int jj1, k1, i1, cpt;
4699:
4700: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4701: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4702: </ul>");
4703: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4704: - 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 4705: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 4706: fprintf(fichtm,"\
4707: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 4708: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 4709: fprintf(fichtm,"\
4710: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4711: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 4712: fprintf(fichtm,"\
1.128 brouard 4713: - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . 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 4714: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4715: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.126 brouard 4716: fprintf(fichtm,"\
4717: - Population projections by age and states: \
1.201 brouard 4718: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.126 brouard 4719:
4720: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4721:
1.145 brouard 4722: m=pow(2,cptcoveff);
1.126 brouard 4723: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4724:
4725: jj1=0;
4726: for(k1=1; k1<=m;k1++){
1.192 brouard 4727: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4728: jj1++;
4729: if (cptcovn > 0) {
4730: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.192 brouard 4731: for (cpt=1; cpt<=cptcoveff;cpt++){
1.198 brouard 4732: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
4733: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
1.192 brouard 4734: }
1.126 brouard 4735: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4736: }
1.201 brouard 4737: /* aij, bij */
4738: fprintf(fichtm,"<br>- Logit model, 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> \
4739: <img src=\"%s_%d-1.svg\">",subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 4740: /* Pij */
1.202 brouard 4741: fprintf(fichtm,"<br>\n- Pij 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 4742: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 4743: /* Quasi-incidences */
1.201 brouard 4744: fprintf(fichtm,"<br>\n- Iij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
4745: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\
4746: incidence (rates) are the limit when h tends to zero of the ratio of the probability hPij \
4747: divided by h: hPij/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
4748: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
4749: /* Survival functions (period) in state j */
4750: for(cpt=1; cpt<=nlstate;cpt++){
4751: 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> \
4752: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
4753: }
4754: /* State specific survival functions (period) */
4755: for(cpt=1; cpt<=nlstate;cpt++){
4756: fprintf(fichtm,"<br>\n- Survival functions from state %d in any different live states and total.\
4757: Or probability to survive in various states (1 to %d) being in state %d at different ages.\
4758: <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);
4759: }
4760: /* Period (stable) prevalence in each health state */
4761: for(cpt=1; cpt<=nlstate;cpt++){
4762: 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> \
4763: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
4764: }
1.126 brouard 4765: for(cpt=1; cpt<=nlstate;cpt++) {
1.201 brouard 4766: 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> \
4767: <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 4768: }
1.192 brouard 4769: /* } /\* end i1 *\/ */
1.126 brouard 4770: }/* End k1 */
4771: fprintf(fichtm,"</ul>");
4772:
4773: fprintf(fichtm,"\
4774: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 4775: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 4776: - 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 4777: But because parameters are usually highly correlated (a higher incidence of disability \
4778: and a higher incidence of recovery can give very close observed transition) it might \
4779: be very useful to look not only at linear confidence intervals estimated from the \
4780: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
4781: (parameters) of the logistic regression, it might be more meaningful to visualize the \
4782: covariance matrix of the one-step probabilities. \
4783: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 4784:
1.193 brouard 4785: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4786: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
1.126 brouard 4787: fprintf(fichtm,"\
4788: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4789: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 4790:
4791: fprintf(fichtm,"\
4792: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4793: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
1.126 brouard 4794: fprintf(fichtm,"\
4795: - 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): \
4796: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 4797: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.126 brouard 4798: fprintf(fichtm,"\
4799: - (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): \
4800: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 4801: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.126 brouard 4802: fprintf(fichtm,"\
1.128 brouard 4803: - 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 4804: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
1.126 brouard 4805: fprintf(fichtm,"\
1.128 brouard 4806: - 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 4807: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
1.126 brouard 4808: fprintf(fichtm,"\
4809: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.201 brouard 4810: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 4811:
4812: /* if(popforecast==1) fprintf(fichtm,"\n */
4813: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4814: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4815: /* <br>",fileres,fileres,fileres,fileres); */
4816: /* else */
4817: /* 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); */
4818: fflush(fichtm);
4819: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4820:
1.145 brouard 4821: m=pow(2,cptcoveff);
1.126 brouard 4822: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4823:
4824: jj1=0;
4825: for(k1=1; k1<=m;k1++){
1.192 brouard 4826: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4827: jj1++;
4828: if (cptcovn > 0) {
4829: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4830: for (cpt=1; cpt<=cptcoveff;cpt++)
1.198 brouard 4831: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 4832: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4833: }
4834: for(cpt=1; cpt<=nlstate;cpt++) {
4835: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.199 brouard 4836: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.svg <br>\
1.201 brouard 4837: <img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);
1.126 brouard 4838: }
4839: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4840: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4841: true period expectancies (those weighted with period prevalences are also\
4842: drawn in addition to the population based expectancies computed using\
1.201 brouard 4843: observed and cahotic prevalences: %s_%d.svg<br>\
4844: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.192 brouard 4845: /* } /\* end i1 *\/ */
1.126 brouard 4846: }/* End k1 */
4847: fprintf(fichtm,"</ul>");
4848: fflush(fichtm);
4849: }
4850:
4851: /******************* Gnuplot file **************/
1.201 brouard 4852: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 4853:
4854: char dirfileres[132],optfileres[132];
1.164 brouard 4855: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.130 brouard 4856: int ng=0;
1.201 brouard 4857: int vpopbased;
1.126 brouard 4858: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4859: /* printf("Problem with file %s",optionfilegnuplot); */
4860: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4861: /* } */
4862:
4863: /*#ifdef windows */
4864: fprintf(ficgp,"cd \"%s\" \n",pathc);
4865: /*#endif */
4866: m=pow(2,cptcoveff);
4867:
1.202 brouard 4868: /* Contribution to likelihood */
4869: /* Plot the probability implied in the likelihood */
4870: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
4871: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
4872: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
4873: fprintf(ficgp,"\nset ter png size 640, 480");
1.204 ! brouard 4874: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 4875: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
4876: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
4877: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
1.204 ! brouard 4878: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
! 4879: fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):5 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
! 4880: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
! 4881: fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):4 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
! 4882: for (i=1; i<= nlstate ; i ++) {
! 4883: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
! 4884: fprintf(ficgp,"unset log;\n plot \"%s\"",subdirf(fileresilk));
! 4885: fprintf(ficgp," u 2:($4 == %d && $5==%d ? $9 : 1/0):5 t \"p%d%d\" with points lc variable \\\n",i,1,i,1);
! 4886: for (j=2; j<= nlstate+ndeath ; j ++) {
! 4887: fprintf(ficgp,", \"\" u 2:($4 == %d && $5==%d ? $9 : 1/0):5 t \"p%d%d\" with points lc variable ",i,j,i,j);
! 4888: }
! 4889: fprintf(ficgp,";\nset out; unset ylabel;\n");
! 4890: }
! 4891: /* 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 */
! 4892: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
! 4893: /* 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 4894: fprintf(ficgp,"\nset out;unset log\n");
1.202 brouard 4895: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
4896:
1.126 brouard 4897: strcpy(dirfileres,optionfilefiname);
4898: strcpy(optfileres,"vpl");
4899: /* 1eme*/
1.201 brouard 4900: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files\n");
1.126 brouard 4901: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 4902: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
1.201 brouard 4903: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
4904: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
1.126 brouard 4905: fprintf(ficgp,"set xlabel \"Age\" \n\
4906: set ylabel \"Probability\" \n\
1.199 brouard 4907: set ter svg size 640, 480\n\
1.201 brouard 4908: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 4909:
4910: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4911: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4912: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4913: }
1.201 brouard 4914: 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 4915: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4916: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4917: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4918: }
1.201 brouard 4919: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 4920: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4921: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4922: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4923: }
1.201 brouard 4924: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
4925: fprintf(ficgp,"\nset out \n");
4926: } /* k1 */
4927: } /* cpt */
1.126 brouard 4928: /*2 eme*/
1.153 brouard 4929: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126 brouard 4930: for (k1=1; k1<= m ; k1 ++) {
1.201 brouard 4931: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
4932: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
4933: if(vpopbased==0)
4934: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
4935: else
4936: fprintf(ficgp,"\nreplot ");
4937: for (i=1; i<= nlstate+1 ; i ++) {
4938: k=2*i;
4939: 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);
4940: for (j=1; j<= nlstate+1 ; j ++) {
4941: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4942: else fprintf(ficgp," %%*lf (%%*lf)");
4943: }
4944: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
4945: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
4946: 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);
4947: for (j=1; j<= nlstate+1 ; j ++) {
4948: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4949: else fprintf(ficgp," %%*lf (%%*lf)");
4950: }
4951: fprintf(ficgp,"\" t\"\" w l lt 0,");
4952: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
4953: for (j=1; j<= nlstate+1 ; j ++) {
4954: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4955: else fprintf(ficgp," %%*lf (%%*lf)");
4956: }
4957: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4958: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
4959: } /* state */
4960: } /* vpopbased */
4961: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
4962: } /* k1 */
1.126 brouard 4963: /*3eme*/
4964:
4965: for (k1=1; k1<= m ; k1 ++) {
4966: for (cpt=1; cpt<= nlstate ; cpt ++) {
4967: /* k=2+nlstate*(2*cpt-2); */
4968: k=2+(nlstate+1)*(cpt-1);
1.201 brouard 4969: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
1.199 brouard 4970: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 4971: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.126 brouard 4972: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4973: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4974: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4975: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4976: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4977: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4978:
4979: */
4980: for (i=1; i< nlstate ; i ++) {
1.201 brouard 4981: 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 4982: /* 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);*/
4983:
4984: }
1.201 brouard 4985: 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 4986: }
4987: }
4988:
1.201 brouard 4989: /* Survival functions (period) from state i in state j by initial state i */
4990: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4991: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
4992: k=3;
4993: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'lij' files, cov=%d state=%d",k1, cpt);
4994: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
4995: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
4996: set ter svg size 640, 480\n\
4997: unset log y\n\
4998: plot [%.f:%.f] ", ageminpar, agemaxpar);
4999: for (i=1; i<= nlstate ; i ++){
5000: if(i==1)
5001: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5002: else
5003: fprintf(ficgp,", '' ");
5004: l=(nlstate+ndeath)*(i-1)+1;
5005: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
5006: for (j=2; j<= nlstate+ndeath ; j ++)
5007: fprintf(ficgp,"+$%d",k+l+j-1);
5008: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
5009: } /* nlstate */
5010: fprintf(ficgp,"\nset out\n");
5011: } /* end cpt state*/
5012: } /* end covariate */
5013:
5014: /* Survival functions (period) from state i in state j by final state j */
1.202 brouard 5015: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.201 brouard 5016: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
5017: k=3;
5018: 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);
5019: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
5020: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
5021: set ter svg size 640, 480\n\
5022: unset log y\n\
5023: plot [%.f:%.f] ", ageminpar, agemaxpar);
5024: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
5025: if(j==1)
5026: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5027: else
5028: fprintf(ficgp,", '' ");
5029: l=(nlstate+ndeath)*(cpt-1) +j;
5030: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
5031: /* for (i=2; i<= nlstate+ndeath ; i ++) */
5032: /* fprintf(ficgp,"+$%d",k+l+i-1); */
5033: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
5034: } /* nlstate */
5035: fprintf(ficgp,", '' ");
5036: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
5037: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
5038: l=(nlstate+ndeath)*(cpt-1) +j;
5039: if(j < nlstate)
5040: fprintf(ficgp,"$%d +",k+l);
5041: else
5042: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
5043: }
5044: fprintf(ficgp,"\nset out\n");
5045: } /* end cpt state*/
5046: } /* end covariate */
5047:
1.202 brouard 5048: /* CV preval stable (period) for each covariate */
5049: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.153 brouard 5050: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126 brouard 5051: k=3;
1.153 brouard 5052: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.201 brouard 5053: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 5054: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.199 brouard 5055: set ter svg size 640, 480\n\
1.126 brouard 5056: unset log y\n\
1.153 brouard 5057: plot [%.f:%.f] ", ageminpar, agemaxpar);
5058: for (i=1; i<= nlstate ; i ++){
5059: if(i==1)
1.201 brouard 5060: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
1.153 brouard 5061: else
5062: fprintf(ficgp,", '' ");
1.154 brouard 5063: l=(nlstate+ndeath)*(i-1)+1;
5064: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.201 brouard 5065: for (j=2; j<= nlstate ; j ++)
5066: fprintf(ficgp,"+$%d",k+l+j-1);
1.153 brouard 5067: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
5068: } /* nlstate */
1.201 brouard 5069: fprintf(ficgp,"\nset out\n");
1.153 brouard 5070: } /* end cpt state*/
5071: } /* end covariate */
1.201 brouard 5072:
1.126 brouard 5073: /* proba elementaires */
1.187 brouard 5074: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 5075: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 5076: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 5077: for(k=1; k <=(nlstate+ndeath); k++){
5078: if (k != i) {
1.187 brouard 5079: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 5080: for(j=1; j <=ncovmodel; j++){
1.187 brouard 5081: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 5082: jk++;
5083: }
1.187 brouard 5084: fprintf(ficgp,"\n");
1.126 brouard 5085: }
5086: }
5087: }
1.187 brouard 5088: fprintf(ficgp,"##############\n#\n");
5089:
1.145 brouard 5090: /*goto avoid;*/
1.200 brouard 5091: fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
1.187 brouard 5092: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
5093: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
5094: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
5095: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
5096: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5097: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
5098: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5099: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
5100: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
5101: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5102: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
5103: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
5104: fprintf(ficgp,"#\n");
1.201 brouard 5105: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.187 brouard 5106: fprintf(ficgp,"# ng=%d\n",ng);
5107: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 5108: for(jk=1; jk <=m; jk++) {
1.187 brouard 5109: fprintf(ficgp,"# jk=%d\n",jk);
1.201 brouard 5110: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
5111: fprintf(ficgp,"\nset ter svg size 640, 480 ");
5112: if (ng==1){
5113: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
5114: fprintf(ficgp,"\nunset log y");
5115: }else if (ng==2){
5116: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
5117: fprintf(ficgp,"\nset log y");
5118: }else if (ng==3){
1.126 brouard 5119: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
1.201 brouard 5120: fprintf(ficgp,"\nset log y");
5121: }else
5122: fprintf(ficgp,"\nunset title ");
5123: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 5124: i=1;
5125: for(k2=1; k2<=nlstate; k2++) {
5126: k3=i;
5127: for(k=1; k<=(nlstate+ndeath); k++) {
5128: if (k != k2){
1.201 brouard 5129: switch( ng) {
5130: case 1:
1.187 brouard 5131: if(nagesqr==0)
1.201 brouard 5132: fprintf(ficgp," p%d+p%d*x",i,i+1);
1.187 brouard 5133: else /* nagesqr =1 */
1.201 brouard 5134: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
5135: break;
5136: case 2: /* ng=2 */
1.187 brouard 5137: if(nagesqr==0)
5138: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
5139: else /* nagesqr =1 */
1.201 brouard 5140: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
5141: break;
5142: case 3:
5143: if(nagesqr==0)
5144: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
5145: else /* nagesqr =1 */
5146: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
5147: break;
5148: }
1.141 brouard 5149: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 brouard 5150: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.197 brouard 5151: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
5152: if(ij <=cptcovage) { /* Bug valgrind */
5153: if((j-2)==Tage[ij]) { /* Bug valgrind */
1.200 brouard 5154: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
5155: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
1.197 brouard 5156: ij++;
5157: }
1.186 brouard 5158: }
5159: else
1.198 brouard 5160: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.126 brouard 5161: }
1.201 brouard 5162: if(ng != 1){
5163: fprintf(ficgp,")/(1");
1.126 brouard 5164:
1.201 brouard 5165: for(k1=1; k1 <=nlstate; k1++){
5166: if(nagesqr==0)
5167: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
5168: else /* nagesqr =1 */
5169: 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);
5170:
5171: ij=1;
5172: for(j=3; j <=ncovmodel-nagesqr; j++){
5173: if(ij <=cptcovage) { /* Bug valgrind */
5174: if((j-2)==Tage[ij]) { /* Bug valgrind */
5175: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
5176: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
5177: ij++;
5178: }
1.197 brouard 5179: }
1.201 brouard 5180: else
5181: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.186 brouard 5182: }
1.201 brouard 5183: fprintf(ficgp,")");
1.126 brouard 5184: }
5185: fprintf(ficgp,")");
1.201 brouard 5186: if(ng ==2)
5187: fprintf(ficgp," t \"p%d%d\" ", k2,k);
5188: else /* ng= 3 */
5189: fprintf(ficgp," t \"i%d%d\" ", k2,k);
5190: }else{ /* end ng <> 1 */
5191: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
1.126 brouard 5192: }
5193: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
5194: i=i+ncovmodel;
5195: }
5196: } /* end k */
5197: } /* end k2 */
1.201 brouard 5198: fprintf(ficgp,"\n set out\n");
1.126 brouard 5199: } /* end jk */
5200: } /* end ng */
1.164 brouard 5201: /* avoid: */
1.126 brouard 5202: fflush(ficgp);
5203: } /* end gnuplot */
5204:
5205:
5206: /*************** Moving average **************/
5207: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
5208:
5209: int i, cpt, cptcod;
5210: int modcovmax =1;
5211: int mobilavrange, mob;
5212: double age;
5213:
5214: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
5215: a covariate has 2 modalities */
5216: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
5217:
5218: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
5219: if(mobilav==1) mobilavrange=5; /* default */
5220: else mobilavrange=mobilav;
5221: for (age=bage; age<=fage; age++)
5222: for (i=1; i<=nlstate;i++)
5223: for (cptcod=1;cptcod<=modcovmax;cptcod++)
5224: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
5225: /* We keep the original values on the extreme ages bage, fage and for
5226: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
5227: we use a 5 terms etc. until the borders are no more concerned.
