Annotation of imach/src/imach.c, revision 1.190
1.190 ! brouard 1: /* $Id: imach.c,v 1.189 2015/04/30 14:45:16 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.190 ! brouard 4: Revision 1.189 2015/04/30 14:45:16 brouard
! 5: Summary: 0.98q2
! 6:
1.189 brouard 7: Revision 1.188 2015/04/30 08:27:53 brouard
8: *** empty log message ***
9:
1.188 brouard 10: Revision 1.187 2015/04/29 09:11:15 brouard
11: *** empty log message ***
12:
1.187 brouard 13: Revision 1.186 2015/04/23 12:01:52 brouard
14: Summary: V1*age is working now, version 0.98q1
15:
16: Some codes had been disabled in order to simplify and Vn*age was
17: working in the optimization phase, ie, giving correct MLE parameters,
18: but, as usual, outputs were not correct and program core dumped.
19:
1.186 brouard 20: Revision 1.185 2015/03/11 13:26:42 brouard
21: Summary: Inclusion of compile and links command line for Intel Compiler
22:
1.185 brouard 23: Revision 1.184 2015/03/11 11:52:39 brouard
24: Summary: Back from Windows 8. Intel Compiler
25:
1.184 brouard 26: Revision 1.183 2015/03/10 20:34:32 brouard
27: Summary: 0.98q0, trying with directest, mnbrak fixed
28:
29: We use directest instead of original Powell test; probably no
30: incidence on the results, but better justifications;
31: We fixed Numerical Recipes mnbrak routine which was wrong and gave
32: wrong results.
33:
1.183 brouard 34: Revision 1.182 2015/02/12 08:19:57 brouard
35: Summary: Trying to keep directest which seems simpler and more general
36: Author: Nicolas Brouard
37:
1.182 brouard 38: Revision 1.181 2015/02/11 23:22:24 brouard
39: Summary: Comments on Powell added
40:
41: Author:
42:
1.181 brouard 43: Revision 1.180 2015/02/11 17:33:45 brouard
44: Summary: Finishing move from main to function (hpijx and prevalence_limit)
45:
1.180 brouard 46: Revision 1.179 2015/01/04 09:57:06 brouard
47: Summary: back to OS/X
48:
1.179 brouard 49: Revision 1.178 2015/01/04 09:35:48 brouard
50: *** empty log message ***
51:
1.178 brouard 52: Revision 1.177 2015/01/03 18:40:56 brouard
53: Summary: Still testing ilc32 on OSX
54:
1.177 brouard 55: Revision 1.176 2015/01/03 16:45:04 brouard
56: *** empty log message ***
57:
1.176 brouard 58: Revision 1.175 2015/01/03 16:33:42 brouard
59: *** empty log message ***
60:
1.175 brouard 61: Revision 1.174 2015/01/03 16:15:49 brouard
62: Summary: Still in cross-compilation
63:
1.174 brouard 64: Revision 1.173 2015/01/03 12:06:26 brouard
65: Summary: trying to detect cross-compilation
66:
1.173 brouard 67: Revision 1.172 2014/12/27 12:07:47 brouard
68: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
69:
1.172 brouard 70: Revision 1.171 2014/12/23 13:26:59 brouard
71: Summary: Back from Visual C
72:
73: Still problem with utsname.h on Windows
74:
1.171 brouard 75: Revision 1.170 2014/12/23 11:17:12 brouard
76: Summary: Cleaning some \%% back to %%
77:
78: The escape was mandatory for a specific compiler (which one?), but too many warnings.
79:
1.170 brouard 80: Revision 1.169 2014/12/22 23:08:31 brouard
81: Summary: 0.98p
82:
83: Outputs some informations on compiler used, OS etc. Testing on different platforms.
84:
1.169 brouard 85: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 86: Summary: update
1.169 brouard 87:
1.168 brouard 88: Revision 1.167 2014/12/22 13:50:56 brouard
89: Summary: Testing uname and compiler version and if compiled 32 or 64
90:
91: Testing on Linux 64
92:
1.167 brouard 93: Revision 1.166 2014/12/22 11:40:47 brouard
94: *** empty log message ***
95:
1.166 brouard 96: Revision 1.165 2014/12/16 11:20:36 brouard
97: Summary: After compiling on Visual C
98:
99: * imach.c (Module): Merging 1.61 to 1.162
100:
1.165 brouard 101: Revision 1.164 2014/12/16 10:52:11 brouard
102: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
103:
104: * imach.c (Module): Merging 1.61 to 1.162
105:
1.164 brouard 106: Revision 1.163 2014/12/16 10:30:11 brouard
107: * imach.c (Module): Merging 1.61 to 1.162
108:
1.163 brouard 109: Revision 1.162 2014/09/25 11:43:39 brouard
110: Summary: temporary backup 0.99!
111:
1.162 brouard 112: Revision 1.1 2014/09/16 11:06:58 brouard
113: Summary: With some code (wrong) for nlopt
114:
115: Author:
116:
117: Revision 1.161 2014/09/15 20:41:41 brouard
118: Summary: Problem with macro SQR on Intel compiler
119:
1.161 brouard 120: Revision 1.160 2014/09/02 09:24:05 brouard
121: *** empty log message ***
122:
1.160 brouard 123: Revision 1.159 2014/09/01 10:34:10 brouard
124: Summary: WIN32
125: Author: Brouard
126:
1.159 brouard 127: Revision 1.158 2014/08/27 17:11:51 brouard
128: *** empty log message ***
129:
1.158 brouard 130: Revision 1.157 2014/08/27 16:26:55 brouard
131: Summary: Preparing windows Visual studio version
132: Author: Brouard
133:
134: In order to compile on Visual studio, time.h is now correct and time_t
135: and tm struct should be used. difftime should be used but sometimes I
136: just make the differences in raw time format (time(&now).
137: Trying to suppress #ifdef LINUX
138: Add xdg-open for __linux in order to open default browser.
139:
1.157 brouard 140: Revision 1.156 2014/08/25 20:10:10 brouard
141: *** empty log message ***
142:
1.156 brouard 143: Revision 1.155 2014/08/25 18:32:34 brouard
144: Summary: New compile, minor changes
145: Author: Brouard
146:
1.155 brouard 147: Revision 1.154 2014/06/20 17:32:08 brouard
148: Summary: Outputs now all graphs of convergence to period prevalence
149:
1.154 brouard 150: Revision 1.153 2014/06/20 16:45:46 brouard
151: Summary: If 3 live state, convergence to period prevalence on same graph
152: Author: Brouard
153:
1.153 brouard 154: Revision 1.152 2014/06/18 17:54:09 brouard
155: Summary: open browser, use gnuplot on same dir than imach if not found in the path
156:
1.152 brouard 157: Revision 1.151 2014/06/18 16:43:30 brouard
158: *** empty log message ***
159:
1.151 brouard 160: Revision 1.150 2014/06/18 16:42:35 brouard
161: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
162: Author: brouard
163:
1.150 brouard 164: Revision 1.149 2014/06/18 15:51:14 brouard
165: Summary: Some fixes in parameter files errors
166: Author: Nicolas Brouard
167:
1.149 brouard 168: Revision 1.148 2014/06/17 17:38:48 brouard
169: Summary: Nothing new
170: Author: Brouard
171:
172: Just a new packaging for OS/X version 0.98nS
173:
1.148 brouard 174: Revision 1.147 2014/06/16 10:33:11 brouard
175: *** empty log message ***
176:
1.147 brouard 177: Revision 1.146 2014/06/16 10:20:28 brouard
178: Summary: Merge
179: Author: Brouard
180:
181: Merge, before building revised version.
