Annotation of imach/src/imach.c, revision 1.199
1.199 ! brouard 1: /* $Id: imach.c,v 1.198 2015/09/03 07:14:39 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.199 ! brouard 4: Revision 1.198 2015/09/03 07:14:39 brouard
! 5: Summary: 0.98q5 Flavia
! 6:
1.198 brouard 7: Revision 1.197 2015/09/01 18:24:39 brouard
8: *** empty log message ***
9:
1.197 brouard 10: Revision 1.196 2015/08/18 23:17:52 brouard
11: Summary: 0.98q5
12:
1.196 brouard 13: Revision 1.195 2015/08/18 16:28:39 brouard
14: Summary: Adding a hack for testing purpose
15:
16: After reading the title, ftol and model lines, if the comment line has
17: a q, starting with #q, the answer at the end of the run is quit. It
18: permits to run test files in batch with ctest. The former workaround was
19: $ echo q | imach foo.imach
20:
1.195 brouard 21: Revision 1.194 2015/08/18 13:32:00 brouard
22: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
23:
1.194 brouard 24: Revision 1.193 2015/08/04 07:17:42 brouard
25: Summary: 0.98q4
26:
1.193 brouard 27: Revision 1.192 2015/07/16 16:49:02 brouard
28: Summary: Fixing some outputs
29:
1.192 brouard 30: Revision 1.191 2015/07/14 10:00:33 brouard
31: Summary: Some fixes
32:
1.191 brouard 33: Revision 1.190 2015/05/05 08:51:13 brouard
34: Summary: Adding digits in output parameters (7 digits instead of 6)
35:
36: Fix 1+age+.
37:
1.190 brouard 38: Revision 1.189 2015/04/30 14:45:16 brouard
39: Summary: 0.98q2
40:
1.189 brouard 41: Revision 1.188 2015/04/30 08:27:53 brouard
42: *** empty log message ***
43:
1.188 brouard 44: Revision 1.187 2015/04/29 09:11:15 brouard
45: *** empty log message ***
46:
1.187 brouard 47: Revision 1.186 2015/04/23 12:01:52 brouard
48: Summary: V1*age is working now, version 0.98q1
49:
50: Some codes had been disabled in order to simplify and Vn*age was
51: working in the optimization phase, ie, giving correct MLE parameters,
52: but, as usual, outputs were not correct and program core dumped.
53:
1.186 brouard 54: Revision 1.185 2015/03/11 13:26:42 brouard
55: Summary: Inclusion of compile and links command line for Intel Compiler
56:
1.185 brouard 57: Revision 1.184 2015/03/11 11:52:39 brouard
58: Summary: Back from Windows 8. Intel Compiler
59:
1.184 brouard 60: Revision 1.183 2015/03/10 20:34:32 brouard
61: Summary: 0.98q0, trying with directest, mnbrak fixed
62:
63: We use directest instead of original Powell test; probably no
64: incidence on the results, but better justifications;
65: We fixed Numerical Recipes mnbrak routine which was wrong and gave
66: wrong results.
67:
1.183 brouard 68: Revision 1.182 2015/02/12 08:19:57 brouard
69: Summary: Trying to keep directest which seems simpler and more general
70: Author: Nicolas Brouard
71:
1.182 brouard 72: Revision 1.181 2015/02/11 23:22:24 brouard
73: Summary: Comments on Powell added
74:
75: Author:
76:
1.181 brouard 77: Revision 1.180 2015/02/11 17:33:45 brouard
78: Summary: Finishing move from main to function (hpijx and prevalence_limit)
79:
1.180 brouard 80: Revision 1.179 2015/01/04 09:57:06 brouard
81: Summary: back to OS/X
82:
1.179 brouard 83: Revision 1.178 2015/01/04 09:35:48 brouard
84: *** empty log message ***
85:
1.178 brouard 86: Revision 1.177 2015/01/03 18:40:56 brouard
87: Summary: Still testing ilc32 on OSX
88:
1.177 brouard 89: Revision 1.176 2015/01/03 16:45:04 brouard
90: *** empty log message ***
91:
1.176 brouard 92: Revision 1.175 2015/01/03 16:33:42 brouard
93: *** empty log message ***
94:
1.175 brouard 95: Revision 1.174 2015/01/03 16:15:49 brouard
96: Summary: Still in cross-compilation
97:
1.174 brouard 98: Revision 1.173 2015/01/03 12:06:26 brouard
99: Summary: trying to detect cross-compilation
100:
1.173 brouard 101: Revision 1.172 2014/12/27 12:07:47 brouard
102: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
103:
1.172 brouard 104: Revision 1.171 2014/12/23 13:26:59 brouard
105: Summary: Back from Visual C
106:
107: Still problem with utsname.h on Windows
108:
1.171 brouard 109: Revision 1.170 2014/12/23 11:17:12 brouard
110: Summary: Cleaning some \%% back to %%
111:
112: The escape was mandatory for a specific compiler (which one?), but too many warnings.
113:
1.170 brouard 114: Revision 1.169 2014/12/22 23:08:31 brouard
115: Summary: 0.98p
116:
117: Outputs some informations on compiler used, OS etc. Testing on different platforms.
118:
1.169 brouard 119: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 120: Summary: update
1.169 brouard 121:
1.168 brouard 122: Revision 1.167 2014/12/22 13:50:56 brouard
123: Summary: Testing uname and compiler version and if compiled 32 or 64
124:
125: Testing on Linux 64
126:
1.167 brouard 127: Revision 1.166 2014/12/22 11:40:47 brouard
128: *** empty log message ***
129:
1.166 brouard 130: Revision 1.165 2014/12/16 11:20:36 brouard
131: Summary: After compiling on Visual C
132:
133: * imach.c (Module): Merging 1.61 to 1.162
134:
1.165 brouard 135: Revision 1.164 2014/12/16 10:52:11 brouard
136: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
137:
138: * imach.c (Module): Merging 1.61 to 1.162
139:
1.164 brouard 140: Revision 1.163 2014/12/16 10:30:11 brouard
141: * imach.c (Module): Merging 1.61 to 1.162
142:
1.163 brouard 143: Revision 1.162 2014/09/25 11:43:39 brouard
144: Summary: temporary backup 0.99!
145:
1.162 brouard 146: Revision 1.1 2014/09/16 11:06:58 brouard
147: Summary: With some code (wrong) for nlopt
148:
149: Author:
150:
151: Revision 1.161 2014/09/15 20:41:41 brouard
152: Summary: Problem with macro SQR on Intel compiler
153:
1.161 brouard 154: Revision 1.160 2014/09/02 09:24:05 brouard
155: *** empty log message ***
156:
1.160 brouard 157: Revision 1.159 2014/09/01 10:34:10 brouard
158: Summary: WIN32
159: Author: Brouard
160:
1.159 brouard 161: Revision 1.158 2014/08/27 17:11:51 brouard
162: *** empty log message ***
163:
1.158 brouard 164: Revision 1.157 2014/08/27 16:26:55 brouard
165: Summary: Preparing windows Visual studio version
166: Author: Brouard
167:
168: In order to compile on Visual studio, time.h is now correct and time_t
169: and tm struct should be used. difftime should be used but sometimes I
170: just make the differences in raw time format (time(&now).
171: Trying to suppress #ifdef LINUX
172: Add xdg-open for __linux in order to open default browser.
173:
1.157 brouard 174: Revision 1.156 2014/08/25 20:10:10 brouard
175: *** empty log message ***
176:
1.156 brouard 177: Revision 1.155 2014/08/25 18:32:34 brouard
178: Summary: New compile, minor changes
179: Author: Brouard
180:
1.155 brouard 181: Revision 1.154 2014/06/20 17:32:08 brouard
182: Summary: Outputs now all graphs of convergence to period prevalence
183:
1.154 brouard 184: Revision 1.153 2014/06/20 16:45:46 brouard
185: Summary: If 3 live state, convergence to period prevalence on same graph
186: Author: Brouard
187:
1.153 brouard 188: Revision 1.152 2014/06/18 17:54:09 brouard
189: Summary: open browser, use gnuplot on same dir than imach if not found in the path
190:
1.152 brouard 191: Revision 1.151 2014/06/18 16:43:30 brouard
192: *** empty log message ***
193:
1.151 brouard 194: Revision 1.150 2014/06/18 16:42:35 brouard
195: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
196: Author: brouard
197:
1.150 brouard 198: Revision 1.149 2014/06/18 15:51:14 brouard
199: Summary: Some fixes in parameter files errors
200: Author: Nicolas Brouard
201:
1.149 brouard 202: Revision 1.148 2014/06/17 17:38:48 brouard
203: Summary: Nothing new
204: Author: Brouard
205:
206: Just a new packaging for OS/X version 0.98nS
207:
1.148 brouard 208: Revision 1.147 2014/06/16 10:33:11 brouard
209: *** empty log message ***
210:
1.147 brouard 211: Revision 1.146 2014/06/16 10:20:28 brouard
212: Summary: Merge
213: Author: Brouard
214:
215: Merge, before building revised version.
216:
1.146 brouard 217: Revision 1.145 2014/06/10 21:23:15 brouard
218: Summary: Debugging with valgrind
219: Author: Nicolas Brouard
220:
221: Lot of changes in order to output the results with some covariates
222: After the Edimburgh REVES conference 2014, it seems mandatory to
223: improve the code.
224: No more memory valgrind error but a lot has to be done in order to
225: continue the work of splitting the code into subroutines.
226: Also, decodemodel has been improved. Tricode is still not
227: optimal. nbcode should be improved. Documentation has been added in
228: the source code.
229:
1.144 brouard 230: Revision 1.143 2014/01/26 09:45:38 brouard
231: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
232:
233: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
234: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
235:
1.143 brouard 236: Revision 1.142 2014/01/26 03:57:36 brouard
237: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
238:
239: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
240:
1.142 brouard 241: Revision 1.141 2014/01/26 02:42:01 brouard
242: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
243:
1.141 brouard 244: Revision 1.140 2011/09/02 10:37:54 brouard
245: Summary: times.h is ok with mingw32 now.
246:
1.140 brouard 247: Revision 1.139 2010/06/14 07:50:17 brouard
248: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
249: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
250:
1.139 brouard 251: Revision 1.138 2010/04/30 18:19:40 brouard
252: *** empty log message ***
253:
1.138 brouard 254: Revision 1.137 2010/04/29 18:11:38 brouard
255: (Module): Checking covariates for more complex models
256: than V1+V2. A lot of change to be done. Unstable.
257:
1.137 brouard 258: Revision 1.136 2010/04/26 20:30:53 brouard
259: (Module): merging some libgsl code. Fixing computation
260: of likelione (using inter/intrapolation if mle = 0) in order to
261: get same likelihood as if mle=1.
262: Some cleaning of code and comments added.
263:
1.136 brouard 264: Revision 1.135 2009/10/29 15:33:14 brouard
265: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
266:
1.135 brouard 267: Revision 1.134 2009/10/29 13:18:53 brouard
268: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
269:
1.134 brouard 270: Revision 1.133 2009/07/06 10:21:25 brouard
271: just nforces
272:
1.133 brouard 273: Revision 1.132 2009/07/06 08:22:05 brouard
274: Many tings
275:
1.132 brouard 276: Revision 1.131 2009/06/20 16:22:47 brouard
277: Some dimensions resccaled
278:
1.131 brouard 279: Revision 1.130 2009/05/26 06:44:34 brouard
280: (Module): Max Covariate is now set to 20 instead of 8. A
281: lot of cleaning with variables initialized to 0. Trying to make
282: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
283:
1.130 brouard 284: Revision 1.129 2007/08/31 13:49:27 lievre
285: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
286:
1.129 lievre 287: Revision 1.128 2006/06/30 13:02:05 brouard
288: (Module): Clarifications on computing e.j
289:
1.128 brouard 290: Revision 1.127 2006/04/28 18:11:50 brouard
291: (Module): Yes the sum of survivors was wrong since
292: imach-114 because nhstepm was no more computed in the age
293: loop. Now we define nhstepma in the age loop.
294: (Module): In order to speed up (in case of numerous covariates) we
295: compute health expectancies (without variances) in a first step
296: and then all the health expectancies with variances or standard
297: deviation (needs data from the Hessian matrices) which slows the
298: computation.
299: In the future we should be able to stop the program is only health
300: expectancies and graph are needed without standard deviations.
301:
1.127 brouard 302: Revision 1.126 2006/04/28 17:23:28 brouard
303: (Module): Yes the sum of survivors was wrong since
304: imach-114 because nhstepm was no more computed in the age
305: loop. Now we define nhstepma in the age loop.
306: Version 0.98h
307:
1.126 brouard 308: Revision 1.125 2006/04/04 15:20:31 lievre
309: Errors in calculation of health expectancies. Age was not initialized.
310: Forecasting file added.
311:
312: Revision 1.124 2006/03/22 17:13:53 lievre
313: Parameters are printed with %lf instead of %f (more numbers after the comma).
314: The log-likelihood is printed in the log file
315:
316: Revision 1.123 2006/03/20 10:52:43 brouard
317: * imach.c (Module): <title> changed, corresponds to .htm file
318: name. <head> headers where missing.
319:
320: * imach.c (Module): Weights can have a decimal point as for
321: English (a comma might work with a correct LC_NUMERIC environment,
322: otherwise the weight is truncated).
323: Modification of warning when the covariates values are not 0 or
324: 1.
325: Version 0.98g
326:
327: Revision 1.122 2006/03/20 09:45:41 brouard
328: (Module): Weights can have a decimal point as for
329: English (a comma might work with a correct LC_NUMERIC environment,
330: otherwise the weight is truncated).
331: Modification of warning when the covariates values are not 0 or
332: 1.
333: Version 0.98g
334:
335: Revision 1.121 2006/03/16 17:45:01 lievre
336: * imach.c (Module): Comments concerning covariates added
337:
338: * imach.c (Module): refinements in the computation of lli if
339: status=-2 in order to have more reliable computation if stepm is
340: not 1 month. Version 0.98f
341:
342: Revision 1.120 2006/03/16 15:10:38 lievre
343: (Module): refinements in the computation of lli if
344: status=-2 in order to have more reliable computation if stepm is
345: not 1 month. Version 0.98f
346:
347: Revision 1.119 2006/03/15 17:42:26 brouard
348: (Module): Bug if status = -2, the loglikelihood was
349: computed as likelihood omitting the logarithm. Version O.98e
350:
351: Revision 1.118 2006/03/14 18:20:07 brouard
352: (Module): varevsij Comments added explaining the second
353: table of variances if popbased=1 .
354: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
355: (Module): Function pstamp added
356: (Module): Version 0.98d
357:
358: Revision 1.117 2006/03/14 17:16:22 brouard
359: (Module): varevsij Comments added explaining the second
360: table of variances if popbased=1 .
361: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
362: (Module): Function pstamp added
363: (Module): Version 0.98d
364:
365: Revision 1.116 2006/03/06 10:29:27 brouard
366: (Module): Variance-covariance wrong links and
367: varian-covariance of ej. is needed (Saito).
368:
369: Revision 1.115 2006/02/27 12:17:45 brouard
370: (Module): One freematrix added in mlikeli! 0.98c
371:
372: Revision 1.114 2006/02/26 12:57:58 brouard
373: (Module): Some improvements in processing parameter
374: filename with strsep.
375:
376: Revision 1.113 2006/02/24 14:20:24 brouard
377: (Module): Memory leaks checks with valgrind and:
378: datafile was not closed, some imatrix were not freed and on matrix
379: allocation too.
380:
381: Revision 1.112 2006/01/30 09:55:26 brouard
382: (Module): Back to gnuplot.exe instead of wgnuplot.exe
383:
384: Revision 1.111 2006/01/25 20:38:18 brouard
385: (Module): Lots of cleaning and bugs added (Gompertz)
386: (Module): Comments can be added in data file. Missing date values
387: can be a simple dot '.'.
388:
389: Revision 1.110 2006/01/25 00:51:50 brouard
390: (Module): Lots of cleaning and bugs added (Gompertz)
391:
392: Revision 1.109 2006/01/24 19:37:15 brouard
393: (Module): Comments (lines starting with a #) are allowed in data.
394:
395: Revision 1.108 2006/01/19 18:05:42 lievre
396: Gnuplot problem appeared...
397: To be fixed
398:
399: Revision 1.107 2006/01/19 16:20:37 brouard
400: Test existence of gnuplot in imach path
401:
402: Revision 1.106 2006/01/19 13:24:36 brouard
403: Some cleaning and links added in html output
404:
405: Revision 1.105 2006/01/05 20:23:19 lievre
406: *** empty log message ***
407:
408: Revision 1.104 2005/09/30 16:11:43 lievre
409: (Module): sump fixed, loop imx fixed, and simplifications.
410: (Module): If the status is missing at the last wave but we know
411: that the person is alive, then we can code his/her status as -2
412: (instead of missing=-1 in earlier versions) and his/her
413: contributions to the likelihood is 1 - Prob of dying from last
414: health status (= 1-p13= p11+p12 in the easiest case of somebody in
415: the healthy state at last known wave). Version is 0.98
416:
417: Revision 1.103 2005/09/30 15:54:49 lievre
418: (Module): sump fixed, loop imx fixed, and simplifications.
419:
420: Revision 1.102 2004/09/15 17:31:30 brouard
421: Add the possibility to read data file including tab characters.
422:
423: Revision 1.101 2004/09/15 10:38:38 brouard
424: Fix on curr_time
425:
426: Revision 1.100 2004/07/12 18:29:06 brouard
427: Add version for Mac OS X. Just define UNIX in Makefile
428:
429: Revision 1.99 2004/06/05 08:57:40 brouard
430: *** empty log message ***
431:
432: Revision 1.98 2004/05/16 15:05:56 brouard
433: New version 0.97 . First attempt to estimate force of mortality
434: directly from the data i.e. without the need of knowing the health
435: state at each age, but using a Gompertz model: log u =a + b*age .
436: This is the basic analysis of mortality and should be done before any
437: other analysis, in order to test if the mortality estimated from the
438: cross-longitudinal survey is different from the mortality estimated
439: from other sources like vital statistic data.
440:
441: The same imach parameter file can be used but the option for mle should be -3.
442:
1.133 brouard 443: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 444: former routines in order to include the new code within the former code.
445:
446: The output is very simple: only an estimate of the intercept and of
447: the slope with 95% confident intervals.
448:
449: Current limitations:
450: A) Even if you enter covariates, i.e. with the
451: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
452: B) There is no computation of Life Expectancy nor Life Table.
453:
454: Revision 1.97 2004/02/20 13:25:42 lievre
455: Version 0.96d. Population forecasting command line is (temporarily)
456: suppressed.
457:
458: Revision 1.96 2003/07/15 15:38:55 brouard
459: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
460: rewritten within the same printf. Workaround: many printfs.
461:
462: Revision 1.95 2003/07/08 07:54:34 brouard
463: * imach.c (Repository):
464: (Repository): Using imachwizard code to output a more meaningful covariance
465: matrix (cov(a12,c31) instead of numbers.
466:
467: Revision 1.94 2003/06/27 13:00:02 brouard
468: Just cleaning
469:
470: Revision 1.93 2003/06/25 16:33:55 brouard
471: (Module): On windows (cygwin) function asctime_r doesn't
472: exist so I changed back to asctime which exists.
473: (Module): Version 0.96b
474:
475: Revision 1.92 2003/06/25 16:30:45 brouard
476: (Module): On windows (cygwin) function asctime_r doesn't
477: exist so I changed back to asctime which exists.
478:
479: Revision 1.91 2003/06/25 15:30:29 brouard
480: * imach.c (Repository): Duplicated warning errors corrected.
481: (Repository): Elapsed time after each iteration is now output. It
482: helps to forecast when convergence will be reached. Elapsed time
483: is stamped in powell. We created a new html file for the graphs
484: concerning matrix of covariance. It has extension -cov.htm.
485:
486: Revision 1.90 2003/06/24 12:34:15 brouard
487: (Module): Some bugs corrected for windows. Also, when
488: mle=-1 a template is output in file "or"mypar.txt with the design
489: of the covariance matrix to be input.
490:
491: Revision 1.89 2003/06/24 12:30:52 brouard
492: (Module): Some bugs corrected for windows. Also, when
493: mle=-1 a template is output in file "or"mypar.txt with the design
494: of the covariance matrix to be input.
495:
496: Revision 1.88 2003/06/23 17:54:56 brouard
497: * 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.
498:
499: Revision 1.87 2003/06/18 12:26:01 brouard
500: Version 0.96
501:
502: Revision 1.86 2003/06/17 20:04:08 brouard
503: (Module): Change position of html and gnuplot routines and added
504: routine fileappend.
505:
506: Revision 1.85 2003/06/17 13:12:43 brouard
507: * imach.c (Repository): Check when date of death was earlier that
508: current date of interview. It may happen when the death was just
509: prior to the death. In this case, dh was negative and likelihood
510: was wrong (infinity). We still send an "Error" but patch by
511: assuming that the date of death was just one stepm after the
512: interview.
513: (Repository): Because some people have very long ID (first column)
514: we changed int to long in num[] and we added a new lvector for
515: memory allocation. But we also truncated to 8 characters (left
516: truncation)
517: (Repository): No more line truncation errors.
518:
519: Revision 1.84 2003/06/13 21:44:43 brouard
520: * imach.c (Repository): Replace "freqsummary" at a correct
521: place. It differs from routine "prevalence" which may be called
522: many times. Probs is memory consuming and must be used with
523: parcimony.
524: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
525:
526: Revision 1.83 2003/06/10 13:39:11 lievre
527: *** empty log message ***
528:
529: Revision 1.82 2003/06/05 15:57:20 brouard
530: Add log in imach.c and fullversion number is now printed.
531:
532: */
533: /*
534: Interpolated Markov Chain
535:
536: Short summary of the programme:
537:
538: This program computes Healthy Life Expectancies from
539: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
540: first survey ("cross") where individuals from different ages are
541: interviewed on their health status or degree of disability (in the
542: case of a health survey which is our main interest) -2- at least a
543: second wave of interviews ("longitudinal") which measure each change
544: (if any) in individual health status. Health expectancies are
545: computed from the time spent in each health state according to a
546: model. More health states you consider, more time is necessary to reach the
547: Maximum Likelihood of the parameters involved in the model. The
548: simplest model is the multinomial logistic model where pij is the
549: probability to be observed in state j at the second wave
550: conditional to be observed in state i at the first wave. Therefore
551: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
552: 'age' is age and 'sex' is a covariate. If you want to have a more
553: complex model than "constant and age", you should modify the program
554: where the markup *Covariates have to be included here again* invites
555: you to do it. More covariates you add, slower the
556: convergence.
557:
558: The advantage of this computer programme, compared to a simple
559: multinomial logistic model, is clear when the delay between waves is not
560: identical for each individual. Also, if a individual missed an
561: intermediate interview, the information is lost, but taken into
562: account using an interpolation or extrapolation.
563:
564: hPijx is the probability to be observed in state i at age x+h
565: conditional to the observed state i at age x. The delay 'h' can be
566: split into an exact number (nh*stepm) of unobserved intermediate
567: states. This elementary transition (by month, quarter,
568: semester or year) is modelled as a multinomial logistic. The hPx
569: matrix is simply the matrix product of nh*stepm elementary matrices
570: and the contribution of each individual to the likelihood is simply
571: hPijx.
572:
573: Also this programme outputs the covariance matrix of the parameters but also
574: of the life expectancies. It also computes the period (stable) prevalence.
575:
1.133 brouard 576: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
577: Institut national d'études démographiques, Paris.
1.126 brouard 578: This software have been partly granted by Euro-REVES, a concerted action
579: from the European Union.
580: It is copyrighted identically to a GNU software product, ie programme and
581: software can be distributed freely for non commercial use. Latest version
582: can be accessed at http://euroreves.ined.fr/imach .
583:
584: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
585: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
586:
587: **********************************************************************/
588: /*
589: main
590: read parameterfile
591: read datafile
592: concatwav
593: freqsummary
594: if (mle >= 1)
595: mlikeli
596: print results files
597: if mle==1
598: computes hessian
599: read end of parameter file: agemin, agemax, bage, fage, estepm
600: begin-prev-date,...
601: open gnuplot file
602: open html file
1.145 brouard 603: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
604: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
605: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
606: freexexit2 possible for memory heap.
607:
608: h Pij x | pij_nom ficrestpij
609: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
610: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
611: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
612:
613: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
614: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
615: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
616: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
617: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
618:
1.126 brouard 619: forecasting if prevfcast==1 prevforecast call prevalence()
620: health expectancies
621: Variance-covariance of DFLE
622: prevalence()
623: movingaverage()
624: varevsij()
625: if popbased==1 varevsij(,popbased)
626: total life expectancies
627: Variance of period (stable) prevalence
628: end
629: */
630:
1.187 brouard 631: /* #define DEBUG */
632: /* #define DEBUGBRENT */
1.165 brouard 633: #define POWELL /* Instead of NLOPT */
1.192 brouard 634: #define POWELLF1F3 /* Skip test */
1.186 brouard 635: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
636: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 637:
638: #include <math.h>
639: #include <stdio.h>
640: #include <stdlib.h>
641: #include <string.h>
1.159 brouard 642:
643: #ifdef _WIN32
644: #include <io.h>
1.172 brouard 645: #include <windows.h>
646: #include <tchar.h>
1.159 brouard 647: #else
1.126 brouard 648: #include <unistd.h>
1.159 brouard 649: #endif
1.126 brouard 650:
651: #include <limits.h>
652: #include <sys/types.h>
1.171 brouard 653:
654: #if defined(__GNUC__)
655: #include <sys/utsname.h> /* Doesn't work on Windows */
656: #endif
657:
1.126 brouard 658: #include <sys/stat.h>
659: #include <errno.h>
1.159 brouard 660: /* extern int errno; */
1.126 brouard 661:
1.157 brouard 662: /* #ifdef LINUX */
663: /* #include <time.h> */
664: /* #include "timeval.h" */
665: /* #else */
666: /* #include <sys/time.h> */
667: /* #endif */
668:
1.126 brouard 669: #include <time.h>
670:
1.136 brouard 671: #ifdef GSL
672: #include <gsl/gsl_errno.h>
673: #include <gsl/gsl_multimin.h>
674: #endif
675:
1.167 brouard 676:
1.162 brouard 677: #ifdef NLOPT
678: #include <nlopt.h>
679: typedef struct {
680: double (* function)(double [] );
681: } myfunc_data ;
682: #endif
683:
1.126 brouard 684: /* #include <libintl.h> */
685: /* #define _(String) gettext (String) */
686:
1.141 brouard 687: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 688:
689: #define GNUPLOTPROGRAM "gnuplot"
690: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
691: #define FILENAMELENGTH 132
692:
693: #define GLOCK_ERROR_NOPATH -1 /* empty path */
694: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
695:
1.144 brouard 696: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
697: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 698:
699: #define NINTERVMAX 8
1.144 brouard 700: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
701: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
702: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 703: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.126 brouard 704: #define MAXN 20000
1.144 brouard 705: #define YEARM 12. /**< Number of months per year */
1.126 brouard 706: #define AGESUP 130
707: #define AGEBASE 40
1.194 brouard 708: #define AGEOVERFLOW 1.e20
1.164 brouard 709: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 710: #ifdef _WIN32
711: #define DIRSEPARATOR '\\'
712: #define CHARSEPARATOR "\\"
713: #define ODIRSEPARATOR '/'
714: #else
1.126 brouard 715: #define DIRSEPARATOR '/'
716: #define CHARSEPARATOR "/"
717: #define ODIRSEPARATOR '\\'
718: #endif
719:
1.199 ! brouard 720: /* $Id: imach.c,v 1.198 2015/09/03 07:14:39 brouard Exp $ */
1.126 brouard 721: /* $State: Exp $ */
1.196 brouard 722: #include "version.h"
723: char version[]=__IMACH_VERSION__;
1.197 brouard 724: char copyright[]="September 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
1.199 ! brouard 725: char fullversion[]="$Revision: 1.198 $ $Date: 2015/09/03 07:14:39 $";
1.126 brouard 726: char strstart[80];
727: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 728: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 729: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 730: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
731: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
732: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
733: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
734: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
735: int cptcovprodnoage=0; /**< Number of covariate products without age */
736: int cptcoveff=0; /* Total number of covariates to vary for printing results */
737: int cptcov=0; /* Working variable */
1.126 brouard 738: int npar=NPARMAX;
739: int nlstate=2; /* Number of live states */
740: int ndeath=1; /* Number of dead states */
1.130 brouard 741: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 742: int popbased=0;
743:
744: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 745: int maxwav=0; /* Maxim number of waves */
746: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
747: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
748: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 749: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 750: int mle=1, weightopt=0;
1.126 brouard 751: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
752: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
753: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
754: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 755: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 756: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 757: double **matprod2(); /* test */
1.126 brouard 758: double **oldm, **newm, **savm; /* Working pointers to matrices */
759: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 760: /*FILE *fic ; */ /* Used in readdata only */
761: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 762: FILE *ficlog, *ficrespow;
1.130 brouard 763: int globpr=0; /* Global variable for printing or not */
1.126 brouard 764: double fretone; /* Only one call to likelihood */
1.130 brouard 765: long ipmx=0; /* Number of contributions */
1.126 brouard 766: double sw; /* Sum of weights */
767: char filerespow[FILENAMELENGTH];
768: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
769: FILE *ficresilk;
770: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
771: FILE *ficresprobmorprev;
772: FILE *fichtm, *fichtmcov; /* Html File */
773: FILE *ficreseij;
774: char filerese[FILENAMELENGTH];
775: FILE *ficresstdeij;
776: char fileresstde[FILENAMELENGTH];
777: FILE *ficrescveij;
778: char filerescve[FILENAMELENGTH];
779: FILE *ficresvij;
780: char fileresv[FILENAMELENGTH];
781: FILE *ficresvpl;
782: char fileresvpl[FILENAMELENGTH];
783: char title[MAXLINE];
784: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
785: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
786: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
787: char command[FILENAMELENGTH];
788: int outcmd=0;
789:
790: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
791:
792: char filelog[FILENAMELENGTH]; /* Log file */
793: char filerest[FILENAMELENGTH];
794: char fileregp[FILENAMELENGTH];
795: char popfile[FILENAMELENGTH];
796:
797: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
798:
1.157 brouard 799: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
800: /* struct timezone tzp; */
801: /* extern int gettimeofday(); */
802: struct tm tml, *gmtime(), *localtime();
803:
804: extern time_t time();
805:
806: struct tm start_time, end_time, curr_time, last_time, forecast_time;
807: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
808: struct tm tm;
809:
1.126 brouard 810: char strcurr[80], strfor[80];
811:
812: char *endptr;
813: long lval;
814: double dval;
815:
816: #define NR_END 1
817: #define FREE_ARG char*
818: #define FTOL 1.0e-10
819:
820: #define NRANSI
821: #define ITMAX 200
822:
823: #define TOL 2.0e-4
824:
825: #define CGOLD 0.3819660
826: #define ZEPS 1.0e-10
827: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
828:
829: #define GOLD 1.618034
830: #define GLIMIT 100.0
831: #define TINY 1.0e-20
832:
833: static double maxarg1,maxarg2;
834: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
835: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
836:
837: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
838: #define rint(a) floor(a+0.5)
1.166 brouard 839: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 840: #define mytinydouble 1.0e-16
1.166 brouard 841: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
842: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
843: /* static double dsqrarg; */
844: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 845: static double sqrarg;
846: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
847: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
848: int agegomp= AGEGOMP;
849:
850: int imx;
851: int stepm=1;
852: /* Stepm, step in month: minimum step interpolation*/
853:
854: int estepm;
855: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
856:
857: int m,nb;
858: long *num;
1.197 brouard 859: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 860: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
861: covariate for which somebody answered excluding
862: undefined. Usually 2: 0 and 1. */
863: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
864: covariate for which somebody answered including
865: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 866: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
867: double **pmmij, ***probs;
868: double *ageexmed,*agecens;
869: double dateintmean=0;
870:
871: double *weight;
872: int **s; /* Status */
1.141 brouard 873: double *agedc;
1.145 brouard 874: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 875: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 876: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 877: double idx;
878: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.197 brouard 879: int *Tage;
1.145 brouard 880: int *Ndum; /** Freq of modality (tricode */
1.141 brouard 881: int **codtab; /**< codtab=imatrix(1,100,1,10); */
882: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 883: double *lsurv, *lpop, *tpop;
884:
1.143 brouard 885: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
886: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 887:
888: /**************** split *************************/
889: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
890: {
891: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
892: the name of the file (name), its extension only (ext) and its first part of the name (finame)
893: */
894: char *ss; /* pointer */
1.186 brouard 895: int l1=0, l2=0; /* length counters */
1.126 brouard 896:
897: l1 = strlen(path ); /* length of path */
898: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
899: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
900: if ( ss == NULL ) { /* no directory, so determine current directory */
901: strcpy( name, path ); /* we got the fullname name because no directory */
902: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
903: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
904: /* get current working directory */
905: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 906: #ifdef WIN32
907: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
908: #else
909: if (getcwd(dirc, FILENAME_MAX) == NULL) {
910: #endif
1.126 brouard 911: return( GLOCK_ERROR_GETCWD );
912: }
913: /* got dirc from getcwd*/
914: printf(" DIRC = %s \n",dirc);
915: } else { /* strip direcotry from path */
916: ss++; /* after this, the filename */
917: l2 = strlen( ss ); /* length of filename */
918: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
919: strcpy( name, ss ); /* save file name */
920: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 921: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 922: printf(" DIRC2 = %s \n",dirc);
923: }
924: /* We add a separator at the end of dirc if not exists */
925: l1 = strlen( dirc ); /* length of directory */
926: if( dirc[l1-1] != DIRSEPARATOR ){
927: dirc[l1] = DIRSEPARATOR;
928: dirc[l1+1] = 0;
929: printf(" DIRC3 = %s \n",dirc);
930: }
931: ss = strrchr( name, '.' ); /* find last / */
932: if (ss >0){
933: ss++;
934: strcpy(ext,ss); /* save extension */
935: l1= strlen( name);
936: l2= strlen(ss)+1;
937: strncpy( finame, name, l1-l2);
938: finame[l1-l2]= 0;
939: }
940:
941: return( 0 ); /* we're done */
942: }
943:
944:
945: /******************************************/
946:
947: void replace_back_to_slash(char *s, char*t)
948: {
949: int i;
950: int lg=0;
951: i=0;
952: lg=strlen(t);
953: for(i=0; i<= lg; i++) {
954: (s[i] = t[i]);
955: if (t[i]== '\\') s[i]='/';
956: }
957: }
958:
1.132 brouard 959: char *trimbb(char *out, char *in)
1.137 brouard 960: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 961: char *s;
962: s=out;
963: while (*in != '\0'){
1.137 brouard 964: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 965: in++;
966: }
967: *out++ = *in++;
968: }
969: *out='\0';
970: return s;
971: }
972:
1.187 brouard 973: /* char *substrchaine(char *out, char *in, char *chain) */
974: /* { */
975: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
976: /* char *s, *t; */
977: /* t=in;s=out; */
978: /* while ((*in != *chain) && (*in != '\0')){ */
979: /* *out++ = *in++; */
980: /* } */
981:
982: /* /\* *in matches *chain *\/ */
983: /* while ((*in++ == *chain++) && (*in != '\0')){ */
984: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
985: /* } */
986: /* in--; chain--; */
987: /* while ( (*in != '\0')){ */
988: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
989: /* *out++ = *in++; */
990: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
991: /* } */
992: /* *out='\0'; */
993: /* out=s; */
994: /* return out; */
995: /* } */
996: char *substrchaine(char *out, char *in, char *chain)
997: {
998: /* Substract chain 'chain' from 'in', return and output 'out' */
999: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1000:
1001: char *strloc;
1002:
1003: strcpy (out, in);
1004: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1005: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1006: if(strloc != NULL){
1007: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1008: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1009: /* strcpy (strloc, strloc +strlen(chain));*/
1010: }
1011: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1012: return out;
1013: }
1014:
1015:
1.145 brouard 1016: char *cutl(char *blocc, char *alocc, char *in, char occ)
1017: {
1.187 brouard 1018: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1019: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1020: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1021: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1022: */
1.160 brouard 1023: char *s, *t;
1.145 brouard 1024: t=in;s=in;
1025: while ((*in != occ) && (*in != '\0')){
1026: *alocc++ = *in++;
1027: }
1028: if( *in == occ){
1029: *(alocc)='\0';
1030: s=++in;
1031: }
1032:
1033: if (s == t) {/* occ not found */
1034: *(alocc-(in-s))='\0';
1035: in=s;
1036: }
1037: while ( *in != '\0'){
1038: *blocc++ = *in++;
1039: }
1040:
1041: *blocc='\0';
1042: return t;
1043: }
1.137 brouard 1044: char *cutv(char *blocc, char *alocc, char *in, char occ)
1045: {
1.187 brouard 1046: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1047: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1048: gives blocc="abcdef2ghi" and alocc="j".