5228: */
5229: for (mob=3;mob <=mobilavrange;mob=mob+2){
5230: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
5231: for (i=1; i<=nlstate;i++){
5232: for (cptcod=1;cptcod<=modcovmax;cptcod++){
5233: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
5234: for (cpt=1;cpt<=(mob-1)/2;cpt++){
5235: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
5236: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
5237: }
5238: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
5239: }
5240: }
5241: }/* end age */
5242: }/* end mob */
5243: }else return -1;
5244: return 0;
5245: }/* End movingaverage */
5246:
5247:
5248: /************** Forecasting ******************/
1.169 brouard 5249: 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 5250: /* proj1, year, month, day of starting projection
5251: agemin, agemax range of age
5252: dateprev1 dateprev2 range of dates during which prevalence is computed
5253: anproj2 year of en of projection (same day and month as proj1).
5254: */
1.164 brouard 5255: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 5256: double agec; /* generic age */
5257: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
5258: double *popeffectif,*popcount;
5259: double ***p3mat;
5260: double ***mobaverage;
5261: char fileresf[FILENAMELENGTH];
5262:
5263: agelim=AGESUP;
5264: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5265:
1.201 brouard 5266: strcpy(fileresf,"F_");
5267: strcat(fileresf,fileresu);
1.126 brouard 5268: if((ficresf=fopen(fileresf,"w"))==NULL) {
5269: printf("Problem with forecast resultfile: %s\n", fileresf);
5270: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
5271: }
5272: printf("Computing forecasting: result on file '%s' \n", fileresf);
5273: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
5274:
5275: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5276:
5277: if (mobilav!=0) {
5278: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5279: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5280: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5281: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5282: }
5283: }
5284:
5285: stepsize=(int) (stepm+YEARM-1)/YEARM;
5286: if (stepm<=12) stepsize=1;
5287: if(estepm < stepm){
5288: printf ("Problem %d lower than %d\n",estepm, stepm);
5289: }
5290: else hstepm=estepm;
5291:
5292: hstepm=hstepm/stepm;
5293: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
5294: fractional in yp1 */
5295: anprojmean=yp;
5296: yp2=modf((yp1*12),&yp);
5297: mprojmean=yp;
5298: yp1=modf((yp2*30.5),&yp);
5299: jprojmean=yp;
5300: if(jprojmean==0) jprojmean=1;
5301: if(mprojmean==0) jprojmean=1;
5302:
5303: i1=cptcoveff;
5304: if (cptcovn < 1){i1=1;}
5305:
5306: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
5307:
5308: fprintf(ficresf,"#****** Routine prevforecast **\n");
5309:
5310: /* if (h==(int)(YEARM*yearp)){ */
5311: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
5312: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5313: k=k+1;
5314: fprintf(ficresf,"\n#******");
5315: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 5316: fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5317: }
5318: fprintf(ficresf,"******\n");
5319: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
5320: for(j=1; j<=nlstate+ndeath;j++){
5321: for(i=1; i<=nlstate;i++)
5322: fprintf(ficresf," p%d%d",i,j);
5323: fprintf(ficresf," p.%d",j);
5324: }
5325: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
5326: fprintf(ficresf,"\n");
5327: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
5328:
5329: for (agec=fage; agec>=(ageminpar-1); agec--){
5330: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
5331: nhstepm = nhstepm/hstepm;
5332: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5333: oldm=oldms;savm=savms;
5334: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
5335:
5336: for (h=0; h<=nhstepm; h++){
5337: if (h*hstepm/YEARM*stepm ==yearp) {
5338: fprintf(ficresf,"\n");
5339: for(j=1;j<=cptcoveff;j++)
1.198 brouard 5340: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5341: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
5342: }
5343: for(j=1; j<=nlstate+ndeath;j++) {
5344: ppij=0.;
5345: for(i=1; i<=nlstate;i++) {
5346: if (mobilav==1)
5347: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
5348: else {
5349: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
5350: }
5351: if (h*hstepm/YEARM*stepm== yearp) {
5352: fprintf(ficresf," %.3f", p3mat[i][j][h]);
5353: }
5354: } /* end i */
5355: if (h*hstepm/YEARM*stepm==yearp) {
5356: fprintf(ficresf," %.3f", ppij);
5357: }
5358: }/* end j */
5359: } /* end h */
5360: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5361: } /* end agec */
5362: } /* end yearp */
5363: } /* end cptcod */
5364: } /* end cptcov */
5365:
5366: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5367:
5368: fclose(ficresf);
5369: }
5370:
5371: /************** Forecasting *****not tested NB*************/
1.169 brouard 5372: 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 5373:
5374: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
5375: int *popage;
5376: double calagedatem, agelim, kk1, kk2;
5377: double *popeffectif,*popcount;
5378: double ***p3mat,***tabpop,***tabpopprev;
5379: double ***mobaverage;
5380: char filerespop[FILENAMELENGTH];
5381:
5382: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5383: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5384: agelim=AGESUP;
5385: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
5386:
5387: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5388:
5389:
1.201 brouard 5390: strcpy(filerespop,"POP_");
5391: strcat(filerespop,fileresu);
1.126 brouard 5392: if((ficrespop=fopen(filerespop,"w"))==NULL) {
5393: printf("Problem with forecast resultfile: %s\n", filerespop);
5394: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
5395: }
5396: printf("Computing forecasting: result on file '%s' \n", filerespop);
5397: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
5398:
5399: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5400:
5401: if (mobilav!=0) {
5402: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5403: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5404: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5405: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5406: }
5407: }
5408:
5409: stepsize=(int) (stepm+YEARM-1)/YEARM;
5410: if (stepm<=12) stepsize=1;
5411:
5412: agelim=AGESUP;
5413:
5414: hstepm=1;
5415: hstepm=hstepm/stepm;
5416:
5417: if (popforecast==1) {
5418: if((ficpop=fopen(popfile,"r"))==NULL) {
5419: printf("Problem with population file : %s\n",popfile);exit(0);
5420: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
5421: }
5422: popage=ivector(0,AGESUP);
5423: popeffectif=vector(0,AGESUP);
5424: popcount=vector(0,AGESUP);
5425:
5426: i=1;
5427: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
5428:
5429: imx=i;
5430: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
5431: }
5432:
5433: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
5434: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5435: k=k+1;
5436: fprintf(ficrespop,"\n#******");
5437: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 5438: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5439: }
5440: fprintf(ficrespop,"******\n");
5441: fprintf(ficrespop,"# Age");
5442: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
5443: if (popforecast==1) fprintf(ficrespop," [Population]");
5444:
5445: for (cpt=0; cpt<=0;cpt++) {
5446: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5447:
5448: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5449: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5450: nhstepm = nhstepm/hstepm;
5451:
5452: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5453: oldm=oldms;savm=savms;
5454: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5455:
5456: for (h=0; h<=nhstepm; h++){
5457: if (h==(int) (calagedatem+YEARM*cpt)) {
5458: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5459: }
5460: for(j=1; j<=nlstate+ndeath;j++) {
5461: kk1=0.;kk2=0;
5462: for(i=1; i<=nlstate;i++) {
5463: if (mobilav==1)
5464: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
5465: else {
5466: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
5467: }
5468: }
5469: if (h==(int)(calagedatem+12*cpt)){
5470: tabpop[(int)(agedeb)][j][cptcod]=kk1;
5471: /*fprintf(ficrespop," %.3f", kk1);
5472: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
5473: }
5474: }
5475: for(i=1; i<=nlstate;i++){
5476: kk1=0.;
5477: for(j=1; j<=nlstate;j++){
5478: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5479: }
5480: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5481: }
5482:
5483: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5484: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5485: }
5486: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5487: }
5488: }
5489:
5490: /******/
5491:
5492: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5493: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5494: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5495: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5496: nhstepm = nhstepm/hstepm;
5497:
5498: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5499: oldm=oldms;savm=savms;
5500: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5501: for (h=0; h<=nhstepm; h++){
5502: if (h==(int) (calagedatem+YEARM*cpt)) {
5503: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5504: }
5505: for(j=1; j<=nlstate+ndeath;j++) {
5506: kk1=0.;kk2=0;
5507: for(i=1; i<=nlstate;i++) {
5508: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5509: }
5510: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5511: }
5512: }
5513: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5514: }
5515: }
5516: }
5517: }
5518:
5519: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5520:
5521: if (popforecast==1) {
5522: free_ivector(popage,0,AGESUP);
5523: free_vector(popeffectif,0,AGESUP);
5524: free_vector(popcount,0,AGESUP);
5525: }
5526: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5527: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5528: fclose(ficrespop);
5529: } /* End of popforecast */
5530:
5531: int fileappend(FILE *fichier, char *optionfich)
5532: {
5533: if((fichier=fopen(optionfich,"a"))==NULL) {
5534: printf("Problem with file: %s\n", optionfich);
5535: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5536: return (0);
5537: }
5538: fflush(fichier);
5539: return (1);
5540: }
5541:
5542:
5543: /**************** function prwizard **********************/
5544: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
5545: {
5546:
5547: /* Wizard to print covariance matrix template */
5548:
1.164 brouard 5549: char ca[32], cb[32];
5550: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 5551: int numlinepar;
5552:
5553: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5554: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5555: for(i=1; i <=nlstate; i++){
5556: jj=0;
5557: for(j=1; j <=nlstate+ndeath; j++){
5558: if(j==i) continue;
5559: jj++;
5560: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5561: printf("%1d%1d",i,j);
5562: fprintf(ficparo,"%1d%1d",i,j);
5563: for(k=1; k<=ncovmodel;k++){
5564: /* printf(" %lf",param[i][j][k]); */
5565: /* fprintf(ficparo," %lf",param[i][j][k]); */
5566: printf(" 0.");
5567: fprintf(ficparo," 0.");
5568: }
5569: printf("\n");
5570: fprintf(ficparo,"\n");
5571: }
5572: }
5573: printf("# Scales (for hessian or gradient estimation)\n");
5574: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
5575: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
5576: for(i=1; i <=nlstate; i++){
5577: jj=0;
5578: for(j=1; j <=nlstate+ndeath; j++){
5579: if(j==i) continue;
5580: jj++;
5581: fprintf(ficparo,"%1d%1d",i,j);
5582: printf("%1d%1d",i,j);
5583: fflush(stdout);
5584: for(k=1; k<=ncovmodel;k++){
5585: /* printf(" %le",delti3[i][j][k]); */
5586: /* fprintf(ficparo," %le",delti3[i][j][k]); */
5587: printf(" 0.");
5588: fprintf(ficparo," 0.");
5589: }
5590: numlinepar++;
5591: printf("\n");
5592: fprintf(ficparo,"\n");
5593: }
5594: }
5595: printf("# Covariance matrix\n");
5596: /* # 121 Var(a12)\n\ */
5597: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5598: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5599: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5600: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5601: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5602: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5603: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5604: fflush(stdout);
5605: fprintf(ficparo,"# Covariance matrix\n");
5606: /* # 121 Var(a12)\n\ */
5607: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5608: /* # ...\n\ */
5609: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5610:
5611: for(itimes=1;itimes<=2;itimes++){
5612: jj=0;
5613: for(i=1; i <=nlstate; i++){
5614: for(j=1; j <=nlstate+ndeath; j++){
5615: if(j==i) continue;
5616: for(k=1; k<=ncovmodel;k++){
5617: jj++;
5618: ca[0]= k+'a'-1;ca[1]='\0';
5619: if(itimes==1){
5620: printf("#%1d%1d%d",i,j,k);
5621: fprintf(ficparo,"#%1d%1d%d",i,j,k);
5622: }else{
5623: printf("%1d%1d%d",i,j,k);
5624: fprintf(ficparo,"%1d%1d%d",i,j,k);
5625: /* printf(" %.5le",matcov[i][j]); */
5626: }
5627: ll=0;
5628: for(li=1;li <=nlstate; li++){
5629: for(lj=1;lj <=nlstate+ndeath; lj++){
5630: if(lj==li) continue;
5631: for(lk=1;lk<=ncovmodel;lk++){
5632: ll++;
5633: if(ll<=jj){
5634: cb[0]= lk +'a'-1;cb[1]='\0';
5635: if(ll<jj){
5636: if(itimes==1){
5637: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5638: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5639: }else{
5640: printf(" 0.");
5641: fprintf(ficparo," 0.");
5642: }
5643: }else{
5644: if(itimes==1){
5645: printf(" Var(%s%1d%1d)",ca,i,j);
5646: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5647: }else{
5648: printf(" 0.");
5649: fprintf(ficparo," 0.");
5650: }
5651: }
5652: }
5653: } /* end lk */
5654: } /* end lj */
5655: } /* end li */
5656: printf("\n");
5657: fprintf(ficparo,"\n");
5658: numlinepar++;
5659: } /* end k*/
5660: } /*end j */
5661: } /* end i */
5662: } /* end itimes */
5663:
5664: } /* end of prwizard */
5665: /******************* Gompertz Likelihood ******************************/
5666: double gompertz(double x[])
5667: {
5668: double A,B,L=0.0,sump=0.,num=0.;
5669: int i,n=0; /* n is the size of the sample */
5670:
5671: for (i=0;i<=imx-1 ; i++) {