182:
1.146 brouard 183: Revision 1.145 2014/06/10 21:23:15 brouard
184: Summary: Debugging with valgrind
185: Author: Nicolas Brouard
186:
187: Lot of changes in order to output the results with some covariates
188: After the Edimburgh REVES conference 2014, it seems mandatory to
189: improve the code.
190: No more memory valgrind error but a lot has to be done in order to
191: continue the work of splitting the code into subroutines.
192: Also, decodemodel has been improved. Tricode is still not
193: optimal. nbcode should be improved. Documentation has been added in
194: the source code.
195:
1.144 brouard 196: Revision 1.143 2014/01/26 09:45:38 brouard
197: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
198:
199: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
200: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
201:
1.143 brouard 202: Revision 1.142 2014/01/26 03:57:36 brouard
203: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
204:
205: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
206:
1.142 brouard 207: Revision 1.141 2014/01/26 02:42:01 brouard
208: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
209:
1.141 brouard 210: Revision 1.140 2011/09/02 10:37:54 brouard
211: Summary: times.h is ok with mingw32 now.
212:
1.140 brouard 213: Revision 1.139 2010/06/14 07:50:17 brouard
214: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
215: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
216:
1.139 brouard 217: Revision 1.138 2010/04/30 18:19:40 brouard
218: *** empty log message ***
219:
1.138 brouard 220: Revision 1.137 2010/04/29 18:11:38 brouard
221: (Module): Checking covariates for more complex models
222: than V1+V2. A lot of change to be done. Unstable.
223:
1.137 brouard 224: Revision 1.136 2010/04/26 20:30:53 brouard
225: (Module): merging some libgsl code. Fixing computation
226: of likelione (using inter/intrapolation if mle = 0) in order to
227: get same likelihood as if mle=1.
228: Some cleaning of code and comments added.
229:
1.136 brouard 230: Revision 1.135 2009/10/29 15:33:14 brouard
231: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
232:
1.135 brouard 233: Revision 1.134 2009/10/29 13:18:53 brouard
234: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
235:
1.134 brouard 236: Revision 1.133 2009/07/06 10:21:25 brouard
237: just nforces
238:
1.133 brouard 239: Revision 1.132 2009/07/06 08:22:05 brouard
240: Many tings
241:
1.132 brouard 242: Revision 1.131 2009/06/20 16:22:47 brouard
243: Some dimensions resccaled
244:
1.131 brouard 245: Revision 1.130 2009/05/26 06:44:34 brouard
246: (Module): Max Covariate is now set to 20 instead of 8. A
247: lot of cleaning with variables initialized to 0. Trying to make
248: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
249:
1.130 brouard 250: Revision 1.129 2007/08/31 13:49:27 lievre
251: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
252:
1.129 lievre 253: Revision 1.128 2006/06/30 13:02:05 brouard
254: (Module): Clarifications on computing e.j
255:
1.128 brouard 256: Revision 1.127 2006/04/28 18:11:50 brouard
257: (Module): Yes the sum of survivors was wrong since
258: imach-114 because nhstepm was no more computed in the age
259: loop. Now we define nhstepma in the age loop.
260: (Module): In order to speed up (in case of numerous covariates) we
261: compute health expectancies (without variances) in a first step
262: and then all the health expectancies with variances or standard
263: deviation (needs data from the Hessian matrices) which slows the
264: computation.
265: In the future we should be able to stop the program is only health
266: expectancies and graph are needed without standard deviations.
267:
1.127 brouard 268: Revision 1.126 2006/04/28 17:23:28 brouard
269: (Module): Yes the sum of survivors was wrong since
270: imach-114 because nhstepm was no more computed in the age
271: loop. Now we define nhstepma in the age loop.
272: Version 0.98h
273:
1.126 brouard 274: Revision 1.125 2006/04/04 15:20:31 lievre
275: Errors in calculation of health expectancies. Age was not initialized.
276: Forecasting file added.
277:
278: Revision 1.124 2006/03/22 17:13:53 lievre
279: Parameters are printed with %lf instead of %f (more numbers after the comma).
280: The log-likelihood is printed in the log file
281:
282: Revision 1.123 2006/03/20 10:52:43 brouard
283: * imach.c (Module): <title> changed, corresponds to .htm file
284: name. <head> headers where missing.
285:
286: * imach.c (Module): Weights can have a decimal point as for
287: English (a comma might work with a correct LC_NUMERIC environment,
288: otherwise the weight is truncated).
289: Modification of warning when the covariates values are not 0 or
290: 1.
291: Version 0.98g
292:
293: Revision 1.122 2006/03/20 09:45:41 brouard
294: (Module): Weights can have a decimal point as for
295: English (a comma might work with a correct LC_NUMERIC environment,
296: otherwise the weight is truncated).
297: Modification of warning when the covariates values are not 0 or
298: 1.
299: Version 0.98g
300:
301: Revision 1.121 2006/03/16 17:45:01 lievre
302: * imach.c (Module): Comments concerning covariates added
303:
304: * imach.c (Module): refinements in the computation of lli if
305: status=-2 in order to have more reliable computation if stepm is
306: not 1 month. Version 0.98f
307:
308: Revision 1.120 2006/03/16 15:10:38 lievre
309: (Module): refinements in the computation of lli if
310: status=-2 in order to have more reliable computation if stepm is
311: not 1 month. Version 0.98f
312:
313: Revision 1.119 2006/03/15 17:42:26 brouard
314: (Module): Bug if status = -2, the loglikelihood was
315: computed as likelihood omitting the logarithm. Version O.98e
316:
317: Revision 1.118 2006/03/14 18:20:07 brouard
318: (Module): varevsij Comments added explaining the second
319: table of variances if popbased=1 .
320: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
321: (Module): Function pstamp added
322: (Module): Version 0.98d
323:
324: Revision 1.117 2006/03/14 17:16:22 brouard
325: (Module): varevsij Comments added explaining the second
326: table of variances if popbased=1 .
327: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
328: (Module): Function pstamp added
329: (Module): Version 0.98d
330:
331: Revision 1.116 2006/03/06 10:29:27 brouard
332: (Module): Variance-covariance wrong links and
333: varian-covariance of ej. is needed (Saito).
334:
335: Revision 1.115 2006/02/27 12:17:45 brouard
336: (Module): One freematrix added in mlikeli! 0.98c
337:
338: Revision 1.114 2006/02/26 12:57:58 brouard
339: (Module): Some improvements in processing parameter
340: filename with strsep.
341:
342: Revision 1.113 2006/02/24 14:20:24 brouard
343: (Module): Memory leaks checks with valgrind and:
344: datafile was not closed, some imatrix were not freed and on matrix
345: allocation too.
346:
347: Revision 1.112 2006/01/30 09:55:26 brouard
348: (Module): Back to gnuplot.exe instead of wgnuplot.exe
349:
350: Revision 1.111 2006/01/25 20:38:18 brouard
351: (Module): Lots of cleaning and bugs added (Gompertz)
352: (Module): Comments can be added in data file. Missing date values
353: can be a simple dot '.'.
354:
355: Revision 1.110 2006/01/25 00:51:50 brouard
356: (Module): Lots of cleaning and bugs added (Gompertz)
357:
358: Revision 1.109 2006/01/24 19:37:15 brouard
359: (Module): Comments (lines starting with a #) are allowed in data.
360:
361: Revision 1.108 2006/01/19 18:05:42 lievre
362: Gnuplot problem appeared...