1049: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1050: */
1051: char *s, *t;
1052: t=in;s=in;
1053: while (*in != '\0'){
1054: while( *in == occ){
1055: *blocc++ = *in++;
1056: s=in;
1057: }
1058: *blocc++ = *in++;
1059: }
1060: if (s == t) /* occ not found */
1061: *(blocc-(in-s))='\0';
1062: else
1063: *(blocc-(in-s)-1)='\0';
1064: in=s;
1065: while ( *in != '\0'){
1066: *alocc++ = *in++;
1067: }
1068:
1069: *alocc='\0';
1070: return s;
1071: }
1072:
1.126 brouard 1073: int nbocc(char *s, char occ)
1074: {
1075: int i,j=0;
1076: int lg=20;
1077: i=0;
1078: lg=strlen(s);
1079: for(i=0; i<= lg; i++) {
1080: if (s[i] == occ ) j++;
1081: }
1082: return j;
1083: }
1084:
1.137 brouard 1085: /* void cutv(char *u,char *v, char*t, char occ) */
1086: /* { */
1087: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1088: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1089: /* gives u="abcdef2ghi" and v="j" *\/ */
1090: /* int i,lg,j,p=0; */
1091: /* i=0; */
1092: /* lg=strlen(t); */
1093: /* for(j=0; j<=lg-1; j++) { */
1094: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1095: /* } */
1.126 brouard 1096:
1.137 brouard 1097: /* for(j=0; j<p; j++) { */
1098: /* (u[j] = t[j]); */
1099: /* } */
1100: /* u[p]='\0'; */
1.126 brouard 1101:
1.137 brouard 1102: /* for(j=0; j<= lg; j++) { */
1103: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1104: /* } */
1105: /* } */
1.126 brouard 1106:
1.160 brouard 1107: #ifdef _WIN32
1108: char * strsep(char **pp, const char *delim)
1109: {
1110: char *p, *q;
1111:
1112: if ((p = *pp) == NULL)
1113: return 0;
1114: if ((q = strpbrk (p, delim)) != NULL)
1115: {
1116: *pp = q + 1;
1117: *q = '\0';
1118: }
1119: else
1120: *pp = 0;
1121: return p;
1122: }
1123: #endif
1124:
1.126 brouard 1125: /********************** nrerror ********************/
1126:
1127: void nrerror(char error_text[])
1128: {
1129: fprintf(stderr,"ERREUR ...\n");
1130: fprintf(stderr,"%s\n",error_text);
1131: exit(EXIT_FAILURE);
1132: }
1133: /*********************** vector *******************/
1134: double *vector(int nl, int nh)
1135: {
1136: double *v;
1137: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1138: if (!v) nrerror("allocation failure in vector");
1139: return v-nl+NR_END;
1140: }
1141:
1142: /************************ free vector ******************/
1143: void free_vector(double*v, int nl, int nh)
1144: {
1145: free((FREE_ARG)(v+nl-NR_END));
1146: }
1147:
1148: /************************ivector *******************************/
1149: int *ivector(long nl,long nh)
1150: {
1151: int *v;
1152: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1153: if (!v) nrerror("allocation failure in ivector");
1154: return v-nl+NR_END;
1155: }
1156:
1157: /******************free ivector **************************/
1158: void free_ivector(int *v, long nl, long nh)
1159: {
1160: free((FREE_ARG)(v+nl-NR_END));
1161: }
1162:
1163: /************************lvector *******************************/
1164: long *lvector(long nl,long nh)
1165: {
1166: long *v;
1167: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1168: if (!v) nrerror("allocation failure in ivector");
1169: return v-nl+NR_END;
1170: }
1171:
1172: /******************free lvector **************************/
1173: void free_lvector(long *v, long nl, long nh)
1174: {
1175: free((FREE_ARG)(v+nl-NR_END));
1176: }
1177:
1178: /******************* imatrix *******************************/
1179: int **imatrix(long nrl, long nrh, long ncl, long nch)
1180: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1181: {
1182: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1183: int **m;
1184:
1185: /* allocate pointers to rows */
1186: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1187: if (!m) nrerror("allocation failure 1 in matrix()");
1188: m += NR_END;
1189: m -= nrl;
1190:
1191:
1192: /* allocate rows and set pointers to them */
1193: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1194: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1195: m[nrl] += NR_END;
1196: m[nrl] -= ncl;
1197:
1198: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1199:
1200: /* return pointer to array of pointers to rows */
1201: return m;
1202: }
1203:
1204: /****************** free_imatrix *************************/
1205: void free_imatrix(m,nrl,nrh,ncl,nch)
1206: int **m;
1207: long nch,ncl,nrh,nrl;
1208: /* free an int matrix allocated by imatrix() */
1209: {
1210: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1211: free((FREE_ARG) (m+nrl-NR_END));
1212: }
1213:
1214: /******************* matrix *******************************/
1215: double **matrix(long nrl, long nrh, long ncl, long nch)
1216: {
1217: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1218: double **m;
1219:
1220: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1221: if (!m) nrerror("allocation failure 1 in matrix()");
1222: m += NR_END;
1223: m -= nrl;
1224:
1225: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1226: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1227: m[nrl] += NR_END;
1228: m[nrl] -= ncl;
1229:
1230: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1231: return m;
1.145 brouard 1232: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1233: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1234: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1235: */
1236: }
1237:
1238: /*************************free matrix ************************/
1239: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1240: {
1241: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1242: free((FREE_ARG)(m+nrl-NR_END));
1243: }
1244:
1245: /******************* ma3x *******************************/
1246: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1247: {
1248: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1249: double ***m;
1250:
1251: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1252: if (!m) nrerror("allocation failure 1 in matrix()");
1253: m += NR_END;
1254: m -= nrl;
1255:
1256: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1257: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1258: m[nrl] += NR_END;
1259: m[nrl] -= ncl;
1260:
1261: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1262:
1263: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1264: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1265: m[nrl][ncl] += NR_END;
1266: m[nrl][ncl] -= nll;
1267: for (j=ncl+1; j<=nch; j++)
1268: m[nrl][j]=m[nrl][j-1]+nlay;
1269:
1270: for (i=nrl+1; i<=nrh; i++) {
1271: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1272: for (j=ncl+1; j<=nch; j++)
1273: m[i][j]=m[i][j-1]+nlay;
1274: }
1275: return m;
1276: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1277: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1278: */
1279: }
1280:
1281: /*************************free ma3x ************************/
1282: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1283: {
1284: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1285: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1286: free((FREE_ARG)(m+nrl-NR_END));
1287: }
1288:
1289: /*************** function subdirf ***********/
1290: char *subdirf(char fileres[])
1291: {
1292: /* Caution optionfilefiname is hidden */
1293: strcpy(tmpout,optionfilefiname);
1294: strcat(tmpout,"/"); /* Add to the right */
1295: strcat(tmpout,fileres);
1296: return tmpout;
1297: }
1298:
1299: /*************** function subdirf2 ***********/
1300: char *subdirf2(char fileres[], char *preop)
1301: {
1302:
1303: /* Caution optionfilefiname is hidden */
1304: strcpy(tmpout,optionfilefiname);
1305: strcat(tmpout,"/");
1306: strcat(tmpout,preop);
1307: strcat(tmpout,fileres);
1308: return tmpout;
1309: }
1310:
1311: /*************** function subdirf3 ***********/
1312: char *subdirf3(char fileres[], char *preop, char *preop2)
1313: {
1314:
1315: /* Caution optionfilefiname is hidden */
1316: strcpy(tmpout,optionfilefiname);
1317: strcat(tmpout,"/");
1318: strcat(tmpout,preop);
1319: strcat(tmpout,preop2);
1320: strcat(tmpout,fileres);
1321: return tmpout;
1322: }
1323:
1.162 brouard 1324: char *asc_diff_time(long time_sec, char ascdiff[])
1325: {
1326: long sec_left, days, hours, minutes;
1327: days = (time_sec) / (60*60*24);
1328: sec_left = (time_sec) % (60*60*24);
1329: hours = (sec_left) / (60*60) ;
1330: sec_left = (sec_left) %(60*60);
1331: minutes = (sec_left) /60;
1332: sec_left = (sec_left) % (60);
1333: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1334: return ascdiff;
1335: }
1336:
1.126 brouard 1337: /***************** f1dim *************************/
1338: extern int ncom;
1339: extern double *pcom,*xicom;
1340: extern double (*nrfunc)(double []);
1341:
1342: double f1dim(double x)
1343: {
1344: int j;
1345: double f;
1346: double *xt;
1347:
1348: xt=vector(1,ncom);
1349: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1350: f=(*nrfunc)(xt);
1351: free_vector(xt,1,ncom);
1352: return f;
1353: }
1354:
1355: /*****************brent *************************/
1356: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1357: {
1358: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1359: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1360: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1361: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1362: * returned function value.
1363: */
1.126 brouard 1364: int iter;
1365: double a,b,d,etemp;
1.159 brouard 1366: double fu=0,fv,fw,fx;
1.164 brouard 1367: double ftemp=0.;
1.126 brouard 1368: double p,q,r,tol1,tol2,u,v,w,x,xm;
1369: double e=0.0;
1370:
1371: a=(ax < cx ? ax : cx);
1372: b=(ax > cx ? ax : cx);
1373: x=w=v=bx;
1374: fw=fv=fx=(*f)(x);
1375: for (iter=1;iter<=ITMAX;iter++) {
1376: xm=0.5*(a+b);
1377: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1378: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1379: printf(".");fflush(stdout);
1380: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1381: #ifdef DEBUGBRENT
1.126 brouard 1382: 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);
1383: 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);
1384: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1385: #endif
1386: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1387: *xmin=x;
1388: return fx;
1389: }
1390: ftemp=fu;
1391: if (fabs(e) > tol1) {
1392: r=(x-w)*(fx-fv);
1393: q=(x-v)*(fx-fw);
1394: p=(x-v)*q-(x-w)*r;
1395: q=2.0*(q-r);
1396: if (q > 0.0) p = -p;
1397: q=fabs(q);
1398: etemp=e;
1399: e=d;
1400: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1401: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1402: else {
1403: d=p/q;
1404: u=x+d;
1405: if (u-a < tol2 || b-u < tol2)
1406: d=SIGN(tol1,xm-x);
1407: }
1408: } else {
1409: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1410: }
1411: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1412: fu=(*f)(u);
1413: if (fu <= fx) {
1414: if (u >= x) a=x; else b=x;
1415: SHFT(v,w,x,u)
1.183 brouard 1416: SHFT(fv,fw,fx,fu)
1417: } else {
1418: if (u < x) a=u; else b=u;
1419: if (fu <= fw || w == x) {
1420: v=w;
1421: w=u;
1422: fv=fw;
1423: fw=fu;
1424: } else if (fu <= fv || v == x || v == w) {
1425: v=u;
1426: fv=fu;
1427: }
1428: }
1.126 brouard 1429: }
1430: nrerror("Too many iterations in brent");
1431: *xmin=x;
1432: return fx;
1433: }
1434:
1435: /****************** mnbrak ***********************/
1436:
1437: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1438: double (*func)(double))
1.183 brouard 1439: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1440: the downhill direction (defined by the function as evaluated at the initial points) and returns
1441: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1442: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1443: */
1.126 brouard 1444: double ulim,u,r,q, dum;
1445: double fu;
1.187 brouard 1446:
1447: double scale=10.;
1448: int iterscale=0;
1449:
1450: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1451: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1452:
1453:
1454: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1455: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1456: /* *bx = *ax - (*ax - *bx)/scale; */
1457: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1458: /* } */
1459:
1.126 brouard 1460: if (*fb > *fa) {
1461: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1462: SHFT(dum,*fb,*fa,dum)
1463: }
1.126 brouard 1464: *cx=(*bx)+GOLD*(*bx-*ax);
1465: *fc=(*func)(*cx);
1.183 brouard 1466: #ifdef DEBUG
1467: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1468: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1469: #endif
1470: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1471: r=(*bx-*ax)*(*fb-*fc);
1472: q=(*bx-*cx)*(*fb-*fa);
1473: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1474: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1475: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1476: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1477: fu=(*func)(u);
1.163 brouard 1478: #ifdef DEBUG
1479: /* f(x)=A(x-u)**2+f(u) */
1480: double A, fparabu;
1481: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1482: fparabu= *fa - A*(*ax-u)*(*ax-u);
1483: 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);
1484: 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 1485: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1486: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1487: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1488: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1489: #endif
1.184 brouard 1490: #ifdef MNBRAKORIGINAL
1.183 brouard 1491: #else
1.191 brouard 1492: /* if (fu > *fc) { */
1493: /* #ifdef DEBUG */
1494: /* printf("mnbrak4 fu > fc \n"); */
1495: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1496: /* #endif */
1497: /* /\* 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 *\\/ *\/ */
1498: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1499: /* dum=u; /\* Shifting c and u *\/ */
1500: /* u = *cx; */
1501: /* *cx = dum; */
1502: /* dum = fu; */
1503: /* fu = *fc; */
1504: /* *fc =dum; */
1505: /* } else { /\* end *\/ */
1506: /* #ifdef DEBUG */
1507: /* printf("mnbrak3 fu < fc \n"); */
1508: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1509: /* #endif */
1510: /* dum=u; /\* Shifting c and u *\/ */
1511: /* u = *cx; */
1512: /* *cx = dum; */
1513: /* dum = fu; */
1514: /* fu = *fc; */
1515: /* *fc =dum; */
1516: /* } */
1.183 brouard 1517: #ifdef DEBUG
1.191 brouard 1518: printf("mnbrak34 fu < or >= fc \n");
1519: fprintf(ficlog, "mnbrak34 fu < fc\n");
1.183 brouard 1520: #endif
1.191 brouard 1521: dum=u; /* Shifting c and u */
1522: u = *cx;
1523: *cx = dum;
1524: dum = fu;
1525: fu = *fc;
1526: *fc =dum;
1.183 brouard 1527: #endif
1.162 brouard 1528: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1529: #ifdef DEBUG
1530: printf("mnbrak2 u after c but before ulim\n");
1531: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1532: #endif
1.126 brouard 1533: fu=(*func)(u);
1534: if (fu < *fc) {
1.183 brouard 1535: #ifdef DEBUG
1536: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1537: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1538: #endif
1.126 brouard 1539: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1540: SHFT(*fb,*fc,fu,(*func)(u))
1541: }
1.162 brouard 1542: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1543: #ifdef DEBUG
1544: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1545: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1546: #endif
1.126 brouard 1547: u=ulim;
1548: fu=(*func)(u);
1.183 brouard 1549: } else { /* u could be left to b (if r > q parabola has a maximum) */
1550: #ifdef DEBUG
1551: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1552: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1553: #endif
1.126 brouard 1554: u=(*cx)+GOLD*(*cx-*bx);
1555: fu=(*func)(u);
1.183 brouard 1556: } /* end tests */
1.126 brouard 1557: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1558: SHFT(*fa,*fb,*fc,fu)
1559: #ifdef DEBUG
1560: 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);
1561: 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);
1562: #endif
1563: } /* 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 1564: }
1565:
1566: /*************** linmin ************************/
1.162 brouard 1567: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1568: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1569: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1570: the value of func at the returned location p . This is actually all accomplished by calling the
1571: routines mnbrak and brent .*/
1.126 brouard 1572: int ncom;
1573: double *pcom,*xicom;
1574: double (*nrfunc)(double []);
1575:
1576: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1577: {
1578: double brent(double ax, double bx, double cx,
1579: double (*f)(double), double tol, double *xmin);
1580: double f1dim(double x);
1581: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1582: double *fc, double (*func)(double));
1583: int j;
1584: double xx,xmin,bx,ax;
1585: double fx,fb,fa;
1.187 brouard 1586:
1587: double scale=10., axs, xxs, xxss; /* Scale added for infinity */
1.126 brouard 1588:
1589: ncom=n;
1590: pcom=vector(1,n);
1591: xicom=vector(1,n);
1592: nrfunc=func;
1593: for (j=1;j<=n;j++) {
1594: pcom[j]=p[j];
1595: xicom[j]=xi[j];
1596: }
1.187 brouard 1597:
1.192 brouard 1598: /* axs=0.0; */
1599: /* xxss=1; /\* 1 and using scale *\/ */
1.187 brouard 1600: xxs=1;
1.192 brouard 1601: /* do{ */
1.187 brouard 1602: ax=0.;
1603: xx= xxs;
1604: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1605: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1606: /* 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)) */
1607: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1608: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1609: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1610: /* 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]]*/
1.192 brouard 1611: /* if (fx != fx){ */
1612: /* xxs=xxs/scale; /\* Trying a smaller xx, closer to initial ax=0 *\/ */
1613: /* 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); */
1614: /* } */
1615: /* }while(fx != fx); */
1.187 brouard 1616:
1.191 brouard 1617: #ifdef DEBUGLINMIN
1618: 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);
1619: #endif
1.187 brouard 1620: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1621: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1622: /* fmin = f(p[j] + xmin * xi[j]) */
1623: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1624: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1625: #ifdef DEBUG
1626: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1627: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1628: #endif
1.191 brouard 1629: #ifdef DEBUGLINMIN
1630: printf("linmin end ");
1631: #endif
1.126 brouard 1632: for (j=1;j<=n;j++) {
1.188 brouard 1633: /* printf(" before xi[%d]=%12.8f", j,xi[j]); */
1.187 brouard 1634: xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
1.189 brouard 1635: /* if(xxs <1.0) */
1636: /* 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 ); */
1.187 brouard 1637: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1638: }
1.189 brouard 1639: /* printf("\n"); */
1.191 brouard 1640: #ifdef DEBUGLINMIN
1641: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1642: for (j=1;j<=n;j++) {
1643: printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]);
1644: if(j % ncovmodel == 0)
1645: printf("\n");
1646: }
1647: #endif
1.126 brouard 1648: free_vector(xicom,1,n);
1649: free_vector(pcom,1,n);
1650: }
1651:
1652:
1653: /*************** powell ************************/
1.162 brouard 1654: /*
1655: Minimization of a function func of n variables. Input consists of an initial starting point
1656: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1657: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1658: such that failure to decrease by more than this amount on one iteration signals doneness. On
1659: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1660: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1661: */
1.126 brouard 1662: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1663: double (*func)(double []))
1664: {
1665: void linmin(double p[], double xi[], int n, double *fret,
1666: double (*func)(double []));
1667: int i,ibig,j;
1668: double del,t,*pt,*ptt,*xit;
1.181 brouard 1669: double directest;
1.126 brouard 1670: double fp,fptt;
1671: double *xits;
1672: int niterf, itmp;
1673:
1674: pt=vector(1,n);
1675: ptt=vector(1,n);
1676: xit=vector(1,n);
1677: xits=vector(1,n);
1678: *fret=(*func)(p);
1679: for (j=1;j<=n;j++) pt[j]=p[j];
1.157 brouard 1680: rcurr_time = time(NULL);
1.126 brouard 1681: for (*iter=1;;++(*iter)) {
1.187 brouard 1682: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1683: ibig=0;
1684: del=0.0;
1.157 brouard 1685: rlast_time=rcurr_time;
1686: /* (void) gettimeofday(&curr_time,&tzp); */
1687: rcurr_time = time(NULL);
1688: curr_time = *localtime(&rcurr_time);
1689: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1690: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1691: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1692: for (i=1;i<=n;i++) {
1.126 brouard 1693: printf(" %d %.12f",i, p[i]);
1694: fprintf(ficlog," %d %.12lf",i, p[i]);
1695: fprintf(ficrespow," %.12lf", p[i]);
1696: }
1697: printf("\n");
1698: fprintf(ficlog,"\n");
1699: fprintf(ficrespow,"\n");fflush(ficrespow);
1700: if(*iter <=3){
1.157 brouard 1701: tml = *localtime(&rcurr_time);
1702: strcpy(strcurr,asctime(&tml));
1703: rforecast_time=rcurr_time;
1.126 brouard 1704: itmp = strlen(strcurr);
1705: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1706: strcurr[itmp-1]='\0';
1.162 brouard 1707: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1708: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1709: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1710: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1711: forecast_time = *localtime(&rforecast_time);
1712: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1713: itmp = strlen(strfor);
1714: if(strfor[itmp-1]=='\n')
1715: strfor[itmp-1]='\0';
1.157 brouard 1716: 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);
1717: 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 1718: }
1719: }
1.187 brouard 1720: for (i=1;i<=n;i++) { /* For each direction i */
1721: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1722: fptt=(*fret);
1723: #ifdef DEBUG
1.164 brouard 1724: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1725: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1726: #endif
1.187 brouard 1727: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1728: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 brouard 1729: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1730: /* Outputs are fret(new point p) p is updated and xit rescaled */
1731: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1732: /* because that direction will be replaced unless the gain del is small */
1733: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1734: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1735: /* with the new direction. */
1.126 brouard 1736: del=fabs(fptt-(*fret));
1737: ibig=i;
1738: }
1739: #ifdef DEBUG
1740: printf("%d %.12e",i,(*fret));
1741: fprintf(ficlog,"%d %.12e",i,(*fret));
1742: for (j=1;j<=n;j++) {
1743: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1744: printf(" x(%d)=%.12e",j,xit[j]);
1745: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1746: }
1747: for(j=1;j<=n;j++) {
1.162 brouard 1748: printf(" p(%d)=%.12e",j,p[j]);
1749: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1750: }
1751: printf("\n");
1752: fprintf(ficlog,"\n");
1753: #endif
1.187 brouard 1754: } /* end loop on each direction i */
1755: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1756: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1757: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1758: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1759: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1760: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1761: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1762: /* decreased of more than 3.84 */
1763: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1764: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1765: /* By adding 10 parameters more the gain should be 18.31 */
1766:
1767: /* Starting the program with initial values given by a former maximization will simply change */
1768: /* the scales of the directions and the directions, because the are reset to canonical directions */
1769: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1770: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1771: #ifdef DEBUG
1772: int k[2],l;
1773: k[0]=1;
1774: k[1]=-1;
1775: printf("Max: %.12e",(*func)(p));
1776: fprintf(ficlog,"Max: %.12e",(*func)(p));
1777: for (j=1;j<=n;j++) {
1778: printf(" %.12e",p[j]);
1779: fprintf(ficlog," %.12e",p[j]);
1780: }
1781: printf("\n");
1782: fprintf(ficlog,"\n");
1783: for(l=0;l<=1;l++) {
1784: for (j=1;j<=n;j++) {
1785: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1786: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1787: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1788: }
1789: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1790: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1791: }
1792: #endif
1793:
1794:
1795: free_vector(xit,1,n);
1796: free_vector(xits,1,n);
1797: free_vector(ptt,1,n);
1798: free_vector(pt,1,n);
1799: return;
1.192 brouard 1800: } /* enough precision */
1.126 brouard 1801: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1802: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1803: ptt[j]=2.0*p[j]-pt[j];
1804: xit[j]=p[j]-pt[j];
1805: pt[j]=p[j];
1806: }
1.181 brouard 1807: fptt=(*func)(ptt); /* f_3 */
1.192 brouard 1808: #ifdef POWELLF1F3
1809: #else
1.161 brouard 1810: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 1811: #endif
1.162 brouard 1812: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1813: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1814: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1815: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1816: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1817: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1818: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1819: #ifdef NRCORIGINAL
1820: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1821: #else
1822: 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 1823: t= t- del*SQR(fp-fptt);
1.183 brouard 1824: #endif
1.182 brouard 1825: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
1.161 brouard 1826: #ifdef DEBUG
1.181 brouard 1827: 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);
1828: 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 1829: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1830: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1831: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1832: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1833: 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);
1834: 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);
1835: #endif
1.183 brouard 1836: #ifdef POWELLORIGINAL
1837: if (t < 0.0) { /* Then we use it for new direction */
1838: #else
1.182 brouard 1839: if (directest*t < 0.0) { /* Contradiction between both tests */
1.192 brouard 1840: printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
1841: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1842: fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1843: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1844: }
1.181 brouard 1845: if (directest < 0.0) { /* Then we use it for new direction */
1846: #endif
1.191 brouard 1847: #ifdef DEBUGLINMIN
1848: printf("Before linmin in direction P%d-P0\n",n);
1849: for (j=1;j<=n;j++) {
1850: printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1851: if(j % ncovmodel == 0)
1852: printf("\n");
1853: }
1854: #endif
1.187 brouard 1855: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.191 brouard 1856: #ifdef DEBUGLINMIN
1857: for (j=1;j<=n;j++) {
1858: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1859: if(j % ncovmodel == 0)
1860: printf("\n");
1861: }
1862: #endif
1.126 brouard 1863: for (j=1;j<=n;j++) {
1.181 brouard 1864: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1865: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 1866: }
1.181 brouard 1867: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1868: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1869:
1.126 brouard 1870: #ifdef DEBUG
1.164 brouard 1871: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1872: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 1873: for(j=1;j<=n;j++){
1874: printf(" %.12e",xit[j]);
1875: fprintf(ficlog," %.12e",xit[j]);
1876: }
1877: printf("\n");
1878: fprintf(ficlog,"\n");
1879: #endif
1.192 brouard 1880: } /* end of t or directest negative */
1881: #ifdef POWELLF1F3
1882: #else
1.162 brouard 1883: } /* end if (fptt < fp) */
1.192 brouard 1884: #endif
1885: } /* loop iteration */
1.126 brouard 1886: }
1887:
1888: /**** Prevalence limit (stable or period prevalence) ****************/
1889:
1890: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1891: {
1892: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1893: matrix by transitions matrix until convergence is reached */
1.169 brouard 1894:
1.126 brouard 1895: int i, ii,j,k;
1896: double min, max, maxmin, maxmax,sumnew=0.;
1.145 brouard 1897: /* double **matprod2(); */ /* test */
1.131 brouard 1898: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1899: double **newm;
1900: double agefin, delaymax=50 ; /* Max number of years to converge */
1.169 brouard 1901:
1.126 brouard 1902: for (ii=1;ii<=nlstate+ndeath;ii++)
1903: for (j=1;j<=nlstate+ndeath;j++){
1904: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1905: }
1.169 brouard 1906:
1907: cov[1]=1.;
1908:
1909: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.126 brouard 1910: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1911: newm=savm;
1912: /* Covariates have to be included here again */
1.138 brouard 1913: cov[2]=agefin;
1.187 brouard 1914: if(nagesqr==1)
1915: cov[3]= agefin*agefin;;
1.138 brouard 1916: for (k=1; k<=cptcovn;k++) {
1.198 brouard 1917: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])];
1918: /* 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 1919: }
1.186 brouard 1920: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.198 brouard 1921: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2];
1.186 brouard 1922: for (k=1; k<=cptcovprod;k++) /* Useless */
1.198 brouard 1923: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])];
1.138 brouard 1924:
1925: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1926: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1927: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 1928: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1929: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 1930: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 1931:
1.126 brouard 1932: savm=oldm;
1933: oldm=newm;
1934: maxmax=0.;
1935: for(j=1;j<=nlstate;j++){
1936: min=1.;
1937: max=0.;
1938: for(i=1; i<=nlstate; i++) {
1939: sumnew=0;
1940: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1941: prlim[i][j]= newm[i][j]/(1-sumnew);
1.145 brouard 1942: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1.126 brouard 1943: max=FMAX(max,prlim[i][j]);
1944: min=FMIN(min,prlim[i][j]);
1945: }
1946: maxmin=max-min;
1947: maxmax=FMAX(maxmax,maxmin);
1.169 brouard 1948: } /* j loop */
1.126 brouard 1949: if(maxmax < ftolpl){
1950: return prlim;
1951: }
1.169 brouard 1952: } /* age loop */
1953: return prlim; /* should not reach here */
1.126 brouard 1954: }
1955:
1956: /*************** transition probabilities ***************/
1957:
1958: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1959: {
1.138 brouard 1960: /* According to parameters values stored in x and the covariate's values stored in cov,
1961: computes the probability to be observed in state j being in state i by appying the
1962: model to the ncovmodel covariates (including constant and age).