5672: sump=sump+weight[i];
5673: /* sump=sump+1;*/
5674: num=num+1;
5675: }
5676:
5677:
5678: /* for (i=0; i<=imx; i++)
5679: 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]);*/
5680:
5681: for (i=1;i<=imx ; i++)
5682: {
5683: if (cens[i] == 1 && wav[i]>1)
5684: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5685:
5686: if (cens[i] == 0 && wav[i]>1)
5687: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5688: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5689:
5690: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5691: if (wav[i] > 1 ) { /* ??? */
5692: L=L+A*weight[i];
5693: /* 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]);*/
5694: }
5695: }
5696:
5697: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5698:
5699: return -2*L*num/sump;
5700: }
5701:
1.136 brouard 5702: #ifdef GSL
5703: /******************* Gompertz_f Likelihood ******************************/
5704: double gompertz_f(const gsl_vector *v, void *params)
5705: {
5706: double A,B,LL=0.0,sump=0.,num=0.;
5707: double *x= (double *) v->data;
5708: int i,n=0; /* n is the size of the sample */
5709:
5710: for (i=0;i<=imx-1 ; i++) {
5711: sump=sump+weight[i];
5712: /* sump=sump+1;*/
5713: num=num+1;
5714: }
5715:
5716:
5717: /* for (i=0; i<=imx; i++)
5718: 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]);*/
5719: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5720: for (i=1;i<=imx ; i++)
5721: {
5722: if (cens[i] == 1 && wav[i]>1)
5723: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5724:
5725: if (cens[i] == 0 && wav[i]>1)
5726: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5727: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5728:
5729: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5730: if (wav[i] > 1 ) { /* ??? */
5731: LL=LL+A*weight[i];
5732: /* 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]);*/
5733: }
5734: }
5735:
5736: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5737: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5738:
5739: return -2*LL*num/sump;
5740: }
5741: #endif
5742:
1.126 brouard 5743: /******************* Printing html file ***********/
1.201 brouard 5744: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 5745: int lastpass, int stepm, int weightopt, char model[],\
5746: int imx, double p[],double **matcov,double agemortsup){
5747: int i,k;
5748:
5749: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5750: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5751: for (i=1;i<=2;i++)
5752: 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 5753: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 5754: fprintf(fichtm,"</ul>");
5755:
5756: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5757:
5758: 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>");
5759:
5760: for (k=agegomp;k<(agemortsup-2);k++)
5761: 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]);
5762:
5763:
5764: fflush(fichtm);
5765: }
5766:
5767: /******************* Gnuplot file **************/
1.201 brouard 5768: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 5769:
5770: char dirfileres[132],optfileres[132];
1.164 brouard 5771:
1.126 brouard 5772: int ng;
5773:
5774:
5775: /*#ifdef windows */
5776: fprintf(ficgp,"cd \"%s\" \n",pathc);
5777: /*#endif */
5778:
5779:
5780: strcpy(dirfileres,optionfilefiname);
5781: strcpy(optfileres,"vpl");
1.199 brouard 5782: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 5783: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 5784: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 5785: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 5786: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5787:
5788: }
5789:
1.136 brouard 5790: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5791: {
1.126 brouard 5792:
1.136 brouard 5793: /*-------- data file ----------*/
5794: FILE *fic;
5795: char dummy[]=" ";
1.164 brouard 5796: int i=0, j=0, n=0;
1.136 brouard 5797: int linei, month, year,iout;
5798: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 5799: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 5800: char *stratrunc;
5801: int lstra;
1.126 brouard 5802:
5803:
1.136 brouard 5804: if((fic=fopen(datafile,"r"))==NULL) {
1.195 brouard 5805: printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
5806: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
1.136 brouard 5807: }
1.126 brouard 5808:
1.136 brouard 5809: i=1;
5810: linei=0;
5811: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5812: linei=linei+1;
5813: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5814: if(line[j] == '\t')
5815: line[j] = ' ';
5816: }
5817: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5818: ;
5819: };
5820: line[j+1]=0; /* Trims blanks at end of line */
5821: if(line[0]=='#'){
5822: fprintf(ficlog,"Comment line\n%s\n",line);
5823: printf("Comment line\n%s\n",line);
5824: continue;
5825: }
5826: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 5827: strcpy(line, linetmp);
1.136 brouard 5828:
1.126 brouard 5829:
1.136 brouard 5830: for (j=maxwav;j>=1;j--){
1.137 brouard 5831: cutv(stra, strb, line, ' ');
1.136 brouard 5832: if(strb[0]=='.') { /* Missing status */
5833: lval=-1;
5834: }else{
5835: errno=0;
5836: lval=strtol(strb,&endptr,10);
5837: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5838: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5839: 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);
5840: 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 5841: return 1;
5842: }
5843: }
5844: s[j][i]=lval;
5845:
5846: strcpy(line,stra);
5847: cutv(stra, strb,line,' ');
1.169 brouard 5848: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5849: }
1.169 brouard 5850: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5851: month=99;
5852: year=9999;
5853: }else{
1.141 brouard 5854: 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);
5855: 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 5856: return 1;
5857: }
5858: anint[j][i]= (double) year;
5859: mint[j][i]= (double)month;
5860: strcpy(line,stra);
5861: } /* ENd Waves */
5862:
5863: cutv(stra, strb,line,' ');
1.169 brouard 5864: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5865: }
1.169 brouard 5866: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5867: month=99;
5868: year=9999;
5869: }else{
1.141 brouard 5870: 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);
5871: 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 5872: return 1;
5873: }
5874: andc[i]=(double) year;
5875: moisdc[i]=(double) month;
5876: strcpy(line,stra);
5877:
5878: cutv(stra, strb,line,' ');
1.169 brouard 5879: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5880: }
1.169 brouard 5881: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 5882: month=99;
5883: year=9999;
5884: }else{
1.141 brouard 5885: 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);
5886: 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 5887: return 1;
5888: }
5889: if (year==9999) {
1.141 brouard 5890: 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);
5891: 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 5892: return 1;
1.126 brouard 5893:
1.136 brouard 5894: }
5895: annais[i]=(double)(year);
5896: moisnais[i]=(double)(month);
5897: strcpy(line,stra);
5898:
5899: cutv(stra, strb,line,' ');
5900: errno=0;
5901: dval=strtod(strb,&endptr);
5902: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5903: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5904: 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 5905: fflush(ficlog);
5906: return 1;
5907: }
5908: weight[i]=dval;
5909: strcpy(line,stra);
5910:
5911: for (j=ncovcol;j>=1;j--){
5912: cutv(stra, strb,line,' ');
5913: if(strb[0]=='.') { /* Missing status */
5914: lval=-1;
5915: }else{
5916: errno=0;
5917: lval=strtol(strb,&endptr,10);
5918: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5919: 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);
5920: 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 5921: return 1;
5922: }
5923: }
5924: if(lval <-1 || lval >1){
1.141 brouard 5925: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5926: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5927: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5928: For example, for multinomial values like 1, 2 and 3,\n \
5929: build V1=0 V2=0 for the reference value (1),\n \
5930: V1=1 V2=0 for (2) \n \
5931: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5932: output of IMaCh is often meaningless.\n \
5933: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 5934: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5935: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5936: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5937: For example, for multinomial values like 1, 2 and 3,\n \
5938: build V1=0 V2=0 for the reference value (1),\n \
5939: V1=1 V2=0 for (2) \n \
5940: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5941: output of IMaCh is often meaningless.\n \
5942: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5943: return 1;
5944: }
5945: covar[j][i]=(double)(lval);
5946: strcpy(line,stra);
5947: }
5948: lstra=strlen(stra);
5949:
5950: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5951: stratrunc = &(stra[lstra-9]);
5952: num[i]=atol(stratrunc);
5953: }
5954: else
5955: num[i]=atol(stra);
5956: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5957: 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;}*/
5958:
5959: i=i+1;
5960: } /* End loop reading data */
1.126 brouard 5961:
1.136 brouard 5962: *imax=i-1; /* Number of individuals */
5963: fclose(fic);
5964:
5965: return (0);
1.164 brouard 5966: /* endread: */
1.136 brouard 5967: printf("Exiting readdata: ");
5968: fclose(fic);
5969: return (1);
1.126 brouard 5970:
5971:
5972:
1.136 brouard 5973: }
1.145 brouard 5974: void removespace(char *str) {
5975: char *p1 = str, *p2 = str;
5976: do
5977: while (*p2 == ' ')
5978: p2++;
1.169 brouard 5979: while (*p1++ == *p2++);
1.145 brouard 5980: }
5981:
5982: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 5983: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
5984: * - nagesqr = 1 if age*age in the model, otherwise 0.
5985: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
5986: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 5987: * - cptcovage number of covariates with age*products =2
5988: * - cptcovs number of simple covariates
5989: * - 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
5990: * which is a new column after the 9 (ncovcol) variables.
5991: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5992: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5993: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5994: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5995: */
1.136 brouard 5996: {
1.145 brouard 5997: int i, j, k, ks;
1.164 brouard 5998: int j1, k1, k2;
1.136 brouard 5999: char modelsav[80];
1.145 brouard 6000: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 6001: char *strpt;
1.136 brouard 6002:
1.145 brouard 6003: /*removespace(model);*/
1.136 brouard 6004: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 6005: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 6006: if (strstr(model,"AGE") !=0){
1.192 brouard 6007: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
6008: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 6009: return 1;
6010: }
1.141 brouard 6011: if (strstr(model,"v") !=0){
6012: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
6013: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
6014: return 1;
6015: }
1.187 brouard 6016: strcpy(modelsav,model);
6017: if ((strpt=strstr(model,"age*age")) !=0){
6018: printf(" strpt=%s, model=%s\n",strpt, model);
6019: if(strpt != model){
6020: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 6021: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 6022: corresponding column of parameters.\n",model);
6023: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 6024: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 6025: corresponding column of parameters.\n",model); fflush(ficlog);
6026: return 1;
6027: }
6028:
6029: nagesqr=1;
6030: if (strstr(model,"+age*age") !=0)
6031: substrchaine(modelsav, model, "+age*age");
6032: else if (strstr(model,"age*age+") !=0)
6033: substrchaine(modelsav, model, "age*age+");
6034: else
6035: substrchaine(modelsav, model, "age*age");
6036: }else
6037: nagesqr=0;
6038: if (strlen(modelsav) >1){
6039: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
6040: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
6041: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
6042: cptcovt= j+1; /* Number of total covariates in the model, not including
6043: * cst, age and age*age
6044: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
6045: /* including age products which are counted in cptcovage.
6046: * but the covariates which are products must be treated
6047: * separately: ncovn=4- 2=2 (V1+V3). */
6048: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
6049: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
6050:
6051:
6052: /* Design
6053: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
6054: * < ncovcol=8 >
6055: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
6056: * k= 1 2 3 4 5 6 7 8
6057: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
6058: * covar[k,i], value of kth covariate if not including age for individual i:
6059: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
6060: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
6061: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
6062: * Tage[++cptcovage]=k
6063: * if products, new covar are created after ncovcol with k1
6064: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
6065: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
6066: * 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
6067: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
6068: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
6069: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
6070: * < ncovcol=8 >
6071: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
6072: * k= 1 2 3 4 5 6 7 8 9 10 11 12
6073: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
6074: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
6075: * p Tprod[1]@2={ 6, 5}
6076: *p Tvard[1][1]@4= {7, 8, 5, 6}
6077: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
6078: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
6079: *How to reorganize?