363: To be fixed
364:
365: Revision 1.107 2006/01/19 16:20:37 brouard
366: Test existence of gnuplot in imach path
367:
368: Revision 1.106 2006/01/19 13:24:36 brouard
369: Some cleaning and links added in html output
370:
371: Revision 1.105 2006/01/05 20:23:19 lievre
372: *** empty log message ***
373:
374: Revision 1.104 2005/09/30 16:11:43 lievre
375: (Module): sump fixed, loop imx fixed, and simplifications.
376: (Module): If the status is missing at the last wave but we know
377: that the person is alive, then we can code his/her status as -2
378: (instead of missing=-1 in earlier versions) and his/her
379: contributions to the likelihood is 1 - Prob of dying from last
380: health status (= 1-p13= p11+p12 in the easiest case of somebody in
381: the healthy state at last known wave). Version is 0.98
382:
383: Revision 1.103 2005/09/30 15:54:49 lievre
384: (Module): sump fixed, loop imx fixed, and simplifications.
385:
386: Revision 1.102 2004/09/15 17:31:30 brouard
387: Add the possibility to read data file including tab characters.
388:
389: Revision 1.101 2004/09/15 10:38:38 brouard
390: Fix on curr_time
391:
392: Revision 1.100 2004/07/12 18:29:06 brouard
393: Add version for Mac OS X. Just define UNIX in Makefile
394:
395: Revision 1.99 2004/06/05 08:57:40 brouard
396: *** empty log message ***
397:
398: Revision 1.98 2004/05/16 15:05:56 brouard
399: New version 0.97 . First attempt to estimate force of mortality
400: directly from the data i.e. without the need of knowing the health
401: state at each age, but using a Gompertz model: log u =a + b*age .
402: This is the basic analysis of mortality and should be done before any
403: other analysis, in order to test if the mortality estimated from the
404: cross-longitudinal survey is different from the mortality estimated
405: from other sources like vital statistic data.
406:
407: The same imach parameter file can be used but the option for mle should be -3.
408:
1.133 brouard 409: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 410: former routines in order to include the new code within the former code.
411:
412: The output is very simple: only an estimate of the intercept and of
413: the slope with 95% confident intervals.
414:
415: Current limitations:
416: A) Even if you enter covariates, i.e. with the
417: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
418: B) There is no computation of Life Expectancy nor Life Table.
419:
420: Revision 1.97 2004/02/20 13:25:42 lievre
421: Version 0.96d. Population forecasting command line is (temporarily)
422: suppressed.
423:
424: Revision 1.96 2003/07/15 15:38:55 brouard
425: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
426: rewritten within the same printf. Workaround: many printfs.
427:
428: Revision 1.95 2003/07/08 07:54:34 brouard
429: * imach.c (Repository):
430: (Repository): Using imachwizard code to output a more meaningful covariance
431: matrix (cov(a12,c31) instead of numbers.
432:
433: Revision 1.94 2003/06/27 13:00:02 brouard
434: Just cleaning
435:
436: Revision 1.93 2003/06/25 16:33:55 brouard
437: (Module): On windows (cygwin) function asctime_r doesn't
438: exist so I changed back to asctime which exists.
439: (Module): Version 0.96b
440:
441: Revision 1.92 2003/06/25 16:30:45 brouard
442: (Module): On windows (cygwin) function asctime_r doesn't
443: exist so I changed back to asctime which exists.
444:
445: Revision 1.91 2003/06/25 15:30:29 brouard
446: * imach.c (Repository): Duplicated warning errors corrected.
447: (Repository): Elapsed time after each iteration is now output. It
448: helps to forecast when convergence will be reached. Elapsed time
449: is stamped in powell. We created a new html file for the graphs
450: concerning matrix of covariance. It has extension -cov.htm.
451:
452: Revision 1.90 2003/06/24 12:34:15 brouard
453: (Module): Some bugs corrected for windows. Also, when
454: mle=-1 a template is output in file "or"mypar.txt with the design
455: of the covariance matrix to be input.
456:
457: Revision 1.89 2003/06/24 12:30:52 brouard
458: (Module): Some bugs corrected for windows. Also, when
459: mle=-1 a template is output in file "or"mypar.txt with the design
460: of the covariance matrix to be input.
461:
462: Revision 1.88 2003/06/23 17:54:56 brouard
463: * 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.
464:
465: Revision 1.87 2003/06/18 12:26:01 brouard
466: Version 0.96
467:
468: Revision 1.86 2003/06/17 20:04:08 brouard
469: (Module): Change position of html and gnuplot routines and added
470: routine fileappend.
471:
472: Revision 1.85 2003/06/17 13:12:43 brouard
473: * imach.c (Repository): Check when date of death was earlier that
474: current date of interview. It may happen when the death was just
475: prior to the death. In this case, dh was negative and likelihood
476: was wrong (infinity). We still send an "Error" but patch by
477: assuming that the date of death was just one stepm after the
478: interview.
479: (Repository): Because some people have very long ID (first column)
480: we changed int to long in num[] and we added a new lvector for
481: memory allocation. But we also truncated to 8 characters (left
482: truncation)
483: (Repository): No more line truncation errors.
484:
485: Revision 1.84 2003/06/13 21:44:43 brouard
486: * imach.c (Repository): Replace "freqsummary" at a correct
487: place. It differs from routine "prevalence" which may be called
488: many times. Probs is memory consuming and must be used with
489: parcimony.
490: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
491:
492: Revision 1.83 2003/06/10 13:39:11 lievre
493: *** empty log message ***
494:
495: Revision 1.82 2003/06/05 15:57:20 brouard
496: Add log in imach.c and fullversion number is now printed.
497:
498: */
499: /*
500: Interpolated Markov Chain
501:
502: Short summary of the programme:
503:
504: This program computes Healthy Life Expectancies from
505: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
506: first survey ("cross") where individuals from different ages are
507: interviewed on their health status or degree of disability (in the
508: case of a health survey which is our main interest) -2- at least a
509: second wave of interviews ("longitudinal") which measure each change
510: (if any) in individual health status. Health expectancies are
511: computed from the time spent in each health state according to a
512: model. More health states you consider, more time is necessary to reach the
513: Maximum Likelihood of the parameters involved in the model. The
514: simplest model is the multinomial logistic model where pij is the
515: probability to be observed in state j at the second wave
516: conditional to be observed in state i at the first wave. Therefore
517: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
518: 'age' is age and 'sex' is a covariate. If you want to have a more
519: complex model than "constant and age", you should modify the program
520: where the markup *Covariates have to be included here again* invites
521: you to do it. More covariates you add, slower the
522: convergence.
523:
524: The advantage of this computer programme, compared to a simple
525: multinomial logistic model, is clear when the delay between waves is not
526: identical for each individual. Also, if a individual missed an
527: intermediate interview, the information is lost, but taken into
528: account using an interpolation or extrapolation.
529:
530: hPijx is the probability to be observed in state i at age x+h
531: conditional to the observed state i at age x. The delay 'h' can be
532: split into an exact number (nh*stepm) of unobserved intermediate
533: states. This elementary transition (by month, quarter,
534: semester or year) is modelled as a multinomial logistic. The hPx
535: matrix is simply the matrix product of nh*stepm elementary matrices
536: and the contribution of each individual to the likelihood is simply
537: hPijx.
538:
539: Also this programme outputs the covariance matrix of the parameters but also
540: of the life expectancies. It also computes the period (stable) prevalence.
541:
1.133 brouard 542: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
543: Institut national d'études démographiques, Paris.