1963: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1964: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1965: ncth covariate in the global vector x is given by the formula:
1966: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1967: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1968: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1969: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1970: Outputs ps[i][j] the probability to be observed in j being in j according to
1971: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1972: */
1973: double s1, lnpijopii;
1.126 brouard 1974: /*double t34;*/
1.164 brouard 1975: int i,j, nc, ii, jj;
1.126 brouard 1976:
1977: for(i=1; i<= nlstate; i++){
1978: for(j=1; j<i;j++){
1.138 brouard 1979: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1980: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1981: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1982: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1983: }
1.138 brouard 1984: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1985: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1986: }
1987: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 1988: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1989: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1990: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1991: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 1992: }
1.138 brouard 1993: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 1994: }
1995: }
1996:
1997: for(i=1; i<= nlstate; i++){
1998: s1=0;
1.131 brouard 1999: for(j=1; j<i; j++){
1.138 brouard 2000: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2001: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2002: }
2003: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 2004: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2005: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2006: }
1.138 brouard 2007: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 2008: ps[i][i]=1./(s1+1.);
1.138 brouard 2009: /* Computing other pijs */
1.126 brouard 2010: for(j=1; j<i; j++)
2011: ps[i][j]= exp(ps[i][j])*ps[i][i];
2012: for(j=i+1; j<=nlstate+ndeath; j++)
2013: ps[i][j]= exp(ps[i][j])*ps[i][i];
2014: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2015: } /* end i */
2016:
2017: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2018: for(jj=1; jj<= nlstate+ndeath; jj++){
2019: ps[ii][jj]=0;
2020: ps[ii][ii]=1;
2021: }
2022: }
2023:
1.145 brouard 2024:
2025: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2026: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2027: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2028: /* } */
2029: /* printf("\n "); */
2030: /* } */
2031: /* printf("\n ");printf("%lf ",cov[2]);*/
2032: /*
1.126 brouard 2033: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2034: goto end;*/
2035: return ps;
2036: }
2037:
2038: /**************** Product of 2 matrices ******************/
2039:
1.145 brouard 2040: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2041: {
2042: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2043: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2044: /* in, b, out are matrice of pointers which should have been initialized
2045: before: only the contents of out is modified. The function returns
2046: a pointer to pointers identical to out */
1.145 brouard 2047: int i, j, k;
1.126 brouard 2048: for(i=nrl; i<= nrh; i++)
1.145 brouard 2049: for(k=ncolol; k<=ncoloh; k++){
2050: out[i][k]=0.;
2051: for(j=ncl; j<=nch; j++)
2052: out[i][k] +=in[i][j]*b[j][k];
2053: }
1.126 brouard 2054: return out;
2055: }
2056:
2057:
2058: /************* Higher Matrix Product ***************/
2059:
2060: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2061: {
2062: /* Computes the transition matrix starting at age 'age' over
2063: 'nhstepm*hstepm*stepm' months (i.e. until
2064: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2065: nhstepm*hstepm matrices.
2066: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2067: (typically every 2 years instead of every month which is too big
2068: for the memory).
2069: Model is determined by parameters x and covariates have to be
2070: included manually here.
2071:
2072: */
2073:
2074: int i, j, d, h, k;
1.131 brouard 2075: double **out, cov[NCOVMAX+1];
1.126 brouard 2076: double **newm;
1.187 brouard 2077: double agexact;
1.126 brouard 2078:
2079: /* Hstepm could be zero and should return the unit matrix */
2080: for (i=1;i<=nlstate+ndeath;i++)
2081: for (j=1;j<=nlstate+ndeath;j++){
2082: oldm[i][j]=(i==j ? 1.0 : 0.0);
2083: po[i][j][0]=(i==j ? 1.0 : 0.0);
2084: }
2085: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2086: for(h=1; h <=nhstepm; h++){
2087: for(d=1; d <=hstepm; d++){
2088: newm=savm;
2089: /* Covariates have to be included here again */
2090: cov[1]=1.;
1.187 brouard 2091: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
2092: cov[2]=agexact;
2093: if(nagesqr==1)
2094: cov[3]= agexact*agexact;
1.131 brouard 2095: for (k=1; k<=cptcovn;k++)
1.198 brouard 2096: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])];
1.186 brouard 2097: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
2098: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.198 brouard 2099: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2];
1.145 brouard 2100: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.198 brouard 2101: 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 2102:
2103:
2104: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2105: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2106: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2107: pmij(pmmij,cov,ncovmodel,x,nlstate));
2108: savm=oldm;
2109: oldm=newm;
2110: }
2111: for(i=1; i<=nlstate+ndeath; i++)
2112: for(j=1;j<=nlstate+ndeath;j++) {
2113: po[i][j][h]=newm[i][j];
1.128 brouard 2114: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2115: }
1.128 brouard 2116: /*printf("h=%d ",h);*/
1.126 brouard 2117: } /* end h */
1.128 brouard 2118: /* printf("\n H=%d \n",h); */
1.126 brouard 2119: return po;
2120: }
2121:
1.162 brouard 2122: #ifdef NLOPT
2123: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2124: double fret;
2125: double *xt;
2126: int j;
2127: myfunc_data *d2 = (myfunc_data *) pd;
2128: /* xt = (p1-1); */
2129: xt=vector(1,n);
2130: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2131:
2132: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2133: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2134: printf("Function = %.12lf ",fret);
2135: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2136: printf("\n");
2137: free_vector(xt,1,n);
2138: return fret;
2139: }
2140: #endif
1.126 brouard 2141:
2142: /*************** log-likelihood *************/
2143: double func( double *x)
2144: {
2145: int i, ii, j, k, mi, d, kk;
1.131 brouard 2146: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2147: double **out;
2148: double sw; /* Sum of weights */
2149: double lli; /* Individual log likelihood */
2150: int s1, s2;
2151: double bbh, survp;
2152: long ipmx;
1.187 brouard 2153: double agexact;
1.126 brouard 2154: /*extern weight */
2155: /* We are differentiating ll according to initial status */
2156: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2157: /*for(i=1;i<imx;i++)
2158: printf(" %d\n",s[4][i]);
2159: */
1.162 brouard 2160:
2161: ++countcallfunc;
2162:
1.126 brouard 2163: cov[1]=1.;
2164:
2165: for(k=1; k<=nlstate; k++) ll[k]=0.;
2166:
2167: if(mle==1){
2168: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2169: /* Computes the values of the ncovmodel covariates of the model
2170: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2171: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2172: to be observed in j being in i according to the model.
2173: */
1.145 brouard 2174: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 brouard 2175: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2176: }
1.137 brouard 2177: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2178: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2179: has been calculated etc */
1.126 brouard 2180: for(mi=1; mi<= wav[i]-1; mi++){
2181: for (ii=1;ii<=nlstate+ndeath;ii++)
2182: for (j=1;j<=nlstate+ndeath;j++){
2183: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2184: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2185: }
2186: for(d=0; d<dh[mi][i]; d++){
2187: newm=savm;
1.187 brouard 2188: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2189: cov[2]=agexact;
2190: if(nagesqr==1)
2191: cov[3]= agexact*agexact;
1.126 brouard 2192: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2193: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2194: }
2195: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2196: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2197: savm=oldm;
2198: oldm=newm;
2199: } /* end mult */
2200:
2201: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2202: /* But now since version 0.9 we anticipate for bias at large stepm.
2203: * If stepm is larger than one month (smallest stepm) and if the exact delay
2204: * (in months) between two waves is not a multiple of stepm, we rounded to
2205: * the nearest (and in case of equal distance, to the lowest) interval but now
2206: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2207: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2208: * probability in order to take into account the bias as a fraction of the way
2209: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2210: * -stepm/2 to stepm/2 .
2211: * For stepm=1 the results are the same as for previous versions of Imach.
2212: * For stepm > 1 the results are less biased than in previous versions.
2213: */
2214: s1=s[mw[mi][i]][i];
2215: s2=s[mw[mi+1][i]][i];
2216: bbh=(double)bh[mi][i]/(double)stepm;
2217: /* bias bh is positive if real duration
2218: * is higher than the multiple of stepm and negative otherwise.
2219: */
2220: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2221: if( s2 > nlstate){
2222: /* i.e. if s2 is a death state and if the date of death is known
2223: then the contribution to the likelihood is the probability to
2224: die between last step unit time and current step unit time,
2225: which is also equal to probability to die before dh
2226: minus probability to die before dh-stepm .
2227: In version up to 0.92 likelihood was computed
2228: as if date of death was unknown. Death was treated as any other
2229: health state: the date of the interview describes the actual state
2230: and not the date of a change in health state. The former idea was
2231: to consider that at each interview the state was recorded
2232: (healthy, disable or death) and IMaCh was corrected; but when we
2233: introduced the exact date of death then we should have modified
2234: the contribution of an exact death to the likelihood. This new
2235: contribution is smaller and very dependent of the step unit
2236: stepm. It is no more the probability to die between last interview
2237: and month of death but the probability to survive from last
2238: interview up to one month before death multiplied by the
2239: probability to die within a month. Thanks to Chris
2240: Jackson for correcting this bug. Former versions increased
2241: mortality artificially. The bad side is that we add another loop
2242: which slows down the processing. The difference can be up to 10%
2243: lower mortality.
2244: */
1.183 brouard 2245: /* If, at the beginning of the maximization mostly, the
2246: cumulative probability or probability to be dead is
2247: constant (ie = 1) over time d, the difference is equal to
2248: 0. out[s1][3] = savm[s1][3]: probability, being at state
2249: s1 at precedent wave, to be dead a month before current
2250: wave is equal to probability, being at state s1 at
2251: precedent wave, to be dead at mont of the current
2252: wave. Then the observed probability (that this person died)
2253: is null according to current estimated parameter. In fact,
2254: it should be very low but not zero otherwise the log go to
2255: infinity.
2256: */
2257: /* #ifdef INFINITYORIGINAL */
2258: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2259: /* #else */
2260: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2261: /* lli=log(mytinydouble); */
2262: /* else */
2263: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2264: /* #endif */
2265: lli=log(out[s1][s2] - savm[s1][s2]);
1.126 brouard 2266:
2267: } else if (s2==-2) {
2268: for (j=1,survp=0. ; j<=nlstate; j++)
2269: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2270: /*survp += out[s1][j]; */
2271: lli= log(survp);
2272: }
2273:
2274: else if (s2==-4) {
2275: for (j=3,survp=0. ; j<=nlstate; j++)
2276: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2277: lli= log(survp);
2278: }
2279:
2280: else if (s2==-5) {
2281: for (j=1,survp=0. ; j<=2; j++)
2282: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2283: lli= log(survp);
2284: }
2285:
2286: else{
2287: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2288: /* 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 */
2289: }
2290: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2291: /*if(lli ==000.0)*/
2292: /*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); */
2293: ipmx +=1;
2294: sw += weight[i];
2295: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2296: /* if (lli < log(mytinydouble)){ */
2297: /* 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); */
2298: /* 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]); */
2299: /* } */
1.126 brouard 2300: } /* end of wave */
2301: } /* end of individual */
2302: } else if(mle==2){
2303: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2304: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2305: for(mi=1; mi<= wav[i]-1; mi++){
2306: for (ii=1;ii<=nlstate+ndeath;ii++)
2307: for (j=1;j<=nlstate+ndeath;j++){
2308: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2309: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2310: }
2311: for(d=0; d<=dh[mi][i]; d++){
2312: newm=savm;
1.187 brouard 2313: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2314: cov[2]=agexact;
2315: if(nagesqr==1)
2316: cov[3]= agexact*agexact;
1.126 brouard 2317: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2318: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2319: }
2320: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2321: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2322: savm=oldm;
2323: oldm=newm;
2324: } /* end mult */
2325:
2326: s1=s[mw[mi][i]][i];
2327: s2=s[mw[mi+1][i]][i];
2328: bbh=(double)bh[mi][i]/(double)stepm;
2329: 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 */
2330: ipmx +=1;
2331: sw += weight[i];
2332: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2333: } /* end of wave */
2334: } /* end of individual */
2335: } else if(mle==3){ /* exponential inter-extrapolation */
2336: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2337: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2338: for(mi=1; mi<= wav[i]-1; mi++){
2339: for (ii=1;ii<=nlstate+ndeath;ii++)
2340: for (j=1;j<=nlstate+ndeath;j++){
2341: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2342: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2343: }
2344: for(d=0; d<dh[mi][i]; d++){
2345: newm=savm;
1.187 brouard 2346: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2347: cov[2]=agexact;
2348: if(nagesqr==1)
2349: cov[3]= agexact*agexact;
1.126 brouard 2350: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2351: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2352: }
2353: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2354: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2355: savm=oldm;
2356: oldm=newm;
2357: } /* end mult */
2358:
2359: s1=s[mw[mi][i]][i];
2360: s2=s[mw[mi+1][i]][i];
2361: bbh=(double)bh[mi][i]/(double)stepm;
2362: 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 */
2363: ipmx +=1;
2364: sw += weight[i];
2365: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2366: } /* end of wave */
2367: } /* end of individual */
2368: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2369: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2370: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2371: for(mi=1; mi<= wav[i]-1; mi++){
2372: for (ii=1;ii<=nlstate+ndeath;ii++)
2373: for (j=1;j<=nlstate+ndeath;j++){
2374: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2375: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2376: }
2377: for(d=0; d<dh[mi][i]; d++){
2378: newm=savm;
1.187 brouard 2379: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2380: cov[2]=agexact;
2381: if(nagesqr==1)
2382: cov[3]= agexact*agexact;
1.126 brouard 2383: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2384: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2385: }
2386:
2387: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2388: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2389: savm=oldm;
2390: oldm=newm;
2391: } /* end mult */
2392:
2393: s1=s[mw[mi][i]][i];
2394: s2=s[mw[mi+1][i]][i];
2395: if( s2 > nlstate){
2396: lli=log(out[s1][s2] - savm[s1][s2]);
2397: }else{
2398: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2399: }
2400: ipmx +=1;
2401: sw += weight[i];
2402: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2403: /* 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]); */
2404: } /* end of wave */
2405: } /* end of individual */
2406: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2407: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2408: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2409: for(mi=1; mi<= wav[i]-1; mi++){
2410: for (ii=1;ii<=nlstate+ndeath;ii++)
2411: for (j=1;j<=nlstate+ndeath;j++){
2412: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2413: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2414: }
2415: for(d=0; d<dh[mi][i]; d++){
2416: newm=savm;
1.187 brouard 2417: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2418: cov[2]=agexact;
2419: if(nagesqr==1)
2420: cov[3]= agexact*agexact;
1.126 brouard 2421: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2422: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2423: }
2424:
2425: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2426: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2427: savm=oldm;
2428: oldm=newm;
2429: } /* end mult */
2430:
2431: s1=s[mw[mi][i]][i];
2432: s2=s[mw[mi+1][i]][i];
2433: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2434: ipmx +=1;
2435: sw += weight[i];
2436: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2437: /*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]);*/
2438: } /* end of wave */
2439: } /* end of individual */
2440: } /* End of if */
2441: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2442: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2443: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2444: return -l;
2445: }
2446:
2447: /*************** log-likelihood *************/
2448: double funcone( double *x)
2449: {
2450: /* Same as likeli but slower because of a lot of printf and if */
2451: int i, ii, j, k, mi, d, kk;
1.131 brouard 2452: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2453: double **out;
2454: double lli; /* Individual log likelihood */
2455: double llt;
2456: int s1, s2;
2457: double bbh, survp;
1.187 brouard 2458: double agexact;
1.126 brouard 2459: /*extern weight */
2460: /* We are differentiating ll according to initial status */
2461: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2462: /*for(i=1;i<imx;i++)
2463: printf(" %d\n",s[4][i]);
2464: */
2465: cov[1]=1.;
2466:
2467: for(k=1; k<=nlstate; k++) ll[k]=0.;
2468:
2469: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2470: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2471: for(mi=1; mi<= wav[i]-1; mi++){
2472: for (ii=1;ii<=nlstate+ndeath;ii++)
2473: for (j=1;j<=nlstate+ndeath;j++){
2474: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2475: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2476: }
2477: for(d=0; d<dh[mi][i]; d++){
2478: newm=savm;
1.187 brouard 2479: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2480: cov[2]=agexact;
2481: if(nagesqr==1)
2482: cov[3]= agexact*agexact;
1.126 brouard 2483: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2484: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2485: }
1.187 brouard 2486:
1.145 brouard 2487: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2488: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2489: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2490: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2491: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2492: savm=oldm;
2493: oldm=newm;
2494: } /* end mult */
2495:
2496: s1=s[mw[mi][i]][i];
2497: s2=s[mw[mi+1][i]][i];
2498: bbh=(double)bh[mi][i]/(double)stepm;
2499: /* bias is positive if real duration
2500: * is higher than the multiple of stepm and negative otherwise.
2501: */
2502: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2503: lli=log(out[s1][s2] - savm[s1][s2]);
2504: } else if (s2==-2) {
2505: for (j=1,survp=0. ; j<=nlstate; j++)
2506: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2507: lli= log(survp);
2508: }else if (mle==1){
2509: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2510: } else if(mle==2){
2511: 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 */
2512: } else if(mle==3){ /* exponential inter-extrapolation */
2513: 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 */
2514: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2515: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2516: } else{ /* mle=0 back to 1 */
2517: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2518: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2519: } /* End of if */
2520: ipmx +=1;
2521: sw += weight[i];
2522: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2523: /*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 2524: if(globpr){
1.141 brouard 2525: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1.126 brouard 2526: %11.6f %11.6f %11.6f ", \
2527: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2528: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2529: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2530: llt +=ll[k]*gipmx/gsw;
2531: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2532: }
2533: fprintf(ficresilk," %10.6f\n", -llt);
2534: }
2535: } /* end of wave */
2536: } /* end of individual */
2537: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2538: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2539: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2540: if(globpr==0){ /* First time we count the contributions and weights */
2541: gipmx=ipmx;
2542: gsw=sw;
2543: }
2544: return -l;
2545: }
2546:
2547:
2548: /*************** function likelione ***********/
2549: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2550: {
2551: /* This routine should help understanding what is done with
2552: the selection of individuals/waves and
2553: to check the exact contribution to the likelihood.
2554: Plotting could be done.
2555: */
2556: int k;
2557:
2558: if(*globpri !=0){ /* Just counts and sums, no printings */
2559: strcpy(fileresilk,"ilk");
2560: strcat(fileresilk,fileres);
2561: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2562: printf("Problem with resultfile: %s\n", fileresilk);
2563: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2564: }
2565: 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");
2566: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2567: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2568: for(k=1; k<=nlstate; k++)
2569: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2570: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2571: }
2572:
2573: *fretone=(*funcone)(p);
2574: if(*globpri !=0){
2575: fclose(ficresilk);
2576: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2577: fflush(fichtm);
2578: }
2579: return;
2580: }
2581:
2582:
2583: /*********** Maximum Likelihood Estimation ***************/
2584:
2585: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2586: {
1.165 brouard 2587: int i,j, iter=0;
1.126 brouard 2588: double **xi;
2589: double fret;
2590: double fretone; /* Only one call to likelihood */
2591: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2592:
2593: #ifdef NLOPT
2594: int creturn;
2595: nlopt_opt opt;
2596: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2597: double *lb;
2598: double minf; /* the minimum objective value, upon return */
2599: double * p1; /* Shifted parameters from 0 instead of 1 */
2600: myfunc_data dinst, *d = &dinst;
2601: #endif
2602:
2603:
1.126 brouard 2604: xi=matrix(1,npar,1,npar);
2605: for (i=1;i<=npar;i++)
2606: for (j=1;j<=npar;j++)
2607: xi[i][j]=(i==j ? 1.0 : 0.0);
2608: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2609: strcpy(filerespow,"pow");
2610: strcat(filerespow,fileres);
2611: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2612: printf("Problem with resultfile: %s\n", filerespow);
2613: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2614: }
2615: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2616: for (i=1;i<=nlstate;i++)
2617: for(j=1;j<=nlstate+ndeath;j++)
2618: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2619: fprintf(ficrespow,"\n");
1.162 brouard 2620: #ifdef POWELL
1.126 brouard 2621: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2622: #endif
1.126 brouard 2623:
1.162 brouard 2624: #ifdef NLOPT
2625: #ifdef NEWUOA
2626: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2627: #else
2628: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2629: #endif
2630: lb=vector(0,npar-1);
2631: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2632: nlopt_set_lower_bounds(opt, lb);
2633: nlopt_set_initial_step1(opt, 0.1);
2634:
2635: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2636: d->function = func;
2637: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2638: nlopt_set_min_objective(opt, myfunc, d);
2639: nlopt_set_xtol_rel(opt, ftol);
2640: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2641: printf("nlopt failed! %d\n",creturn);
2642: }
2643: else {
2644: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2645: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2646: iter=1; /* not equal */
2647: }
2648: nlopt_destroy(opt);
2649: #endif
1.126 brouard 2650: free_matrix(xi,1,npar,1,npar);
2651: fclose(ficrespow);
1.180 brouard 2652: printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2653: fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2654: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2655:
2656: }
2657:
2658: /**** Computes Hessian and covariance matrix ***/
2659: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2660: {
2661: double **a,**y,*x,pd;
2662: double **hess;
1.164 brouard 2663: int i, j;
1.126 brouard 2664: int *indx;
2665:
2666: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2667: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2668: void lubksb(double **a, int npar, int *indx, double b[]) ;
2669: void ludcmp(double **a, int npar, int *indx, double *d) ;
2670: double gompertz(double p[]);
2671: hess=matrix(1,npar,1,npar);
2672:
2673: printf("\nCalculation of the hessian matrix. Wait...\n");
2674: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2675: for (i=1;i<=npar;i++){
2676: printf("%d",i);fflush(stdout);
2677: fprintf(ficlog,"%d",i);fflush(ficlog);
2678:
2679: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2680:
2681: /* printf(" %f ",p[i]);
2682: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2683: }
2684:
2685: for (i=1;i<=npar;i++) {
2686: for (j=1;j<=npar;j++) {
2687: if (j>i) {
2688: printf(".%d%d",i,j);fflush(stdout);
2689: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2690: hess[i][j]=hessij(p,delti,i,j,func,npar);
2691:
2692: hess[j][i]=hess[i][j];
2693: /*printf(" %lf ",hess[i][j]);*/
2694: }
2695: }
2696: }
2697: printf("\n");
2698: fprintf(ficlog,"\n");
2699:
2700: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2701: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2702:
2703: a=matrix(1,npar,1,npar);
2704: y=matrix(1,npar,1,npar);
2705: x=vector(1,npar);
2706: indx=ivector(1,npar);
2707: for (i=1;i<=npar;i++)
2708: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2709: ludcmp(a,npar,indx,&pd);
2710:
2711: for (j=1;j<=npar;j++) {
2712: for (i=1;i<=npar;i++) x[i]=0;
2713: x[j]=1;
2714: lubksb(a,npar,indx,x);
2715: for (i=1;i<=npar;i++){
2716: matcov[i][j]=x[i];
2717: }
2718: }
2719:
2720: printf("\n#Hessian matrix#\n");
2721: fprintf(ficlog,"\n#Hessian matrix#\n");
2722: for (i=1;i<=npar;i++) {
2723: for (j=1;j<=npar;j++) {
2724: printf("%.3e ",hess[i][j]);
2725: fprintf(ficlog,"%.3e ",hess[i][j]);
2726: }
2727: printf("\n");
2728: fprintf(ficlog,"\n");
2729: }
2730:
2731: /* Recompute Inverse */
2732: for (i=1;i<=npar;i++)
2733: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2734: ludcmp(a,npar,indx,&pd);
2735:
2736: /* printf("\n#Hessian matrix recomputed#\n");
2737:
2738: for (j=1;j<=npar;j++) {
2739: for (i=1;i<=npar;i++) x[i]=0;
2740: x[j]=1;
2741: lubksb(a,npar,indx,x);
2742: for (i=1;i<=npar;i++){
2743: y[i][j]=x[i];
2744: printf("%.3e ",y[i][j]);
2745: fprintf(ficlog,"%.3e ",y[i][j]);
2746: }
2747: printf("\n");
2748: fprintf(ficlog,"\n");
2749: }
2750: */
2751:
2752: free_matrix(a,1,npar,1,npar);
2753: free_matrix(y,1,npar,1,npar);
2754: free_vector(x,1,npar);
2755: free_ivector(indx,1,npar);
2756: free_matrix(hess,1,npar,1,npar);
2757:
2758:
2759: }
2760:
2761: /*************** hessian matrix ****************/
2762: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2763: {
2764: int i;
2765: int l=1, lmax=20;
2766: double k1,k2;
1.132 brouard 2767: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2768: double res;
2769: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2770: double fx;
2771: int k=0,kmax=10;
2772: double l1;
2773:
2774: fx=func(x);
2775: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2776: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2777: l1=pow(10,l);
2778: delts=delt;
2779: for(k=1 ; k <kmax; k=k+1){
2780: delt = delta*(l1*k);
2781: p2[theta]=x[theta] +delt;
1.145 brouard 2782: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2783: p2[theta]=x[theta]-delt;
2784: k2=func(p2)-fx;
2785: /*res= (k1-2.0*fx+k2)/delt/delt; */
2786: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2787:
1.132 brouard 2788: #ifdef DEBUGHESS
1.126 brouard 2789: 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);
2790: 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);
2791: #endif
2792: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2793: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2794: k=kmax;
2795: }
2796: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 2797: k=kmax; l=lmax*10;
1.126 brouard 2798: }
2799: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2800: delts=delt;
2801: }
2802: }
2803: }
2804: delti[theta]=delts;
2805: return res;
2806:
2807: }
2808:
2809: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2810: {
2811: int i;
1.164 brouard 2812: int l=1, lmax=20;
1.126 brouard 2813: double k1,k2,k3,k4,res,fx;
1.132 brouard 2814: double p2[MAXPARM+1];
1.126 brouard 2815: int k;
2816:
2817: fx=func(x);
2818: for (k=1; k<=2; k++) {
2819: for (i=1;i<=npar;i++) p2[i]=x[i];
2820: p2[thetai]=x[thetai]+delti[thetai]/k;
2821: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2822: k1=func(p2)-fx;
2823:
2824: p2[thetai]=x[thetai]+delti[thetai]/k;
2825: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2826: k2=func(p2)-fx;
2827:
2828: p2[thetai]=x[thetai]-delti[thetai]/k;
2829: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2830: k3=func(p2)-fx;
2831:
2832: p2[thetai]=x[thetai]-delti[thetai]/k;
2833: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2834: k4=func(p2)-fx;
2835: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2836: #ifdef DEBUG
2837: 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);
2838: 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);
2839: #endif
2840: }
2841: return res;
2842: }
2843:
2844: /************** Inverse of matrix **************/
2845: void ludcmp(double **a, int n, int *indx, double *d)
2846: {
2847: int i,imax,j,k;
2848: double big,dum,sum,temp;
2849: double *vv;
2850:
2851: vv=vector(1,n);
2852: *d=1.0;
2853: for (i=1;i<=n;i++) {
2854: big=0.0;
2855: for (j=1;j<=n;j++)
2856: if ((temp=fabs(a[i][j])) > big) big=temp;
2857: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2858: vv[i]=1.0/big;
2859: }
2860: for (j=1;j<=n;j++) {
2861: for (i=1;i<j;i++) {
2862: sum=a[i][j];
2863: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2864: a[i][j]=sum;
2865: }
2866: big=0.0;
2867: for (i=j;i<=n;i++) {
2868: sum=a[i][j];
2869: for (k=1;k<j;k++)
2870: sum -= a[i][k]*a[k][j];
2871: a[i][j]=sum;
2872: if ( (dum=vv[i]*fabs(sum)) >= big) {
2873: big=dum;
2874: imax=i;
2875: }
2876: }
2877: if (j != imax) {
2878: for (k=1;k<=n;k++) {
2879: dum=a[imax][k];
2880: a[imax][k]=a[j][k];
2881: a[j][k]=dum;
2882: }
2883: *d = -(*d);
2884: vv[imax]=vv[j];
2885: }
2886: indx[j]=imax;
2887: if (a[j][j] == 0.0) a[j][j]=TINY;
2888: if (j != n) {
2889: dum=1.0/(a[j][j]);
2890: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2891: }
2892: }
2893: free_vector(vv,1,n); /* Doesn't work */
2894: ;
2895: }
2896:
2897: void lubksb(double **a, int n, int *indx, double b[])
2898: {
2899: int i,ii=0,ip,j;
2900: double sum;
2901:
2902: for (i=1;i<=n;i++) {
2903: ip=indx[i];
2904: sum=b[ip];
2905: b[ip]=b[i];
2906: if (ii)
2907: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2908: else if (sum) ii=i;
2909: b[i]=sum;
2910: }
2911: for (i=n;i>=1;i--) {
2912: sum=b[i];
2913: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2914: b[i]=sum/a[i][i];
2915: }
2916: }
2917:
2918: void pstamp(FILE *fichier)
2919: {
1.196 brouard 2920: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 2921: }
2922:
2923: /************ Frequencies ********************/
2924: 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[])
2925: { /* Some frequencies */
2926:
1.164 brouard 2927: int i, m, jk, j1, bool, z1,j;
1.126 brouard 2928: int first;
2929: double ***freq; /* Frequencies */
2930: double *pp, **prop;
2931: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2932: char fileresp[FILENAMELENGTH];
2933:
2934: pp=vector(1,nlstate);
2935: prop=matrix(1,nlstate,iagemin,iagemax+3);
2936: strcpy(fileresp,"p");
2937: strcat(fileresp,fileres);
2938: if((ficresp=fopen(fileresp,"w"))==NULL) {
2939: printf("Problem with prevalence resultfile: %s\n", fileresp);
2940: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2941: exit(0);
2942: }
2943: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2944: j1=0;
2945:
2946: j=cptcoveff;
2947: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2948:
2949: first=1;
2950:
1.169 brouard 2951: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2952: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2953: /* j1++; */
1.145 brouard 2954: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 2955: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2956: scanf("%d", i);*/
2957: for (i=-5; i<=nlstate+ndeath; i++)
2958: for (jk=-5; jk<=nlstate+ndeath; jk++)
2959: for(m=iagemin; m <= iagemax+3; m++)
2960: freq[i][jk][m]=0;
1.143 brouard 2961:
2962: for (i=1; i<=nlstate; i++)
2963: for(m=iagemin; m <= iagemax+3; m++)
2964: prop[i][m]=0;
1.126 brouard 2965:
2966: dateintsum=0;
2967: k2cpt=0;
2968: for (i=1; i<=imx; i++) {
2969: bool=1;
1.144 brouard 2970: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2971: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 2972: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
1.145 brouard 2973: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 2974: bool=0;
1.198 brouard 2975: /* 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",
2976: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
2977: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
2978: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
1.144 brouard 2979: }
1.126 brouard 2980: }
1.144 brouard 2981:
1.126 brouard 2982: if (bool==1){
2983: for(m=firstpass; m<=lastpass; m++){
2984: k2=anint[m][i]+(mint[m][i]/12.);
2985: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2986: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2987: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2988: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2989: if (m<lastpass) {
2990: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2991: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2992: }
2993:
2994: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2995: dateintsum=dateintsum+k2;
2996: k2cpt++;
2997: }
2998: /*}*/
2999: }
3000: }
1.145 brouard 3001: } /* end i */
1.126 brouard 3002:
3003: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
3004: pstamp(ficresp);
3005: if (cptcovn>0) {
3006: fprintf(ficresp, "\n#********** Variable ");
1.198 brouard 3007: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 3008: fprintf(ficresp, "**********\n#");
1.143 brouard 3009: fprintf(ficlog, "\n#********** Variable ");
1.198 brouard 3010: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.143 brouard 3011: fprintf(ficlog, "**********\n#");
1.126 brouard 3012: }
3013: for(i=1; i<=nlstate;i++)
3014: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
3015: fprintf(ficresp, "\n");
3016:
3017: for(i=iagemin; i <= iagemax+3; i++){
3018: if(i==iagemax+3){
3019: fprintf(ficlog,"Total");
3020: }else{
3021: if(first==1){
3022: first=0;
3023: printf("See log file for details...\n");
3024: }
3025: fprintf(ficlog,"Age %d", i);
3026: }
3027: for(jk=1; jk <=nlstate ; jk++){
3028: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
3029: pp[jk] += freq[jk][m][i];
3030: }
3031: for(jk=1; jk <=nlstate ; jk++){
3032: for(m=-1, pos=0; m <=0 ; m++)
3033: pos += freq[jk][m][i];
3034: if(pp[jk]>=1.e-10){
3035: if(first==1){
1.132 brouard 3036: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 3037: }
3038: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3039: }else{
3040: if(first==1)
3041: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3042: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3043: }
3044: }
3045:
3046: for(jk=1; jk <=nlstate ; jk++){
3047: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
3048: pp[jk] += freq[jk][m][i];
3049: }
3050: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
3051: pos += pp[jk];
3052: posprop += prop[jk][i];
3053: }
3054: for(jk=1; jk <=nlstate ; jk++){
3055: if(pos>=1.e-5){
3056: if(first==1)
3057: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3058: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3059: }else{
3060: if(first==1)
3061: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3062: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3063: }
3064: if( i <= iagemax){
3065: if(pos>=1.e-5){
3066: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
3067: /*probs[i][jk][j1]= pp[jk]/pos;*/
3068: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
3069: }
3070: else
3071: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
3072: }
3073: }
3074:
3075: for(jk=-1; jk <=nlstate+ndeath; jk++)
3076: for(m=-1; m <=nlstate+ndeath; m++)
3077: if(freq[jk][m][i] !=0 ) {
3078: if(first==1)
3079: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
3080: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
3081: }
3082: if(i <= iagemax)
3083: fprintf(ficresp,"\n");
3084: if(first==1)
3085: printf("Others in log...\n");
3086: fprintf(ficlog,"\n");
3087: }
1.145 brouard 3088: /*}*/
1.126 brouard 3089: }
3090: dateintmean=dateintsum/k2cpt;
3091:
3092: fclose(ficresp);
3093: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
3094: free_vector(pp,1,nlstate);
3095: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
3096: /* End of Freq */
3097: }
3098:
3099: /************ Prevalence ********************/
3100: 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)
3101: {
3102: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3103: in each health status at the date of interview (if between dateprev1 and dateprev2).