6080: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
6081: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
6082: * {2, 1, 4, 8, 5, 6, 3, 7}
6083: * Struct []
6084: */
1.145 brouard 6085:
1.187 brouard 6086: /* This loop fills the array Tvar from the string 'model'.*/
6087: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
6088: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
6089: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
6090: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
6091: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
6092: /* k=1 Tvar[1]=2 (from V2) */
6093: /* k=5 Tvar[5] */
6094: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 6095: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 6096: /* } */
1.198 brouard 6097: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 6098: /*
6099: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
6100: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 6101: Tvar[k]=0;
1.187 brouard 6102: cptcovage=0;
6103: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
6104: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
6105: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
6106: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
6107: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
6108: /*scanf("%d",i);*/
6109: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
6110: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
6111: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
6112: /* covar is not filled and then is empty */
6113: cptcovprod--;
6114: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
6115: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
6116: cptcovage++; /* Sums the number of covariates which include age as a product */
6117: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
6118: /*printf("stre=%s ", stre);*/
6119: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
6120: cptcovprod--;
6121: cutl(stre,strb,strc,'V');
6122: Tvar[k]=atoi(stre);
6123: cptcovage++;
6124: Tage[cptcovage]=k;
6125: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
6126: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
6127: cptcovn++;
6128: cptcovprodnoage++;k1++;
6129: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
6130: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
6131: because this model-covariate is a construction we invent a new column
6132: ncovcol + k1
6133: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
6134: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
6135: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
6136: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
6137: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
6138: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
6139: k2=k2+2;
6140: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
6141: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
6142: for (i=1; i<=lastobs;i++){
6143: /* Computes the new covariate which is a product of
6144: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
6145: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
6146: }
6147: } /* End age is not in the model */
6148: } /* End if model includes a product */
6149: else { /* no more sum */
6150: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
6151: /* scanf("%d",i);*/
6152: cutl(strd,strc,strb,'V');
6153: ks++; /**< Number of simple covariates */
1.145 brouard 6154: cptcovn++;
1.187 brouard 6155: Tvar[k]=atoi(strd);
6156: }
6157: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
6158: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
6159: scanf("%d",i);*/
6160: } /* end of loop + on total covariates */
6161: } /* end if strlen(modelsave == 0) age*age might exist */
6162: } /* end if strlen(model == 0) */
1.136 brouard 6163:
6164: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
6165: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
6166:
6167: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
6168: printf("cptcovprod=%d ", cptcovprod);
6169: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
6170:
6171: scanf("%d ",i);*/
6172:
6173:
1.137 brouard 6174: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 6175: /*endread:*/
1.136 brouard 6176: printf("Exiting decodemodel: ");
6177: return (1);
6178: }
6179:
1.169 brouard 6180: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 6181: {
6182: int i, m;
6183:
6184: for (i=1; i<=imx; i++) {
6185: for(m=2; (m<= maxwav); m++) {
6186: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
6187: anint[m][i]=9999;
6188: s[m][i]=-1;
6189: }
6190: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 6191: *nberr = *nberr + 1;
6192: 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);
6193: 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 6194: s[m][i]=-1;
6195: }
6196: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 6197: (*nberr)++;
1.136 brouard 6198: 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]);
6199: 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]);
6200: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
6201: }
6202: }
6203: }
6204:
6205: for (i=1; i<=imx; i++) {
6206: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
6207: for(m=firstpass; (m<= lastpass); m++){
6208: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
6209: if (s[m][i] >= nlstate+1) {
1.169 brouard 6210: if(agedc[i]>0){
6211: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 6212: agev[m][i]=agedc[i];
6213: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 6214: }else {
1.136 brouard 6215: if ((int)andc[i]!=9999){
6216: nbwarn++;
6217: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
6218: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
6219: agev[m][i]=-1;
6220: }
6221: }
1.169 brouard 6222: } /* agedc > 0 */
1.136 brouard 6223: }
6224: else if(s[m][i] !=9){ /* Standard case, age in fractional
6225: years but with the precision of a month */
6226: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
6227: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
6228: agev[m][i]=1;
6229: else if(agev[m][i] < *agemin){
6230: *agemin=agev[m][i];
6231: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
6232: }
6233: else if(agev[m][i] >*agemax){
6234: *agemax=agev[m][i];
1.156 brouard 6235: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 6236: }
6237: /*agev[m][i]=anint[m][i]-annais[i];*/
6238: /* agev[m][i] = age[i]+2*m;*/
6239: }
6240: else { /* =9 */
6241: agev[m][i]=1;
6242: s[m][i]=-1;
6243: }
6244: }
6245: else /*= 0 Unknown */
6246: agev[m][i]=1;
6247: }
6248:
6249: }
6250: for (i=1; i<=imx; i++) {
6251: for(m=firstpass; (m<=lastpass); m++){
6252: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 6253: (*nberr)++;
1.136 brouard 6254: 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);
6255: 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);
6256: return 1;
6257: }
6258: }
6259: }
6260:
6261: /*for (i=1; i<=imx; i++){
6262: for (m=firstpass; (m<lastpass); m++){
6263: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
6264: }
6265:
6266: }*/
6267:
6268:
1.139 brouard 6269: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
6270: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 6271:
6272: return (0);
1.164 brouard 6273: /* endread:*/
1.136 brouard 6274: printf("Exiting calandcheckages: ");
6275: return (1);
6276: }
6277:
1.172 brouard 6278: #if defined(_MSC_VER)
6279: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6280: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6281: //#include "stdafx.h"
6282: //#include <stdio.h>
6283: //#include <tchar.h>
6284: //#include <windows.h>
6285: //#include <iostream>
6286: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
6287:
6288: LPFN_ISWOW64PROCESS fnIsWow64Process;
6289:
6290: BOOL IsWow64()
6291: {
6292: BOOL bIsWow64 = FALSE;
6293:
6294: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
6295: // (HANDLE, PBOOL);
6296:
6297: //LPFN_ISWOW64PROCESS fnIsWow64Process;
6298:
6299: HMODULE module = GetModuleHandle(_T("kernel32"));
6300: const char funcName[] = "IsWow64Process";
6301: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
6302: GetProcAddress(module, funcName);
6303:
6304: if (NULL != fnIsWow64Process)
6305: {
6306: if (!fnIsWow64Process(GetCurrentProcess(),
6307: &bIsWow64))
6308: //throw std::exception("Unknown error");
6309: printf("Unknown error\n");
6310: }
6311: return bIsWow64 != FALSE;
6312: }
6313: #endif
1.177 brouard 6314:
1.191 brouard 6315: void syscompilerinfo(int logged)
1.167 brouard 6316: {
6317: /* #include "syscompilerinfo.h"*/
1.185 brouard 6318: /* command line Intel compiler 32bit windows, XP compatible:*/
6319: /* /GS /W3 /Gy
6320: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
6321: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
6322: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 6323: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
6324: */
6325: /* 64 bits */
1.185 brouard 6326: /*
6327: /GS /W3 /Gy
6328: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
6329: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
6330: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
6331: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
6332: /* Optimization are useless and O3 is slower than O2 */
6333: /*
6334: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
6335: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
6336: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
6337: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
6338: */
1.186 brouard 6339: /* Link is */ /* /OUT:"visual studio
1.185 brouard 6340: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
6341: /PDB:"visual studio
6342: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
6343: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
6344: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
6345: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
6346: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
6347: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
6348: uiAccess='false'"
6349: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
6350: /NOLOGO /TLBID:1
6351: */
1.177 brouard 6352: #if defined __INTEL_COMPILER
1.178 brouard 6353: #if defined(__GNUC__)
6354: struct utsname sysInfo; /* For Intel on Linux and OS/X */
6355: #endif
1.177 brouard 6356: #elif defined(__GNUC__)
1.179 brouard 6357: #ifndef __APPLE__
1.174 brouard 6358: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 6359: #endif
1.177 brouard 6360: struct utsname sysInfo;
1.178 brouard 6361: int cross = CROSS;
6362: if (cross){
6363: printf("Cross-");
1.191 brouard 6364: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 6365: }
1.174 brouard 6366: #endif
6367:
1.171 brouard 6368: #include <stdint.h>
1.178 brouard 6369:
1.191 brouard 6370: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 6371: #if defined(__clang__)
1.191 brouard 6372: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 6373: #endif
6374: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 6375: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 6376: #endif
6377: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 6378: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 6379: #endif
6380: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 6381: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 6382: #endif
6383: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 6384: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 6385: #endif
6386: #if defined(_MSC_VER)
1.191 brouard 6387: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 6388: #endif
6389: #if defined(__PGI)
1.191 brouard 6390: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 6391: #endif
6392: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 6393: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 6394: #endif
1.191 brouard 6395: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 6396:
1.167 brouard 6397: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
6398: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
6399: // Windows (x64 and x86)
1.191 brouard 6400: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 6401: #elif __unix__ // all unices, not all compilers
6402: // Unix
1.191 brouard 6403: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 6404: #elif __linux__
6405: // linux
1.191 brouard 6406: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 6407: #elif __APPLE__
1.174 brouard 6408: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 6409: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 6410: #endif
6411:
6412: /* __MINGW32__ */
6413: /* __CYGWIN__ */
6414: /* __MINGW64__ */
6415: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
6416: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
6417: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
6418: /* _WIN64 // Defined for applications for Win64. */
6419: /* _M_X64 // Defined for compilations that target x64 processors. */
6420: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 6421:
1.167 brouard 6422: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 6423: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 6424: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 6425: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 6426: #else
1.191 brouard 6427: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 6428: #endif
6429:
1.169 brouard 6430: #if defined(__GNUC__)
6431: # if defined(__GNUC_PATCHLEVEL__)
6432: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6433: + __GNUC_MINOR__ * 100 \
6434: + __GNUC_PATCHLEVEL__)
6435: # else
6436: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6437: + __GNUC_MINOR__ * 100)
6438: # endif
1.174 brouard 6439: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 6440: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 6441:
6442: if (uname(&sysInfo) != -1) {
6443: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 6444: 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 6445: }
6446: else
6447: perror("uname() error");
1.179 brouard 6448: //#ifndef __INTEL_COMPILER
6449: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 6450: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 6451: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 6452: #endif
1.169 brouard 6453: #endif
1.172 brouard 6454:
6455: // void main()
6456: // {
1.169 brouard 6457: #if defined(_MSC_VER)
1.174 brouard 6458: if (IsWow64()){
1.191 brouard 6459: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6460: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 6461: }
6462: else{
1.191 brouard 6463: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
6464: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 6465: }
1.172 brouard 6466: // printf("\nPress Enter to continue...");
6467: // getchar();
6468: // }
6469:
1.169 brouard 6470: #endif
6471:
1.167 brouard 6472:
6473: }
1.136 brouard 6474:
1.203 brouard 6475: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyear){
1.180 brouard 6476: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6477: int i, j, k, i1 ;
1.202 brouard 6478: /* double ftolpl = 1.e-10; */
1.180 brouard 6479: double age, agebase, agelim;
1.203 brouard 6480: double tot;
1.180 brouard 6481:
1.202 brouard 6482: strcpy(filerespl,"PL_");
6483: strcat(filerespl,fileresu);
6484: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6485: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6486: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6487: }
6488: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6489: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6490: pstamp(ficrespl);
1.203 brouard 6491: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 6492: fprintf(ficrespl,"#Age ");
6493: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6494: fprintf(ficrespl,"\n");
1.180 brouard 6495:
6496: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6497:
6498: agebase=ageminpar;
6499: agelim=agemaxpar;
6500:
6501: i1=pow(2,cptcoveff);
6502: if (cptcovn < 1){i1=1;}
6503:
6504: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6505: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6506: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6507: k=k+1;
6508: /* to clean */
1.198 brouard 6509: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
1.200 brouard 6510: fprintf(ficrespl,"#******");
6511: printf("#******");
6512: fprintf(ficlog,"#******");