1.126 brouard 544: This software have been partly granted by Euro-REVES, a concerted action
545: from the European Union.
546: It is copyrighted identically to a GNU software product, ie programme and
547: software can be distributed freely for non commercial use. Latest version
548: can be accessed at http://euroreves.ined.fr/imach .
549:
550: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
551: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
552:
553: **********************************************************************/
554: /*
555: main
556: read parameterfile
557: read datafile
558: concatwav
559: freqsummary
560: if (mle >= 1)
561: mlikeli
562: print results files
563: if mle==1
564: computes hessian
565: read end of parameter file: agemin, agemax, bage, fage, estepm
566: begin-prev-date,...
567: open gnuplot file
568: open html file
1.145 brouard 569: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
570: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
571: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
572: freexexit2 possible for memory heap.
573:
574: h Pij x | pij_nom ficrestpij
575: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
576: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
577: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
578:
579: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
580: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
581: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
582: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
583: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
584:
1.126 brouard 585: forecasting if prevfcast==1 prevforecast call prevalence()
586: health expectancies
587: Variance-covariance of DFLE
588: prevalence()
589: movingaverage()
590: varevsij()
591: if popbased==1 varevsij(,popbased)
592: total life expectancies
593: Variance of period (stable) prevalence
594: end
595: */
596:
1.187 brouard 597: /* #define DEBUG */
598: /* #define DEBUGBRENT */
1.165 brouard 599: #define POWELL /* Instead of NLOPT */
1.186 brouard 600: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
601: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 602:
603: #include <math.h>
604: #include <stdio.h>
605: #include <stdlib.h>
606: #include <string.h>
1.159 brouard 607:
608: #ifdef _WIN32
609: #include <io.h>
1.172 brouard 610: #include <windows.h>
611: #include <tchar.h>
1.159 brouard 612: #else
1.126 brouard 613: #include <unistd.h>
1.159 brouard 614: #endif
1.126 brouard 615:
616: #include <limits.h>
617: #include <sys/types.h>
1.171 brouard 618:
619: #if defined(__GNUC__)
620: #include <sys/utsname.h> /* Doesn't work on Windows */
621: #endif
622:
1.126 brouard 623: #include <sys/stat.h>
624: #include <errno.h>
1.159 brouard 625: /* extern int errno; */
1.126 brouard 626:
1.157 brouard 627: /* #ifdef LINUX */
628: /* #include <time.h> */
629: /* #include "timeval.h" */
630: /* #else */
631: /* #include <sys/time.h> */
632: /* #endif */
633:
1.126 brouard 634: #include <time.h>
635:
1.136 brouard 636: #ifdef GSL
637: #include <gsl/gsl_errno.h>
638: #include <gsl/gsl_multimin.h>
639: #endif
640:
1.167 brouard 641:
1.162 brouard 642: #ifdef NLOPT
643: #include <nlopt.h>
644: typedef struct {
645: double (* function)(double [] );
646: } myfunc_data ;
647: #endif
648:
1.126 brouard 649: /* #include <libintl.h> */
650: /* #define _(String) gettext (String) */
651:
1.141 brouard 652: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 653:
654: #define GNUPLOTPROGRAM "gnuplot"
655: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
656: #define FILENAMELENGTH 132
657:
658: #define GLOCK_ERROR_NOPATH -1 /* empty path */
659: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
660:
1.144 brouard 661: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
662: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 663:
664: #define NINTERVMAX 8
1.144 brouard 665: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
666: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
667: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.145 brouard 668: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
1.126 brouard 669: #define MAXN 20000
1.144 brouard 670: #define YEARM 12. /**< Number of months per year */
1.126 brouard 671: #define AGESUP 130
672: #define AGEBASE 40
1.164 brouard 673: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 674: #ifdef _WIN32
675: #define DIRSEPARATOR '\\'
676: #define CHARSEPARATOR "\\"
677: #define ODIRSEPARATOR '/'
678: #else
1.126 brouard 679: #define DIRSEPARATOR '/'
680: #define CHARSEPARATOR "/"
681: #define ODIRSEPARATOR '\\'
682: #endif
683:
1.190 ! brouard 684: /* $Id: imach.c,v 1.189 2015/04/30 14:45:16 brouard Exp $ */
1.126 brouard 685: /* $State: Exp $ */
686:
1.189 brouard 687: char version[]="Imach version 0.98q2, April 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
1.190 ! brouard 688: char fullversion[]="$Revision: 1.189 $ $Date: 2015/04/30 14:45:16 $";
1.126 brouard 689: char strstart[80];
690: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 691: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 692: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 693: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
694: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
695: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
696: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
697: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
698: int cptcovprodnoage=0; /**< Number of covariate products without age */
699: int cptcoveff=0; /* Total number of covariates to vary for printing results */
700: int cptcov=0; /* Working variable */
1.126 brouard 701: int npar=NPARMAX;
702: int nlstate=2; /* Number of live states */
703: int ndeath=1; /* Number of dead states */
1.130 brouard 704: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 705: int popbased=0;
706:
707: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 708: int maxwav=0; /* Maxim number of waves */
709: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
710: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
711: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 712: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 713: int mle=1, weightopt=0;
1.126 brouard 714: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
715: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
716: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
717: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 718: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 719: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 720: double **matprod2(); /* test */
1.126 brouard 721: double **oldm, **newm, **savm; /* Working pointers to matrices */
722: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 723: /*FILE *fic ; */ /* Used in readdata only */
724: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 725: FILE *ficlog, *ficrespow;
1.130 brouard 726: int globpr=0; /* Global variable for printing or not */
1.126 brouard 727: double fretone; /* Only one call to likelihood */
1.130 brouard 728: long ipmx=0; /* Number of contributions */
1.126 brouard 729: double sw; /* Sum of weights */
730: char filerespow[FILENAMELENGTH];
731: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
732: FILE *ficresilk;
733: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
734: FILE *ficresprobmorprev;
735: FILE *fichtm, *fichtmcov; /* Html File */
736: FILE *ficreseij;
737: char filerese[FILENAMELENGTH];
738: FILE *ficresstdeij;
739: char fileresstde[FILENAMELENGTH];
740: FILE *ficrescveij;
741: char filerescve[FILENAMELENGTH];
742: FILE *ficresvij;
743: char fileresv[FILENAMELENGTH];
744: FILE *ficresvpl;
745: char fileresvpl[FILENAMELENGTH];
746: char title[MAXLINE];
747: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
748: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
749: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
750: char command[FILENAMELENGTH];
751: int outcmd=0;
752:
753: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