3104: We still use firstpass and lastpass as another selection.
3105: */
3106:
1.164 brouard 3107: int i, m, jk, j1, bool, z1,j;
3108:
3109: double **prop;
3110: double posprop;
1.126 brouard 3111: double y2; /* in fractional years */
3112: int iagemin, iagemax;
1.145 brouard 3113: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 3114:
3115: iagemin= (int) agemin;
3116: iagemax= (int) agemax;
3117: /*pp=vector(1,nlstate);*/
3118: prop=matrix(1,nlstate,iagemin,iagemax+3);
3119: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3120: j1=0;
3121:
1.145 brouard 3122: /*j=cptcoveff;*/
1.126 brouard 3123: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3124:
1.145 brouard 3125: first=1;
3126: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
3127: /*for(i1=1; i1<=ncodemax[k1];i1++){
3128: j1++;*/
1.126 brouard 3129:
3130: for (i=1; i<=nlstate; i++)
3131: for(m=iagemin; m <= iagemax+3; m++)
3132: prop[i][m]=0.0;
3133:
3134: for (i=1; i<=imx; i++) { /* Each individual */
3135: bool=1;
3136: if (cptcovn>0) {
3137: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 3138: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
1.126 brouard 3139: bool=0;
3140: }
3141: if (bool==1) {
3142: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
3143: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3144: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3145: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3146: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3147: 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);
3148: if (s[m][i]>0 && s[m][i]<=nlstate) {
3149: /*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]]);*/
3150: prop[s[m][i]][(int)agev[m][i]] += weight[i];
3151: prop[s[m][i]][iagemax+3] += weight[i];
3152: }
3153: }
3154: } /* end selection of waves */
3155: }
3156: }
3157: for(i=iagemin; i <= iagemax+3; i++){
3158: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3159: posprop += prop[jk][i];
3160: }
1.145 brouard 3161:
1.126 brouard 3162: for(jk=1; jk <=nlstate ; jk++){
3163: if( i <= iagemax){
3164: if(posprop>=1.e-5){
3165: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 3166: } else{
3167: if(first==1){
3168: first=0;
3169: 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]);
3170: }
3171: }
1.126 brouard 3172: }
3173: }/* end jk */
3174: }/* end i */
1.145 brouard 3175: /*} *//* end i1 */
3176: } /* end j1 */
1.126 brouard 3177:
3178: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3179: /*free_vector(pp,1,nlstate);*/
3180: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3181: } /* End of prevalence */
3182:
3183: /************* Waves Concatenation ***************/
3184:
3185: 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)
3186: {
3187: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3188: Death is a valid wave (if date is known).
3189: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3190: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3191: and mw[mi+1][i]. dh depends on stepm.
3192: */
3193:
3194: int i, mi, m;
3195: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3196: double sum=0., jmean=0.;*/
3197: int first;
3198: int j, k=0,jk, ju, jl;
3199: double sum=0.;
3200: first=0;
1.164 brouard 3201: jmin=100000;
1.126 brouard 3202: jmax=-1;
3203: jmean=0.;
3204: for(i=1; i<=imx; i++){
3205: mi=0;
3206: m=firstpass;
3207: while(s[m][i] <= nlstate){
3208: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
3209: mw[++mi][i]=m;
3210: if(m >=lastpass)
3211: break;
3212: else
3213: m++;
3214: }/* end while */
3215: if (s[m][i] > nlstate){
3216: mi++; /* Death is another wave */
3217: /* if(mi==0) never been interviewed correctly before death */
3218: /* Only death is a correct wave */
3219: mw[mi][i]=m;
3220: }
3221:
3222: wav[i]=mi;
3223: if(mi==0){
3224: nbwarn++;
3225: if(first==0){
3226: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3227: first=1;
3228: }
3229: if(first==1){
3230: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3231: }
3232: } /* end mi==0 */
3233: } /* End individuals */
3234:
3235: for(i=1; i<=imx; i++){
3236: for(mi=1; mi<wav[i];mi++){
3237: if (stepm <=0)
3238: dh[mi][i]=1;
3239: else{
3240: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3241: if (agedc[i] < 2*AGESUP) {
3242: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3243: if(j==0) j=1; /* Survives at least one month after exam */
3244: else if(j<0){
3245: nberr++;
3246: 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]);
3247: j=1; /* Temporary Dangerous patch */
3248: 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);
3249: 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]);
3250: 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);
3251: }
3252: k=k+1;
3253: if (j >= jmax){
3254: jmax=j;
3255: ijmax=i;
3256: }
3257: if (j <= jmin){
3258: jmin=j;
3259: ijmin=i;
3260: }
3261: sum=sum+j;
3262: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3263: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3264: }
3265: }
3266: else{
3267: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3268: /* 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]); */
3269:
3270: k=k+1;
3271: if (j >= jmax) {
3272: jmax=j;
3273: ijmax=i;
3274: }
3275: else if (j <= jmin){
3276: jmin=j;
3277: ijmin=i;
3278: }
3279: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3280: /*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]);*/
3281: if(j<0){
3282: nberr++;
3283: 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]);
3284: 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]);
3285: }
3286: sum=sum+j;
3287: }
3288: jk= j/stepm;
3289: jl= j -jk*stepm;
3290: ju= j -(jk+1)*stepm;
3291: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3292: if(jl==0){
3293: dh[mi][i]=jk;
3294: bh[mi][i]=0;
3295: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 3296: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 3297: dh[mi][i]=jk+1;
3298: bh[mi][i]=ju;
3299: }
3300: }else{
3301: if(jl <= -ju){
3302: dh[mi][i]=jk;
3303: bh[mi][i]=jl; /* bias is positive if real duration
3304: * is higher than the multiple of stepm and negative otherwise.
3305: */
3306: }
3307: else{
3308: dh[mi][i]=jk+1;
3309: bh[mi][i]=ju;
3310: }
3311: if(dh[mi][i]==0){
3312: dh[mi][i]=1; /* At least one step */
3313: bh[mi][i]=ju; /* At least one step */
3314: /* 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);*/
3315: }
3316: } /* end if mle */
3317: }
3318: } /* end wave */
3319: }
3320: jmean=sum/k;
3321: 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 3322: 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 3323: }
3324:
3325: /*********** Tricode ****************************/
1.145 brouard 3326: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 3327: {
1.144 brouard 3328: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3329: /* 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 3330: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 3331: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 3332: * nbcode[Tvar[j]][1]=
1.144 brouard 3333: */
1.130 brouard 3334:
1.145 brouard 3335: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 3336: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 3337: int cptcode=0; /* Modality max of covariates j */
3338: int modmincovj=0; /* Modality min of covariates j */
3339:
3340:
1.126 brouard 3341: cptcoveff=0;
3342:
1.144 brouard 3343: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 3344:
1.145 brouard 3345: /* Loop on covariates without age and products */
1.186 brouard 3346: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
1.192 brouard 3347: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.186 brouard 3348: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.136 brouard 3349: modality of this covariate Vj*/
1.145 brouard 3350: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3351: * If product of Vn*Vm, still boolean *:
3352: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3353: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3354: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 3355: modality of the nth covariate of individual i. */
1.145 brouard 3356: if (ij > modmaxcovj)
3357: modmaxcovj=ij;
3358: else if (ij < modmincovj)
3359: modmincovj=ij;
3360: if ((ij < -1) && (ij > NCOVMAX)){
3361: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3362: exit(1);
3363: }else
1.136 brouard 3364: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 3365: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 3366: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 3367: /* getting the maximum value of the modality of the covariate
3368: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3369: female is 1, then modmaxcovj=1.*/
1.192 brouard 3370: } /* end for loop on individuals i */
1.145 brouard 3371: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.192 brouard 3372: 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 3373: cptcode=modmaxcovj;
1.137 brouard 3374: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 3375: /*for (i=0; i<=cptcode; i++) {*/
1.192 brouard 3376: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
3377: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3378: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3379: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
3380: if( k != -1){
3381: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
3382: covariate for which somebody answered excluding
3383: undefined. Usually 2: 0 and 1. */
3384: }
3385: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
3386: covariate for which somebody answered including
3387: undefined. Usually 3: -1, 0 and 1. */
1.145 brouard 3388: }
3389: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3390: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3391: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3392:
1.136 brouard 3393: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 3394: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3395: 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 3396: modmincovj=3; modmaxcovj = 7;
1.186 brouard 3397: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3398: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3399: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 3400: nbcode[Tvar[j]][ij]=k;
3401: nbcode[Tvar[j]][1]=0;
3402: nbcode[Tvar[j]][2]=1;
3403: nbcode[Tvar[j]][3]=2;
1.197 brouard 3404: To be continued (not working yet).
1.145 brouard 3405: */
1.197 brouard 3406: ij=0; /* ij is similar to i but can jump over null modalities */
3407: 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*/
3408: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
1.192 brouard 3409: break;
3410: }
3411: ij++;
1.197 brouard 3412: 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 3413: cptcode = ij; /* New max modality for covar j */
3414: } /* end of loop on modality i=-1 to 1 or more */
3415:
3416: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
3417: /* /\*recode from 0 *\/ */
3418: /* k is a modality. If we have model=V1+V1*sex */
3419: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3420: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
3421: /* } */
3422: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
3423: /* if (ij > ncodemax[j]) { */
3424: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3425: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3426: /* break; */
3427: /* } */
3428: /* } /\* end of loop on modality k *\/ */
1.137 brouard 3429: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3430:
1.145 brouard 3431: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3432:
1.187 brouard 3433: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.145 brouard 3434: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3435: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.187 brouard 3436: Ndum[ij]++; /* Might be supersed V1 + V1*age */
1.145 brouard 3437: }
1.126 brouard 3438:
1.192 brouard 3439: ij=0;
1.145 brouard 3440: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3441: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3442: if((Ndum[i]!=0) && (i<=ncovcol)){
1.192 brouard 3443: ij++;
1.145 brouard 3444: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3445: Tvaraff[ij]=i; /*For printing (unclear) */
1.192 brouard 3446: }else{
3447: /* Tvaraff[ij]=0; */
3448: }
1.126 brouard 3449: }
1.192 brouard 3450: /* ij--; */
1.144 brouard 3451: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3452:
1.126 brouard 3453: }
3454:
1.145 brouard 3455:
1.126 brouard 3456: /*********** Health Expectancies ****************/
3457:
1.127 brouard 3458: 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 3459:
3460: {
3461: /* Health expectancies, no variances */
1.164 brouard 3462: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3463: int nhstepma, nstepma; /* Decreasing with age */
3464: double age, agelim, hf;
3465: double ***p3mat;
3466: double eip;
3467:
3468: pstamp(ficreseij);
3469: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3470: fprintf(ficreseij,"# Age");
3471: for(i=1; i<=nlstate;i++){
3472: for(j=1; j<=nlstate;j++){
3473: fprintf(ficreseij," e%1d%1d ",i,j);
3474: }
3475: fprintf(ficreseij," e%1d. ",i);
3476: }
3477: fprintf(ficreseij,"\n");
3478:
3479:
3480: if(estepm < stepm){
3481: printf ("Problem %d lower than %d\n",estepm, stepm);
3482: }
3483: else hstepm=estepm;
3484: /* We compute the life expectancy from trapezoids spaced every estepm months
3485: * This is mainly to measure the difference between two models: for example
3486: * if stepm=24 months pijx are given only every 2 years and by summing them
3487: * we are calculating an estimate of the Life Expectancy assuming a linear
3488: * progression in between and thus overestimating or underestimating according
3489: * to the curvature of the survival function. If, for the same date, we
3490: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3491: * to compare the new estimate of Life expectancy with the same linear
3492: * hypothesis. A more precise result, taking into account a more precise
3493: * curvature will be obtained if estepm is as small as stepm. */
3494:
3495: /* For example we decided to compute the life expectancy with the smallest unit */
3496: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3497: nhstepm is the number of hstepm from age to agelim
3498: nstepm is the number of stepm from age to agelin.
3499: Look at hpijx to understand the reason of that which relies in memory size
3500: and note for a fixed period like estepm months */
3501: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3502: survival function given by stepm (the optimization length). Unfortunately it
3503: means that if the survival funtion is printed only each two years of age and if
3504: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3505: results. So we changed our mind and took the option of the best precision.
3506: */
3507: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3508:
3509: agelim=AGESUP;
3510: /* If stepm=6 months */
3511: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3512: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3513:
3514: /* nhstepm age range expressed in number of stepm */
3515: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3516: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3517: /* if (stepm >= YEARM) hstepm=1;*/
3518: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3519: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3520:
3521: for (age=bage; age<=fage; age ++){
3522: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3523: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3524: /* if (stepm >= YEARM) hstepm=1;*/
3525: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3526:
3527: /* If stepm=6 months */
3528: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3529: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3530:
3531: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3532:
3533: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3534:
3535: printf("%d|",(int)age);fflush(stdout);
3536: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3537:
3538: /* Computing expectancies */
3539: for(i=1; i<=nlstate;i++)
3540: for(j=1; j<=nlstate;j++)
3541: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3542: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3543:
3544: /* 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]);*/
3545:
3546: }
3547:
3548: fprintf(ficreseij,"%3.0f",age );
3549: for(i=1; i<=nlstate;i++){
3550: eip=0;
3551: for(j=1; j<=nlstate;j++){
3552: eip +=eij[i][j][(int)age];
3553: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3554: }
3555: fprintf(ficreseij,"%9.4f", eip );
3556: }
3557: fprintf(ficreseij,"\n");
3558:
3559: }
3560: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3561: printf("\n");
3562: fprintf(ficlog,"\n");
3563:
3564: }
3565:
1.127 brouard 3566: 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 3567:
3568: {
3569: /* Covariances of health expectancies eij and of total life expectancies according
3570: to initial status i, ei. .
3571: */
3572: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3573: int nhstepma, nstepma; /* Decreasing with age */
3574: double age, agelim, hf;
3575: double ***p3matp, ***p3matm, ***varhe;
3576: double **dnewm,**doldm;
3577: double *xp, *xm;
3578: double **gp, **gm;
3579: double ***gradg, ***trgradg;
3580: int theta;
3581:
3582: double eip, vip;
3583:
3584: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3585: xp=vector(1,npar);
3586: xm=vector(1,npar);
3587: dnewm=matrix(1,nlstate*nlstate,1,npar);
3588: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3589:
3590: pstamp(ficresstdeij);
3591: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3592: fprintf(ficresstdeij,"# Age");
3593: for(i=1; i<=nlstate;i++){
3594: for(j=1; j<=nlstate;j++)
3595: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3596: fprintf(ficresstdeij," e%1d. ",i);
3597: }
3598: fprintf(ficresstdeij,"\n");
3599:
3600: pstamp(ficrescveij);
3601: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3602: fprintf(ficrescveij,"# Age");
3603: for(i=1; i<=nlstate;i++)
3604: for(j=1; j<=nlstate;j++){
3605: cptj= (j-1)*nlstate+i;
3606: for(i2=1; i2<=nlstate;i2++)
3607: for(j2=1; j2<=nlstate;j2++){
3608: cptj2= (j2-1)*nlstate+i2;
3609: if(cptj2 <= cptj)
3610: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3611: }
3612: }
3613: fprintf(ficrescveij,"\n");
3614:
3615: if(estepm < stepm){
3616: printf ("Problem %d lower than %d\n",estepm, stepm);
3617: }
3618: else hstepm=estepm;
3619: /* We compute the life expectancy from trapezoids spaced every estepm months
3620: * This is mainly to measure the difference between two models: for example
3621: * if stepm=24 months pijx are given only every 2 years and by summing them
3622: * we are calculating an estimate of the Life Expectancy assuming a linear
3623: * progression in between and thus overestimating or underestimating according
3624: * to the curvature of the survival function. If, for the same date, we
3625: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3626: * to compare the new estimate of Life expectancy with the same linear
3627: * hypothesis. A more precise result, taking into account a more precise
3628: * curvature will be obtained if estepm is as small as stepm. */
3629:
3630: /* For example we decided to compute the life expectancy with the smallest unit */
3631: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3632: nhstepm is the number of hstepm from age to agelim
3633: nstepm is the number of stepm from age to agelin.
3634: Look at hpijx to understand the reason of that which relies in memory size
3635: and note for a fixed period like estepm months */
3636: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3637: survival function given by stepm (the optimization length). Unfortunately it
3638: means that if the survival funtion is printed only each two years of age and if
3639: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3640: results. So we changed our mind and took the option of the best precision.
3641: */
3642: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3643:
3644: /* If stepm=6 months */
3645: /* nhstepm age range expressed in number of stepm */
3646: agelim=AGESUP;
3647: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3648: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3649: /* if (stepm >= YEARM) hstepm=1;*/
3650: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3651:
3652: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3653: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3654: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3655: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3656: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3657: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3658:
3659: for (age=bage; age<=fage; age ++){
3660: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3661: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3662: /* if (stepm >= YEARM) hstepm=1;*/
3663: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3664:
3665: /* If stepm=6 months */
3666: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3667: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3668:
3669: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3670:
3671: /* Computing Variances of health expectancies */
3672: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3673: decrease memory allocation */
3674: for(theta=1; theta <=npar; theta++){
3675: for(i=1; i<=npar; i++){
3676: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3677: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3678: }
3679: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3680: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3681:
3682: for(j=1; j<= nlstate; j++){
3683: for(i=1; i<=nlstate; i++){
3684: for(h=0; h<=nhstepm-1; h++){
3685: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3686: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3687: }
3688: }
3689: }
3690:
3691: for(ij=1; ij<= nlstate*nlstate; ij++)
3692: for(h=0; h<=nhstepm-1; h++){
3693: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3694: }
3695: }/* End theta */
3696:
3697:
3698: for(h=0; h<=nhstepm-1; h++)
3699: for(j=1; j<=nlstate*nlstate;j++)
3700: for(theta=1; theta <=npar; theta++)
3701: trgradg[h][j][theta]=gradg[h][theta][j];
3702:
3703:
3704: for(ij=1;ij<=nlstate*nlstate;ij++)
3705: for(ji=1;ji<=nlstate*nlstate;ji++)
3706: varhe[ij][ji][(int)age] =0.;
3707:
3708: printf("%d|",(int)age);fflush(stdout);
3709: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3710: for(h=0;h<=nhstepm-1;h++){
3711: for(k=0;k<=nhstepm-1;k++){
3712: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3713: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3714: for(ij=1;ij<=nlstate*nlstate;ij++)
3715: for(ji=1;ji<=nlstate*nlstate;ji++)
3716: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3717: }
3718: }
3719:
3720: /* Computing expectancies */
3721: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3722: for(i=1; i<=nlstate;i++)
3723: for(j=1; j<=nlstate;j++)
3724: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3725: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3726:
3727: /* 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]);*/
3728:
3729: }
3730:
3731: fprintf(ficresstdeij,"%3.0f",age );
3732: for(i=1; i<=nlstate;i++){
3733: eip=0.;
3734: vip=0.;
3735: for(j=1; j<=nlstate;j++){
3736: eip += eij[i][j][(int)age];
3737: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3738: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3739: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3740: }
3741: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3742: }
3743: fprintf(ficresstdeij,"\n");
3744:
3745: fprintf(ficrescveij,"%3.0f",age );
3746: for(i=1; i<=nlstate;i++)
3747: for(j=1; j<=nlstate;j++){
3748: cptj= (j-1)*nlstate+i;
3749: for(i2=1; i2<=nlstate;i2++)
3750: for(j2=1; j2<=nlstate;j2++){
3751: cptj2= (j2-1)*nlstate+i2;
3752: if(cptj2 <= cptj)
3753: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3754: }
3755: }
3756: fprintf(ficrescveij,"\n");
3757:
3758: }
3759: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3760: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3761: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3762: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3763: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3764: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3765: printf("\n");
3766: fprintf(ficlog,"\n");
3767:
3768: free_vector(xm,1,npar);
3769: free_vector(xp,1,npar);
3770: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3771: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3772: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3773: }
3774:
3775: /************ Variance ******************/
3776: 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 ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
3777: {
3778: /* Variance of health expectancies */
3779: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3780: /* double **newm;*/
1.169 brouard 3781: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3782:
3783: int movingaverage();
1.126 brouard 3784: double **dnewm,**doldm;
3785: double **dnewmp,**doldmp;
3786: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 3787: int k;
1.126 brouard 3788: double *xp;
3789: double **gp, **gm; /* for var eij */
3790: double ***gradg, ***trgradg; /*for var eij */
3791: double **gradgp, **trgradgp; /* for var p point j */
3792: double *gpp, *gmp; /* for var p point j */
3793: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3794: double ***p3mat;
3795: double age,agelim, hf;
3796: double ***mobaverage;
3797: int theta;
3798: char digit[4];
3799: char digitp[25];
3800:
3801: char fileresprobmorprev[FILENAMELENGTH];
3802:
3803: if(popbased==1){
3804: if(mobilav!=0)
3805: strcpy(digitp,"-populbased-mobilav-");
3806: else strcpy(digitp,"-populbased-nomobil-");
3807: }
3808: else
3809: strcpy(digitp,"-stablbased-");
3810:
3811: if (mobilav!=0) {
3812: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3813: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3814: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3815: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3816: }
3817: }
3818:
3819: strcpy(fileresprobmorprev,"prmorprev");
3820: sprintf(digit,"%-d",ij);
3821: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3822: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3823: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3824: strcat(fileresprobmorprev,fileres);
3825: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3826: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3827: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3828: }
3829: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3830:
3831: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3832: pstamp(ficresprobmorprev);
3833: 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);
3834: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3835: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3836: fprintf(ficresprobmorprev," p.%-d SE",j);
3837: for(i=1; i<=nlstate;i++)
3838: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3839: }
3840: fprintf(ficresprobmorprev,"\n");
3841: fprintf(ficgp,"\n# Routine varevsij");
3842: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3843: 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");
3844: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3845: /* } */
3846: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3847: pstamp(ficresvij);
3848: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3849: if(popbased==1)
1.128 brouard 3850: 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 3851: else
3852: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3853: fprintf(ficresvij,"# Age");
3854: for(i=1; i<=nlstate;i++)
3855: for(j=1; j<=nlstate;j++)
3856: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3857: fprintf(ficresvij,"\n");
3858:
3859: xp=vector(1,npar);
3860: dnewm=matrix(1,nlstate,1,npar);
3861: doldm=matrix(1,nlstate,1,nlstate);
3862: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3863: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3864:
3865: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3866: gpp=vector(nlstate+1,nlstate+ndeath);
3867: gmp=vector(nlstate+1,nlstate+ndeath);
3868: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3869:
3870: if(estepm < stepm){
3871: printf ("Problem %d lower than %d\n",estepm, stepm);
3872: }
3873: else hstepm=estepm;
3874: /* For example we decided to compute the life expectancy with the smallest unit */
3875: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3876: nhstepm is the number of hstepm from age to agelim
3877: nstepm is the number of stepm from age to agelin.
1.128 brouard 3878: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 3879: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3880: survival function given by stepm (the optimization length). Unfortunately it
3881: means that if the survival funtion is printed every two years of age and if
3882: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3883: results. So we changed our mind and took the option of the best precision.
3884: */
3885: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3886: agelim = AGESUP;
3887: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3888: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3889: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3890: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3891: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3892: gp=matrix(0,nhstepm,1,nlstate);
3893: gm=matrix(0,nhstepm,1,nlstate);
3894:
3895:
3896: for(theta=1; theta <=npar; theta++){
3897: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3898: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3899: }
3900: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3901: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3902:
3903: if (popbased==1) {
3904: if(mobilav ==0){
3905: for(i=1; i<=nlstate;i++)
3906: prlim[i][i]=probs[(int)age][i][ij];
3907: }else{ /* mobilav */
3908: for(i=1; i<=nlstate;i++)
3909: prlim[i][i]=mobaverage[(int)age][i][ij];
3910: }
3911: }
3912:
3913: for(j=1; j<= nlstate; j++){
3914: for(h=0; h<=nhstepm; h++){
3915: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3916: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3917: }
3918: }
3919: /* This for computing probability of death (h=1 means
3920: computed over hstepm matrices product = hstepm*stepm months)
3921: as a weighted average of prlim.