1.180 brouard 6513: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 6514: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6515: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6516: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6517: }
6518: fprintf(ficrespl,"******\n");
6519: printf("******\n");
6520: fprintf(ficlog,"******\n");
6521:
6522: fprintf(ficrespl,"#Age ");
6523: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 6524: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6525: }
1.203 brouard 6526: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
6527: fprintf(ficrespl,"Total Years_to_converge\n");
1.180 brouard 6528:
6529: for (age=agebase; age<=agelim; age++){
6530: /* for (age=agebase; age<=agebase; age++){ */
1.203 brouard 6531: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k);
1.180 brouard 6532: fprintf(ficrespl,"%.0f ",age );
6533: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6534: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.203 brouard 6535: tot=0.;
6536: for(i=1; i<=nlstate;i++){
6537: tot += prlim[i][i];
1.180 brouard 6538: fprintf(ficrespl," %.5f", prlim[i][i]);
1.203 brouard 6539: }
6540: fprintf(ficrespl," %.3f %d\n", tot, *ncvyear);
1.180 brouard 6541: } /* Age */
6542: /* was end of cptcod */
6543: } /* cptcov */
1.184 brouard 6544: return 0;
1.180 brouard 6545: }
6546:
6547: int hPijx(double *p, int bage, int fage){
6548: /*------------- h Pij x at various ages ------------*/
6549:
6550: int stepsize;
6551: int agelim;
6552: int hstepm;
6553: int nhstepm;
6554: int h, i, i1, j, k;
6555:
6556: double agedeb;
6557: double ***p3mat;
6558:
1.201 brouard 6559: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 6560: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6561: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
6562: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
6563: }
6564: printf("Computing pij: result on file '%s' \n", filerespij);
6565: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6566:
6567: stepsize=(int) (stepm+YEARM-1)/YEARM;
6568: /*if (stepm<=24) stepsize=2;*/
6569:
6570: agelim=AGESUP;
6571: hstepm=stepsize*YEARM; /* Every year of age */
6572: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6573:
6574: /* hstepm=1; aff par mois*/
6575: pstamp(ficrespij);
6576: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6577: i1= pow(2,cptcoveff);
1.183 brouard 6578: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
6579: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
6580: /* k=k+1; */
6581: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6582: fprintf(ficrespij,"\n#****** ");
6583: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6584: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.183 brouard 6585: fprintf(ficrespij,"******\n");
6586:
6587: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6588: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6589: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6590:
6591: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 6592:
1.183 brouard 6593: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6594: oldm=oldms;savm=savms;
6595: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6596: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6597: for(i=1; i<=nlstate;i++)
6598: for(j=1; j<=nlstate+ndeath;j++)
6599: fprintf(ficrespij," %1d-%1d",i,j);
6600: fprintf(ficrespij,"\n");
6601: for (h=0; h<=nhstepm; h++){
6602: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
6603: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 6604: for(i=1; i<=nlstate;i++)
6605: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 6606: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 6607: fprintf(ficrespij,"\n");
6608: }
1.183 brouard 6609: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6610: fprintf(ficrespij,"\n");
6611: }
1.180 brouard 6612: /*}*/
6613: }
1.184 brouard 6614: return 0;
1.180 brouard 6615: }
6616:
6617:
1.136 brouard 6618: /***********************************************/
6619: /**************** Main Program *****************/
6620: /***********************************************/
6621:
6622: int main(int argc, char *argv[])
6623: {
6624: #ifdef GSL
6625: const gsl_multimin_fminimizer_type *T;
6626: size_t iteri = 0, it;
6627: int rval = GSL_CONTINUE;
6628: int status = GSL_SUCCESS;
6629: double ssval;
6630: #endif
6631: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 6632: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.203 brouard 6633: int ncvyearnp=0;
6634: int *ncvyear=&ncvyearnp; /* Number of years needed for the period prevalence to converge */
1.164 brouard 6635: int jj, ll, li, lj, lk;
1.136 brouard 6636: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 6637: int num_filled;
1.136 brouard 6638: int itimes;
6639: int NDIM=2;
6640: int vpopbased=0;
6641:
1.164 brouard 6642: char ca[32], cb[32];
1.136 brouard 6643: /* FILE *fichtm; *//* Html File */
6644: /* FILE *ficgp;*/ /*Gnuplot File */
6645: struct stat info;
1.191 brouard 6646: double agedeb=0.;
1.194 brouard 6647:
6648: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.136 brouard 6649:
1.165 brouard 6650: double fret;
1.191 brouard 6651: double dum=0.; /* Dummy variable */
1.136 brouard 6652: double ***p3mat;
6653: double ***mobaverage;
1.164 brouard 6654:
6655: char line[MAXLINE];
1.197 brouard 6656: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
6657:
6658: char model[MAXLINE], modeltemp[MAXLINE];
1.136 brouard 6659: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 6660: char *tok, *val; /* pathtot */
1.136 brouard 6661: int firstobs=1, lastobs=10;
1.195 brouard 6662: int c, h , cpt, c2;
1.191 brouard 6663: int jl=0;
6664: int i1, j1, jk, stepsize=0;
1.194 brouard 6665: int count=0;
6666:
1.164 brouard 6667: int *tab;
1.136 brouard 6668: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
6669: int mobilav=0,popforecast=0;
1.191 brouard 6670: int hstepm=0, nhstepm=0;
1.136 brouard 6671: int agemortsup;
6672: float sumlpop=0.;
6673: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
6674: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
6675:
1.191 brouard 6676: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 6677: double ftolpl=FTOL;
6678: double **prlim;
6679: double ***param; /* Matrix of parameters */
6680: double *p;
6681: double **matcov; /* Matrix of covariance */
1.203 brouard 6682: double **hess; /* Hessian matrix */
1.136 brouard 6683: double ***delti3; /* Scale */
6684: double *delti; /* Scale */
6685: double ***eij, ***vareij;
6686: double **varpl; /* Variances of prevalence limits by age */
6687: double *epj, vepp;
1.164 brouard 6688:
1.136 brouard 6689: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6690: double **ximort;
1.145 brouard 6691: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 6692: int *dcwave;
6693:
1.164 brouard 6694: char z[1]="c";
1.136 brouard 6695:
6696: /*char *strt;*/
6697: char strtend[80];
1.126 brouard 6698:
1.164 brouard 6699:
1.126 brouard 6700: /* setlocale (LC_ALL, ""); */
6701: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6702: /* textdomain (PACKAGE); */
6703: /* setlocale (LC_CTYPE, ""); */
6704: /* setlocale (LC_MESSAGES, ""); */
6705:
6706: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 6707: rstart_time = time(NULL);
6708: /* (void) gettimeofday(&start_time,&tzp);*/
6709: start_time = *localtime(&rstart_time);
1.126 brouard 6710: curr_time=start_time;
1.157 brouard 6711: /*tml = *localtime(&start_time.tm_sec);*/
6712: /* strcpy(strstart,asctime(&tml)); */
6713: strcpy(strstart,asctime(&start_time));
1.126 brouard 6714:
6715: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 6716: /* tp.tm_sec = tp.tm_sec +86400; */
6717: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 6718: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6719: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6720: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 6721: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 6722: /* strt=asctime(&tmg); */
6723: /* printf("Time(after) =%s",strstart); */
6724: /* (void) time (&time_value);
6725: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6726: * tm = *localtime(&time_value);
6727: * strstart=asctime(&tm);
6728: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6729: */
6730:
6731: nberr=0; /* Number of errors and warnings */
6732: nbwarn=0;
1.184 brouard 6733: #ifdef WIN32
6734: _getcwd(pathcd, size);
6735: #else
1.126 brouard 6736: getcwd(pathcd, size);
1.184 brouard 6737: #endif
1.191 brouard 6738: syscompilerinfo(0);
1.196 brouard 6739: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 6740: if(argc <=1){
6741: printf("\nEnter the parameter file name: ");
6742: fgets(pathr,FILENAMELENGTH,stdin);
6743: i=strlen(pathr);
6744: if(pathr[i-1]=='\n')
6745: pathr[i-1]='\0';
1.156 brouard 6746: i=strlen(pathr);
6747: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
6748: pathr[i-1]='\0';
1.126 brouard 6749: for (tok = pathr; tok != NULL; ){
6750: printf("Pathr |%s|\n",pathr);
6751: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6752: printf("val= |%s| pathr=%s\n",val,pathr);
6753: strcpy (pathtot, val);
6754: if(pathr[0] == '\0') break; /* Dirty */
6755: }
6756: }
6757: else{
6758: strcpy(pathtot,argv[1]);
6759: }
6760: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6761: /*cygwin_split_path(pathtot,path,optionfile);
6762: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6763: /* cutv(path,optionfile,pathtot,'\\');*/
6764:
6765: /* Split argv[0], imach program to get pathimach */
6766: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6767: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6768: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6769: /* strcpy(pathimach,argv[0]); */
6770: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6771: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6772: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 6773: #ifdef WIN32
6774: _chdir(path); /* Can be a relative path */
6775: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
6776: #else
1.126 brouard 6777: chdir(path); /* Can be a relative path */
1.184 brouard 6778: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
6779: #endif
6780: printf("Current directory %s!\n",pathcd);
1.126 brouard 6781: strcpy(command,"mkdir ");
6782: strcat(command,optionfilefiname);
6783: if((outcmd=system(command)) != 0){
1.169 brouard 6784: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 6785: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6786: /* fclose(ficlog); */
6787: /* exit(1); */
6788: }
6789: /* if((imk=mkdir(optionfilefiname))<0){ */
6790: /* perror("mkdir"); */
6791: /* } */
6792:
6793: /*-------- arguments in the command line --------*/
6794:
1.186 brouard 6795: /* Main Log file */
1.126 brouard 6796: strcat(filelog, optionfilefiname);
6797: strcat(filelog,".log"); /* */
6798: if((ficlog=fopen(filelog,"w"))==NULL) {
6799: printf("Problem with logfile %s\n",filelog);
6800: goto end;
6801: }
6802: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 6803: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 6804: fprintf(ficlog,"\nEnter the parameter file name: \n");
6805: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6806: path=%s \n\
6807: optionfile=%s\n\
6808: optionfilext=%s\n\
1.156 brouard 6809: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 6810:
1.197 brouard 6811: syscompilerinfo(1);
1.167 brouard 6812:
1.126 brouard 6813: printf("Local time (at start):%s",strstart);
6814: fprintf(ficlog,"Local time (at start): %s",strstart);
6815: fflush(ficlog);
6816: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 6817: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 6818:
6819: /* */
6820: strcpy(fileres,"r");
6821: strcat(fileres, optionfilefiname);
1.201 brouard 6822: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 6823: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 6824: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 6825:
1.186 brouard 6826: /* Main ---------arguments file --------*/
1.126 brouard 6827:
6828: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 6829: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6830: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 6831: fflush(ficlog);
1.149 brouard 6832: /* goto end; */
6833: exit(70);
1.126 brouard 6834: }
6835:
6836:
6837:
6838: strcpy(filereso,"o");
1.201 brouard 6839: strcat(filereso,fileresu);
1.126 brouard 6840: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6841: printf("Problem with Output resultfile: %s\n", filereso);
6842: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6843: fflush(ficlog);
6844: goto end;
6845: }
6846:
6847: /* Reads comments: lines beginning with '#' */
6848: numlinepar=0;
1.197 brouard 6849:
6850: /* First parameter line */
6851: while(fgets(line, MAXLINE, ficpar)) {
6852: /* If line starts with a # it is a comment */
6853: if (line[0] == '#') {
6854: numlinepar++;
6855: fputs(line,stdout);
6856: fputs(line,ficparo);
6857: fputs(line,ficlog);
6858: continue;
6859: }else
6860: break;
6861: }
6862: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
6863: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
6864: if (num_filled != 5) {
6865: printf("Should be 5 parameters\n");
6866: }
1.126 brouard 6867: numlinepar++;
1.197 brouard 6868: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
6869: }
6870: /* Second parameter line */
6871: while(fgets(line, MAXLINE, ficpar)) {
6872: /* If line starts with a # it is a comment */
6873: if (line[0] == '#') {
6874: numlinepar++;
6875: fputs(line,stdout);
6876: fputs(line,ficparo);
6877: fputs(line,ficlog);
6878: continue;
6879: }else
6880: break;
6881: }
6882: if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
6883: &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
6884: if (num_filled != 8) {
6885: printf("Not 8\n");
6886: }
6887: 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 6888: }
1.203 brouard 6889: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
6890: ftolpl=6.e-3; /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 6891: /* Third parameter line */
6892: while(fgets(line, MAXLINE, ficpar)) {
6893: /* If line starts with a # it is a comment */
6894: if (line[0] == '#') {
6895: numlinepar++;
6896: fputs(line,stdout);
6897: fputs(line,ficparo);
6898: fputs(line,ficlog);
6899: continue;
6900: }else
6901: break;
6902: }
1.201 brouard 6903: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
6904: if (num_filled == 0)
6905: model[0]='\0';
6906: else if (num_filled != 1){
1.197 brouard 6907: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
6908: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
6909: model[0]='\0';
6910: goto end;
6911: }
6912: else{
6913: if (model[0]=='+'){
6914: for(i=1; i<=strlen(model);i++)
6915: modeltemp[i-1]=model[i];
1.201 brouard 6916: strcpy(model,modeltemp);
1.197 brouard 6917: }
6918: }
1.199 brouard 6919: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 6920: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 6921: }
6922: /* 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); */
6923: /* numlinepar=numlinepar+3; /\* In general *\/ */
6924: /* 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 6925: 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);
6926: 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 6927: fflush(ficlog);
1.190 brouard 6928: /* if(model[0]=='#'|| model[0]== '\0'){ */
6929: if(model[0]=='#'){
1.187 brouard 6930: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
6931: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
6932: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
6933: if(mle != -1){
6934: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
6935: exit(1);
6936: }
6937: }
1.126 brouard 6938: while((c=getc(ficpar))=='#' && c!= EOF){
6939: ungetc(c,ficpar);
6940: fgets(line, MAXLINE, ficpar);
6941: numlinepar++;
1.195 brouard 6942: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
6943: z[0]=line[1];
6944: }
6945: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 6946: fputs(line, stdout);
6947: //puts(line);
1.126 brouard 6948: fputs(line,ficparo);
6949: fputs(line,ficlog);
6950: }
6951: ungetc(c,ficpar);
6952:
6953:
1.145 brouard 6954: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 6955: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
6956: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
6957: v1+v2*age+v2*v3 makes cptcovn = 3
6958: */
6959: if (strlen(model)>1)
1.187 brouard 6960: 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 6961: else