754:
755: char filelog[FILENAMELENGTH]; /* Log file */
756: char filerest[FILENAMELENGTH];
757: char fileregp[FILENAMELENGTH];
758: char popfile[FILENAMELENGTH];
759:
760: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
761:
1.157 brouard 762: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
763: /* struct timezone tzp; */
764: /* extern int gettimeofday(); */
765: struct tm tml, *gmtime(), *localtime();
766:
767: extern time_t time();
768:
769: struct tm start_time, end_time, curr_time, last_time, forecast_time;
770: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
771: struct tm tm;
772:
1.126 brouard 773: char strcurr[80], strfor[80];
774:
775: char *endptr;
776: long lval;
777: double dval;
778:
779: #define NR_END 1
780: #define FREE_ARG char*
781: #define FTOL 1.0e-10
782:
783: #define NRANSI
784: #define ITMAX 200
785:
786: #define TOL 2.0e-4
787:
788: #define CGOLD 0.3819660
789: #define ZEPS 1.0e-10
790: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
791:
792: #define GOLD 1.618034
793: #define GLIMIT 100.0
794: #define TINY 1.0e-20
795:
796: static double maxarg1,maxarg2;
797: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
798: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
799:
800: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
801: #define rint(a) floor(a+0.5)
1.166 brouard 802: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 803: #define mytinydouble 1.0e-16
1.166 brouard 804: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
805: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
806: /* static double dsqrarg; */
807: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 808: static double sqrarg;
809: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
810: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
811: int agegomp= AGEGOMP;
812:
813: int imx;
814: int stepm=1;
815: /* Stepm, step in month: minimum step interpolation*/
816:
817: int estepm;
818: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
819:
820: int m,nb;
821: long *num;
822: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
823: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
824: double **pmmij, ***probs;
825: double *ageexmed,*agecens;
826: double dateintmean=0;
827:
828: double *weight;
829: int **s; /* Status */
1.141 brouard 830: double *agedc;
1.145 brouard 831: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 832: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 833: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 834: double idx;
835: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.145 brouard 836: int *Ndum; /** Freq of modality (tricode */
1.141 brouard 837: int **codtab; /**< codtab=imatrix(1,100,1,10); */
838: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 839: double *lsurv, *lpop, *tpop;
840:
1.143 brouard 841: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
842: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 843:
844: /**************** split *************************/
845: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
846: {
847: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
848: the name of the file (name), its extension only (ext) and its first part of the name (finame)
849: */
850: char *ss; /* pointer */
1.186 brouard 851: int l1=0, l2=0; /* length counters */
1.126 brouard 852:
853: l1 = strlen(path ); /* length of path */
854: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
855: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
856: if ( ss == NULL ) { /* no directory, so determine current directory */
857: strcpy( name, path ); /* we got the fullname name because no directory */
858: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
859: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
860: /* get current working directory */
861: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 862: #ifdef WIN32
863: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
864: #else
865: if (getcwd(dirc, FILENAME_MAX) == NULL) {
866: #endif
1.126 brouard 867: return( GLOCK_ERROR_GETCWD );
868: }
869: /* got dirc from getcwd*/
870: printf(" DIRC = %s \n",dirc);
871: } else { /* strip direcotry from path */
872: ss++; /* after this, the filename */
873: l2 = strlen( ss ); /* length of filename */
874: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
875: strcpy( name, ss ); /* save file name */
876: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 877: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 878: printf(" DIRC2 = %s \n",dirc);
879: }
880: /* We add a separator at the end of dirc if not exists */
881: l1 = strlen( dirc ); /* length of directory */
882: if( dirc[l1-1] != DIRSEPARATOR ){
883: dirc[l1] = DIRSEPARATOR;
884: dirc[l1+1] = 0;
885: printf(" DIRC3 = %s \n",dirc);
886: }
887: ss = strrchr( name, '.' ); /* find last / */
888: if (ss >0){
889: ss++;
890: strcpy(ext,ss); /* save extension */
891: l1= strlen( name);
892: l2= strlen(ss)+1;
893: strncpy( finame, name, l1-l2);
894: finame[l1-l2]= 0;
895: }
896:
897: return( 0 ); /* we're done */
898: }
899:
900:
901: /******************************************/
902:
903: void replace_back_to_slash(char *s, char*t)
904: {
905: int i;
906: int lg=0;
907: i=0;
908: lg=strlen(t);
909: for(i=0; i<= lg; i++) {
910: (s[i] = t[i]);
911: if (t[i]== '\\') s[i]='/';
912: }
913: }
914:
1.132 brouard 915: char *trimbb(char *out, char *in)
1.137 brouard 916: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 917: char *s;
918: s=out;
919: while (*in != '\0'){
1.137 brouard 920: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 921: in++;
922: }
923: *out++ = *in++;
924: }
925: *out='\0';
926: return s;
927: }
928:
1.187 brouard 929: /* char *substrchaine(char *out, char *in, char *chain) */
930: /* { */
931: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
932: /* char *s, *t; */
933: /* t=in;s=out; */
934: /* while ((*in != *chain) && (*in != '\0')){ */
935: /* *out++ = *in++; */
936: /* } */
937:
938: /* /\* *in matches *chain *\/ */
939: /* while ((*in++ == *chain++) && (*in != '\0')){ */
940: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
941: /* } */
942: /* in--; chain--; */
943: /* while ( (*in != '\0')){ */
944: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
945: /* *out++ = *in++; */
946: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
947: /* } */
948: /* *out='\0'; */
949: /* out=s; */
950: /* return out; */
951: /* } */
952: char *substrchaine(char *out, char *in, char *chain)
953: {
954: /* Substract chain 'chain' from 'in', return and output 'out' */
955: /* in="V1+V1*age+age*age+V2", chain="age*age" */
956:
957: char *strloc;
958:
959: strcpy (out, in);
960: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
961: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
962: if(strloc != NULL){
963: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
964: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
965: /* strcpy (strloc, strloc +strlen(chain));*/
966: }
967: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
968: return out;
969: }
970:
971:
1.145 brouard 972: char *cutl(char *blocc, char *alocc, char *in, char occ)
973: {
1.187 brouard 974: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 975: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 976: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 977: If occ is not found blocc is null and alocc is equal to in. Returns blocc
978: */
1.160 brouard 979: char *s, *t;
1.145 brouard 980: t=in;s=in;
981: while ((*in != occ) && (*in != '\0')){
982: *alocc++ = *in++;
983: }
984: if( *in == occ){
985: *(alocc)='\0';
986: s=++in;
987: }
988:
989: if (s == t) {/* occ not found */
990: *(alocc-(in-s))='\0';
991: in=s;
992: }
993: while ( *in != '\0'){
994: *blocc++ = *in++;
995: }
996:
997: *blocc='\0';
998: return t;
999: }
1.137 brouard 1000: char *cutv(char *blocc, char *alocc, char *in, char occ)
1001: {
1.187 brouard 1002: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1003: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1004: gives blocc="abcdef2ghi" and alocc="j".