3922: */
3923: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3924: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3925: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3926: }
3927: /* end probability of death */
3928:
3929: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3930: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3931: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3932: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3933:
3934: if (popbased==1) {
3935: if(mobilav ==0){
3936: for(i=1; i<=nlstate;i++)
3937: prlim[i][i]=probs[(int)age][i][ij];
3938: }else{ /* mobilav */
3939: for(i=1; i<=nlstate;i++)
3940: prlim[i][i]=mobaverage[(int)age][i][ij];
3941: }
3942: }
3943:
1.128 brouard 3944: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 3945: for(h=0; h<=nhstepm; h++){
3946: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3947: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3948: }
3949: }
3950: /* This for computing probability of death (h=1 means
3951: computed over hstepm matrices product = hstepm*stepm months)
3952: as a weighted average of prlim.
3953: */
3954: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3955: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3956: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3957: }
3958: /* end probability of death */
3959:
3960: for(j=1; j<= nlstate; j++) /* vareij */
3961: for(h=0; h<=nhstepm; h++){
3962: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3963: }
3964:
3965: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3966: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3967: }
3968:
3969: } /* End theta */
3970:
3971: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3972:
3973: for(h=0; h<=nhstepm; h++) /* veij */
3974: for(j=1; j<=nlstate;j++)
3975: for(theta=1; theta <=npar; theta++)
3976: trgradg[h][j][theta]=gradg[h][theta][j];
3977:
3978: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3979: for(theta=1; theta <=npar; theta++)
3980: trgradgp[j][theta]=gradgp[theta][j];
3981:
3982:
3983: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3984: for(i=1;i<=nlstate;i++)
3985: for(j=1;j<=nlstate;j++)
3986: vareij[i][j][(int)age] =0.;
3987:
3988: for(h=0;h<=nhstepm;h++){
3989: for(k=0;k<=nhstepm;k++){
3990: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3991: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3992: for(i=1;i<=nlstate;i++)
3993: for(j=1;j<=nlstate;j++)
3994: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3995: }
3996: }
3997:
3998: /* pptj */
3999: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
4000: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
4001: for(j=nlstate+1;j<=nlstate+ndeath;j++)
4002: for(i=nlstate+1;i<=nlstate+ndeath;i++)
4003: varppt[j][i]=doldmp[j][i];
4004: /* end ppptj */
4005: /* x centered again */
4006: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
4007: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
4008:
4009: if (popbased==1) {
4010: if(mobilav ==0){
4011: for(i=1; i<=nlstate;i++)
4012: prlim[i][i]=probs[(int)age][i][ij];
4013: }else{ /* mobilav */
4014: for(i=1; i<=nlstate;i++)
4015: prlim[i][i]=mobaverage[(int)age][i][ij];
4016: }
4017: }
4018:
4019: /* This for computing probability of death (h=1 means
4020: computed over hstepm (estepm) matrices product = hstepm*stepm months)
4021: as a weighted average of prlim.
4022: */
4023: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4024: for(i=1,gmp[j]=0.;i<= nlstate; i++)
4025: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4026: }
4027: /* end probability of death */
4028:
4029: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
4030: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4031: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
4032: for(i=1; i<=nlstate;i++){
4033: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
4034: }
4035: }
4036: fprintf(ficresprobmorprev,"\n");
4037:
4038: fprintf(ficresvij,"%.0f ",age );
4039: for(i=1; i<=nlstate;i++)
4040: for(j=1; j<=nlstate;j++){
4041: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
4042: }
4043: fprintf(ficresvij,"\n");
4044: free_matrix(gp,0,nhstepm,1,nlstate);
4045: free_matrix(gm,0,nhstepm,1,nlstate);
4046: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
4047: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
4048: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4049: } /* End age */
4050: free_vector(gpp,nlstate+1,nlstate+ndeath);
4051: free_vector(gmp,nlstate+1,nlstate+ndeath);
4052: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
4053: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.199 ! brouard 4054: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
! 4055: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
1.126 brouard 4056: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 4057: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.126 brouard 4058: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
4059: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
4060: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 4061: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 4062: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 4063: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 4064: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
1.199 ! brouard 4065: 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);
! 4066: /* 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 4067: */
1.199 ! brouard 4068: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
! 4069: fprintf(ficgp,"\nset out \"%s%s.svg\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
1.126 brouard 4070:
4071: free_vector(xp,1,npar);
4072: free_matrix(doldm,1,nlstate,1,nlstate);
4073: free_matrix(dnewm,1,nlstate,1,npar);
4074: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4075: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
4076: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4077: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4078: fclose(ficresprobmorprev);
4079: fflush(ficgp);
4080: fflush(fichtm);
4081: } /* end varevsij */
4082:
4083: /************ Variance of prevlim ******************/
4084: 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 ij, char strstart[])
4085: {
4086: /* Variance of prevalence limit */
4087: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 4088:
1.126 brouard 4089: double **dnewm,**doldm;
4090: int i, j, nhstepm, hstepm;
4091: double *xp;
4092: double *gp, *gm;
4093: double **gradg, **trgradg;
4094: double age,agelim;
4095: int theta;
4096:
4097: pstamp(ficresvpl);
4098: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
4099: fprintf(ficresvpl,"# Age");
4100: for(i=1; i<=nlstate;i++)
4101: fprintf(ficresvpl," %1d-%1d",i,i);
4102: fprintf(ficresvpl,"\n");
4103:
4104: xp=vector(1,npar);
4105: dnewm=matrix(1,nlstate,1,npar);
4106: doldm=matrix(1,nlstate,1,nlstate);
4107:
4108: hstepm=1*YEARM; /* Every year of age */
4109: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
4110: agelim = AGESUP;
4111: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4112: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4113: if (stepm >= YEARM) hstepm=1;
4114: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4115: gradg=matrix(1,npar,1,nlstate);
4116: gp=vector(1,nlstate);
4117: gm=vector(1,nlstate);
4118:
4119: for(theta=1; theta <=npar; theta++){
4120: for(i=1; i<=npar; i++){ /* Computes gradient */
4121: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4122: }
4123: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4124: for(i=1;i<=nlstate;i++)
4125: gp[i] = prlim[i][i];
4126:
4127: for(i=1; i<=npar; i++) /* Computes gradient */
4128: xp[i] = x[i] - (i==theta ?delti[theta]:0);
4129: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4130: for(i=1;i<=nlstate;i++)
4131: gm[i] = prlim[i][i];
4132:
4133: for(i=1;i<=nlstate;i++)
4134: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
4135: } /* End theta */
4136:
4137: trgradg =matrix(1,nlstate,1,npar);
4138:
4139: for(j=1; j<=nlstate;j++)
4140: for(theta=1; theta <=npar; theta++)
4141: trgradg[j][theta]=gradg[theta][j];
4142:
4143: for(i=1;i<=nlstate;i++)
4144: varpl[i][(int)age] =0.;
4145: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4146: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4147: for(i=1;i<=nlstate;i++)
4148: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4149:
4150: fprintf(ficresvpl,"%.0f ",age );
4151: for(i=1; i<=nlstate;i++)
4152: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4153: fprintf(ficresvpl,"\n");
4154: free_vector(gp,1,nlstate);
4155: free_vector(gm,1,nlstate);
4156: free_matrix(gradg,1,npar,1,nlstate);
4157: free_matrix(trgradg,1,nlstate,1,npar);
4158: } /* End age */
4159:
4160: free_vector(xp,1,npar);
4161: free_matrix(doldm,1,nlstate,1,npar);
4162: free_matrix(dnewm,1,nlstate,1,nlstate);
4163:
4164: }
4165:
4166: /************ Variance of one-step probabilities ******************/
4167: 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[])
4168: {
1.164 brouard 4169: int i, j=0, k1, l1, tj;
1.126 brouard 4170: int k2, l2, j1, z1;
1.164 brouard 4171: int k=0, l;
1.145 brouard 4172: int first=1, first1, first2;
1.126 brouard 4173: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4174: double **dnewm,**doldm;
4175: double *xp;
4176: double *gp, *gm;
4177: double **gradg, **trgradg;
4178: double **mu;
1.164 brouard 4179: double age, cov[NCOVMAX+1];
1.126 brouard 4180: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4181: int theta;
4182: char fileresprob[FILENAMELENGTH];
4183: char fileresprobcov[FILENAMELENGTH];
4184: char fileresprobcor[FILENAMELENGTH];
4185: double ***varpij;
4186:
4187: strcpy(fileresprob,"prob");
4188: strcat(fileresprob,fileres);
4189: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4190: printf("Problem with resultfile: %s\n", fileresprob);
4191: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4192: }
4193: strcpy(fileresprobcov,"probcov");
4194: strcat(fileresprobcov,fileres);
4195: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4196: printf("Problem with resultfile: %s\n", fileresprobcov);
4197: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4198: }
4199: strcpy(fileresprobcor,"probcor");
4200: strcat(fileresprobcor,fileres);
4201: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4202: printf("Problem with resultfile: %s\n", fileresprobcor);
4203: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4204: }
4205: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4206: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4207: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4208: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4209: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4210: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4211: pstamp(ficresprob);
4212: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4213: fprintf(ficresprob,"# Age");
4214: pstamp(ficresprobcov);
4215: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4216: fprintf(ficresprobcov,"# Age");
4217: pstamp(ficresprobcor);
4218: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4219: fprintf(ficresprobcor,"# Age");
4220:
4221:
4222: for(i=1; i<=nlstate;i++)
4223: for(j=1; j<=(nlstate+ndeath);j++){
4224: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4225: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4226: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4227: }
4228: /* fprintf(ficresprob,"\n");
4229: fprintf(ficresprobcov,"\n");
4230: fprintf(ficresprobcor,"\n");
4231: */
1.131 brouard 4232: xp=vector(1,npar);
1.126 brouard 4233: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4234: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4235: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4236: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4237: first=1;
4238: fprintf(ficgp,"\n# Routine varprob");
4239: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4240: fprintf(fichtm,"\n");
4241:
1.197 brouard 4242: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4></br>this page is important in order to visualize confidence intervals and especially correlation between disability and recovery</li>\n",optionfilehtmcov);
4243: 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);
4244: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 4245: and drawn. It helps understanding how is the covariance between two incidences.\
4246: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4247: 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. \
4248: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4249: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4250: standard deviations wide on each axis. <br>\
4251: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4252: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4253: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4254:
4255: cov[1]=1;
1.145 brouard 4256: /* tj=cptcoveff; */
4257: tj = (int) pow(2,cptcoveff);
1.126 brouard 4258: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4259: j1=0;
1.145 brouard 4260: for(j1=1; j1<=tj;j1++){
4261: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4262: /*j1++;*/
1.126 brouard 4263: if (cptcovn>0) {
4264: fprintf(ficresprob, "\n#********** Variable ");
1.198 brouard 4265: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4266: fprintf(ficresprob, "**********\n#\n");
4267: fprintf(ficresprobcov, "\n#********** Variable ");
1.198 brouard 4268: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4269: fprintf(ficresprobcov, "**********\n#\n");
4270:
4271: fprintf(ficgp, "\n#********** Variable ");
1.198 brouard 4272: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4273: fprintf(ficgp, "**********\n#\n");
4274:
4275:
4276: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.198 brouard 4277: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4278: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4279:
4280: fprintf(ficresprobcor, "\n#********** Variable ");
1.198 brouard 4281: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4282: fprintf(ficresprobcor, "**********\n#");
4283: }
4284:
1.145 brouard 4285: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4286: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4287: gp=vector(1,(nlstate)*(nlstate+ndeath));
4288: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 4289: for (age=bage; age<=fage; age ++){
4290: cov[2]=age;
1.187 brouard 4291: if(nagesqr==1)
4292: cov[3]= age*age;
1.126 brouard 4293: for (k=1; k<=cptcovn;k++) {
1.198 brouard 4294: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];/* j1 1 2 3 4
1.145 brouard 4295: * 1 1 1 1 1
4296: * 2 2 1 1 1
4297: * 3 1 2 1 1
4298: */
4299: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 4300: }
1.186 brouard 4301: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.198 brouard 4302: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2];
1.126 brouard 4303: for (k=1; k<=cptcovprod;k++)
1.198 brouard 4304: 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 4305:
4306:
4307: for(theta=1; theta <=npar; theta++){
4308: for(i=1; i<=npar; i++)
4309: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4310:
4311: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4312:
4313: k=0;
4314: for(i=1; i<= (nlstate); i++){
4315: for(j=1; j<=(nlstate+ndeath);j++){
4316: k=k+1;
4317: gp[k]=pmmij[i][j];
4318: }
4319: }
4320:
4321: for(i=1; i<=npar; i++)
4322: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4323:
4324: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4325: k=0;
4326: for(i=1; i<=(nlstate); i++){
4327: for(j=1; j<=(nlstate+ndeath);j++){
4328: k=k+1;
4329: gm[k]=pmmij[i][j];
4330: }
4331: }
4332:
4333: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4334: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4335: }
4336:
4337: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4338: for(theta=1; theta <=npar; theta++)
4339: trgradg[j][theta]=gradg[theta][j];
4340:
4341: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4342: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4343:
4344: pmij(pmmij,cov,ncovmodel,x,nlstate);
4345:
4346: k=0;
4347: for(i=1; i<=(nlstate); i++){
4348: for(j=1; j<=(nlstate+ndeath);j++){
4349: k=k+1;
4350: mu[k][(int) age]=pmmij[i][j];
4351: }
4352: }
4353: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4354: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4355: varpij[i][j][(int)age] = doldm[i][j];
4356:
4357: /*printf("\n%d ",(int)age);
4358: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4359: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4360: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4361: }*/
4362:
4363: fprintf(ficresprob,"\n%d ",(int)age);
4364: fprintf(ficresprobcov,"\n%d ",(int)age);
4365: fprintf(ficresprobcor,"\n%d ",(int)age);
4366:
4367: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4368: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4369: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4370: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4371: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4372: }
4373: i=0;
4374: for (k=1; k<=(nlstate);k++){
4375: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 4376: i++;
1.126 brouard 4377: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4378: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4379: for (j=1; j<=i;j++){
1.145 brouard 4380: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 4381: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4382: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4383: }
4384: }
4385: }/* end of loop for state */
4386: } /* end of loop for age */
1.145 brouard 4387: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4388: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4389: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4390: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4391:
1.126 brouard 4392: /* Confidence intervalle of pij */
4393: /*
1.131 brouard 4394: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 4395: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4396: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4397: 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);
4398: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4399: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4400: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4401: */
4402:
4403: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 4404: first1=1;first2=2;
1.126 brouard 4405: for (k2=1; k2<=(nlstate);k2++){
4406: for (l2=1; l2<=(nlstate+ndeath);l2++){
4407: if(l2==k2) continue;
4408: j=(k2-1)*(nlstate+ndeath)+l2;
4409: for (k1=1; k1<=(nlstate);k1++){
4410: for (l1=1; l1<=(nlstate+ndeath);l1++){
4411: if(l1==k1) continue;
4412: i=(k1-1)*(nlstate+ndeath)+l1;
4413: if(i<=j) continue;
4414: for (age=bage; age<=fage; age ++){
4415: if ((int)age %5==0){
4416: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4417: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4418: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4419: mu1=mu[i][(int) age]/stepm*YEARM ;
4420: mu2=mu[j][(int) age]/stepm*YEARM;
4421: c12=cv12/sqrt(v1*v2);
4422: /* Computing eigen value of matrix of covariance */
4423: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4424: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4425: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4426: if(first2==1){
4427: first1=0;
4428: 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);
4429: }
4430: 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);
4431: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4432: /* lc2=fabs(lc2); */
1.135 brouard 4433: }
4434:
1.126 brouard 4435: /* Eigen vectors */
4436: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4437: /*v21=sqrt(1.-v11*v11); *//* error */
4438: v21=(lc1-v1)/cv12*v11;
4439: v12=-v21;
4440: v22=v11;
4441: tnalp=v21/v11;
4442: if(first1==1){
4443: first1=0;
4444: 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);
4445: }
4446: 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);
4447: /*printf(fignu*/
4448: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4449: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4450: if(first==1){
4451: first=0;
4452: fprintf(ficgp,"\nset parametric;unset label");
4453: 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 4454: fprintf(ficgp,"\nset ter svg size 640, 480");
1.126 brouard 4455: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.199 ! brouard 4456: :<a href=\"%s%d%1d%1d-%1d%1d.svg\">\
! 4457: %s%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.126 brouard 4458: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4459: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.199 ! brouard 4460: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.126 brouard 4461: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.199 ! brouard 4462: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.126 brouard 4463: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4464: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4465: 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",\
4466: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4467: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4468: }else{
4469: first=0;
4470: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4471: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4472: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4473: 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",\
4474: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4475: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4476: }/* if first */
4477: } /* age mod 5 */
4478: } /* end loop age */
1.199 ! brouard 4479: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.svg\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.126 brouard 4480: first=1;
4481: } /*l12 */
4482: } /* k12 */
4483: } /*l1 */
4484: }/* k1 */
1.169 brouard 4485: /* } */ /* loop covariates */
1.126 brouard 4486: }
4487: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4488: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4489: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4490: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4491: free_vector(xp,1,npar);
4492: fclose(ficresprob);
4493: fclose(ficresprobcov);
4494: fclose(ficresprobcor);
4495: fflush(ficgp);
4496: fflush(fichtmcov);
4497: }
4498:
4499:
4500: /******************* Printing html file ***********/
4501: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4502: int lastpass, int stepm, int weightopt, char model[],\
4503: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4504: int popforecast, int estepm ,\
4505: double jprev1, double mprev1,double anprev1, \
4506: double jprev2, double mprev2,double anprev2){
4507: int jj1, k1, i1, cpt;
4508:
4509: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4510: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4511: </ul>");
4512: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4513: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4514: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4515: fprintf(fichtm,"\
4516: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4517: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4518: fprintf(fichtm,"\
4519: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4520: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4521: fprintf(fichtm,"\
1.128 brouard 4522: - (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 4523: <a href=\"%s\">%s</a> <br>\n",
4524: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4525: fprintf(fichtm,"\
4526: - Population projections by age and states: \
4527: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4528:
4529: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4530:
1.145 brouard 4531: m=pow(2,cptcoveff);
1.126 brouard 4532: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4533:
4534: jj1=0;
4535: for(k1=1; k1<=m;k1++){
1.192 brouard 4536: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4537: jj1++;
4538: if (cptcovn > 0) {
4539: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.192 brouard 4540: for (cpt=1; cpt<=cptcoveff;cpt++){
1.198 brouard 4541: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
4542: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
1.192 brouard 4543: }
1.126 brouard 4544: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4545: }
4546: /* Pij */
1.199 ! brouard 4547: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.svg\">%s%d_1.svg</a><br> \
! 4548: <img src=\"%s%d_1.svg\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4549: /* Quasi-incidences */
4550: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.199 ! brouard 4551: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.svg\">%s%d_2.svg</a><br> \
! 4552: <img src=\"%s%d_2.svg\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4553: /* Period (stable) prevalence in each health state */
1.154 brouard 4554: for(cpt=1; cpt<=nlstate;cpt++){
1.199 ! brouard 4555: fprintf(fichtm,"<br>- 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> \
! 4556: <img src=\"%s%d_%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.126 brouard 4557: }
4558: for(cpt=1; cpt<=nlstate;cpt++) {
1.199 ! brouard 4559: 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) : <a href=\"%s%d%d.svg\">%s%d%d.svg</a> <br> \
! 4560: <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 4561: }
1.192 brouard 4562: /* } /\* end i1 *\/ */
1.126 brouard 4563: }/* End k1 */
4564: fprintf(fichtm,"</ul>");
4565:
4566: fprintf(fichtm,"\
4567: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 4568: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.197 brouard 4569: - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file.<br> \
4570: But because parameters are usually highly correlated (a higher incidence of disability \
4571: and a higher incidence of recovery can give very close observed transition) it might \
4572: be very useful to look not only at linear confidence intervals estimated from the \
4573: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
4574: (parameters) of the logistic regression, it might be more meaningful to visualize the \
4575: covariance matrix of the one-step probabilities. \
4576: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 4577:
1.193 brouard 4578: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.126 brouard 4579: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4580: fprintf(fichtm,"\
4581: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4582: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4583:
4584: fprintf(fichtm,"\
4585: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4586: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4587: fprintf(fichtm,"\
4588: - 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): \
4589: <a href=\"%s\">%s</a> <br>\n</li>",
4590: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4591: fprintf(fichtm,"\
4592: - (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): \
4593: <a href=\"%s\">%s</a> <br>\n</li>",
4594: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4595: fprintf(fichtm,"\
1.128 brouard 4596: - 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",
1.126 brouard 4597: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4598: fprintf(fichtm,"\
1.128 brouard 4599: - 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",
4600: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
1.126 brouard 4601: fprintf(fichtm,"\
4602: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4603: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4604:
4605: /* if(popforecast==1) fprintf(fichtm,"\n */
4606: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4607: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4608: /* <br>",fileres,fileres,fileres,fileres); */
4609: /* else */
4610: /* 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); */
4611: fflush(fichtm);
4612: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4613:
1.145 brouard 4614: m=pow(2,cptcoveff);
1.126 brouard 4615: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4616:
4617: jj1=0;
4618: for(k1=1; k1<=m;k1++){
1.192 brouard 4619: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4620: jj1++;
4621: if (cptcovn > 0) {
4622: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4623: for (cpt=1; cpt<=cptcoveff;cpt++)
1.198 brouard 4624: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 4625: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4626: }
4627: for(cpt=1; cpt<=nlstate;cpt++) {
4628: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.199 ! brouard 4629: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.svg <br>\
! 4630: <img src=\"%s%d_%d.svg\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.126 brouard 4631: }
4632: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4633: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4634: true period expectancies (those weighted with period prevalences are also\
4635: drawn in addition to the population based expectancies computed using\
1.199 ! brouard 4636: observed and cahotic prevalences: %s%d.svg<br>\
! 4637: <img src=\"%s%d.svg\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
1.192 brouard 4638: /* } /\* end i1 *\/ */
1.126 brouard 4639: }/* End k1 */
4640: fprintf(fichtm,"</ul>");
4641: fflush(fichtm);
4642: }
4643:
4644: /******************* Gnuplot file **************/
4645: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4646:
4647: char dirfileres[132],optfileres[132];
1.164 brouard 4648: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.130 brouard 4649: int ng=0;
1.126 brouard 4650: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4651: /* printf("Problem with file %s",optionfilegnuplot); */
4652: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4653: /* } */
4654:
4655: /*#ifdef windows */
4656: fprintf(ficgp,"cd \"%s\" \n",pathc);
4657: /*#endif */
4658: m=pow(2,cptcoveff);
4659:
4660: strcpy(dirfileres,optionfilefiname);
4661: strcpy(optfileres,"vpl");
4662: /* 1eme*/
1.153 brouard 4663: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
1.126 brouard 4664: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 4665: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
1.199 ! brouard 4666: fprintf(ficgp,"\nset out \"%s%d_%d.svg\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
! 4667: fprintf(ficgp,"\n#set out \"v%s%d_%d.svg\" \n",optionfilefiname,cpt,k1);
1.126 brouard 4668: fprintf(ficgp,"set xlabel \"Age\" \n\
4669: set ylabel \"Probability\" \n\
1.199 ! brouard 4670: set ter svg size 640, 480\n\
1.170 brouard 4671: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4672:
4673: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4674: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4675: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4676: }
1.170 brouard 4677: fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4678: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4679: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4680: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4681: }
1.170 brouard 4682: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4683: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4684: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4685: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4686: }
1.145 brouard 4687: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.126 brouard 4688: }
4689: }
4690: /*2 eme*/
1.153 brouard 4691: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126 brouard 4692: for (k1=1; k1<= m ; k1 ++) {
1.199 ! brouard 4693: fprintf(ficgp,"\nset out \"%s%d.svg\" \n",subdirf2(optionfilefiname,"e"),k1);
! 4694: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
1.126 brouard 4695:
4696: for (i=1; i<= nlstate+1 ; i ++) {
4697: k=2*i;
1.170 brouard 4698: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4699: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4700: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4701: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4702: }
4703: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4704: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.170 brouard 4705: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4706: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4707: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4708: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4709: }
1.145 brouard 4710: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.170 brouard 4711: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4712: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4713: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4714: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4715: }
1.145 brouard 4716: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4717: else fprintf(ficgp,"\" t\"\" w l lt 0,");
1.126 brouard 4718: }
4719: }
4720:
4721: /*3eme*/
4722:
4723: for (k1=1; k1<= m ; k1 ++) {
4724: for (cpt=1; cpt<= nlstate ; cpt ++) {
4725: /* k=2+nlstate*(2*cpt-2); */
4726: k=2+(nlstate+1)*(cpt-1);
1.199 ! brouard 4727: fprintf(ficgp,"\nset out \"%s%d%d.svg\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
! 4728: fprintf(ficgp,"set ter svg size 640, 480\n\
1.126 brouard 4729: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4730: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4731: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4732: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4733: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4734: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4735: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4736:
4737: */
4738: for (i=1; i< nlstate ; i ++) {
4739: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
4740: /* 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);*/
4741:
4742: }
4743: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4744: }
4745: }
4746:
4747: /* CV preval stable (period) */
1.153 brouard 4748: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4749: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126 brouard 4750: k=3;
1.153 brouard 4751: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.199 ! brouard 4752: fprintf(ficgp,"\nset out \"%s%d_%d.svg\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
1.126 brouard 4753: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.199 ! brouard 4754: set ter svg size 640, 480\n\
1.126 brouard 4755: unset log y\n\
1.153 brouard 4756: plot [%.f:%.f] ", ageminpar, agemaxpar);
4757: for (i=1; i<= nlstate ; i ++){
4758: if(i==1)
4759: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4760: else
4761: fprintf(ficgp,", '' ");
1.154 brouard 4762: l=(nlstate+ndeath)*(i-1)+1;
4763: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.153 brouard 4764: for (j=1; j<= (nlstate-1) ; j ++)
4765: fprintf(ficgp,"+$%d",k+l+j);
4766: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4767: } /* nlstate */
4768: fprintf(ficgp,"\n");
4769: } /* end cpt state*/
4770: } /* end covariate */
1.126 brouard 4771:
4772: /* proba elementaires */
1.187 brouard 4773: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 4774: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 4775: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 4776: for(k=1; k <=(nlstate+ndeath); k++){
4777: if (k != i) {
1.187 brouard 4778: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 4779: for(j=1; j <=ncovmodel; j++){
1.187 brouard 4780: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 4781: jk++;
4782: }
1.187 brouard 4783: fprintf(ficgp,"\n");
1.126 brouard 4784: }
4785: }
4786: }
1.187 brouard 4787: fprintf(ficgp,"##############\n#\n");
4788:
1.145 brouard 4789: /*goto avoid;*/
1.187 brouard 4790: fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n");
4791: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
4792: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
4793: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
4794: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
4795: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4796: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4797: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4798: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4799: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
4800: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4801: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
4802: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
4803: fprintf(ficgp,"#\n");
1.126 brouard 4804: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
1.187 brouard 4805: fprintf(ficgp,"# ng=%d\n",ng);
4806: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 4807: for(jk=1; jk <=m; jk++) {
1.187 brouard 4808: fprintf(ficgp,"# jk=%d\n",jk);
1.199 ! brouard 4809: fprintf(ficgp,"\nset out \"%s%d_%d.svg\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.126 brouard 4810: if (ng==2)
4811: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4812: else
4813: fprintf(ficgp,"\nset title \"Probability\"\n");
1.199 ! brouard 4814: fprintf(ficgp,"\nset ter svg size 640, 480\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 4815: i=1;
4816: for(k2=1; k2<=nlstate; k2++) {
4817: k3=i;
4818: for(k=1; k<=(nlstate+ndeath); k++) {
4819: if (k != k2){
4820: if(ng==2)
1.187 brouard 4821: if(nagesqr==0)
4822: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4823: else /* nagesqr =1 */
4824: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
1.126 brouard 4825: else
1.187 brouard 4826: if(nagesqr==0)
4827: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4828: else /* nagesqr =1 */
4829: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
1.141 brouard 4830: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 brouard 4831: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.197 brouard 4832: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
4833: if(ij <=cptcovage) { /* Bug valgrind */
4834: if((j-2)==Tage[ij]) { /* Bug valgrind */
1.198 brouard 4835: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]);
1.197 brouard 4836: ij++;
4837: }
1.186 brouard 4838: }
4839: else
1.198 brouard 4840: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.126 brouard 4841: }
4842: fprintf(ficgp,")/(1");
4843:
1.187 brouard 4844: for(k1=1; k1 <=nlstate; k1++){
4845: if(nagesqr==0)
4846: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4847: else /* nagesqr =1 */
4848: 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);
4849:
1.126 brouard 4850: ij=1;
1.187 brouard 4851: for(j=3; j <=ncovmodel-nagesqr; j++){
1.197 brouard 4852: if(ij <=cptcovage) { /* Bug valgrind */
4853: if((j-2)==Tage[ij]) { /* Bug valgrind */
1.198 brouard 4854: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]);
1.197 brouard 4855: ij++;
4856: }
1.186 brouard 4857: }
4858: else
1.198 brouard 4859: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.126 brouard 4860: }
4861: fprintf(ficgp,")");
4862: }
4863: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4864: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4865: i=i+ncovmodel;
4866: }
4867: } /* end k */
4868: } /* end k2 */
4869: } /* end jk */
4870: } /* end ng */
1.164 brouard 4871: /* avoid: */
1.126 brouard 4872: fflush(ficgp);
4873: } /* end gnuplot */
4874:
4875:
4876: /*************** Moving average **************/
4877: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4878:
4879: int i, cpt, cptcod;
4880: int modcovmax =1;
4881: int mobilavrange, mob;
4882: double age;
4883:
4884: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4885: a covariate has 2 modalities */
4886: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4887:
4888: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4889: if(mobilav==1) mobilavrange=5; /* default */
4890: else mobilavrange=mobilav;
4891: for (age=bage; age<=fage; age++)
4892: for (i=1; i<=nlstate;i++)
4893: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4894: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4895: /* We keep the original values on the extreme ages bage, fage and for
4896: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4897: we use a 5 terms etc. until the borders are no more concerned.
4898: */
4899: for (mob=3;mob <=mobilavrange;mob=mob+2){
4900: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4901: for (i=1; i<=nlstate;i++){
4902: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4903: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4904: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4905: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4906: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4907: }
4908: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4909: }
4910: }
4911: }/* end age */
4912: }/* end mob */
4913: }else return -1;
4914: return 0;
4915: }/* End movingaverage */
4916:
4917:
4918: /************** Forecasting ******************/
1.169 brouard 4919: 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 4920: /* proj1, year, month, day of starting projection
4921: agemin, agemax range of age
4922: dateprev1 dateprev2 range of dates during which prevalence is computed
4923: anproj2 year of en of projection (same day and month as proj1).