1.187 brouard 6962: ncovmodel=2; /* Constant and age */
1.133 brouard 6963: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
6964: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 6965: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
6966: 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);
6967: 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);
6968: fflush(stdout);
6969: fclose (ficlog);
6970: goto end;
6971: }
1.126 brouard 6972: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6973: delti=delti3[1][1];
6974: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
6975: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
6976: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 6977: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6978: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 6979: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6980: fclose (ficparo);
6981: fclose (ficlog);
6982: goto end;
6983: exit(0);
6984: }
1.186 brouard 6985: else if(mle==-3) { /* Main Wizard */
1.126 brouard 6986: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 6987: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6988: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 6989: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6990: matcov=matrix(1,npar,1,npar);
1.203 brouard 6991: hess=matrix(1,npar,1,npar);
1.126 brouard 6992: }
6993: else{
1.145 brouard 6994: /* Read guessed parameters */
1.126 brouard 6995: /* Reads comments: lines beginning with '#' */
6996: while((c=getc(ficpar))=='#' && c!= EOF){
6997: ungetc(c,ficpar);
6998: fgets(line, MAXLINE, ficpar);
6999: numlinepar++;
1.141 brouard 7000: fputs(line,stdout);
1.126 brouard 7001: fputs(line,ficparo);
7002: fputs(line,ficlog);
7003: }
7004: ungetc(c,ficpar);
7005:
7006: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7007: for(i=1; i <=nlstate; i++){
7008: j=0;
7009: for(jj=1; jj <=nlstate+ndeath; jj++){
7010: if(jj==i) continue;
7011: j++;
7012: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.193 brouard 7013: if ((i1 != i) || (j1 != jj)){
1.126 brouard 7014: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
7015: It might be a problem of design; if ncovcol and the model are correct\n \
7016: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
7017: exit(1);
7018: }
7019: fprintf(ficparo,"%1d%1d",i1,j1);
7020: if(mle==1)
1.193 brouard 7021: printf("%1d%1d",i,jj);
7022: fprintf(ficlog,"%1d%1d",i,jj);
1.126 brouard 7023: for(k=1; k<=ncovmodel;k++){
7024: fscanf(ficpar," %lf",¶m[i][j][k]);
7025: if(mle==1){
7026: printf(" %lf",param[i][j][k]);
7027: fprintf(ficlog," %lf",param[i][j][k]);
7028: }
7029: else
7030: fprintf(ficlog," %lf",param[i][j][k]);
7031: fprintf(ficparo," %lf",param[i][j][k]);
7032: }
7033: fscanf(ficpar,"\n");
7034: numlinepar++;
7035: if(mle==1)
7036: printf("\n");
7037: fprintf(ficlog,"\n");
7038: fprintf(ficparo,"\n");
7039: }
7040: }
7041: fflush(ficlog);
7042:
1.145 brouard 7043: /* Reads scales values */
1.126 brouard 7044: p=param[1][1];
7045:
7046: /* Reads comments: lines beginning with '#' */
7047: while((c=getc(ficpar))=='#' && c!= EOF){
7048: ungetc(c,ficpar);
7049: fgets(line, MAXLINE, ficpar);
7050: numlinepar++;
1.141 brouard 7051: fputs(line,stdout);
1.126 brouard 7052: fputs(line,ficparo);
7053: fputs(line,ficlog);
7054: }
7055: ungetc(c,ficpar);
7056:
7057: for(i=1; i <=nlstate; i++){
7058: for(j=1; j <=nlstate+ndeath-1; j++){
7059: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 7060: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 7061: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
7062: exit(1);
7063: }
7064: printf("%1d%1d",i,j);
7065: fprintf(ficparo,"%1d%1d",i1,j1);
7066: fprintf(ficlog,"%1d%1d",i1,j1);
7067: for(k=1; k<=ncovmodel;k++){
7068: fscanf(ficpar,"%le",&delti3[i][j][k]);
7069: printf(" %le",delti3[i][j][k]);
7070: fprintf(ficparo," %le",delti3[i][j][k]);
7071: fprintf(ficlog," %le",delti3[i][j][k]);
7072: }
7073: fscanf(ficpar,"\n");
7074: numlinepar++;
7075: printf("\n");
7076: fprintf(ficparo,"\n");
7077: fprintf(ficlog,"\n");
7078: }
7079: }
7080: fflush(ficlog);
7081:
1.145 brouard 7082: /* Reads covariance matrix */
1.126 brouard 7083: delti=delti3[1][1];
7084:
7085:
7086: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
7087:
7088: /* Reads comments: lines beginning with '#' */
7089: while((c=getc(ficpar))=='#' && c!= EOF){
7090: ungetc(c,ficpar);
7091: fgets(line, MAXLINE, ficpar);
7092: numlinepar++;
1.141 brouard 7093: fputs(line,stdout);
1.126 brouard 7094: fputs(line,ficparo);
7095: fputs(line,ficlog);
7096: }
7097: ungetc(c,ficpar);
7098:
7099: matcov=matrix(1,npar,1,npar);
1.203 brouard 7100: hess=matrix(1,npar,1,npar);
1.131 brouard 7101: for(i=1; i <=npar; i++)
7102: for(j=1; j <=npar; j++) matcov[i][j]=0.;
7103:
1.194 brouard 7104: /* Scans npar lines */
1.126 brouard 7105: for(i=1; i <=npar; i++){
1.194 brouard 7106: count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
7107: if(count != 3){
7108: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
7109: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
7110: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
7111: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
7112: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
7113: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
7114: exit(1);
7115: }else
1.126 brouard 7116: if(mle==1)
1.194 brouard 7117: printf("%1d%1d%1d",i1,j1,jk);
7118: fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
7119: fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
1.126 brouard 7120: for(j=1; j <=i; j++){
7121: fscanf(ficpar," %le",&matcov[i][j]);
7122: if(mle==1){
7123: printf(" %.5le",matcov[i][j]);
7124: }
7125: fprintf(ficlog," %.5le",matcov[i][j]);
7126: fprintf(ficparo," %.5le",matcov[i][j]);
7127: }
7128: fscanf(ficpar,"\n");
7129: numlinepar++;
7130: if(mle==1)
7131: printf("\n");
7132: fprintf(ficlog,"\n");
7133: fprintf(ficparo,"\n");
7134: }
1.194 brouard 7135: /* End of read covariance matrix npar lines */
1.126 brouard 7136: for(i=1; i <=npar; i++)
7137: for(j=i+1;j<=npar;j++)
7138: matcov[i][j]=matcov[j][i];
7139:
7140: if(mle==1)
7141: printf("\n");
7142: fprintf(ficlog,"\n");
7143:
7144: fflush(ficlog);
7145:
7146: /*-------- Rewriting parameter file ----------*/
7147: strcpy(rfileres,"r"); /* "Rparameterfile */
7148: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
7149: strcat(rfileres,"."); /* */
7150: strcat(rfileres,optionfilext); /* Other files have txt extension */
7151: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 7152: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
7153: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 7154: }
7155: fprintf(ficres,"#%s\n",version);
7156: } /* End of mle != -3 */
7157:
1.186 brouard 7158: /* Main data
7159: */
1.126 brouard 7160: n= lastobs;
7161: num=lvector(1,n);
7162: moisnais=vector(1,n);
7163: annais=vector(1,n);
7164: moisdc=vector(1,n);
7165: andc=vector(1,n);
7166: agedc=vector(1,n);
7167: cod=ivector(1,n);
7168: weight=vector(1,n);
7169: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
7170: mint=matrix(1,maxwav,1,n);
7171: anint=matrix(1,maxwav,1,n);
1.131 brouard 7172: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 7173: tab=ivector(1,NCOVMAX);
1.144 brouard 7174: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 7175: 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 7176:
1.136 brouard 7177: /* Reads data from file datafile */
7178: if (readdata(datafile, firstobs, lastobs, &imx)==1)
7179: goto end;
7180:
7181: /* Calculation of the number of parameters from char model */
1.137 brouard 7182: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
7183: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
7184: k=3 V4 Tvar[k=3]= 4 (from V4)
7185: k=2 V1 Tvar[k=2]= 1 (from V1)
7186: k=1 Tvar[1]=2 (from V2)
7187: */
7188: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
7189: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
7190: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
7191: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
7192: */
7193: /* For model-covariate k tells which data-covariate to use but
7194: because this model-covariate is a construction we invent a new column
7195: ncovcol + k1
7196: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
7197: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 7198: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 7199: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
7200: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
7201: */
1.145 brouard 7202: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
7203: 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 7204: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
7205: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 7206: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 7207: 4 covariates (3 plus signs)
7208: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
7209: */
1.136 brouard 7210:
1.186 brouard 7211: /* Main decodemodel */
7212:
1.187 brouard 7213:
1.136 brouard 7214: if(decodemodel(model, lastobs) == 1)
7215: goto end;
7216:
1.137 brouard 7217: if((double)(lastobs-imx)/(double)imx > 1.10){
7218: nbwarn++;
7219: 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);
7220: 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);
7221: }
1.136 brouard 7222: /* if(mle==1){*/
1.137 brouard 7223: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
7224: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 7225: }
7226:
7227: /*-calculation of age at interview from date of interview and age at death -*/
7228: agev=matrix(1,maxwav,1,imx);
7229:
7230: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
7231: goto end;
7232:
1.126 brouard 7233:
1.136 brouard 7234: agegomp=(int)agemin;
7235: free_vector(moisnais,1,n);
7236: free_vector(annais,1,n);
1.126 brouard 7237: /* free_matrix(mint,1,maxwav,1,n);
7238: free_matrix(anint,1,maxwav,1,n);*/
7239: free_vector(moisdc,1,n);
7240: free_vector(andc,1,n);
1.145 brouard 7241: /* */
7242:
1.126 brouard 7243: wav=ivector(1,imx);
7244: dh=imatrix(1,lastpass-firstpass+1,1,imx);
7245: bh=imatrix(1,lastpass-firstpass+1,1,imx);
7246: mw=imatrix(1,lastpass-firstpass+1,1,imx);
7247:
7248: /* Concatenates waves */
7249: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 7250: /* */
7251:
1.126 brouard 7252: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
7253:
7254: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
7255: ncodemax[1]=1;
1.145 brouard 7256: Ndum =ivector(-1,NCOVMAX);
1.187 brouard 7257: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
1.145 brouard 7258: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.186 brouard 7259: /* Nbcode gives the value of the lth modality of jth covariate, in
7260: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
7261: /* 1 to ncodemax[j] is the maximum value of this jth covariate */
1.145 brouard 7262:
1.200 brouard 7263: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 7264: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 7265: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.145 brouard 7266: h=0;
7267:
7268:
7269: /*if (cptcovn > 0) */
1.126 brouard 7270:
1.145 brouard 7271:
1.126 brouard 7272: m=pow(2,cptcoveff);
7273:
1.144 brouard 7274: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.186 brouard 7275: * For k=4 covariates, h goes from 1 to 2**k
7276: * codtabm(h,k)= 1 & (h-1) >> (k-1) ;
7277: * h\k 1 2 3 4
1.143 brouard 7278: *______________________________
7279: * 1 i=1 1 i=1 1 i=1 1 i=1 1
7280: * 2 2 1 1 1
7281: * 3 i=2 1 2 1 1
7282: * 4 2 2 1 1
7283: * 5 i=3 1 i=2 1 2 1
7284: * 6 2 1 2 1
7285: * 7 i=4 1 2 2 1
7286: * 8 2 2 2 1
1.197 brouard 7287: * 9 i=5 1 i=3 1 i=2 1 2
7288: * 10 2 1 1 2
7289: * 11 i=6 1 2 1 2
7290: * 12 2 2 1 2
7291: * 13 i=7 1 i=4 1 2 2
7292: * 14 2 1 2 2
7293: * 15 i=8 1 2 2 2
7294: * 16 2 2 2 2
1.143 brouard 7295: */
1.202 brouard 7296: /* /\* for(h=1; h <=100 ;h++){ *\/ */
7297: /* /\* printf("h=%2d ", h); *\/ */
7298: /* /\* for(k=1; k <=10; k++){ *\/ */
7299: /* /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */
7300: /* /\* codtab[h][k]=codtabm(h,k); *\/ */
7301: /* /\* } *\/ */
7302: /* /\* printf("\n"); *\/ */
7303: /* } */
1.197 brouard 7304: /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
7305: /* 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 *\/ */
7306: /* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
7307: /* for(cpt=1; cpt <=pow(2,k-1); cpt++){ /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/ */
7308: /* h++; */
7309: /* if (h>m) */
7310: /* h=1; */
7311: /* codtab[h][k]=j; */
7312: /* /\* codtab[12][3]=1; *\/ */
7313: /* /\*codtab[h][Tvar[k]]=j;*\/ */
7314: /* /\* 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]]); *\/ */
7315: /* } */
7316: /* } */
7317: /* } */
7318: /* } */
1.126 brouard 7319: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
7320: codtab[1][2]=1;codtab[2][2]=2; */
1.197 brouard 7321: /* for(i=1; i <=m ;i++){ */
7322: /* for(k=1; k <=cptcovn; k++){ */
7323: /* printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
7324: /* } */
7325: /* printf("\n"); */
7326: /* } */
7327: /* scanf("%d",i);*/
1.145 brouard 7328:
7329: free_ivector(Ndum,-1,NCOVMAX);
7330:
7331:
1.126 brouard 7332:
1.186 brouard 7333: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 7334: strcpy(optionfilegnuplot,optionfilefiname);
7335: if(mle==-3)
1.201 brouard 7336: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 7337: strcat(optionfilegnuplot,".gp");
7338:
7339: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
7340: printf("Problem with file %s",optionfilegnuplot);
7341: }
7342: else{
1.204 ! brouard 7343: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 7344: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 7345: //fprintf(ficgp,"set missing 'NaNq'\n");
7346: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 7347: }
7348: /* fclose(ficgp);*/
1.186 brouard 7349:
7350:
7351: /* Initialisation of --------- index.htm --------*/
1.126 brouard 7352:
7353: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
7354: if(mle==-3)
1.201 brouard 7355: strcat(optionfilehtm,"-MORT_");
1.126 brouard 7356: strcat(optionfilehtm,".htm");
7357: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 7358: printf("Problem with %s \n",optionfilehtm);
7359: exit(0);
1.126 brouard 7360: }
7361:
7362: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
7363: strcat(optionfilehtmcov,"-cov.htm");
7364: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
7365: printf("Problem with %s \n",optionfilehtmcov), exit(0);
7366: }
7367: else{
7368: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
7369: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 ! brouard 7370: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 7371: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
7372: }
7373:
1.204 ! brouard 7374: 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> \
! 7375: <hr size=\"2\" color=\"#EC5E5E\"> \n\
! 7376: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 7377: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 ! brouard 7378: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 7379: \n\
7380: <hr size=\"2\" color=\"#EC5E5E\">\
7381: <ul><li><h4>Parameter files</h4>\n\
7382: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
7383: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
7384: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
7385: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
7386: - Date and time at start: %s</ul>\n",\
7387: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
7388: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
7389: fileres,fileres,\
7390: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
7391: fflush(fichtm);
7392:
7393: strcpy(pathr,path);
7394: strcat(pathr,optionfilefiname);
1.184 brouard 7395: #ifdef WIN32
7396: _chdir(optionfilefiname); /* Move to directory named optionfile */
7397: #else
1.126 brouard 7398: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 7399: #endif
7400:
1.126 brouard 7401:
7402: /* Calculates basic frequencies. Computes observed prevalence at single age
7403: and prints on file fileres'p'. */
7404: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
7405:
7406: fprintf(fichtm,"\n");
7407: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
7408: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
7409: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