1005: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1006: */
1007: char *s, *t;
1008: t=in;s=in;
1009: while (*in != '\0'){
1010: while( *in == occ){
1011: *blocc++ = *in++;
1012: s=in;
1013: }
1014: *blocc++ = *in++;
1015: }
1016: if (s == t) /* occ not found */
1017: *(blocc-(in-s))='\0';
1018: else
1019: *(blocc-(in-s)-1)='\0';
1020: in=s;
1021: while ( *in != '\0'){
1022: *alocc++ = *in++;
1023: }
1024:
1025: *alocc='\0';
1026: return s;
1027: }
1028:
1.126 brouard 1029: int nbocc(char *s, char occ)
1030: {
1031: int i,j=0;
1032: int lg=20;
1033: i=0;
1034: lg=strlen(s);
1035: for(i=0; i<= lg; i++) {
1036: if (s[i] == occ ) j++;
1037: }
1038: return j;
1039: }
1040:
1.137 brouard 1041: /* void cutv(char *u,char *v, char*t, char occ) */
1042: /* { */
1043: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1044: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1045: /* gives u="abcdef2ghi" and v="j" *\/ */
1046: /* int i,lg,j,p=0; */
1047: /* i=0; */
1048: /* lg=strlen(t); */
1049: /* for(j=0; j<=lg-1; j++) { */
1050: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1051: /* } */
1.126 brouard 1052:
1.137 brouard 1053: /* for(j=0; j<p; j++) { */
1054: /* (u[j] = t[j]); */
1055: /* } */
1056: /* u[p]='\0'; */
1.126 brouard 1057:
1.137 brouard 1058: /* for(j=0; j<= lg; j++) { */
1059: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1060: /* } */
1061: /* } */
1.126 brouard 1062:
1.160 brouard 1063: #ifdef _WIN32
1064: char * strsep(char **pp, const char *delim)
1065: {
1066: char *p, *q;
1067:
1068: if ((p = *pp) == NULL)
1069: return 0;
1070: if ((q = strpbrk (p, delim)) != NULL)
1071: {
1072: *pp = q + 1;
1073: *q = '\0';
1074: }
1075: else
1076: *pp = 0;
1077: return p;
1078: }
1079: #endif
1080:
1.126 brouard 1081: /********************** nrerror ********************/
1082:
1083: void nrerror(char error_text[])
1084: {
1085: fprintf(stderr,"ERREUR ...\n");
1086: fprintf(stderr,"%s\n",error_text);
1087: exit(EXIT_FAILURE);
1088: }
1089: /*********************** vector *******************/
1090: double *vector(int nl, int nh)
1091: {
1092: double *v;
1093: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1094: if (!v) nrerror("allocation failure in vector");
1095: return v-nl+NR_END;
1096: }
1097:
1098: /************************ free vector ******************/
1099: void free_vector(double*v, int nl, int nh)
1100: {
1101: free((FREE_ARG)(v+nl-NR_END));
1102: }
1103:
1104: /************************ivector *******************************/
1105: int *ivector(long nl,long nh)
1106: {
1107: int *v;
1108: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1109: if (!v) nrerror("allocation failure in ivector");
1110: return v-nl+NR_END;
1111: }
1112:
1113: /******************free ivector **************************/
1114: void free_ivector(int *v, long nl, long nh)
1115: {
1116: free((FREE_ARG)(v+nl-NR_END));
1117: }
1118:
1119: /************************lvector *******************************/
1120: long *lvector(long nl,long nh)
1121: {
1122: long *v;
1123: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1124: if (!v) nrerror("allocation failure in ivector");
1125: return v-nl+NR_END;
1126: }
1127:
1128: /******************free lvector **************************/
1129: void free_lvector(long *v, long nl, long nh)
1130: {
1131: free((FREE_ARG)(v+nl-NR_END));
1132: }
1133:
1134: /******************* imatrix *******************************/
1135: int **imatrix(long nrl, long nrh, long ncl, long nch)
1136: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1137: {
1138: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1139: int **m;
1140:
1141: /* allocate pointers to rows */
1142: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1143: if (!m) nrerror("allocation failure 1 in matrix()");
1144: m += NR_END;
1145: m -= nrl;
1146:
1147:
1148: /* allocate rows and set pointers to them */
1149: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1150: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1151: m[nrl] += NR_END;
1152: m[nrl] -= ncl;
1153:
1154: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1155:
1156: /* return pointer to array of pointers to rows */
1157: return m;
1158: }
1159:
1160: /****************** free_imatrix *************************/
1161: void free_imatrix(m,nrl,nrh,ncl,nch)
1162: int **m;
1163: long nch,ncl,nrh,nrl;
1164: /* free an int matrix allocated by imatrix() */
1165: {
1166: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1167: free((FREE_ARG) (m+nrl-NR_END));
1168: }
1169:
1170: /******************* matrix *******************************/
1171: double **matrix(long nrl, long nrh, long ncl, long nch)
1172: {
1173: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1174: double **m;
1175:
1176: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1177: if (!m) nrerror("allocation failure 1 in matrix()");
1178: m += NR_END;
1179: m -= nrl;
1180:
1181: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1182: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1183: m[nrl] += NR_END;
1184: m[nrl] -= ncl;
1185:
1186: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1187: return m;
1.145 brouard 1188: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1189: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1190: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1191: */
1192: }
1193:
1194: /*************************free matrix ************************/
1195: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1196: {
1197: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1198: free((FREE_ARG)(m+nrl-NR_END));
1199: }
1200:
1201: /******************* ma3x *******************************/
1202: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1203: {
1204: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1205: double ***m;
1206:
1207: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1208: if (!m) nrerror("allocation failure 1 in matrix()");
1209: m += NR_END;
1210: m -= nrl;
1211:
1212: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1213: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1214: m[nrl] += NR_END;
1215: m[nrl] -= ncl;
1216:
1217: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1218:
1219: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1220: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1221: m[nrl][ncl] += NR_END;
1222: m[nrl][ncl] -= nll;
1223: for (j=ncl+1; j<=nch; j++)
1224: m[nrl][j]=m[nrl][j-1]+nlay;
1225:
1226: for (i=nrl+1; i<=nrh; i++) {
1227: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1228: for (j=ncl+1; j<=nch; j++)
1229: m[i][j]=m[i][j-1]+nlay;
1230: }
1231: return m;
1232: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1233: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1234: */
1235: }
1236:
1237: /*************************free ma3x ************************/
1238: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1239: {
1240: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1241: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1242: free((FREE_ARG)(m+nrl-NR_END));
1243: }
1244:
1245: /*************** function subdirf ***********/
1246: char *subdirf(char fileres[])
1247: {
1248: /* Caution optionfilefiname is hidden */
1249: strcpy(tmpout,optionfilefiname);
1250: strcat(tmpout,"/"); /* Add to the right */
1251: strcat(tmpout,fileres);
1252: return tmpout;
1253: }
1254:
1255: /*************** function subdirf2 ***********/
1256: char *subdirf2(char fileres[], char *preop)
1257: {
1258:
1259: /* Caution optionfilefiname is hidden */
1260: strcpy(tmpout,optionfilefiname);
1261: strcat(tmpout,"/");
1262: strcat(tmpout,preop);
1263: strcat(tmpout,fileres);
1264: return tmpout;
1265: }
1266:
1267: /*************** function subdirf3 ***********/
1268: char *subdirf3(char fileres[], char *preop, char *preop2)
1269: {
1270:
1271: /* Caution optionfilefiname is hidden */
1272: strcpy(tmpout,optionfilefiname);
1273: strcat(tmpout,"/");
1274: strcat(tmpout,preop);
1275: strcat(tmpout,preop2);
1276: strcat(tmpout,fileres);
1277: return tmpout;
1278: }
1279:
1.162 brouard 1280: char *asc_diff_time(long time_sec, char ascdiff[])
1281: {
1282: long sec_left, days, hours, minutes;
1283: days = (time_sec) / (60*60*24);
1284: sec_left = (time_sec) % (60*60*24);
1285: hours = (sec_left) / (60*60) ;
1286: sec_left = (sec_left) %(60*60);
1287: minutes = (sec_left) /60;
1288: sec_left = (sec_left) % (60);
1289: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1290: return ascdiff;
1291: }
1292:
1.126 brouard 1293: /***************** f1dim *************************/
1294: extern int ncom;
1295: extern double *pcom,*xicom;
1296: extern double (*nrfunc)(double []);
1297:
1298: double f1dim(double x)
1299: {
1300: int j;
1301: double f;
1302: double *xt;
1303:
1304: xt=vector(1,ncom);
1305: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1306: f=(*nrfunc)(xt);
1307: free_vector(xt,1,ncom);
1308: return f;
1309: }
1310:
1311: /*****************brent *************************/
1312: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1313: {
1314: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1315: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1316: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1317: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1318: * returned function value.