4924: */
1.164 brouard 4925: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 4926: double agec; /* generic age */
4927: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4928: double *popeffectif,*popcount;
4929: double ***p3mat;
4930: double ***mobaverage;
4931: char fileresf[FILENAMELENGTH];
4932:
4933: agelim=AGESUP;
4934: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4935:
4936: strcpy(fileresf,"f");
4937: strcat(fileresf,fileres);
4938: if((ficresf=fopen(fileresf,"w"))==NULL) {
4939: printf("Problem with forecast resultfile: %s\n", fileresf);
4940: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4941: }
4942: printf("Computing forecasting: result on file '%s' \n", fileresf);
4943: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4944:
4945: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4946:
4947: if (mobilav!=0) {
4948: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4949: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4950: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4951: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4952: }
4953: }
4954:
4955: stepsize=(int) (stepm+YEARM-1)/YEARM;
4956: if (stepm<=12) stepsize=1;
4957: if(estepm < stepm){
4958: printf ("Problem %d lower than %d\n",estepm, stepm);
4959: }
4960: else hstepm=estepm;
4961:
4962: hstepm=hstepm/stepm;
4963: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4964: fractional in yp1 */
4965: anprojmean=yp;
4966: yp2=modf((yp1*12),&yp);
4967: mprojmean=yp;
4968: yp1=modf((yp2*30.5),&yp);
4969: jprojmean=yp;
4970: if(jprojmean==0) jprojmean=1;
4971: if(mprojmean==0) jprojmean=1;
4972:
4973: i1=cptcoveff;
4974: if (cptcovn < 1){i1=1;}
4975:
4976: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4977:
4978: fprintf(ficresf,"#****** Routine prevforecast **\n");
4979:
4980: /* if (h==(int)(YEARM*yearp)){ */
4981: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4982: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4983: k=k+1;
4984: fprintf(ficresf,"\n#******");
4985: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 4986: 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 4987: }
4988: fprintf(ficresf,"******\n");
4989: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4990: for(j=1; j<=nlstate+ndeath;j++){
4991: for(i=1; i<=nlstate;i++)
4992: fprintf(ficresf," p%d%d",i,j);
4993: fprintf(ficresf," p.%d",j);
4994: }
4995: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4996: fprintf(ficresf,"\n");
4997: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4998:
4999: for (agec=fage; agec>=(ageminpar-1); agec--){
5000: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
5001: nhstepm = nhstepm/hstepm;
5002: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5003: oldm=oldms;savm=savms;
5004: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
5005:
5006: for (h=0; h<=nhstepm; h++){
5007: if (h*hstepm/YEARM*stepm ==yearp) {
5008: fprintf(ficresf,"\n");
5009: for(j=1;j<=cptcoveff;j++)
1.198 brouard 5010: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5011: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
5012: }
5013: for(j=1; j<=nlstate+ndeath;j++) {
5014: ppij=0.;
5015: for(i=1; i<=nlstate;i++) {
5016: if (mobilav==1)
5017: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
5018: else {
5019: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
5020: }
5021: if (h*hstepm/YEARM*stepm== yearp) {
5022: fprintf(ficresf," %.3f", p3mat[i][j][h]);
5023: }
5024: } /* end i */
5025: if (h*hstepm/YEARM*stepm==yearp) {
5026: fprintf(ficresf," %.3f", ppij);
5027: }
5028: }/* end j */
5029: } /* end h */
5030: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5031: } /* end agec */
5032: } /* end yearp */
5033: } /* end cptcod */
5034: } /* end cptcov */
5035:
5036: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5037:
5038: fclose(ficresf);
5039: }
5040:
5041: /************** Forecasting *****not tested NB*************/
1.169 brouard 5042: 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 5043:
5044: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
5045: int *popage;
5046: double calagedatem, agelim, kk1, kk2;
5047: double *popeffectif,*popcount;
5048: double ***p3mat,***tabpop,***tabpopprev;
5049: double ***mobaverage;
5050: char filerespop[FILENAMELENGTH];
5051:
5052: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5053: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5054: agelim=AGESUP;
5055: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
5056:
5057: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5058:
5059:
5060: strcpy(filerespop,"pop");
5061: strcat(filerespop,fileres);
5062: if((ficrespop=fopen(filerespop,"w"))==NULL) {
5063: printf("Problem with forecast resultfile: %s\n", filerespop);
5064: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
5065: }
5066: printf("Computing forecasting: result on file '%s' \n", filerespop);
5067: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
5068:
5069: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5070:
5071: if (mobilav!=0) {
5072: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5073: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5074: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5075: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5076: }
5077: }
5078:
5079: stepsize=(int) (stepm+YEARM-1)/YEARM;
5080: if (stepm<=12) stepsize=1;
5081:
5082: agelim=AGESUP;
5083:
5084: hstepm=1;
5085: hstepm=hstepm/stepm;
5086:
5087: if (popforecast==1) {
5088: if((ficpop=fopen(popfile,"r"))==NULL) {
5089: printf("Problem with population file : %s\n",popfile);exit(0);
5090: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
5091: }
5092: popage=ivector(0,AGESUP);
5093: popeffectif=vector(0,AGESUP);
5094: popcount=vector(0,AGESUP);
5095:
5096: i=1;
5097: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
5098:
5099: imx=i;
5100: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
5101: }
5102:
5103: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
5104: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5105: k=k+1;
5106: fprintf(ficrespop,"\n#******");
5107: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 5108: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5109: }
5110: fprintf(ficrespop,"******\n");
5111: fprintf(ficrespop,"# Age");
5112: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
5113: if (popforecast==1) fprintf(ficrespop," [Population]");
5114:
5115: for (cpt=0; cpt<=0;cpt++) {
5116: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5117:
5118: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5119: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5120: nhstepm = nhstepm/hstepm;
5121:
5122: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5123: oldm=oldms;savm=savms;
5124: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5125:
5126: for (h=0; h<=nhstepm; h++){
5127: if (h==(int) (calagedatem+YEARM*cpt)) {
5128: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5129: }
5130: for(j=1; j<=nlstate+ndeath;j++) {
5131: kk1=0.;kk2=0;
5132: for(i=1; i<=nlstate;i++) {
5133: if (mobilav==1)
5134: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
5135: else {
5136: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
5137: }
5138: }
5139: if (h==(int)(calagedatem+12*cpt)){
5140: tabpop[(int)(agedeb)][j][cptcod]=kk1;
5141: /*fprintf(ficrespop," %.3f", kk1);
5142: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
5143: }
5144: }
5145: for(i=1; i<=nlstate;i++){
5146: kk1=0.;
5147: for(j=1; j<=nlstate;j++){
5148: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5149: }
5150: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5151: }
5152:
5153: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5154: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5155: }
5156: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5157: }
5158: }
5159:
5160: /******/
5161:
5162: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5163: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5164: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5165: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5166: nhstepm = nhstepm/hstepm;
5167:
5168: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5169: oldm=oldms;savm=savms;
5170: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5171: for (h=0; h<=nhstepm; h++){
5172: if (h==(int) (calagedatem+YEARM*cpt)) {
5173: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5174: }
5175: for(j=1; j<=nlstate+ndeath;j++) {
5176: kk1=0.;kk2=0;
5177: for(i=1; i<=nlstate;i++) {
5178: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5179: }
5180: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5181: }
5182: }
5183: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5184: }
5185: }
5186: }
5187: }
5188:
5189: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5190:
5191: if (popforecast==1) {
5192: free_ivector(popage,0,AGESUP);
5193: free_vector(popeffectif,0,AGESUP);
5194: free_vector(popcount,0,AGESUP);
5195: }
5196: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5197: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5198: fclose(ficrespop);
5199: } /* End of popforecast */
5200:
5201: int fileappend(FILE *fichier, char *optionfich)
5202: {
5203: if((fichier=fopen(optionfich,"a"))==NULL) {
5204: printf("Problem with file: %s\n", optionfich);
5205: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5206: return (0);
5207: }
5208: fflush(fichier);
5209: return (1);
5210: }
5211:
5212:
5213: /**************** function prwizard **********************/
5214: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
5215: {
5216:
5217: /* Wizard to print covariance matrix template */
5218:
1.164 brouard 5219: char ca[32], cb[32];
5220: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 5221: int numlinepar;
5222:
5223: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5224: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5225: for(i=1; i <=nlstate; i++){
5226: jj=0;
5227: for(j=1; j <=nlstate+ndeath; j++){
5228: if(j==i) continue;
5229: jj++;
5230: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5231: printf("%1d%1d",i,j);
5232: fprintf(ficparo,"%1d%1d",i,j);
5233: for(k=1; k<=ncovmodel;k++){
5234: /* printf(" %lf",param[i][j][k]); */
5235: /* fprintf(ficparo," %lf",param[i][j][k]); */
5236: printf(" 0.");
5237: fprintf(ficparo," 0.");
5238: }
5239: printf("\n");
5240: fprintf(ficparo,"\n");
5241: }
5242: }
5243: printf("# Scales (for hessian or gradient estimation)\n");
5244: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
5245: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
5246: for(i=1; i <=nlstate; i++){
5247: jj=0;
5248: for(j=1; j <=nlstate+ndeath; j++){
5249: if(j==i) continue;
5250: jj++;
5251: fprintf(ficparo,"%1d%1d",i,j);
5252: printf("%1d%1d",i,j);
5253: fflush(stdout);
5254: for(k=1; k<=ncovmodel;k++){
5255: /* printf(" %le",delti3[i][j][k]); */
5256: /* fprintf(ficparo," %le",delti3[i][j][k]); */
5257: printf(" 0.");
5258: fprintf(ficparo," 0.");
5259: }
5260: numlinepar++;
5261: printf("\n");
5262: fprintf(ficparo,"\n");
5263: }
5264: }
5265: printf("# Covariance matrix\n");
5266: /* # 121 Var(a12)\n\ */
5267: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5268: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5269: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5270: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5271: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5272: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5273: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5274: fflush(stdout);
5275: fprintf(ficparo,"# Covariance matrix\n");
5276: /* # 121 Var(a12)\n\ */
5277: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5278: /* # ...\n\ */
5279: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5280:
5281: for(itimes=1;itimes<=2;itimes++){
5282: jj=0;
5283: for(i=1; i <=nlstate; i++){
5284: for(j=1; j <=nlstate+ndeath; j++){
5285: if(j==i) continue;
5286: for(k=1; k<=ncovmodel;k++){
5287: jj++;
5288: ca[0]= k+'a'-1;ca[1]='\0';
5289: if(itimes==1){
5290: printf("#%1d%1d%d",i,j,k);
5291: fprintf(ficparo,"#%1d%1d%d",i,j,k);
5292: }else{
5293: printf("%1d%1d%d",i,j,k);
5294: fprintf(ficparo,"%1d%1d%d",i,j,k);
5295: /* printf(" %.5le",matcov[i][j]); */
5296: }
5297: ll=0;
5298: for(li=1;li <=nlstate; li++){
5299: for(lj=1;lj <=nlstate+ndeath; lj++){
5300: if(lj==li) continue;
5301: for(lk=1;lk<=ncovmodel;lk++){
5302: ll++;
5303: if(ll<=jj){
5304: cb[0]= lk +'a'-1;cb[1]='\0';
5305: if(ll<jj){
5306: if(itimes==1){
5307: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5308: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5309: }else{
5310: printf(" 0.");
5311: fprintf(ficparo," 0.");
5312: }
5313: }else{
5314: if(itimes==1){
5315: printf(" Var(%s%1d%1d)",ca,i,j);
5316: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5317: }else{
5318: printf(" 0.");
5319: fprintf(ficparo," 0.");
5320: }
5321: }
5322: }
5323: } /* end lk */
5324: } /* end lj */
5325: } /* end li */
5326: printf("\n");
5327: fprintf(ficparo,"\n");
5328: numlinepar++;
5329: } /* end k*/
5330: } /*end j */
5331: } /* end i */
5332: } /* end itimes */
5333:
5334: } /* end of prwizard */
5335: /******************* Gompertz Likelihood ******************************/
5336: double gompertz(double x[])
5337: {
5338: double A,B,L=0.0,sump=0.,num=0.;
5339: int i,n=0; /* n is the size of the sample */
5340:
5341: for (i=0;i<=imx-1 ; i++) {
5342: sump=sump+weight[i];
5343: /* sump=sump+1;*/
5344: num=num+1;
5345: }
5346:
5347:
5348: /* for (i=0; i<=imx; i++)
5349: 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]);*/
5350:
5351: for (i=1;i<=imx ; i++)
5352: {
5353: if (cens[i] == 1 && wav[i]>1)
5354: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5355:
5356: if (cens[i] == 0 && wav[i]>1)
5357: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5358: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5359:
5360: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5361: if (wav[i] > 1 ) { /* ??? */
5362: L=L+A*weight[i];
5363: /* 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]);*/
5364: }
5365: }
5366:
5367: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5368:
5369: return -2*L*num/sump;
5370: }
5371:
1.136 brouard 5372: #ifdef GSL
5373: /******************* Gompertz_f Likelihood ******************************/
5374: double gompertz_f(const gsl_vector *v, void *params)
5375: {
5376: double A,B,LL=0.0,sump=0.,num=0.;
5377: double *x= (double *) v->data;
5378: int i,n=0; /* n is the size of the sample */
5379:
5380: for (i=0;i<=imx-1 ; i++) {
5381: sump=sump+weight[i];
5382: /* sump=sump+1;*/
5383: num=num+1;
5384: }
5385:
5386:
5387: /* for (i=0; i<=imx; i++)
5388: 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]);*/
5389: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5390: for (i=1;i<=imx ; i++)
5391: {
5392: if (cens[i] == 1 && wav[i]>1)
5393: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5394:
5395: if (cens[i] == 0 && wav[i]>1)
5396: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5397: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5398:
5399: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5400: if (wav[i] > 1 ) { /* ??? */
5401: LL=LL+A*weight[i];
5402: /* 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]);*/
5403: }
5404: }
5405:
5406: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5407: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5408:
5409: return -2*LL*num/sump;
5410: }
5411: #endif
5412:
1.126 brouard 5413: /******************* Printing html file ***********/
5414: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
5415: int lastpass, int stepm, int weightopt, char model[],\
5416: int imx, double p[],double **matcov,double agemortsup){
5417: int i,k;
5418:
5419: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5420: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5421: for (i=1;i<=2;i++)
5422: 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 5423: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 5424: fprintf(fichtm,"</ul>");
5425:
5426: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5427:
5428: 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>");
5429:
5430: for (k=agegomp;k<(agemortsup-2);k++)
5431: 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]);
5432:
5433:
5434: fflush(fichtm);
5435: }
5436:
5437: /******************* Gnuplot file **************/
5438: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
5439:
5440: char dirfileres[132],optfileres[132];
1.164 brouard 5441:
1.126 brouard 5442: int ng;
5443:
5444:
5445: /*#ifdef windows */
5446: fprintf(ficgp,"cd \"%s\" \n",pathc);
5447: /*#endif */
5448:
5449:
5450: strcpy(dirfileres,optionfilefiname);
5451: strcpy(optfileres,"vpl");
1.199 ! brouard 5452: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 5453: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 ! brouard 5454: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 5455: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 5456: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5457:
5458: }
5459:
1.136 brouard 5460: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5461: {
1.126 brouard 5462:
1.136 brouard 5463: /*-------- data file ----------*/
5464: FILE *fic;
5465: char dummy[]=" ";
1.164 brouard 5466: int i=0, j=0, n=0;
1.136 brouard 5467: int linei, month, year,iout;
5468: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 5469: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 5470: char *stratrunc;
5471: int lstra;
1.126 brouard 5472:
5473:
1.136 brouard 5474: if((fic=fopen(datafile,"r"))==NULL) {
1.195 brouard 5475: printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
5476: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
1.136 brouard 5477: }
1.126 brouard 5478:
1.136 brouard 5479: i=1;
5480: linei=0;
5481: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5482: linei=linei+1;
5483: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5484: if(line[j] == '\t')
5485: line[j] = ' ';
5486: }
5487: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5488: ;
5489: };
5490: line[j+1]=0; /* Trims blanks at end of line */
5491: if(line[0]=='#'){
5492: fprintf(ficlog,"Comment line\n%s\n",line);
5493: printf("Comment line\n%s\n",line);
5494: continue;
5495: }
5496: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 5497: strcpy(line, linetmp);
1.136 brouard 5498:
1.126 brouard 5499:
1.136 brouard 5500: for (j=maxwav;j>=1;j--){
1.137 brouard 5501: cutv(stra, strb, line, ' ');
1.136 brouard 5502: if(strb[0]=='.') { /* Missing status */
5503: lval=-1;
5504: }else{
5505: errno=0;
5506: lval=strtol(strb,&endptr,10);
5507: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5508: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5509: 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);
5510: 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 5511: return 1;
5512: }
5513: }
5514: s[j][i]=lval;
5515:
5516: strcpy(line,stra);
5517: cutv(stra, strb,line,' ');
1.169 brouard 5518: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5519: }
1.169 brouard 5520: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5521: month=99;
5522: year=9999;
5523: }else{
1.141 brouard 5524: 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);
5525: 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 5526: return 1;
5527: }
5528: anint[j][i]= (double) year;
5529: mint[j][i]= (double)month;
5530: strcpy(line,stra);
5531: } /* ENd Waves */
5532:
5533: cutv(stra, strb,line,' ');
1.169 brouard 5534: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5535: }
1.169 brouard 5536: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5537: month=99;
5538: year=9999;
5539: }else{
1.141 brouard 5540: 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);
5541: 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 5542: return 1;
5543: }
5544: andc[i]=(double) year;
5545: moisdc[i]=(double) month;
5546: strcpy(line,stra);
5547:
5548: cutv(stra, strb,line,' ');
1.169 brouard 5549: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5550: }
1.169 brouard 5551: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 5552: month=99;
5553: year=9999;
5554: }else{
1.141 brouard 5555: 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);
5556: 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 5557: return 1;
5558: }
5559: if (year==9999) {
1.141 brouard 5560: 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);
5561: 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 5562: return 1;
1.126 brouard 5563:
1.136 brouard 5564: }
5565: annais[i]=(double)(year);
5566: moisnais[i]=(double)(month);
5567: strcpy(line,stra);
5568:
5569: cutv(stra, strb,line,' ');
5570: errno=0;
5571: dval=strtod(strb,&endptr);
5572: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5573: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5574: 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 5575: fflush(ficlog);
5576: return 1;
5577: }
5578: weight[i]=dval;
5579: strcpy(line,stra);
5580:
5581: for (j=ncovcol;j>=1;j--){
5582: cutv(stra, strb,line,' ');
5583: if(strb[0]=='.') { /* Missing status */
5584: lval=-1;
5585: }else{
5586: errno=0;
5587: lval=strtol(strb,&endptr,10);
5588: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5589: 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);
5590: 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 5591: return 1;
5592: }
5593: }
5594: if(lval <-1 || lval >1){
1.141 brouard 5595: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5596: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5597: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5598: For example, for multinomial values like 1, 2 and 3,\n \
5599: build V1=0 V2=0 for the reference value (1),\n \
5600: V1=1 V2=0 for (2) \n \
5601: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5602: output of IMaCh is often meaningless.\n \
5603: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 5604: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5605: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5606: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5607: For example, for multinomial values like 1, 2 and 3,\n \
5608: build V1=0 V2=0 for the reference value (1),\n \
5609: V1=1 V2=0 for (2) \n \
5610: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5611: output of IMaCh is often meaningless.\n \
5612: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5613: return 1;
5614: }
5615: covar[j][i]=(double)(lval);
5616: strcpy(line,stra);
5617: }
5618: lstra=strlen(stra);
5619:
5620: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5621: stratrunc = &(stra[lstra-9]);
5622: num[i]=atol(stratrunc);
5623: }
5624: else
5625: num[i]=atol(stra);
5626: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5627: 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;}*/
5628:
5629: i=i+1;
5630: } /* End loop reading data */
1.126 brouard 5631:
1.136 brouard 5632: *imax=i-1; /* Number of individuals */
5633: fclose(fic);
5634:
5635: return (0);
1.164 brouard 5636: /* endread: */
1.136 brouard 5637: printf("Exiting readdata: ");
5638: fclose(fic);
5639: return (1);
1.126 brouard 5640:
5641:
5642:
1.136 brouard 5643: }
1.145 brouard 5644: void removespace(char *str) {
5645: char *p1 = str, *p2 = str;
5646: do
5647: while (*p2 == ' ')
5648: p2++;
1.169 brouard 5649: while (*p1++ == *p2++);
1.145 brouard 5650: }
5651:
5652: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 5653: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
5654: * - nagesqr = 1 if age*age in the model, otherwise 0.
5655: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
5656: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 5657: * - cptcovage number of covariates with age*products =2
5658: * - cptcovs number of simple covariates
5659: * - 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
5660: * which is a new column after the 9 (ncovcol) variables.
5661: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5662: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5663: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5664: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5665: */
1.136 brouard 5666: {
1.145 brouard 5667: int i, j, k, ks;
1.164 brouard 5668: int j1, k1, k2;
1.136 brouard 5669: char modelsav[80];
1.145 brouard 5670: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 5671: char *strpt;
1.136 brouard 5672:
1.145 brouard 5673: /*removespace(model);*/
1.136 brouard 5674: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 5675: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 5676: if (strstr(model,"AGE") !=0){
1.192 brouard 5677: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
5678: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 5679: return 1;
5680: }
1.141 brouard 5681: if (strstr(model,"v") !=0){
5682: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5683: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5684: return 1;
5685: }
1.187 brouard 5686: strcpy(modelsav,model);
5687: if ((strpt=strstr(model,"age*age")) !=0){
5688: printf(" strpt=%s, model=%s\n",strpt, model);
5689: if(strpt != model){
5690: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 5691: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 5692: corresponding column of parameters.\n",model);
5693: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 5694: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 5695: corresponding column of parameters.\n",model); fflush(ficlog);
5696: return 1;
5697: }
5698:
5699: nagesqr=1;
5700: if (strstr(model,"+age*age") !=0)
5701: substrchaine(modelsav, model, "+age*age");
5702: else if (strstr(model,"age*age+") !=0)
5703: substrchaine(modelsav, model, "age*age+");
5704: else
5705: substrchaine(modelsav, model, "age*age");
5706: }else
5707: nagesqr=0;
5708: if (strlen(modelsav) >1){
5709: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
5710: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
5711: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
5712: cptcovt= j+1; /* Number of total covariates in the model, not including
5713: * cst, age and age*age
5714: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
5715: /* including age products which are counted in cptcovage.
5716: * but the covariates which are products must be treated
5717: * separately: ncovn=4- 2=2 (V1+V3). */
5718: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5719: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5720:
5721:
5722: /* Design
5723: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5724: * < ncovcol=8 >
5725: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5726: * k= 1 2 3 4 5 6 7 8
5727: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5728: * covar[k,i], value of kth covariate if not including age for individual i:
5729: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5730: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5731: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5732: * Tage[++cptcovage]=k
5733: * if products, new covar are created after ncovcol with k1
5734: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5735: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5736: * 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
5737: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5738: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5739: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5740: * < ncovcol=8 >
5741: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5742: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5743: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5744: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5745: * p Tprod[1]@2={ 6, 5}
5746: *p Tvard[1][1]@4= {7, 8, 5, 6}
5747: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5748: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5749: *How to reorganize?