7410: imx,agemin,agemax,jmin,jmax,jmean);
7411: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7412: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7413: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7414: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7415: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
7416:
7417:
7418: /* For Powell, parameters are in a vector p[] starting at p[1]
7419: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
7420: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
7421:
7422: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 7423: /* For mortality only */
1.126 brouard 7424: if (mle==-3){
1.136 brouard 7425: ximort=matrix(1,NDIM,1,NDIM);
1.186 brouard 7426: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 7427: cens=ivector(1,n);
7428: ageexmed=vector(1,n);
7429: agecens=vector(1,n);
7430: dcwave=ivector(1,n);
7431:
7432: for (i=1; i<=imx; i++){
7433: dcwave[i]=-1;
7434: for (m=firstpass; m<=lastpass; m++)
7435: if (s[m][i]>nlstate) {
7436: dcwave[i]=m;
7437: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
7438: break;
7439: }
7440: }
7441:
7442: for (i=1; i<=imx; i++) {
7443: if (wav[i]>0){
7444: ageexmed[i]=agev[mw[1][i]][i];
7445: j=wav[i];
7446: agecens[i]=1.;
7447:
7448: if (ageexmed[i]> 1 && wav[i] > 0){
7449: agecens[i]=agev[mw[j][i]][i];
7450: cens[i]= 1;
7451: }else if (ageexmed[i]< 1)
7452: cens[i]= -1;
7453: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
7454: cens[i]=0 ;
7455: }
7456: else cens[i]=-1;
7457: }
7458:
7459: for (i=1;i<=NDIM;i++) {
7460: for (j=1;j<=NDIM;j++)
7461: ximort[i][j]=(i == j ? 1.0 : 0.0);
7462: }
7463:
1.145 brouard 7464: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 7465: /*printf("%lf %lf", p[1], p[2]);*/
7466:
7467:
1.136 brouard 7468: #ifdef GSL
7469: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 7470: #else
1.126 brouard 7471: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 7472: #endif
1.201 brouard 7473: strcpy(filerespow,"POW-MORT_");
7474: strcat(filerespow,fileresu);
1.126 brouard 7475: if((ficrespow=fopen(filerespow,"w"))==NULL) {
7476: printf("Problem with resultfile: %s\n", filerespow);
7477: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
7478: }
1.136 brouard 7479: #ifdef GSL
7480: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 7481: #else
1.126 brouard 7482: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 7483: #endif
1.126 brouard 7484: /* for (i=1;i<=nlstate;i++)
7485: for(j=1;j<=nlstate+ndeath;j++)
7486: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
7487: */
7488: fprintf(ficrespow,"\n");
1.136 brouard 7489: #ifdef GSL
7490: /* gsl starts here */
7491: T = gsl_multimin_fminimizer_nmsimplex;
7492: gsl_multimin_fminimizer *sfm = NULL;
7493: gsl_vector *ss, *x;
7494: gsl_multimin_function minex_func;
7495:
7496: /* Initial vertex size vector */
7497: ss = gsl_vector_alloc (NDIM);
7498:
7499: if (ss == NULL){
7500: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
7501: }
7502: /* Set all step sizes to 1 */
7503: gsl_vector_set_all (ss, 0.001);
7504:
7505: /* Starting point */
1.126 brouard 7506:
1.136 brouard 7507: x = gsl_vector_alloc (NDIM);
7508:
7509: if (x == NULL){
7510: gsl_vector_free(ss);
7511: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
7512: }
7513:
7514: /* Initialize method and iterate */
7515: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 7516: /* gsl_vector_set(x, 0, 0.0268); */
7517: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 7518: gsl_vector_set(x, 0, p[1]);
7519: gsl_vector_set(x, 1, p[2]);
7520:
7521: minex_func.f = &gompertz_f;
7522: minex_func.n = NDIM;
7523: minex_func.params = (void *)&p; /* ??? */
7524:
7525: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
7526: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
7527:
7528: printf("Iterations beginning .....\n\n");
7529: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
7530:
7531: iteri=0;
7532: while (rval == GSL_CONTINUE){
7533: iteri++;
7534: status = gsl_multimin_fminimizer_iterate(sfm);
7535:
7536: if (status) printf("error: %s\n", gsl_strerror (status));
7537: fflush(0);
7538:
7539: if (status)
7540: break;
7541:
7542: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
7543: ssval = gsl_multimin_fminimizer_size (sfm);
7544:
7545: if (rval == GSL_SUCCESS)
7546: printf ("converged to a local maximum at\n");
7547:
7548: printf("%5d ", iteri);
7549: for (it = 0; it < NDIM; it++){
7550: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
7551: }
7552: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
7553: }
7554:
7555: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
7556:
7557: gsl_vector_free(x); /* initial values */
7558: gsl_vector_free(ss); /* inital step size */
7559: for (it=0; it<NDIM; it++){
7560: p[it+1]=gsl_vector_get(sfm->x,it);
7561: fprintf(ficrespow," %.12lf", p[it]);
7562: }
7563: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
7564: #endif
7565: #ifdef POWELL
7566: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
7567: #endif
1.126 brouard 7568: fclose(ficrespow);
7569:
1.203 brouard 7570: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 7571:
7572: for(i=1; i <=NDIM; i++)
7573: for(j=i+1;j<=NDIM;j++)
7574: matcov[i][j]=matcov[j][i];
7575:
7576: printf("\nCovariance matrix\n ");
1.203 brouard 7577: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 7578: for(i=1; i <=NDIM; i++) {
7579: for(j=1;j<=NDIM;j++){
7580: printf("%f ",matcov[i][j]);
1.203 brouard 7581: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 7582: }
1.203 brouard 7583: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 7584: }
7585:
7586: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 7587: for (i=1;i<=NDIM;i++) {
1.126 brouard 7588: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 7589: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
7590: }
1.126 brouard 7591: lsurv=vector(1,AGESUP);
7592: lpop=vector(1,AGESUP);
7593: tpop=vector(1,AGESUP);
7594: lsurv[agegomp]=100000;
7595:
7596: for (k=agegomp;k<=AGESUP;k++) {
7597: agemortsup=k;
7598: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
7599: }
7600:
7601: for (k=agegomp;k<agemortsup;k++)
7602: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
7603:
7604: for (k=agegomp;k<agemortsup;k++){
7605: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
7606: sumlpop=sumlpop+lpop[k];
7607: }
7608:
7609: tpop[agegomp]=sumlpop;
7610: for (k=agegomp;k<(agemortsup-3);k++){
7611: /* tpop[k+1]=2;*/
7612: tpop[k+1]=tpop[k]-lpop[k];
7613: }
7614:
7615:
7616: printf("\nAge lx qx dx Lx Tx e(x)\n");
7617: for (k=agegomp;k<(agemortsup-2);k++)
7618: 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]);
7619:
7620:
7621: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 7622: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
7623: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7624: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7625: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7626: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7627: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7628: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7629: }else
1.201 brouard 7630: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7631: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 7632: stepm, weightopt,\
7633: model,imx,p,matcov,agemortsup);
7634:
7635: free_vector(lsurv,1,AGESUP);
7636: free_vector(lpop,1,AGESUP);
7637: free_vector(tpop,1,AGESUP);
1.136 brouard 7638: #ifdef GSL
7639: free_ivector(cens,1,n);
7640: free_vector(agecens,1,n);
7641: free_ivector(dcwave,1,n);
7642: free_matrix(ximort,1,NDIM,1,NDIM);
7643: #endif
1.186 brouard 7644: } /* Endof if mle==-3 mortality only */
7645: /* Standard maximisation */
1.203 brouard 7646: else{ /* For mle !=- 3 */
1.132 brouard 7647: globpr=0;/* debug */
1.186 brouard 7648: /* Computes likelihood for initial parameters */
1.132 brouard 7649: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 7650: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7651: for (k=1; k<=npar;k++)
7652: printf(" %d %8.5f",k,p[k]);
7653: printf("\n");
1.186 brouard 7654: globpr=1; /* again, to print the contributions */
1.126 brouard 7655: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7656: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7657: for (k=1; k<=npar;k++)
7658: printf(" %d %8.5f",k,p[k]);
7659: printf("\n");
1.186 brouard 7660: if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
1.126 brouard 7661: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
7662: }
7663:
7664: /*--------- results files --------------*/
1.192 brouard 7665: 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 7666:
7667:
7668: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7669: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7670: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7671: for(i=1,jk=1; i <=nlstate; i++){
7672: for(k=1; k <=(nlstate+ndeath); k++){
7673: if (k != i) {
7674: printf("%d%d ",i,k);
7675: fprintf(ficlog,"%d%d ",i,k);
7676: fprintf(ficres,"%1d%1d ",i,k);
7677: for(j=1; j <=ncovmodel; j++){
1.190 brouard 7678: printf("%12.7f ",p[jk]);
7679: fprintf(ficlog,"%12.7f ",p[jk]);
7680: fprintf(ficres,"%12.7f ",p[jk]);
1.126 brouard 7681: jk++;
7682: }
7683: printf("\n");
7684: fprintf(ficlog,"\n");
7685: fprintf(ficres,"\n");
7686: }
7687: }
7688: }
1.203 brouard 7689: if(mle != 0){
7690: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 7691: ftolhess=ftol; /* Usually correct */
1.203 brouard 7692: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
7693: 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");
7694: 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");
7695: for(i=1,jk=1; i <=nlstate; i++){
7696: for(k=1; k <=(nlstate+ndeath); k++){
7697: if (k != i) {
7698: printf("%d%d ",i,k);
7699: fprintf(ficlog,"%d%d ",i,k);
7700: for(j=1; j <=ncovmodel; j++){
7701: 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]));
7702: 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]));
7703: jk++;
7704: }
7705: printf("\n");
7706: fprintf(ficlog,"\n");
1.193 brouard 7707: }
7708: }
7709: }
1.203 brouard 7710: } /* end of hesscov and Wald tests */
1.193 brouard 7711:
1.203 brouard 7712: /* */
1.126 brouard 7713: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
7714: printf("# Scales (for hessian or gradient estimation)\n");
7715: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
7716: for(i=1,jk=1; i <=nlstate; i++){
7717: for(j=1; j <=nlstate+ndeath; j++){
7718: if (j!=i) {
7719: fprintf(ficres,"%1d%1d",i,j);
7720: printf("%1d%1d",i,j);
7721: fprintf(ficlog,"%1d%1d",i,j);
7722: for(k=1; k<=ncovmodel;k++){
7723: printf(" %.5e",delti[jk]);
7724: fprintf(ficlog," %.5e",delti[jk]);
7725: fprintf(ficres," %.5e",delti[jk]);
7726: jk++;
7727: }
7728: printf("\n");
7729: fprintf(ficlog,"\n");
7730: fprintf(ficres,"\n");
7731: }
7732: }
7733: }
7734:
7735: 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 7736: if(mle >= 1) /* To big for the screen */
1.126 brouard 7737: 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");
7738: 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");
7739: /* # 121 Var(a12)\n\ */
7740: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7741: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7742: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7743: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7744: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7745: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7746: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7747:
7748:
7749: /* Just to have a covariance matrix which will be more understandable
7750: even is we still don't want to manage dictionary of variables
7751: */
7752: for(itimes=1;itimes<=2;itimes++){
7753: jj=0;
7754: for(i=1; i <=nlstate; i++){
7755: for(j=1; j <=nlstate+ndeath; j++){
7756: if(j==i) continue;
7757: for(k=1; k<=ncovmodel;k++){
7758: jj++;
7759: ca[0]= k+'a'-1;ca[1]='\0';
7760: if(itimes==1){
7761: if(mle>=1)
7762: printf("#%1d%1d%d",i,j,k);
7763: fprintf(ficlog,"#%1d%1d%d",i,j,k);
7764: fprintf(ficres,"#%1d%1d%d",i,j,k);
7765: }else{
7766: if(mle>=1)
7767: printf("%1d%1d%d",i,j,k);
7768: fprintf(ficlog,"%1d%1d%d",i,j,k);
7769: fprintf(ficres,"%1d%1d%d",i,j,k);
7770: }
7771: ll=0;
7772: for(li=1;li <=nlstate; li++){
7773: for(lj=1;lj <=nlstate+ndeath; lj++){
7774: if(lj==li) continue;
7775: for(lk=1;lk<=ncovmodel;lk++){
7776: ll++;
7777: if(ll<=jj){
7778: cb[0]= lk +'a'-1;cb[1]='\0';
7779: if(ll<jj){
7780: if(itimes==1){
7781: if(mle>=1)
7782: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7783: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7784: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7785: }else{
7786: if(mle>=1)
7787: printf(" %.5e",matcov[jj][ll]);
7788: fprintf(ficlog," %.5e",matcov[jj][ll]);
7789: fprintf(ficres," %.5e",matcov[jj][ll]);
7790: }
7791: }else{
7792: if(itimes==1){
7793: if(mle>=1)
7794: printf(" Var(%s%1d%1d)",ca,i,j);
7795: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
7796: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
7797: }else{
7798: if(mle>=1)
1.203 brouard 7799: printf(" %.7e",matcov[jj][ll]);
7800: fprintf(ficlog," %.7e",matcov[jj][ll]);
7801: fprintf(ficres," %.7e",matcov[jj][ll]);
1.126 brouard 7802: }
7803: }
7804: }
7805: } /* end lk */
7806: } /* end lj */
7807: } /* end li */
7808: if(mle>=1)
7809: printf("\n");
7810: fprintf(ficlog,"\n");
7811: fprintf(ficres,"\n");
7812: numlinepar++;
7813: } /* end k*/
7814: } /*end j */
7815: } /* end i */
7816: } /* end itimes */
7817:
7818: fflush(ficlog);
7819: fflush(ficres);
7820:
7821: while((c=getc(ficpar))=='#' && c!= EOF){
7822: ungetc(c,ficpar);
7823: fgets(line, MAXLINE, ficpar);
1.141 brouard 7824: fputs(line,stdout);
1.126 brouard 7825: fputs(line,ficparo);
7826: }
7827: ungetc(c,ficpar);
7828:
7829: estepm=0;
7830: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
7831: if (estepm==0 || estepm < stepm) estepm=stepm;
7832: if (fage <= 2) {
7833: bage = ageminpar;
7834: fage = agemaxpar;
7835: }
7836:
7837: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
7838: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7839: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.186 brouard 7840:
7841: /* Other stuffs, more or less useful */
1.126 brouard 7842: while((c=getc(ficpar))=='#' && c!= EOF){
7843: ungetc(c,ficpar);
7844: fgets(line, MAXLINE, ficpar);
1.141 brouard 7845: fputs(line,stdout);
1.126 brouard 7846: fputs(line,ficparo);
7847: }
7848: ungetc(c,ficpar);
7849:
7850: 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);
7851: 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);
7852: 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);
7853: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7854: 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);
7855:
7856: while((c=getc(ficpar))=='#' && c!= EOF){
7857: ungetc(c,ficpar);
7858: fgets(line, MAXLINE, ficpar);
1.141 brouard 7859: fputs(line,stdout);
1.126 brouard 7860: fputs(line,ficparo);
7861: }
7862: ungetc(c,ficpar);
7863:
7864:
7865: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
7866: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
7867:
7868: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 7869: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 7870: fprintf(ficparo,"pop_based=%d\n",popbased);
7871: fprintf(ficres,"pop_based=%d\n",popbased);
7872:
7873: while((c=getc(ficpar))=='#' && c!= EOF){
7874: ungetc(c,ficpar);
7875: fgets(line, MAXLINE, ficpar);
1.141 brouard 7876: fputs(line,stdout);
1.126 brouard 7877: fputs(line,ficparo);
7878: }
7879: ungetc(c,ficpar);
7880:
7881: 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);
7882: 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);
7883: 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);
7884: 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);
7885: 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);
7886: /* day and month of proj2 are not used but only year anproj2.*/
7887:
7888:
7889:
1.145 brouard 7890: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
7891: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 7892:
7893: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 7894: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