1319: */
1.126 brouard 1320: int iter;
1321: double a,b,d,etemp;
1.159 brouard 1322: double fu=0,fv,fw,fx;
1.164 brouard 1323: double ftemp=0.;
1.126 brouard 1324: double p,q,r,tol1,tol2,u,v,w,x,xm;
1325: double e=0.0;
1326:
1327: a=(ax < cx ? ax : cx);
1328: b=(ax > cx ? ax : cx);
1329: x=w=v=bx;
1330: fw=fv=fx=(*f)(x);
1331: for (iter=1;iter<=ITMAX;iter++) {
1332: xm=0.5*(a+b);
1333: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1334: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1335: printf(".");fflush(stdout);
1336: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1337: #ifdef DEBUGBRENT
1.126 brouard 1338: 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);
1339: 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);
1340: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1341: #endif
1342: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1343: *xmin=x;
1344: return fx;
1345: }
1346: ftemp=fu;
1347: if (fabs(e) > tol1) {
1348: r=(x-w)*(fx-fv);
1349: q=(x-v)*(fx-fw);
1350: p=(x-v)*q-(x-w)*r;
1351: q=2.0*(q-r);
1352: if (q > 0.0) p = -p;
1353: q=fabs(q);
1354: etemp=e;
1355: e=d;
1356: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1357: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1358: else {
1359: d=p/q;
1360: u=x+d;
1361: if (u-a < tol2 || b-u < tol2)
1362: d=SIGN(tol1,xm-x);
1363: }
1364: } else {
1365: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1366: }
1367: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1368: fu=(*f)(u);
1369: if (fu <= fx) {
1370: if (u >= x) a=x; else b=x;
1371: SHFT(v,w,x,u)
1.183 brouard 1372: SHFT(fv,fw,fx,fu)
1373: } else {
1374: if (u < x) a=u; else b=u;
1375: if (fu <= fw || w == x) {
1376: v=w;
1377: w=u;
1378: fv=fw;
1379: fw=fu;
1380: } else if (fu <= fv || v == x || v == w) {
1381: v=u;
1382: fv=fu;
1383: }
1384: }
1.126 brouard 1385: }
1386: nrerror("Too many iterations in brent");
1387: *xmin=x;
1388: return fx;
1389: }
1390:
1391: /****************** mnbrak ***********************/
1392:
1393: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1394: double (*func)(double))
1.183 brouard 1395: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1396: the downhill direction (defined by the function as evaluated at the initial points) and returns
1397: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1398: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1399: */
1.126 brouard 1400: double ulim,u,r,q, dum;
1401: double fu;
1.187 brouard 1402:
1403: double scale=10.;
1404: int iterscale=0;
1405:
1406: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1407: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1408:
1409:
1410: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1411: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1412: /* *bx = *ax - (*ax - *bx)/scale; */
1413: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1414: /* } */
1415:
1.126 brouard 1416: if (*fb > *fa) {
1417: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1418: SHFT(dum,*fb,*fa,dum)
1419: }
1.126 brouard 1420: *cx=(*bx)+GOLD*(*bx-*ax);
1421: *fc=(*func)(*cx);
1.183 brouard 1422: #ifdef DEBUG
1423: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1424: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1425: #endif
1426: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1427: r=(*bx-*ax)*(*fb-*fc);
1428: q=(*bx-*cx)*(*fb-*fa);
1429: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1430: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1431: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1432: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1433: fu=(*func)(u);
1.163 brouard 1434: #ifdef DEBUG
1435: /* f(x)=A(x-u)**2+f(u) */
1436: double A, fparabu;
1437: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1438: fparabu= *fa - A*(*ax-u)*(*ax-u);
1439: 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);
1440: 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 1441: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1442: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1443: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1444: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1445: #endif
1.184 brouard 1446: #ifdef MNBRAKORIGINAL
1.183 brouard 1447: #else
1448: if (fu > *fc) {
1449: #ifdef DEBUG
1450: printf("mnbrak4 fu > fc \n");
1451: fprintf(ficlog, "mnbrak4 fu > fc\n");
1452: #endif
1453: /* 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 *\/ */
1454: /* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\/ */
1455: dum=u; /* Shifting c and u */
1456: u = *cx;
1457: *cx = dum;
1458: dum = fu;
1459: fu = *fc;
1460: *fc =dum;
1461: } else { /* end */
1462: #ifdef DEBUG
1463: printf("mnbrak3 fu < fc \n");
1464: fprintf(ficlog, "mnbrak3 fu < fc\n");
1465: #endif
1466: dum=u; /* Shifting c and u */
1467: u = *cx;
1468: *cx = dum;
1469: dum = fu;
1470: fu = *fc;
1471: *fc =dum;
1472: }
1473: #endif
1.162 brouard 1474: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1475: #ifdef DEBUG
1476: printf("mnbrak2 u after c but before ulim\n");
1477: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1478: #endif
1.126 brouard 1479: fu=(*func)(u);
1480: if (fu < *fc) {
1.183 brouard 1481: #ifdef DEBUG
1482: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1483: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1484: #endif
1.126 brouard 1485: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1486: SHFT(*fb,*fc,fu,(*func)(u))
1487: }
1.162 brouard 1488: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1489: #ifdef DEBUG
1490: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1491: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1492: #endif
1.126 brouard 1493: u=ulim;
1494: fu=(*func)(u);
1.183 brouard 1495: } else { /* u could be left to b (if r > q parabola has a maximum) */
1496: #ifdef DEBUG
1497: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1498: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1499: #endif
1.126 brouard 1500: u=(*cx)+GOLD*(*cx-*bx);
1501: fu=(*func)(u);
1.183 brouard 1502: } /* end tests */
1.126 brouard 1503: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1504: SHFT(*fa,*fb,*fc,fu)
1505: #ifdef DEBUG
1506: 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);
1507: 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);
1508: #endif
1509: } /* 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 1510: }
1511:
1512: /*************** linmin ************************/
1.162 brouard 1513: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1514: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1515: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1516: the value of func at the returned location p . This is actually all accomplished by calling the
1517: routines mnbrak and brent .*/
1.126 brouard 1518: int ncom;
1519: double *pcom,*xicom;
1520: double (*nrfunc)(double []);
1521:
1522: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1523: {
1524: double brent(double ax, double bx, double cx,
1525: double (*f)(double), double tol, double *xmin);
1526: double f1dim(double x);
1527: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1528: double *fc, double (*func)(double));
1529: int j;
1530: double xx,xmin,bx,ax;
1531: double fx,fb,fa;
1.187 brouard 1532:
1533: double scale=10., axs, xxs, xxss; /* Scale added for infinity */
1.126 brouard 1534:
1535: ncom=n;
1536: pcom=vector(1,n);
1537: xicom=vector(1,n);
1538: nrfunc=func;
1539: for (j=1;j<=n;j++) {
1540: pcom[j]=p[j];
1541: xicom[j]=xi[j];
1542: }
1.187 brouard 1543:
1544: axs=0.0;
1545: xxss=1; /* 1 and using scale */
1546: xxs=1;
1547: do{
1548: ax=0.;
1549: xx= xxs;
1550: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1551: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1552: /* 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)) */
1553: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1554: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1555: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1556: /* 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]]*/
1557: if (fx != fx){
1558: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1559: 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);
1560: }
1561: }while(fx != fx);
1562:
1563: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1564: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1565: /* fmin = f(p[j] + xmin * xi[j]) */
1566: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1567: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1568: #ifdef DEBUG
1569: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1570: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1571: #endif
1.189 brouard 1572: /* printf("linmin end "); */
1.126 brouard 1573: for (j=1;j<=n;j++) {
1.188 brouard 1574: /* printf(" before xi[%d]=%12.8f", j,xi[j]); */
1.187 brouard 1575: xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
1.189 brouard 1576: /* if(xxs <1.0) */
1577: /* 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 1578: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1579: }
1.189 brouard 1580: /* printf("\n"); */
1581: /* printf("Comparing last *frec(xmin)=%12.8f from Brent and frec(0.)=%12.8f \n", *fret, (*func)(p)); */
1.126 brouard 1582: free_vector(xicom,1,n);