5750: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5751: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5752: * {2, 1, 4, 8, 5, 6, 3, 7}
5753: * Struct []
5754: */
1.145 brouard 5755:
1.187 brouard 5756: /* This loop fills the array Tvar from the string 'model'.*/
5757: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5758: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5759: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5760: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5761: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5762: /* k=1 Tvar[1]=2 (from V2) */
5763: /* k=5 Tvar[5] */
5764: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 5765: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 5766: /* } */
1.198 brouard 5767: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 5768: /*
5769: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5770: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 5771: Tvar[k]=0;
1.187 brouard 5772: cptcovage=0;
5773: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5774: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5775: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5776: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5777: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5778: /*scanf("%d",i);*/
5779: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5780: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5781: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5782: /* covar is not filled and then is empty */
5783: cptcovprod--;
5784: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5785: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
5786: cptcovage++; /* Sums the number of covariates which include age as a product */
5787: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
5788: /*printf("stre=%s ", stre);*/
5789: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5790: cptcovprod--;
5791: cutl(stre,strb,strc,'V');
5792: Tvar[k]=atoi(stre);
5793: cptcovage++;
5794: Tage[cptcovage]=k;
5795: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5796: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5797: cptcovn++;
5798: cptcovprodnoage++;k1++;
5799: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5800: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5801: because this model-covariate is a construction we invent a new column
5802: ncovcol + k1
5803: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5804: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5805: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5806: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5807: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5808: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5809: k2=k2+2;
5810: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5811: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5812: for (i=1; i<=lastobs;i++){
5813: /* Computes the new covariate which is a product of
5814: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5815: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5816: }
5817: } /* End age is not in the model */
5818: } /* End if model includes a product */
5819: else { /* no more sum */
5820: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5821: /* scanf("%d",i);*/
5822: cutl(strd,strc,strb,'V');
5823: ks++; /**< Number of simple covariates */
1.145 brouard 5824: cptcovn++;
1.187 brouard 5825: Tvar[k]=atoi(strd);
5826: }
5827: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5828: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5829: scanf("%d",i);*/
5830: } /* end of loop + on total covariates */
5831: } /* end if strlen(modelsave == 0) age*age might exist */
5832: } /* end if strlen(model == 0) */
1.136 brouard 5833:
5834: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5835: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5836:
5837: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5838: printf("cptcovprod=%d ", cptcovprod);
5839: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5840:
5841: scanf("%d ",i);*/
5842:
5843:
1.137 brouard 5844: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 5845: /*endread:*/
1.136 brouard 5846: printf("Exiting decodemodel: ");
5847: return (1);
5848: }
5849:
1.169 brouard 5850: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 5851: {
5852: int i, m;
5853:
5854: for (i=1; i<=imx; i++) {
5855: for(m=2; (m<= maxwav); m++) {
5856: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5857: anint[m][i]=9999;
5858: s[m][i]=-1;
5859: }
5860: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 5861: *nberr = *nberr + 1;
5862: 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);
5863: 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 5864: s[m][i]=-1;
5865: }
5866: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 5867: (*nberr)++;
1.136 brouard 5868: 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]);
5869: 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]);
5870: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5871: }
5872: }
5873: }
5874:
5875: for (i=1; i<=imx; i++) {
5876: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5877: for(m=firstpass; (m<= lastpass); m++){
5878: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5879: if (s[m][i] >= nlstate+1) {
1.169 brouard 5880: if(agedc[i]>0){
5881: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 5882: agev[m][i]=agedc[i];
5883: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 5884: }else {
1.136 brouard 5885: if ((int)andc[i]!=9999){
5886: nbwarn++;
5887: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5888: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5889: agev[m][i]=-1;
5890: }
5891: }
1.169 brouard 5892: } /* agedc > 0 */
1.136 brouard 5893: }
5894: else if(s[m][i] !=9){ /* Standard case, age in fractional
5895: years but with the precision of a month */
5896: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5897: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5898: agev[m][i]=1;
5899: else if(agev[m][i] < *agemin){
5900: *agemin=agev[m][i];
5901: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5902: }
5903: else if(agev[m][i] >*agemax){
5904: *agemax=agev[m][i];
1.156 brouard 5905: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 5906: }
5907: /*agev[m][i]=anint[m][i]-annais[i];*/
5908: /* agev[m][i] = age[i]+2*m;*/
5909: }
5910: else { /* =9 */
5911: agev[m][i]=1;
5912: s[m][i]=-1;
5913: }
5914: }
5915: else /*= 0 Unknown */
5916: agev[m][i]=1;
5917: }
5918:
5919: }
5920: for (i=1; i<=imx; i++) {
5921: for(m=firstpass; (m<=lastpass); m++){
5922: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 5923: (*nberr)++;
1.136 brouard 5924: 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);
5925: 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);
5926: return 1;
5927: }
5928: }
5929: }
5930:
5931: /*for (i=1; i<=imx; i++){
5932: for (m=firstpass; (m<lastpass); m++){
5933: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5934: }
5935:
5936: }*/
5937:
5938:
1.139 brouard 5939: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5940: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 5941:
5942: return (0);
1.164 brouard 5943: /* endread:*/
1.136 brouard 5944: printf("Exiting calandcheckages: ");
5945: return (1);
5946: }
5947:
1.172 brouard 5948: #if defined(_MSC_VER)
5949: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5950: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5951: //#include "stdafx.h"
5952: //#include <stdio.h>
5953: //#include <tchar.h>
5954: //#include <windows.h>
5955: //#include <iostream>
5956: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
5957:
5958: LPFN_ISWOW64PROCESS fnIsWow64Process;
5959:
5960: BOOL IsWow64()
5961: {
5962: BOOL bIsWow64 = FALSE;
5963:
5964: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
5965: // (HANDLE, PBOOL);
5966:
5967: //LPFN_ISWOW64PROCESS fnIsWow64Process;
5968:
5969: HMODULE module = GetModuleHandle(_T("kernel32"));
5970: const char funcName[] = "IsWow64Process";
5971: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
5972: GetProcAddress(module, funcName);
5973:
5974: if (NULL != fnIsWow64Process)
5975: {
5976: if (!fnIsWow64Process(GetCurrentProcess(),
5977: &bIsWow64))
5978: //throw std::exception("Unknown error");
5979: printf("Unknown error\n");
5980: }
5981: return bIsWow64 != FALSE;
5982: }
5983: #endif
1.177 brouard 5984:
1.191 brouard 5985: void syscompilerinfo(int logged)
1.167 brouard 5986: {
5987: /* #include "syscompilerinfo.h"*/
1.185 brouard 5988: /* command line Intel compiler 32bit windows, XP compatible:*/
5989: /* /GS /W3 /Gy
5990: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
5991: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
5992: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 5993: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
5994: */
5995: /* 64 bits */
1.185 brouard 5996: /*
5997: /GS /W3 /Gy
5998: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
5999: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
6000: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
6001: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
6002: /* Optimization are useless and O3 is slower than O2 */
6003: /*
6004: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
6005: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
6006: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
6007: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
6008: */
1.186 brouard 6009: /* Link is */ /* /OUT:"visual studio
1.185 brouard 6010: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
6011: /PDB:"visual studio
6012: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
6013: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
6014: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
6015: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
6016: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
6017: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
6018: uiAccess='false'"
6019: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
6020: /NOLOGO /TLBID:1
6021: */
1.177 brouard 6022: #if defined __INTEL_COMPILER
1.178 brouard 6023: #if defined(__GNUC__)
6024: struct utsname sysInfo; /* For Intel on Linux and OS/X */
6025: #endif
1.177 brouard 6026: #elif defined(__GNUC__)
1.179 brouard 6027: #ifndef __APPLE__
1.174 brouard 6028: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 6029: #endif
1.177 brouard 6030: struct utsname sysInfo;
1.178 brouard 6031: int cross = CROSS;
6032: if (cross){
6033: printf("Cross-");
1.191 brouard 6034: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 6035: }
1.174 brouard 6036: #endif
6037:
1.171 brouard 6038: #include <stdint.h>
1.178 brouard 6039:
1.191 brouard 6040: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 6041: #if defined(__clang__)
1.191 brouard 6042: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 6043: #endif
6044: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 6045: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 6046: #endif
6047: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 6048: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 6049: #endif
6050: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 6051: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 6052: #endif
6053: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 6054: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 6055: #endif
6056: #if defined(_MSC_VER)
1.191 brouard 6057: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 6058: #endif
6059: #if defined(__PGI)
1.191 brouard 6060: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 6061: #endif
6062: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 6063: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 6064: #endif
1.191 brouard 6065: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 6066:
1.167 brouard 6067: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
6068: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
6069: // Windows (x64 and x86)
1.191 brouard 6070: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 6071: #elif __unix__ // all unices, not all compilers
6072: // Unix
1.191 brouard 6073: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 6074: #elif __linux__
6075: // linux
1.191 brouard 6076: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 6077: #elif __APPLE__
1.174 brouard 6078: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 6079: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 6080: #endif
6081:
6082: /* __MINGW32__ */
6083: /* __CYGWIN__ */
6084: /* __MINGW64__ */
6085: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
6086: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
6087: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
6088: /* _WIN64 // Defined for applications for Win64. */
6089: /* _M_X64 // Defined for compilations that target x64 processors. */
6090: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 6091:
1.167 brouard 6092: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 6093: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 6094: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 6095: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 6096: #else
1.191 brouard 6097: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 6098: #endif
6099:
1.169 brouard 6100: #if defined(__GNUC__)
6101: # if defined(__GNUC_PATCHLEVEL__)
6102: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6103: + __GNUC_MINOR__ * 100 \
6104: + __GNUC_PATCHLEVEL__)
6105: # else
6106: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6107: + __GNUC_MINOR__ * 100)
6108: # endif
1.174 brouard 6109: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 6110: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 6111:
6112: if (uname(&sysInfo) != -1) {
6113: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 6114: 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 6115: }
6116: else
6117: perror("uname() error");
1.179 brouard 6118: //#ifndef __INTEL_COMPILER
6119: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 6120: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 6121: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 6122: #endif
1.169 brouard 6123: #endif
1.172 brouard 6124:
6125: // void main()
6126: // {
1.169 brouard 6127: #if defined(_MSC_VER)
1.174 brouard 6128: if (IsWow64()){
1.191 brouard 6129: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6130: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 6131: }
6132: else{
1.191 brouard 6133: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
6134: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 6135: }
1.172 brouard 6136: // printf("\nPress Enter to continue...");
6137: // getchar();
6138: // }
6139:
1.169 brouard 6140: #endif
6141:
1.167 brouard 6142:
6143: }
1.136 brouard 6144:
1.180 brouard 6145: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
6146: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6147: int i, j, k, i1 ;
6148: double ftolpl = 1.e-10;
6149: double age, agebase, agelim;
6150:
6151: strcpy(filerespl,"pl");
6152: strcat(filerespl,fileres);
6153: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6154: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6155: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6156: }
6157: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6158: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6159: pstamp(ficrespl);
6160: fprintf(ficrespl,"# Period (stable) prevalence \n");
6161: fprintf(ficrespl,"#Age ");
6162: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6163: fprintf(ficrespl,"\n");
6164:
6165: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6166:
6167: agebase=ageminpar;
6168: agelim=agemaxpar;
6169:
6170: i1=pow(2,cptcoveff);
6171: if (cptcovn < 1){i1=1;}
6172:
6173: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6174: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6175: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6176: k=k+1;
6177: /* to clean */
1.198 brouard 6178: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
1.180 brouard 6179: fprintf(ficrespl,"\n#******");
6180: printf("\n#******");
6181: fprintf(ficlog,"\n#******");
6182: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 6183: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6184: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6185: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6186: }
6187: fprintf(ficrespl,"******\n");
6188: printf("******\n");
6189: fprintf(ficlog,"******\n");
6190:
6191: fprintf(ficrespl,"#Age ");
6192: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 6193: fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6194: }
6195: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6196: fprintf(ficrespl,"\n");
6197:
6198: for (age=agebase; age<=agelim; age++){
6199: /* for (age=agebase; age<=agebase; age++){ */
6200: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6201: fprintf(ficrespl,"%.0f ",age );
6202: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6203: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6204: for(i=1; i<=nlstate;i++)
6205: fprintf(ficrespl," %.5f", prlim[i][i]);
6206: fprintf(ficrespl,"\n");
6207: } /* Age */
6208: /* was end of cptcod */
6209: } /* cptcov */
1.184 brouard 6210: return 0;
1.180 brouard 6211: }
6212:
6213: int hPijx(double *p, int bage, int fage){
6214: /*------------- h Pij x at various ages ------------*/
6215:
6216: int stepsize;
6217: int agelim;
6218: int hstepm;
6219: int nhstepm;
6220: int h, i, i1, j, k;
6221:
6222: double agedeb;
6223: double ***p3mat;
6224:
6225: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
6226: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6227: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
6228: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
6229: }
6230: printf("Computing pij: result on file '%s' \n", filerespij);
6231: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6232:
6233: stepsize=(int) (stepm+YEARM-1)/YEARM;
6234: /*if (stepm<=24) stepsize=2;*/
6235:
6236: agelim=AGESUP;
6237: hstepm=stepsize*YEARM; /* Every year of age */
6238: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6239:
6240: /* hstepm=1; aff par mois*/
6241: pstamp(ficrespij);
6242: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6243: i1= pow(2,cptcoveff);
1.183 brouard 6244: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
6245: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
6246: /* k=k+1; */
6247: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6248: fprintf(ficrespij,"\n#****** ");
6249: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6250: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.183 brouard 6251: fprintf(ficrespij,"******\n");
6252:
6253: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6254: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6255: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6256:
6257: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 6258:
1.183 brouard 6259: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6260: oldm=oldms;savm=savms;
6261: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6262: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6263: for(i=1; i<=nlstate;i++)
6264: for(j=1; j<=nlstate+ndeath;j++)
6265: fprintf(ficrespij," %1d-%1d",i,j);
6266: fprintf(ficrespij,"\n");
6267: for (h=0; h<=nhstepm; h++){
6268: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
6269: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 6270: for(i=1; i<=nlstate;i++)
6271: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 6272: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 6273: fprintf(ficrespij,"\n");
6274: }
1.183 brouard 6275: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6276: fprintf(ficrespij,"\n");
6277: }
1.180 brouard 6278: /*}*/
6279: }
1.184 brouard 6280: return 0;
1.180 brouard 6281: }
6282:
6283:
1.136 brouard 6284: /***********************************************/
6285: /**************** Main Program *****************/
6286: /***********************************************/
6287:
6288: int main(int argc, char *argv[])
6289: {
6290: #ifdef GSL
6291: const gsl_multimin_fminimizer_type *T;
6292: size_t iteri = 0, it;
6293: int rval = GSL_CONTINUE;
6294: int status = GSL_SUCCESS;
6295: double ssval;
6296: #endif
6297: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 6298: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
6299:
6300: int jj, ll, li, lj, lk;
1.136 brouard 6301: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 6302: int num_filled;
1.136 brouard 6303: int itimes;
6304: int NDIM=2;
6305: int vpopbased=0;
6306:
1.164 brouard 6307: char ca[32], cb[32];
1.136 brouard 6308: /* FILE *fichtm; *//* Html File */
6309: /* FILE *ficgp;*/ /*Gnuplot File */
6310: struct stat info;
1.191 brouard 6311: double agedeb=0.;
1.194 brouard 6312:
6313: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.136 brouard 6314:
1.165 brouard 6315: double fret;
1.191 brouard 6316: double dum=0.; /* Dummy variable */
1.136 brouard 6317: double ***p3mat;
6318: double ***mobaverage;
1.164 brouard 6319:
6320: char line[MAXLINE];
1.197 brouard 6321: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
6322:
6323: char model[MAXLINE], modeltemp[MAXLINE];
1.136 brouard 6324: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 6325: char *tok, *val; /* pathtot */
1.136 brouard 6326: int firstobs=1, lastobs=10;
1.195 brouard 6327: int c, h , cpt, c2;
1.191 brouard 6328: int jl=0;
6329: int i1, j1, jk, stepsize=0;
1.194 brouard 6330: int count=0;
6331:
1.164 brouard 6332: int *tab;
1.136 brouard 6333: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
6334: int mobilav=0,popforecast=0;
1.191 brouard 6335: int hstepm=0, nhstepm=0;
1.136 brouard 6336: int agemortsup;
6337: float sumlpop=0.;
6338: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
6339: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
6340:
1.191 brouard 6341: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 6342: double ftolpl=FTOL;
6343: double **prlim;
6344: double ***param; /* Matrix of parameters */
6345: double *p;
6346: double **matcov; /* Matrix of covariance */
6347: double ***delti3; /* Scale */
6348: double *delti; /* Scale */
6349: double ***eij, ***vareij;
6350: double **varpl; /* Variances of prevalence limits by age */
6351: double *epj, vepp;
1.164 brouard 6352:
1.136 brouard 6353: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6354: double **ximort;
1.145 brouard 6355: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 6356: int *dcwave;
6357:
1.164 brouard 6358: char z[1]="c";
1.136 brouard 6359:
6360: /*char *strt;*/
6361: char strtend[80];
1.126 brouard 6362:
1.164 brouard 6363:
1.126 brouard 6364: /* setlocale (LC_ALL, ""); */
6365: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6366: /* textdomain (PACKAGE); */
6367: /* setlocale (LC_CTYPE, ""); */
6368: /* setlocale (LC_MESSAGES, ""); */
6369:
6370: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 6371: rstart_time = time(NULL);
6372: /* (void) gettimeofday(&start_time,&tzp);*/
6373: start_time = *localtime(&rstart_time);
1.126 brouard 6374: curr_time=start_time;
1.157 brouard 6375: /*tml = *localtime(&start_time.tm_sec);*/
6376: /* strcpy(strstart,asctime(&tml)); */
6377: strcpy(strstart,asctime(&start_time));
1.126 brouard 6378:
6379: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 6380: /* tp.tm_sec = tp.tm_sec +86400; */
6381: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 6382: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6383: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6384: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 6385: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 6386: /* strt=asctime(&tmg); */
6387: /* printf("Time(after) =%s",strstart); */
6388: /* (void) time (&time_value);
6389: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6390: * tm = *localtime(&time_value);
6391: * strstart=asctime(&tm);
6392: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6393: */
6394:
6395: nberr=0; /* Number of errors and warnings */
6396: nbwarn=0;
1.184 brouard 6397: #ifdef WIN32
6398: _getcwd(pathcd, size);
6399: #else
1.126 brouard 6400: getcwd(pathcd, size);
1.184 brouard 6401: #endif
1.191 brouard 6402: syscompilerinfo(0);
1.196 brouard 6403: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 6404: if(argc <=1){
6405: printf("\nEnter the parameter file name: ");
6406: fgets(pathr,FILENAMELENGTH,stdin);
6407: i=strlen(pathr);
6408: if(pathr[i-1]=='\n')
6409: pathr[i-1]='\0';
1.156 brouard 6410: i=strlen(pathr);
6411: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
6412: pathr[i-1]='\0';
1.126 brouard 6413: for (tok = pathr; tok != NULL; ){
6414: printf("Pathr |%s|\n",pathr);
6415: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6416: printf("val= |%s| pathr=%s\n",val,pathr);
6417: strcpy (pathtot, val);
6418: if(pathr[0] == '\0') break; /* Dirty */
6419: }
6420: }
6421: else{
6422: strcpy(pathtot,argv[1]);
6423: }
6424: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6425: /*cygwin_split_path(pathtot,path,optionfile);
6426: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6427: /* cutv(path,optionfile,pathtot,'\\');*/
6428:
6429: /* Split argv[0], imach program to get pathimach */
6430: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6431: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6432: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6433: /* strcpy(pathimach,argv[0]); */
6434: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6435: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6436: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 6437: #ifdef WIN32
6438: _chdir(path); /* Can be a relative path */
6439: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
6440: #else
1.126 brouard 6441: chdir(path); /* Can be a relative path */
1.184 brouard 6442: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
6443: #endif
6444: printf("Current directory %s!\n",pathcd);
1.126 brouard 6445: strcpy(command,"mkdir ");
6446: strcat(command,optionfilefiname);
6447: if((outcmd=system(command)) != 0){
1.169 brouard 6448: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 6449: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6450: /* fclose(ficlog); */
6451: /* exit(1); */
6452: }
6453: /* if((imk=mkdir(optionfilefiname))<0){ */
6454: /* perror("mkdir"); */
6455: /* } */
6456:
6457: /*-------- arguments in the command line --------*/
6458:
1.186 brouard 6459: /* Main Log file */
1.126 brouard 6460: strcat(filelog, optionfilefiname);
6461: strcat(filelog,".log"); /* */
6462: if((ficlog=fopen(filelog,"w"))==NULL) {
6463: printf("Problem with logfile %s\n",filelog);
6464: goto end;
6465: }
6466: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 6467: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 6468: fprintf(ficlog,"\nEnter the parameter file name: \n");
6469: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6470: path=%s \n\
6471: optionfile=%s\n\
6472: optionfilext=%s\n\
1.156 brouard 6473: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 6474:
1.197 brouard 6475: syscompilerinfo(1);
1.167 brouard 6476:
1.126 brouard 6477: printf("Local time (at start):%s",strstart);
6478: fprintf(ficlog,"Local time (at start): %s",strstart);
6479: fflush(ficlog);
6480: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 6481: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 6482:
6483: /* */
6484: strcpy(fileres,"r");
6485: strcat(fileres, optionfilefiname);
6486: strcat(fileres,".txt"); /* Other files have txt extension */
6487:
1.186 brouard 6488: /* Main ---------arguments file --------*/
1.126 brouard 6489:
6490: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 6491: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6492: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 6493: fflush(ficlog);
1.149 brouard 6494: /* goto end; */
6495: exit(70);
1.126 brouard 6496: }
6497:
6498:
6499:
6500: strcpy(filereso,"o");
6501: strcat(filereso,fileres);
6502: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6503: printf("Problem with Output resultfile: %s\n", filereso);
6504: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6505: fflush(ficlog);
6506: goto end;
6507: }
6508:
6509: /* Reads comments: lines beginning with '#' */
6510: numlinepar=0;
1.197 brouard 6511:
6512: /* First parameter line */
6513: while(fgets(line, MAXLINE, ficpar)) {
6514: /* If line starts with a # it is a comment */
6515: if (line[0] == '#') {
6516: numlinepar++;
6517: fputs(line,stdout);
6518: fputs(line,ficparo);
6519: fputs(line,ficlog);
6520: continue;
6521: }else
6522: break;
6523: }
6524: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
6525: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
6526: if (num_filled != 5) {
6527: printf("Should be 5 parameters\n");
6528: }
1.126 brouard 6529: numlinepar++;
1.197 brouard 6530: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
6531: }
6532: /* Second parameter line */
6533: while(fgets(line, MAXLINE, ficpar)) {
6534: /* If line starts with a # it is a comment */
6535: if (line[0] == '#') {
6536: numlinepar++;
6537: fputs(line,stdout);
6538: fputs(line,ficparo);
6539: fputs(line,ficlog);
6540: continue;
6541: }else
6542: break;
6543: }
6544: if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
6545: &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
6546: if (num_filled != 8) {
6547: printf("Not 8\n");
6548: }
6549: 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 6550: }
6551:
1.197 brouard 6552: /* Third parameter line */
6553: while(fgets(line, MAXLINE, ficpar)) {
6554: /* If line starts with a # it is a comment */
6555: if (line[0] == '#') {
6556: numlinepar++;
6557: fputs(line,stdout);
6558: fputs(line,ficparo);
6559: fputs(line,ficlog);
6560: continue;
6561: }else
6562: break;
6563: }
6564: if((num_filled=sscanf(line,"model=1+age%[^.\n]\n", model)) !=EOF){
6565: if (num_filled != 1) {
6566: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
6567: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
6568: model[0]='\0';
6569: goto end;
6570: }
6571: else{
6572: if (model[0]=='+'){
6573: for(i=1; i<=strlen(model);i++)
6574: modeltemp[i-1]=model[i];
6575: }
6576: strcpy(model,modeltemp);
6577: }
1.199 ! brouard 6578: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.197 brouard 6579: }
6580: /* 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); */
6581: /* numlinepar=numlinepar+3; /\* In general *\/ */
6582: /* 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); */
1.187 brouard 6583: if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
6584: model[strlen(model)-1]='\0';
1.197 brouard 6585: 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);
6586: 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 6587: fflush(ficlog);
1.190 brouard 6588: /* if(model[0]=='#'|| model[0]== '\0'){ */
6589: if(model[0]=='#'){
1.187 brouard 6590: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
6591: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
6592: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
6593: if(mle != -1){
6594: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
6595: exit(1);
6596: }
6597: }
1.126 brouard 6598: while((c=getc(ficpar))=='#' && c!= EOF){
6599: ungetc(c,ficpar);
6600: fgets(line, MAXLINE, ficpar);
6601: numlinepar++;
1.195 brouard 6602: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
6603: z[0]=line[1];
6604: }
6605: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 6606: fputs(line, stdout);
6607: //puts(line);
1.126 brouard 6608: fputs(line,ficparo);
6609: fputs(line,ficlog);
6610: }
6611: ungetc(c,ficpar);
6612:
6613:
1.145 brouard 6614: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 6615: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
6616: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
6617: v1+v2*age+v2*v3 makes cptcovn = 3
6618: */
6619: if (strlen(model)>1)
1.187 brouard 6620: 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 6621: else
1.187 brouard 6622: ncovmodel=2; /* Constant and age */
1.133 brouard 6623: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
6624: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 6625: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
6626: 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);
6627: 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);
6628: fflush(stdout);
6629: fclose (ficlog);
6630: goto end;
6631: }
1.126 brouard 6632: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6633: delti=delti3[1][1];
6634: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
6635: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
6636: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 6637: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6638: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 6639: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6640: fclose (ficparo);
6641: fclose (ficlog);
6642: goto end;
6643: exit(0);
6644: }
1.186 brouard 6645: else if(mle==-3) { /* Main Wizard */
1.126 brouard 6646: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 6647: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6648: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 6649: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6650: matcov=matrix(1,npar,1,npar);
6651: }
6652: else{
1.145 brouard 6653: /* Read guessed parameters */
1.126 brouard 6654: /* Reads comments: lines beginning with '#' */
6655: while((c=getc(ficpar))=='#' && c!= EOF){
6656: ungetc(c,ficpar);
6657: fgets(line, MAXLINE, ficpar);
6658: numlinepar++;
1.141 brouard 6659: fputs(line,stdout);
1.126 brouard 6660: fputs(line,ficparo);
6661: fputs(line,ficlog);
6662: }
6663: ungetc(c,ficpar);
6664:
6665: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6666: for(i=1; i <=nlstate; i++){
6667: j=0;
6668: for(jj=1; jj <=nlstate+ndeath; jj++){
6669: if(jj==i) continue;
6670: j++;
6671: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.193 brouard 6672: if ((i1 != i) || (j1 != jj)){
1.126 brouard 6673: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
6674: It might be a problem of design; if ncovcol and the model are correct\n \
6675: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
6676: exit(1);
6677: }
6678: fprintf(ficparo,"%1d%1d",i1,j1);
6679: if(mle==1)
1.193 brouard 6680: printf("%1d%1d",i,jj);
6681: fprintf(ficlog,"%1d%1d",i,jj);
1.126 brouard 6682: for(k=1; k<=ncovmodel;k++){
6683: fscanf(ficpar," %lf",¶m[i][j][k]);
6684: if(mle==1){
6685: printf(" %lf",param[i][j][k]);
6686: fprintf(ficlog," %lf",param[i][j][k]);
6687: }
6688: else
6689: fprintf(ficlog," %lf",param[i][j][k]);
6690: fprintf(ficparo," %lf",param[i][j][k]);
6691: }
6692: fscanf(ficpar,"\n");
6693: numlinepar++;
6694: if(mle==1)
6695: printf("\n");
6696: fprintf(ficlog,"\n");
6697: fprintf(ficparo,"\n");
6698: }
6699: }
6700: fflush(ficlog);
6701:
1.145 brouard 6702: /* Reads scales values */
1.126 brouard 6703: p=param[1][1];
6704:
6705: /* Reads comments: lines beginning with '#' */
6706: while((c=getc(ficpar))=='#' && c!= EOF){
6707: ungetc(c,ficpar);
6708: fgets(line, MAXLINE, ficpar);
6709: numlinepar++;
1.141 brouard 6710: fputs(line,stdout);
1.126 brouard 6711: fputs(line,ficparo);
6712: fputs(line,ficlog);
6713: }
6714: ungetc(c,ficpar);
6715:
6716: for(i=1; i <=nlstate; i++){
6717: for(j=1; j <=nlstate+ndeath-1; j++){
6718: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 6719: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 6720: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
6721: exit(1);
6722: }
6723: printf("%1d%1d",i,j);
6724: fprintf(ficparo,"%1d%1d",i1,j1);
6725: fprintf(ficlog,"%1d%1d",i1,j1);
6726: for(k=1; k<=ncovmodel;k++){
6727: fscanf(ficpar,"%le",&delti3[i][j][k]);
6728: printf(" %le",delti3[i][j][k]);
6729: fprintf(ficparo," %le",delti3[i][j][k]);
6730: fprintf(ficlog," %le",delti3[i][j][k]);
6731: }
6732: fscanf(ficpar,"\n");
6733: numlinepar++;
6734: printf("\n");
6735: fprintf(ficparo,"\n");
6736: fprintf(ficlog,"\n");
6737: }
6738: }
6739: fflush(ficlog);
6740:
1.145 brouard 6741: /* Reads covariance matrix */
1.126 brouard 6742: delti=delti3[1][1];
6743:
6744:
6745: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
6746:
6747: /* Reads comments: lines beginning with '#' */
6748: while((c=getc(ficpar))=='#' && c!= EOF){
6749: ungetc(c,ficpar);
6750: fgets(line, MAXLINE, ficpar);
6751: numlinepar++;
1.141 brouard 6752: fputs(line,stdout);
1.126 brouard 6753: fputs(line,ficparo);
6754: fputs(line,ficlog);
6755: }
6756: ungetc(c,ficpar);
6757:
6758: matcov=matrix(1,npar,1,npar);
1.131 brouard 6759: for(i=1; i <=npar; i++)
6760: for(j=1; j <=npar; j++) matcov[i][j]=0.;
6761:
1.194 brouard 6762: /* Scans npar lines */
1.126 brouard 6763: for(i=1; i <=npar; i++){
1.194 brouard 6764: count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
6765: if(count != 3){
6766: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
6767: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
6768: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
6769: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
6770: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
6771: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
6772: exit(1);
6773: }else
1.126 brouard 6774: if(mle==1)
1.194 brouard 6775: printf("%1d%1d%1d",i1,j1,jk);
6776: fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
6777: fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
1.126 brouard 6778: for(j=1; j <=i; j++){
6779: fscanf(ficpar," %le",&matcov[i][j]);
6780: if(mle==1){
6781: printf(" %.5le",matcov[i][j]);
6782: }
6783: fprintf(ficlog," %.5le",matcov[i][j]);
6784: fprintf(ficparo," %.5le",matcov[i][j]);
6785: }
6786: fscanf(ficpar,"\n");
6787: numlinepar++;
6788: if(mle==1)
6789: printf("\n");
6790: fprintf(ficlog,"\n");
6791: fprintf(ficparo,"\n");
6792: }
1.194 brouard 6793: /* End of read covariance matrix npar lines */
1.126 brouard 6794: for(i=1; i <=npar; i++)
6795: for(j=i+1;j<=npar;j++)
6796: matcov[i][j]=matcov[j][i];
6797:
6798: if(mle==1)
6799: printf("\n");
6800: fprintf(ficlog,"\n");
6801:
6802: fflush(ficlog);
6803:
6804: /*-------- Rewriting parameter file ----------*/
6805: strcpy(rfileres,"r"); /* "Rparameterfile */
6806: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
6807: strcat(rfileres,"."); /* */
6808: strcat(rfileres,optionfilext); /* Other files have txt extension */
6809: if((ficres =fopen(rfileres,"w"))==NULL) {
6810: printf("Problem writing new parameter file: %s\n", fileres);goto end;
6811: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
6812: }
6813: fprintf(ficres,"#%s\n",version);
6814: } /* End of mle != -3 */
6815:
1.186 brouard 6816: /* Main data
6817: */
1.126 brouard 6818: n= lastobs;
6819: num=lvector(1,n);
6820: moisnais=vector(1,n);
6821: annais=vector(1,n);
6822: moisdc=vector(1,n);
6823: andc=vector(1,n);
6824: agedc=vector(1,n);
6825: cod=ivector(1,n);
6826: weight=vector(1,n);
6827: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
6828: mint=matrix(1,maxwav,1,n);
6829: anint=matrix(1,maxwav,1,n);
1.131 brouard 6830: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 6831: tab=ivector(1,NCOVMAX);
1.144 brouard 6832: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 6833: 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 6834:
1.136 brouard 6835: /* Reads data from file datafile */
6836: if (readdata(datafile, firstobs, lastobs, &imx)==1)
6837: goto end;
6838:
6839: /* Calculation of the number of parameters from char model */
1.137 brouard 6840: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
6841: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
6842: k=3 V4 Tvar[k=3]= 4 (from V4)
6843: k=2 V1 Tvar[k=2]= 1 (from V1)
6844: k=1 Tvar[1]=2 (from V2)
6845: */
6846: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6847: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6848: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6849: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6850: */