7895: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7896: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7897: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7898: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7899: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7900: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7901: }else
1.201 brouard 7902: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.126 brouard 7903:
1.201 brouard 7904: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\
1.126 brouard 7905: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
7906: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
7907:
7908: /*------------ free_vector -------------*/
7909: /* chdir(path); */
7910:
7911: free_ivector(wav,1,imx);
7912: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
7913: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
7914: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
7915: free_lvector(num,1,n);
7916: free_vector(agedc,1,n);
7917: /*free_matrix(covar,0,NCOVMAX,1,n);*/
7918: /*free_matrix(covar,1,NCOVMAX,1,n);*/
7919: fclose(ficparo);
7920: fclose(ficres);
7921:
7922:
1.186 brouard 7923: /* Other results (useful)*/
7924:
7925:
1.126 brouard 7926: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 7927: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
7928: prlim=matrix(1,nlstate,1,nlstate);
1.203 brouard 7929: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, ncvyear);
1.126 brouard 7930: fclose(ficrespl);
7931:
1.145 brouard 7932: #ifdef FREEEXIT2
7933: #include "freeexit2.h"
7934: #endif
7935:
1.126 brouard 7936: /*------------- h Pij x at various ages ------------*/
1.180 brouard 7937: /*#include "hpijx.h"*/
7938: hPijx(p, bage, fage);
1.145 brouard 7939: fclose(ficrespij);
1.126 brouard 7940:
1.145 brouard 7941: /*-------------- Variance of one-step probabilities---*/
7942: k=1;
1.126 brouard 7943: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
7944:
7945:
7946: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7947: for(i=1;i<=AGESUP;i++)
7948: for(j=1;j<=NCOVMAX;j++)
7949: for(k=1;k<=NCOVMAX;k++)
7950: probs[i][j][k]=0.;
7951:
7952: /*---------- Forecasting ------------------*/
7953: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
7954: if(prevfcast==1){
7955: /* if(stepm ==1){*/
1.201 brouard 7956: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 7957: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
7958: /* } */
7959: /* else{ */
7960: /* erreur=108; */
7961: /* 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); */
7962: /* 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); */
7963: /* } */
7964: }
1.186 brouard 7965:
7966: /* ------ Other prevalence ratios------------ */
1.126 brouard 7967:
1.127 brouard 7968: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
7969:
7970: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
7971: /* 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",\
7972: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
7973: */
1.126 brouard 7974:
1.127 brouard 7975: if (mobilav!=0) {
7976: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7977: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
7978: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
7979: printf(" Error in movingaverage mobilav=%d\n",mobilav);
7980: }
1.126 brouard 7981: }
7982:
7983:
1.127 brouard 7984: /*---------- Health expectancies, no variances ------------*/
7985:
1.201 brouard 7986: strcpy(filerese,"E_");
7987: strcat(filerese,fileresu);
1.126 brouard 7988: if((ficreseij=fopen(filerese,"w"))==NULL) {
7989: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7990: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7991: }
7992: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
7993: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145 brouard 7994: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7995: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7996:
7997: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 7998: fprintf(ficreseij,"\n#****** ");
7999: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 8000: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.127 brouard 8001: }
8002: fprintf(ficreseij,"******\n");
8003:
8004: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8005: oldm=oldms;savm=savms;
8006: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
8007:
8008: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 8009: /*}*/
1.127 brouard 8010: }
8011: fclose(ficreseij);
8012:
8013:
8014: /*---------- Health expectancies and variances ------------*/
8015:
8016:
1.201 brouard 8017: strcpy(filerest,"T_");
8018: strcat(filerest,fileresu);
1.127 brouard 8019: if((ficrest=fopen(filerest,"w"))==NULL) {
8020: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
8021: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
8022: }
8023: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
8024: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
8025:
1.126 brouard 8026:
1.201 brouard 8027: strcpy(fileresstde,"STDE_");
8028: strcat(fileresstde,fileresu);
1.126 brouard 8029: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
8030: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
8031: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
8032: }
8033: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
8034: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
8035:
1.201 brouard 8036: strcpy(filerescve,"CVE_");
8037: strcat(filerescve,fileresu);
1.126 brouard 8038: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
8039: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
8040: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
8041: }
8042: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
8043: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
8044:
1.201 brouard 8045: strcpy(fileresv,"V_");
8046: strcat(fileresv,fileresu);
1.126 brouard 8047: if((ficresvij=fopen(fileresv,"w"))==NULL) {
8048: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
8049: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
8050: }
8051: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
8052: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
8053:
1.145 brouard 8054: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8055: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8056:
8057: for (k=1; k <= (int) pow(2,cptcoveff); k++){
8058: fprintf(ficrest,"\n#****** ");
1.126 brouard 8059: for(j=1;j<=cptcoveff;j++)
1.200 brouard 8060: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 8061: fprintf(ficrest,"******\n");
8062:
8063: fprintf(ficresstdeij,"\n#****** ");
8064: fprintf(ficrescveij,"\n#****** ");
8065: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 8066: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8067: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 8068: }
8069: fprintf(ficresstdeij,"******\n");
8070: fprintf(ficrescveij,"******\n");
8071:
8072: fprintf(ficresvij,"\n#****** ");
8073: for(j=1;j<=cptcoveff;j++)
1.200 brouard 8074: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 8075: fprintf(ficresvij,"******\n");
8076:
8077: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8078: oldm=oldms;savm=savms;
1.127 brouard 8079: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.145 brouard 8080: /*
8081: */
8082: /* goto endfree; */
1.126 brouard 8083:
8084: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8085: pstamp(ficrest);
1.145 brouard 8086:
8087:
1.128 brouard 8088: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.199 brouard 8089: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
1.161 brouard 8090: cptcod= 0; /* To be deleted */
1.203 brouard 8091: 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 */
1.145 brouard 8092: 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 ");
1.128 brouard 8093: if(vpopbased==1)
8094: 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);
8095: else
8096: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
1.201 brouard 8097: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
1.128 brouard 8098: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
8099: fprintf(ficrest,"\n");
1.199 brouard 8100: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
1.128 brouard 8101: epj=vector(1,nlstate+1);
8102: for(age=bage; age <=fage ;age++){
1.203 brouard 8103: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k); /*ZZ Is it the correct prevalim */
1.128 brouard 8104: if (vpopbased==1) {
8105: if(mobilav ==0){
8106: for(i=1; i<=nlstate;i++)
8107: prlim[i][i]=probs[(int)age][i][k];
8108: }else{ /* mobilav */
8109: for(i=1; i<=nlstate;i++)
8110: prlim[i][i]=mobaverage[(int)age][i][k];
8111: }
1.126 brouard 8112: }
8113:
1.201 brouard 8114: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
1.199 brouard 8115: /* printf(" age %4.0f ",age); */
1.128 brouard 8116: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
8117: for(i=1, epj[j]=0.;i <=nlstate;i++) {
8118: epj[j] += prlim[i][i]*eij[i][j][(int)age];
1.199 brouard 8119: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
8120: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
1.128 brouard 8121: }
8122: epj[nlstate+1] +=epj[j];
1.126 brouard 8123: }
1.199 brouard 8124: /* printf(" age %4.0f \n",age); */
1.126 brouard 8125:
1.128 brouard 8126: for(i=1, vepp=0.;i <=nlstate;i++)
8127: for(j=1;j <=nlstate;j++)
8128: vepp += vareij[i][j][(int)age];
8129: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
8130: for(j=1;j <=nlstate;j++){
8131: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
8132: }
8133: fprintf(ficrest,"\n");
1.126 brouard 8134: }
8135: }
8136: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
8137: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
8138: free_vector(epj,1,nlstate+1);
1.145 brouard 8139: /*}*/
1.126 brouard 8140: }
8141: free_vector(weight,1,n);
1.145 brouard 8142: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 8143: free_imatrix(s,1,maxwav+1,1,n);
8144: free_matrix(anint,1,maxwav,1,n);
8145: free_matrix(mint,1,maxwav,1,n);
8146: free_ivector(cod,1,n);
8147: free_ivector(tab,1,NCOVMAX);
8148: fclose(ficresstdeij);
8149: fclose(ficrescveij);
8150: fclose(ficresvij);
8151: fclose(ficrest);
8152: fclose(ficpar);
8153:
8154: /*------- Variance of period (stable) prevalence------*/
8155:
1.201 brouard 8156: strcpy(fileresvpl,"VPL_");
8157: strcat(fileresvpl,fileresu);
1.126 brouard 8158: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
8159: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
8160: exit(0);
8161: }
8162: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
8163:
1.145 brouard 8164: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8165: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8166:
8167: for (k=1; k <= (int) pow(2,cptcoveff); k++){
8168: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 8169: for(j=1;j<=cptcoveff;j++)
1.200 brouard 8170: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 8171: fprintf(ficresvpl,"******\n");
8172:
8173: varpl=matrix(1,nlstate,(int) bage, (int) fage);
8174: oldm=oldms;savm=savms;
1.203 brouard 8175: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyear, k, strstart);
1.126 brouard 8176: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 8177: /*}*/
1.126 brouard 8178: }
8179:
8180: fclose(ficresvpl);
8181:
8182: /*---------- End : free ----------------*/
8183: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
8184: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
8185: } /* mle==-3 arrives here for freeing */
1.164 brouard 8186: /* endfree:*/
1.141 brouard 8187: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 8188: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
8189: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
8190: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
8191: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
8192: free_matrix(covar,0,NCOVMAX,1,n);
8193: free_matrix(matcov,1,npar,1,npar);
1.203 brouard 8194: free_matrix(hess,1,npar,1,npar);
1.126 brouard 8195: /*free_vector(delti,1,npar);*/
8196: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8197: free_matrix(agev,1,maxwav,1,imx);
8198: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8199:
1.145 brouard 8200: free_ivector(ncodemax,1,NCOVMAX);
1.192 brouard 8201: free_ivector(ncodemaxwundef,1,NCOVMAX);
1.145 brouard 8202: free_ivector(Tvar,1,NCOVMAX);
8203: free_ivector(Tprod,1,NCOVMAX);
8204: free_ivector(Tvaraff,1,NCOVMAX);
8205: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 8206:
8207: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
1.200 brouard 8208: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 8209: fflush(fichtm);
8210: fflush(ficgp);
8211:
8212:
8213: if((nberr >0) || (nbwarn>0)){
8214: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
8215: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
8216: }else{
8217: printf("End of Imach\n");
8218: fprintf(ficlog,"End of Imach\n");
8219: }
8220: printf("See log file on %s\n",filelog);
8221: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 8222: /*(void) gettimeofday(&end_time,&tzp);*/
8223: rend_time = time(NULL);
8224: end_time = *localtime(&rend_time);
8225: /* tml = *localtime(&end_time.tm_sec); */
8226: strcpy(strtend,asctime(&end_time));
1.126 brouard 8227: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
8228: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 8229: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 8230:
1.157 brouard 8231: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
8232: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
8233: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 8234: /* printf("Total time was %d uSec.\n", total_usecs);*/
8235: /* if(fileappend(fichtm,optionfilehtm)){ */
8236: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8237: fclose(fichtm);
8238: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8239: fclose(fichtmcov);
8240: fclose(ficgp);
8241: fclose(ficlog);
8242: /*------ End -----------*/
8243:
8244:
8245: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 8246: #ifdef WIN32
8247: if (_chdir(pathcd) != 0)
8248: printf("Can't move to directory %s!\n",path);
8249: if(_getcwd(pathcd,MAXLINE) > 0)
8250: #else
1.126 brouard 8251: if(chdir(pathcd) != 0)
1.184 brouard 8252: printf("Can't move to directory %s!\n", path);
8253: if (getcwd(pathcd, MAXLINE) > 0)
8254: #endif
1.126 brouard 8255: printf("Current directory %s!\n",pathcd);
8256: /*strcat(plotcmd,CHARSEPARATOR);*/
8257: sprintf(plotcmd,"gnuplot");
1.157 brouard 8258: #ifdef _WIN32
1.126 brouard 8259: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
8260: #endif
8261: if(!stat(plotcmd,&info)){
1.158 brouard 8262: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8263: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 8264: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 8265: }else
8266: strcpy(pplotcmd,plotcmd);
1.157 brouard 8267: #ifdef __unix
1.126 brouard 8268: strcpy(plotcmd,GNUPLOTPROGRAM);
8269: if(!stat(plotcmd,&info)){
1.158 brouard 8270: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8271: }else
8272: strcpy(pplotcmd,plotcmd);
8273: #endif
8274: }else
8275: strcpy(pplotcmd,plotcmd);
8276:
8277: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 8278: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8279:
8280: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 8281: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 8282: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 8283: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 8284: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 8285: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 8286: }
1.158 brouard 8287: printf(" Successful, please wait...");
1.126 brouard 8288: while (z[0] != 'q') {
8289: /* chdir(path); */
1.154 brouard 8290: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 8291: scanf("%s",z);
8292: /* if (z[0] == 'c') system("./imach"); */
8293: if (z[0] == 'e') {
1.158 brouard 8294: #ifdef __APPLE__
1.152 brouard 8295: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 8296: #elif __linux
8297: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 8298: #else
1.152 brouard 8299: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 8300: #endif
8301: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
8302: system(pplotcmd);
1.126 brouard 8303: }
8304: else if (z[0] == 'g') system(plotcmd);
8305: else if (z[0] == 'q') exit(0);
8306: }
8307: end:
8308: while (z[0] != 'q') {
1.195 brouard 8309: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 8310: scanf("%s",z);
8311: }
8312: }
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