6851: /* For model-covariate k tells which data-covariate to use but
6852: because this model-covariate is a construction we invent a new column
6853: ncovcol + k1
6854: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6855: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 6856: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 6857: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6858: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6859: */
1.145 brouard 6860: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6861: 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 6862: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6863: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 6864: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 6865: 4 covariates (3 plus signs)
6866: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6867: */
1.136 brouard 6868:
1.186 brouard 6869: /* Main decodemodel */
6870:
1.187 brouard 6871:
1.136 brouard 6872: if(decodemodel(model, lastobs) == 1)
6873: goto end;
6874:
1.137 brouard 6875: if((double)(lastobs-imx)/(double)imx > 1.10){
6876: nbwarn++;
6877: 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);
6878: 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);
6879: }
1.136 brouard 6880: /* if(mle==1){*/
1.137 brouard 6881: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6882: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 6883: }
6884:
6885: /*-calculation of age at interview from date of interview and age at death -*/
6886: agev=matrix(1,maxwav,1,imx);
6887:
6888: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6889: goto end;
6890:
1.126 brouard 6891:
1.136 brouard 6892: agegomp=(int)agemin;
6893: free_vector(moisnais,1,n);
6894: free_vector(annais,1,n);
1.126 brouard 6895: /* free_matrix(mint,1,maxwav,1,n);
6896: free_matrix(anint,1,maxwav,1,n);*/
6897: free_vector(moisdc,1,n);
6898: free_vector(andc,1,n);
1.145 brouard 6899: /* */
6900:
1.126 brouard 6901: wav=ivector(1,imx);
6902: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6903: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6904: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6905:
6906: /* Concatenates waves */
6907: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 6908: /* */
6909:
1.126 brouard 6910: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6911:
6912: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6913: ncodemax[1]=1;
1.145 brouard 6914: Ndum =ivector(-1,NCOVMAX);
1.187 brouard 6915: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
1.145 brouard 6916: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.186 brouard 6917: /* Nbcode gives the value of the lth modality of jth covariate, in
6918: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
6919: /* 1 to ncodemax[j] is the maximum value of this jth covariate */
1.145 brouard 6920:
6921: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 6922: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 6923: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.145 brouard 6924: h=0;
6925:
6926:
6927: /*if (cptcovn > 0) */
1.126 brouard 6928:
1.145 brouard 6929:
1.126 brouard 6930: m=pow(2,cptcoveff);
6931:
1.144 brouard 6932: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.186 brouard 6933: * For k=4 covariates, h goes from 1 to 2**k
6934: * codtabm(h,k)= 1 & (h-1) >> (k-1) ;
6935: * h\k 1 2 3 4
1.143 brouard 6936: *______________________________
6937: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6938: * 2 2 1 1 1
6939: * 3 i=2 1 2 1 1
6940: * 4 2 2 1 1
6941: * 5 i=3 1 i=2 1 2 1
6942: * 6 2 1 2 1
6943: * 7 i=4 1 2 2 1
6944: * 8 2 2 2 1
1.197 brouard 6945: * 9 i=5 1 i=3 1 i=2 1 2
6946: * 10 2 1 1 2
6947: * 11 i=6 1 2 1 2
6948: * 12 2 2 1 2
6949: * 13 i=7 1 i=4 1 2 2
6950: * 14 2 1 2 2
6951: * 15 i=8 1 2 2 2
6952: * 16 2 2 2 2
1.143 brouard 6953: */
1.197 brouard 6954: for(h=1; h <=100 ;h++){
6955: /* printf("h=%2d ", h); */
6956: for(k=1; k <=10; k++){
6957: /* printf("k=%d %d ",k,codtabm(h,k)); */
6958: codtab[h][k]=codtabm(h,k);
6959: }
6960: /* printf("\n"); */
6961: }
6962: /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
6963: /* 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 *\/ */
6964: /* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
6965: /* for(cpt=1; cpt <=pow(2,k-1); cpt++){ /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/ */
6966: /* h++; */
6967: /* if (h>m) */
6968: /* h=1; */
6969: /* codtab[h][k]=j; */
6970: /* /\* codtab[12][3]=1; *\/ */
6971: /* /\*codtab[h][Tvar[k]]=j;*\/ */
6972: /* /\* 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]]); *\/ */
6973: /* } */
6974: /* } */
6975: /* } */
6976: /* } */
1.126 brouard 6977: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6978: codtab[1][2]=1;codtab[2][2]=2; */
1.197 brouard 6979: /* for(i=1; i <=m ;i++){ */
6980: /* for(k=1; k <=cptcovn; k++){ */
6981: /* printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
6982: /* } */
6983: /* printf("\n"); */
6984: /* } */
6985: /* scanf("%d",i);*/
1.145 brouard 6986:
6987: free_ivector(Ndum,-1,NCOVMAX);
6988:
6989:
1.126 brouard 6990:
1.186 brouard 6991: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 6992: strcpy(optionfilegnuplot,optionfilefiname);
6993: if(mle==-3)
6994: strcat(optionfilegnuplot,"-mort");
6995: strcat(optionfilegnuplot,".gp");
6996:
6997: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6998: printf("Problem with file %s",optionfilegnuplot);
6999: }
7000: else{
7001: fprintf(ficgp,"\n# %s\n", version);
7002: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 7003: //fprintf(ficgp,"set missing 'NaNq'\n");
7004: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 7005: }
7006: /* fclose(ficgp);*/
1.186 brouard 7007:
7008:
7009: /* Initialisation of --------- index.htm --------*/
1.126 brouard 7010:
7011: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
7012: if(mle==-3)
7013: strcat(optionfilehtm,"-mort");
7014: strcat(optionfilehtm,".htm");
7015: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 7016: printf("Problem with %s \n",optionfilehtm);
7017: exit(0);
1.126 brouard 7018: }
7019:
7020: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
7021: strcat(optionfilehtmcov,"-cov.htm");
7022: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
7023: printf("Problem with %s \n",optionfilehtmcov), exit(0);
7024: }
7025: else{
7026: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
7027: <hr size=\"2\" color=\"#EC5E5E\"> \n\
7028: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
7029: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
7030: }
7031:
7032: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
7033: <hr size=\"2\" color=\"#EC5E5E\"> \n\
7034: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
7035: \n\
7036: <hr size=\"2\" color=\"#EC5E5E\">\
7037: <ul><li><h4>Parameter files</h4>\n\
7038: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
7039: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
7040: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
7041: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
7042: - Date and time at start: %s</ul>\n",\
7043: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
7044: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
7045: fileres,fileres,\
7046: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
7047: fflush(fichtm);
7048:
7049: strcpy(pathr,path);
7050: strcat(pathr,optionfilefiname);
1.184 brouard 7051: #ifdef WIN32
7052: _chdir(optionfilefiname); /* Move to directory named optionfile */
7053: #else
1.126 brouard 7054: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 7055: #endif
7056:
1.126 brouard 7057:
7058: /* Calculates basic frequencies. Computes observed prevalence at single age
7059: and prints on file fileres'p'. */
7060: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
7061:
7062: fprintf(fichtm,"\n");
7063: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
7064: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
7065: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
7066: imx,agemin,agemax,jmin,jmax,jmean);
7067: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7068: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7069: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7070: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7071: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
7072:
7073:
7074: /* For Powell, parameters are in a vector p[] starting at p[1]
7075: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
7076: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
7077:
7078: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 7079: /* For mortality only */
1.126 brouard 7080: if (mle==-3){
1.136 brouard 7081: ximort=matrix(1,NDIM,1,NDIM);
1.186 brouard 7082: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 7083: cens=ivector(1,n);
7084: ageexmed=vector(1,n);
7085: agecens=vector(1,n);
7086: dcwave=ivector(1,n);
7087:
7088: for (i=1; i<=imx; i++){
7089: dcwave[i]=-1;
7090: for (m=firstpass; m<=lastpass; m++)
7091: if (s[m][i]>nlstate) {
7092: dcwave[i]=m;
7093: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
7094: break;
7095: }
7096: }
7097:
7098: for (i=1; i<=imx; i++) {
7099: if (wav[i]>0){
7100: ageexmed[i]=agev[mw[1][i]][i];
7101: j=wav[i];
7102: agecens[i]=1.;
7103:
7104: if (ageexmed[i]> 1 && wav[i] > 0){
7105: agecens[i]=agev[mw[j][i]][i];
7106: cens[i]= 1;
7107: }else if (ageexmed[i]< 1)
7108: cens[i]= -1;
7109: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
7110: cens[i]=0 ;
7111: }
7112: else cens[i]=-1;
7113: }
7114:
7115: for (i=1;i<=NDIM;i++) {
7116: for (j=1;j<=NDIM;j++)
7117: ximort[i][j]=(i == j ? 1.0 : 0.0);
7118: }
7119:
1.145 brouard 7120: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 7121: /*printf("%lf %lf", p[1], p[2]);*/
7122:
7123:
1.136 brouard 7124: #ifdef GSL
7125: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 7126: #else
1.126 brouard 7127: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 7128: #endif
1.126 brouard 7129: strcpy(filerespow,"pow-mort");
7130: strcat(filerespow,fileres);
7131: if((ficrespow=fopen(filerespow,"w"))==NULL) {
7132: printf("Problem with resultfile: %s\n", filerespow);
7133: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
7134: }
1.136 brouard 7135: #ifdef GSL
7136: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 7137: #else
1.126 brouard 7138: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 7139: #endif
1.126 brouard 7140: /* for (i=1;i<=nlstate;i++)
7141: for(j=1;j<=nlstate+ndeath;j++)
7142: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
7143: */
7144: fprintf(ficrespow,"\n");
1.136 brouard 7145: #ifdef GSL
7146: /* gsl starts here */
7147: T = gsl_multimin_fminimizer_nmsimplex;
7148: gsl_multimin_fminimizer *sfm = NULL;
7149: gsl_vector *ss, *x;
7150: gsl_multimin_function minex_func;
7151:
7152: /* Initial vertex size vector */
7153: ss = gsl_vector_alloc (NDIM);
7154:
7155: if (ss == NULL){
7156: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
7157: }
7158: /* Set all step sizes to 1 */
7159: gsl_vector_set_all (ss, 0.001);
7160:
7161: /* Starting point */
1.126 brouard 7162:
1.136 brouard 7163: x = gsl_vector_alloc (NDIM);
7164:
7165: if (x == NULL){
7166: gsl_vector_free(ss);
7167: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
7168: }
7169:
7170: /* Initialize method and iterate */
7171: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 7172: /* gsl_vector_set(x, 0, 0.0268); */
7173: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 7174: gsl_vector_set(x, 0, p[1]);
7175: gsl_vector_set(x, 1, p[2]);
7176:
7177: minex_func.f = &gompertz_f;
7178: minex_func.n = NDIM;
7179: minex_func.params = (void *)&p; /* ??? */
7180:
7181: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
7182: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
7183:
7184: printf("Iterations beginning .....\n\n");
7185: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
7186:
7187: iteri=0;
7188: while (rval == GSL_CONTINUE){
7189: iteri++;
7190: status = gsl_multimin_fminimizer_iterate(sfm);
7191:
7192: if (status) printf("error: %s\n", gsl_strerror (status));
7193: fflush(0);
7194:
7195: if (status)
7196: break;
7197:
7198: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
7199: ssval = gsl_multimin_fminimizer_size (sfm);
7200:
7201: if (rval == GSL_SUCCESS)
7202: printf ("converged to a local maximum at\n");
7203:
7204: printf("%5d ", iteri);
7205: for (it = 0; it < NDIM; it++){
7206: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
7207: }
7208: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
7209: }
7210:
7211: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
7212:
7213: gsl_vector_free(x); /* initial values */
7214: gsl_vector_free(ss); /* inital step size */
7215: for (it=0; it<NDIM; it++){
7216: p[it+1]=gsl_vector_get(sfm->x,it);
7217: fprintf(ficrespow," %.12lf", p[it]);
7218: }
7219: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
7220: #endif
7221: #ifdef POWELL
7222: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
7223: #endif
1.126 brouard 7224: fclose(ficrespow);
7225:
7226: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
7227:
7228: for(i=1; i <=NDIM; i++)
7229: for(j=i+1;j<=NDIM;j++)
7230: matcov[i][j]=matcov[j][i];
7231:
7232: printf("\nCovariance matrix\n ");
7233: for(i=1; i <=NDIM; i++) {
7234: for(j=1;j<=NDIM;j++){
7235: printf("%f ",matcov[i][j]);
7236: }
7237: printf("\n ");
7238: }
7239:
7240: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 7241: for (i=1;i<=NDIM;i++) {
1.126 brouard 7242: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 7243: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
7244: }
1.126 brouard 7245: lsurv=vector(1,AGESUP);
7246: lpop=vector(1,AGESUP);
7247: tpop=vector(1,AGESUP);
7248: lsurv[agegomp]=100000;
7249:
7250: for (k=agegomp;k<=AGESUP;k++) {
7251: agemortsup=k;
7252: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
7253: }
7254:
7255: for (k=agegomp;k<agemortsup;k++)
7256: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
7257:
7258: for (k=agegomp;k<agemortsup;k++){
7259: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
7260: sumlpop=sumlpop+lpop[k];
7261: }
7262:
7263: tpop[agegomp]=sumlpop;
7264: for (k=agegomp;k<(agemortsup-3);k++){
7265: /* tpop[k+1]=2;*/
7266: tpop[k+1]=tpop[k]-lpop[k];
7267: }
7268:
7269:
7270: printf("\nAge lx qx dx Lx Tx e(x)\n");
7271: for (k=agegomp;k<(agemortsup-2);k++)
7272: 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]);
7273:
7274:
7275: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 7276: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
7277: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7278: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7279: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7280: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7281: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7282: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7283: }else
7284: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.126 brouard 7285: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
7286: stepm, weightopt,\
7287: model,imx,p,matcov,agemortsup);
7288:
7289: free_vector(lsurv,1,AGESUP);
7290: free_vector(lpop,1,AGESUP);
7291: free_vector(tpop,1,AGESUP);
1.136 brouard 7292: #ifdef GSL
7293: free_ivector(cens,1,n);
7294: free_vector(agecens,1,n);
7295: free_ivector(dcwave,1,n);
7296: free_matrix(ximort,1,NDIM,1,NDIM);
7297: #endif
1.186 brouard 7298: } /* Endof if mle==-3 mortality only */
7299: /* Standard maximisation */
1.126 brouard 7300: else{ /* For mle >=1 */
1.132 brouard 7301: globpr=0;/* debug */
1.186 brouard 7302: /* Computes likelihood for initial parameters */
1.132 brouard 7303: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 7304: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7305: for (k=1; k<=npar;k++)
7306: printf(" %d %8.5f",k,p[k]);
7307: printf("\n");
1.186 brouard 7308: globpr=1; /* again, to print the contributions */
1.126 brouard 7309: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7310: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7311: for (k=1; k<=npar;k++)
7312: printf(" %d %8.5f",k,p[k]);
7313: printf("\n");
1.186 brouard 7314: if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
1.126 brouard 7315: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
7316: }
7317:
7318: /*--------- results files --------------*/
1.192 brouard 7319: 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 7320:
7321:
7322: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7323: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7324: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7325: for(i=1,jk=1; i <=nlstate; i++){
7326: for(k=1; k <=(nlstate+ndeath); k++){
7327: if (k != i) {
7328: printf("%d%d ",i,k);
7329: fprintf(ficlog,"%d%d ",i,k);
7330: fprintf(ficres,"%1d%1d ",i,k);
7331: for(j=1; j <=ncovmodel; j++){
1.190 brouard 7332: printf("%12.7f ",p[jk]);
7333: fprintf(ficlog,"%12.7f ",p[jk]);
7334: fprintf(ficres,"%12.7f ",p[jk]);
1.126 brouard 7335: jk++;
7336: }
7337: printf("\n");
7338: fprintf(ficlog,"\n");
7339: fprintf(ficres,"\n");
7340: }
7341: }
7342: }
7343: if(mle!=0){
7344: /* Computing hessian and covariance matrix */
7345: ftolhess=ftol; /* Usually correct */
7346: hesscov(matcov, p, npar, delti, ftolhess, func);
7347: }
1.197 brouard 7348: 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");
7349: 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");
1.193 brouard 7350: for(i=1,jk=1; i <=nlstate; i++){
7351: for(k=1; k <=(nlstate+ndeath); k++){
7352: if (k != i) {
7353: printf("%d%d ",i,k);
7354: fprintf(ficlog,"%d%d ",i,k);
7355: for(j=1; j <=ncovmodel; j++){
1.197 brouard 7356: 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]));
7357: 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]));
1.193 brouard 7358: jk++;
7359: }
7360: printf("\n");
7361: fprintf(ficlog,"\n");
7362: }
7363: }
7364: }
7365:
1.126 brouard 7366: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
7367: printf("# Scales (for hessian or gradient estimation)\n");
7368: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
7369: for(i=1,jk=1; i <=nlstate; i++){
7370: for(j=1; j <=nlstate+ndeath; j++){
7371: if (j!=i) {
7372: fprintf(ficres,"%1d%1d",i,j);
7373: printf("%1d%1d",i,j);
7374: fprintf(ficlog,"%1d%1d",i,j);
7375: for(k=1; k<=ncovmodel;k++){
7376: printf(" %.5e",delti[jk]);
7377: fprintf(ficlog," %.5e",delti[jk]);
7378: fprintf(ficres," %.5e",delti[jk]);
7379: jk++;
7380: }
7381: printf("\n");
7382: fprintf(ficlog,"\n");
7383: fprintf(ficres,"\n");
7384: }
7385: }
7386: }
7387:
7388: 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");
7389: if(mle>=1)
7390: 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");
7391: 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");
7392: /* # 121 Var(a12)\n\ */
7393: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7394: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7395: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7396: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7397: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7398: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7399: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7400:
7401:
7402: /* Just to have a covariance matrix which will be more understandable
7403: even is we still don't want to manage dictionary of variables
7404: */
7405: for(itimes=1;itimes<=2;itimes++){
7406: jj=0;
7407: for(i=1; i <=nlstate; i++){
7408: for(j=1; j <=nlstate+ndeath; j++){
7409: if(j==i) continue;
7410: for(k=1; k<=ncovmodel;k++){
7411: jj++;
7412: ca[0]= k+'a'-1;ca[1]='\0';
7413: if(itimes==1){
7414: if(mle>=1)
7415: printf("#%1d%1d%d",i,j,k);
7416: fprintf(ficlog,"#%1d%1d%d",i,j,k);
7417: fprintf(ficres,"#%1d%1d%d",i,j,k);
7418: }else{
7419: if(mle>=1)
7420: printf("%1d%1d%d",i,j,k);
7421: fprintf(ficlog,"%1d%1d%d",i,j,k);
7422: fprintf(ficres,"%1d%1d%d",i,j,k);
7423: }
7424: ll=0;
7425: for(li=1;li <=nlstate; li++){
7426: for(lj=1;lj <=nlstate+ndeath; lj++){
7427: if(lj==li) continue;
7428: for(lk=1;lk<=ncovmodel;lk++){
7429: ll++;
7430: if(ll<=jj){
7431: cb[0]= lk +'a'-1;cb[1]='\0';
7432: if(ll<jj){
7433: if(itimes==1){
7434: if(mle>=1)
7435: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7436: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7437: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7438: }else{
7439: if(mle>=1)
7440: printf(" %.5e",matcov[jj][ll]);
7441: fprintf(ficlog," %.5e",matcov[jj][ll]);
7442: fprintf(ficres," %.5e",matcov[jj][ll]);
7443: }
7444: }else{
7445: if(itimes==1){
7446: if(mle>=1)
7447: printf(" Var(%s%1d%1d)",ca,i,j);
7448: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
7449: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
7450: }else{
7451: if(mle>=1)
7452: printf(" %.5e",matcov[jj][ll]);
7453: fprintf(ficlog," %.5e",matcov[jj][ll]);
7454: fprintf(ficres," %.5e",matcov[jj][ll]);
7455: }
7456: }
7457: }
7458: } /* end lk */
7459: } /* end lj */
7460: } /* end li */
7461: if(mle>=1)
7462: printf("\n");
7463: fprintf(ficlog,"\n");
7464: fprintf(ficres,"\n");
7465: numlinepar++;
7466: } /* end k*/
7467: } /*end j */
7468: } /* end i */
7469: } /* end itimes */
7470:
7471: fflush(ficlog);
7472: fflush(ficres);
7473:
7474: while((c=getc(ficpar))=='#' && c!= EOF){
7475: ungetc(c,ficpar);
7476: fgets(line, MAXLINE, ficpar);
1.141 brouard 7477: fputs(line,stdout);
1.126 brouard 7478: fputs(line,ficparo);
7479: }
7480: ungetc(c,ficpar);
7481:
7482: estepm=0;
7483: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
7484: if (estepm==0 || estepm < stepm) estepm=stepm;
7485: if (fage <= 2) {
7486: bage = ageminpar;
7487: fage = agemaxpar;
7488: }
7489:
7490: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
7491: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7492: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.186 brouard 7493:
7494: /* Other stuffs, more or less useful */
1.126 brouard 7495: while((c=getc(ficpar))=='#' && c!= EOF){
7496: ungetc(c,ficpar);
7497: fgets(line, MAXLINE, ficpar);
1.141 brouard 7498: fputs(line,stdout);
1.126 brouard 7499: fputs(line,ficparo);
7500: }
7501: ungetc(c,ficpar);
7502:
7503: 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);
7504: 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);
7505: 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);
7506: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7507: 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);
7508:
7509: while((c=getc(ficpar))=='#' && c!= EOF){
7510: ungetc(c,ficpar);
7511: fgets(line, MAXLINE, ficpar);
1.141 brouard 7512: fputs(line,stdout);
1.126 brouard 7513: fputs(line,ficparo);
7514: }
7515: ungetc(c,ficpar);
7516:
7517:
7518: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
7519: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
7520:
7521: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 7522: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 7523: fprintf(ficparo,"pop_based=%d\n",popbased);
7524: fprintf(ficres,"pop_based=%d\n",popbased);
7525:
7526: while((c=getc(ficpar))=='#' && c!= EOF){
7527: ungetc(c,ficpar);
7528: fgets(line, MAXLINE, ficpar);
1.141 brouard 7529: fputs(line,stdout);
1.126 brouard 7530: fputs(line,ficparo);
7531: }
7532: ungetc(c,ficpar);
7533:
7534: 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);
7535: 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);
7536: 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);
7537: 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);
7538: 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);
7539: /* day and month of proj2 are not used but only year anproj2.*/
7540:
7541:
7542:
1.145 brouard 7543: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
7544: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 7545:
7546: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 7547: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
7548: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7549: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7550: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7551: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7552: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7553: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7554: }else
7555: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.126 brouard 7556:
7557: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
7558: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
7559: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
7560:
7561: /*------------ free_vector -------------*/
7562: /* chdir(path); */
7563:
7564: free_ivector(wav,1,imx);
7565: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
7566: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
7567: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
7568: free_lvector(num,1,n);
7569: free_vector(agedc,1,n);
7570: /*free_matrix(covar,0,NCOVMAX,1,n);*/
7571: /*free_matrix(covar,1,NCOVMAX,1,n);*/
7572: fclose(ficparo);
7573: fclose(ficres);
7574:
7575:
1.186 brouard 7576: /* Other results (useful)*/
7577:
7578:
1.126 brouard 7579: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 7580: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
7581: prlim=matrix(1,nlstate,1,nlstate);
7582: prevalence_limit(p, prlim, ageminpar, agemaxpar);
1.126 brouard 7583: fclose(ficrespl);
7584:
1.145 brouard 7585: #ifdef FREEEXIT2
7586: #include "freeexit2.h"
7587: #endif
7588:
1.126 brouard 7589: /*------------- h Pij x at various ages ------------*/
1.180 brouard 7590: /*#include "hpijx.h"*/
7591: hPijx(p, bage, fage);
1.145 brouard 7592: fclose(ficrespij);
1.126 brouard 7593:
1.145 brouard 7594: /*-------------- Variance of one-step probabilities---*/
7595: k=1;
1.126 brouard 7596: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
7597:
7598:
7599: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7600: for(i=1;i<=AGESUP;i++)
7601: for(j=1;j<=NCOVMAX;j++)
7602: for(k=1;k<=NCOVMAX;k++)
7603: probs[i][j][k]=0.;
7604:
7605: /*---------- Forecasting ------------------*/
7606: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
7607: if(prevfcast==1){
7608: /* if(stepm ==1){*/
7609: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
7610: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
7611: /* } */
7612: /* else{ */
7613: /* erreur=108; */
7614: /* 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); */
7615: /* 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); */
7616: /* } */
7617: }
1.186 brouard 7618:
7619: /* ------ Other prevalence ratios------------ */
1.126 brouard 7620:
1.127 brouard 7621: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
7622:
7623: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
7624: /* 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",\
7625: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
7626: */
1.126 brouard 7627:
1.127 brouard 7628: if (mobilav!=0) {
7629: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7630: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
7631: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
7632: printf(" Error in movingaverage mobilav=%d\n",mobilav);
7633: }
1.126 brouard 7634: }
7635:
7636:
1.127 brouard 7637: /*---------- Health expectancies, no variances ------------*/
7638:
1.126 brouard 7639: strcpy(filerese,"e");
7640: strcat(filerese,fileres);
7641: if((ficreseij=fopen(filerese,"w"))==NULL) {
7642: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7643: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7644: }
7645: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
7646: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145 brouard 7647: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7648: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7649:
7650: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 7651: fprintf(ficreseij,"\n#****** ");
7652: for(j=1;j<=cptcoveff;j++) {
7653: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7654: }
7655: fprintf(ficreseij,"******\n");
7656:
7657: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7658: oldm=oldms;savm=savms;
7659: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
7660:
7661: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7662: /*}*/
1.127 brouard 7663: }
7664: fclose(ficreseij);
7665:
7666:
7667: /*---------- Health expectancies and variances ------------*/
7668:
7669:
7670: strcpy(filerest,"t");
7671: strcat(filerest,fileres);
7672: if((ficrest=fopen(filerest,"w"))==NULL) {
7673: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
7674: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
7675: }
7676: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7677: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7678:
1.126 brouard 7679:
7680: strcpy(fileresstde,"stde");
7681: strcat(fileresstde,fileres);
7682: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
7683: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7684: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7685: }
7686: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7687: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7688:
7689: strcpy(filerescve,"cve");
7690: strcat(filerescve,fileres);
7691: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
7692: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7693: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7694: }
7695: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7696: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7697:
7698: strcpy(fileresv,"v");
7699: strcat(fileresv,fileres);
7700: if((ficresvij=fopen(fileresv,"w"))==NULL) {
7701: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
7702: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
7703: }
7704: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7705: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7706:
1.145 brouard 7707: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7708: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7709:
7710: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7711: fprintf(ficrest,"\n#****** ");
1.126 brouard 7712: for(j=1;j<=cptcoveff;j++)
7713: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7714: fprintf(ficrest,"******\n");
7715:
7716: fprintf(ficresstdeij,"\n#****** ");
7717: fprintf(ficrescveij,"\n#****** ");
7718: for(j=1;j<=cptcoveff;j++) {
7719: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7720: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7721: }
7722: fprintf(ficresstdeij,"******\n");
7723: fprintf(ficrescveij,"******\n");
7724:
7725: fprintf(ficresvij,"\n#****** ");
7726: for(j=1;j<=cptcoveff;j++)
7727: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7728: fprintf(ficresvij,"******\n");
7729:
7730: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7731: oldm=oldms;savm=savms;
1.127 brouard 7732: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.145 brouard 7733: /*
7734: */
7735: /* goto endfree; */
1.126 brouard 7736:
7737: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7738: pstamp(ficrest);
1.145 brouard 7739:
7740:
1.128 brouard 7741: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.199 ! brouard 7742: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
1.161 brouard 7743: cptcod= 0; /* To be deleted */
7744: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
1.145 brouard 7745: 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 7746: if(vpopbased==1)
7747: 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);
7748: else
7749: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
7750: fprintf(ficrest,"# Age e.. (std) ");
7751: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
7752: fprintf(ficrest,"\n");
1.199 ! brouard 7753: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
1.128 brouard 7754: epj=vector(1,nlstate+1);
7755: for(age=bage; age <=fage ;age++){
1.199 ! brouard 7756: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); /*ZZ Is it the correct prevalim */
1.128 brouard 7757: if (vpopbased==1) {
7758: if(mobilav ==0){
7759: for(i=1; i<=nlstate;i++)
7760: prlim[i][i]=probs[(int)age][i][k];
7761: }else{ /* mobilav */
7762: for(i=1; i<=nlstate;i++)
7763: prlim[i][i]=mobaverage[(int)age][i][k];
7764: }
1.126 brouard 7765: }
7766:
1.128 brouard 7767: fprintf(ficrest," %4.0f",age);
1.199 ! brouard 7768: /* printf(" age %4.0f ",age); */
1.128 brouard 7769: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
7770: for(i=1, epj[j]=0.;i <=nlstate;i++) {
7771: epj[j] += prlim[i][i]*eij[i][j][(int)age];
1.199 ! brouard 7772: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
! 7773: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
1.128 brouard 7774: }
7775: epj[nlstate+1] +=epj[j];
1.126 brouard 7776: }
1.199 ! brouard 7777: /* printf(" age %4.0f \n",age); */
1.126 brouard 7778:
1.128 brouard 7779: for(i=1, vepp=0.;i <=nlstate;i++)
7780: for(j=1;j <=nlstate;j++)
7781: vepp += vareij[i][j][(int)age];
7782: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
7783: for(j=1;j <=nlstate;j++){
7784: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
7785: }
7786: fprintf(ficrest,"\n");
1.126 brouard 7787: }
7788: }
7789: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7790: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7791: free_vector(epj,1,nlstate+1);
1.145 brouard 7792: /*}*/
1.126 brouard 7793: }
7794: free_vector(weight,1,n);
1.145 brouard 7795: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 7796: free_imatrix(s,1,maxwav+1,1,n);
7797: free_matrix(anint,1,maxwav,1,n);
7798: free_matrix(mint,1,maxwav,1,n);
7799: free_ivector(cod,1,n);
7800: free_ivector(tab,1,NCOVMAX);
7801: fclose(ficresstdeij);
7802: fclose(ficrescveij);
7803: fclose(ficresvij);
7804: fclose(ficrest);
7805: fclose(ficpar);
7806:
7807: /*------- Variance of period (stable) prevalence------*/
7808:
7809: strcpy(fileresvpl,"vpl");
7810: strcat(fileresvpl,fileres);
7811: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
7812: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
7813: exit(0);
7814: }
7815: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
7816:
1.145 brouard 7817: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7818: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7819:
7820: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7821: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 7822: for(j=1;j<=cptcoveff;j++)
7823: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7824: fprintf(ficresvpl,"******\n");
7825:
7826: varpl=matrix(1,nlstate,(int) bage, (int) fage);
7827: oldm=oldms;savm=savms;
7828: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
7829: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7830: /*}*/
1.126 brouard 7831: }
7832:
7833: fclose(ficresvpl);
7834:
7835: /*---------- End : free ----------------*/
7836: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7837: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7838: } /* mle==-3 arrives here for freeing */
1.164 brouard 7839: /* endfree:*/
1.141 brouard 7840: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 7841: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
7842: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
7843: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
7844: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
7845: free_matrix(covar,0,NCOVMAX,1,n);
7846: free_matrix(matcov,1,npar,1,npar);
7847: /*free_vector(delti,1,npar);*/
7848: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7849: free_matrix(agev,1,maxwav,1,imx);
7850: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7851:
1.145 brouard 7852: free_ivector(ncodemax,1,NCOVMAX);
1.192 brouard 7853: free_ivector(ncodemaxwundef,1,NCOVMAX);
1.145 brouard 7854: free_ivector(Tvar,1,NCOVMAX);
7855: free_ivector(Tprod,1,NCOVMAX);
7856: free_ivector(Tvaraff,1,NCOVMAX);
7857: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 7858:
7859: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
7860: free_imatrix(codtab,1,100,1,10);
7861: fflush(fichtm);
7862: fflush(ficgp);
7863:
7864:
7865: if((nberr >0) || (nbwarn>0)){
7866: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
7867: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
7868: }else{
7869: printf("End of Imach\n");
7870: fprintf(ficlog,"End of Imach\n");
7871: }
7872: printf("See log file on %s\n",filelog);
7873: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 7874: /*(void) gettimeofday(&end_time,&tzp);*/
7875: rend_time = time(NULL);
7876: end_time = *localtime(&rend_time);
7877: /* tml = *localtime(&end_time.tm_sec); */
7878: strcpy(strtend,asctime(&end_time));
1.126 brouard 7879: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
7880: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 7881: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 7882:
1.157 brouard 7883: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7884: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7885: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 7886: /* printf("Total time was %d uSec.\n", total_usecs);*/
7887: /* if(fileappend(fichtm,optionfilehtm)){ */
7888: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7889: fclose(fichtm);
7890: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7891: fclose(fichtmcov);
7892: fclose(ficgp);
7893: fclose(ficlog);
7894: /*------ End -----------*/
7895:
7896:
7897: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 7898: #ifdef WIN32
7899: if (_chdir(pathcd) != 0)
7900: printf("Can't move to directory %s!\n",path);
7901: if(_getcwd(pathcd,MAXLINE) > 0)
7902: #else
1.126 brouard 7903: if(chdir(pathcd) != 0)
1.184 brouard 7904: printf("Can't move to directory %s!\n", path);
7905: if (getcwd(pathcd, MAXLINE) > 0)
7906: #endif
1.126 brouard 7907: printf("Current directory %s!\n",pathcd);
7908: /*strcat(plotcmd,CHARSEPARATOR);*/
7909: sprintf(plotcmd,"gnuplot");
1.157 brouard 7910: #ifdef _WIN32
1.126 brouard 7911: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
7912: #endif
7913: if(!stat(plotcmd,&info)){
1.158 brouard 7914: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7915: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 7916: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 7917: }else
7918: strcpy(pplotcmd,plotcmd);
1.157 brouard 7919: #ifdef __unix
1.126 brouard 7920: strcpy(plotcmd,GNUPLOTPROGRAM);
7921: if(!stat(plotcmd,&info)){
1.158 brouard 7922: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7923: }else
7924: strcpy(pplotcmd,plotcmd);
7925: #endif
7926: }else
7927: strcpy(pplotcmd,plotcmd);
7928:
7929: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 7930: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7931:
7932: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 7933: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 7934: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 7935: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 7936: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 7937: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 7938: }
1.158 brouard 7939: printf(" Successful, please wait...");
1.126 brouard 7940: while (z[0] != 'q') {
7941: /* chdir(path); */
1.154 brouard 7942: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 7943: scanf("%s",z);
7944: /* if (z[0] == 'c') system("./imach"); */
7945: if (z[0] == 'e') {
1.158 brouard 7946: #ifdef __APPLE__
1.152 brouard 7947: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 7948: #elif __linux
7949: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 7950: #else
1.152 brouard 7951: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 7952: #endif
7953: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7954: system(pplotcmd);
1.126 brouard 7955: }
7956: else if (z[0] == 'g') system(plotcmd);
7957: else if (z[0] == 'q') exit(0);
7958: }
7959: end:
7960: while (z[0] != 'q') {
1.195 brouard 7961: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 7962: scanf("%s",z);
7963: }
7964: }
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