1583: free_vector(pcom,1,n);
1584: }
1585:
1586:
1587: /*************** powell ************************/
1.162 brouard 1588: /*
1589: Minimization of a function func of n variables. Input consists of an initial starting point
1590: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1591: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1592: such that failure to decrease by more than this amount on one iteration signals doneness. On
1593: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1594: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1595: */
1.126 brouard 1596: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1597: double (*func)(double []))
1598: {
1599: void linmin(double p[], double xi[], int n, double *fret,
1600: double (*func)(double []));
1601: int i,ibig,j;
1602: double del,t,*pt,*ptt,*xit;
1.181 brouard 1603: double directest;
1.126 brouard 1604: double fp,fptt;
1605: double *xits;
1606: int niterf, itmp;
1607:
1608: pt=vector(1,n);
1609: ptt=vector(1,n);
1610: xit=vector(1,n);
1611: xits=vector(1,n);
1612: *fret=(*func)(p);
1613: for (j=1;j<=n;j++) pt[j]=p[j];
1.157 brouard 1614: rcurr_time = time(NULL);
1.126 brouard 1615: for (*iter=1;;++(*iter)) {
1.187 brouard 1616: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1617: ibig=0;
1618: del=0.0;
1.157 brouard 1619: rlast_time=rcurr_time;
1620: /* (void) gettimeofday(&curr_time,&tzp); */
1621: rcurr_time = time(NULL);
1622: curr_time = *localtime(&rcurr_time);
1623: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1624: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1625: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.126 brouard 1626: for (i=1;i<=n;i++) {
1627: printf(" %d %.12f",i, p[i]);
1628: fprintf(ficlog," %d %.12lf",i, p[i]);
1629: fprintf(ficrespow," %.12lf", p[i]);
1630: }
1631: printf("\n");
1632: fprintf(ficlog,"\n");
1633: fprintf(ficrespow,"\n");fflush(ficrespow);
1634: if(*iter <=3){
1.157 brouard 1635: tml = *localtime(&rcurr_time);
1636: strcpy(strcurr,asctime(&tml));
1637: rforecast_time=rcurr_time;
1.126 brouard 1638: itmp = strlen(strcurr);
1639: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1640: strcurr[itmp-1]='\0';
1.162 brouard 1641: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1642: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1643: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1644: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1645: forecast_time = *localtime(&rforecast_time);
1646: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1647: itmp = strlen(strfor);
1648: if(strfor[itmp-1]=='\n')
1649: strfor[itmp-1]='\0';
1.157 brouard 1650: 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);
1651: 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 1652: }
1653: }
1.187 brouard 1654: for (i=1;i<=n;i++) { /* For each direction i */
1655: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1656: fptt=(*fret);
1657: #ifdef DEBUG
1.164 brouard 1658: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1659: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1660: #endif
1.187 brouard 1661: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1662: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 brouard 1663: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1664: /* Outputs are fret(new point p) p is updated and xit rescaled */
1665: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1666: /* because that direction will be replaced unless the gain del is small */
1667: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1668: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1669: /* with the new direction. */
1.126 brouard 1670: del=fabs(fptt-(*fret));
1671: ibig=i;
1672: }
1673: #ifdef DEBUG
1674: printf("%d %.12e",i,(*fret));
1675: fprintf(ficlog,"%d %.12e",i,(*fret));
1676: for (j=1;j<=n;j++) {
1677: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1678: printf(" x(%d)=%.12e",j,xit[j]);
1679: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1680: }
1681: for(j=1;j<=n;j++) {
1.162 brouard 1682: printf(" p(%d)=%.12e",j,p[j]);
1683: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1684: }
1685: printf("\n");
1686: fprintf(ficlog,"\n");
1687: #endif
1.187 brouard 1688: } /* end loop on each direction i */
1689: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1690: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1691: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1692: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1693: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1694: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1695: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1696: /* decreased of more than 3.84 */
1697: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1698: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1699: /* By adding 10 parameters more the gain should be 18.31 */
1700:
1701: /* Starting the program with initial values given by a former maximization will simply change */
1702: /* the scales of the directions and the directions, because the are reset to canonical directions */
1703: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1704: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1705: #ifdef DEBUG
1706: int k[2],l;
1707: k[0]=1;
1708: k[1]=-1;
1709: printf("Max: %.12e",(*func)(p));
1710: fprintf(ficlog,"Max: %.12e",(*func)(p));
1711: for (j=1;j<=n;j++) {
1712: printf(" %.12e",p[j]);
1713: fprintf(ficlog," %.12e",p[j]);
1714: }
1715: printf("\n");
1716: fprintf(ficlog,"\n");
1717: for(l=0;l<=1;l++) {
1718: for (j=1;j<=n;j++) {
1719: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1720: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1721: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1722: }
1723: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1724: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1725: }
1726: #endif
1727:
1728:
1729: free_vector(xit,1,n);
1730: free_vector(xits,1,n);
1731: free_vector(ptt,1,n);
1732: free_vector(pt,1,n);
1733: return;
1734: }
1735: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1736: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1737: ptt[j]=2.0*p[j]-pt[j];
1738: xit[j]=p[j]-pt[j];
1739: pt[j]=p[j];
1740: }
1.181 brouard 1741: fptt=(*func)(ptt); /* f_3 */
1.161 brouard 1742: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.162 brouard 1743: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1744: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1745: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1746: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1747: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1748: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1749: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1750: #ifdef NRCORIGINAL
1751: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1752: #else
1753: 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 1754: t= t- del*SQR(fp-fptt);
1.183 brouard 1755: #endif
1.182 brouard 1756: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
1.161 brouard 1757: #ifdef DEBUG
1.181 brouard 1758: 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);
1759: 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 1760: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1761: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1762: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1763: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1764: 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);
1765: 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);
1766: #endif
1.183 brouard 1767: #ifdef POWELLORIGINAL
1768: if (t < 0.0) { /* Then we use it for new direction */
1769: #else
1.182 brouard 1770: if (directest*t < 0.0) { /* Contradiction between both tests */
1.184 brouard 1771: printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
1.182 brouard 1772: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1.184 brouard 1773: fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1.182 brouard 1774: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1775: }
1.181 brouard 1776: if (directest < 0.0) { /* Then we use it for new direction */
1777: #endif
1.187 brouard 1778: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.126 brouard 1779: for (j=1;j<=n;j++) {
1.181 brouard 1780: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1781: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 1782: }
1.181 brouard 1783: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1784: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1785:
1.126 brouard 1786: #ifdef DEBUG
1.164 brouard 1787: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1788: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 1789: for(j=1;j<=n;j++){
1790: printf(" %.12e",xit[j]);
1791: fprintf(ficlog," %.12e",xit[j]);
1792: }
1793: printf("\n");
1794: fprintf(ficlog,"\n");
1795: #endif
1.162 brouard 1796: } /* end of t negative */
1797: } /* end if (fptt < fp) */
1.126 brouard 1798: }
1799: }
1800:
1801: /**** Prevalence limit (stable or period prevalence) ****************/
1802:
1803: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1804: {
1805: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1806: matrix by transitions matrix until convergence is reached */
1.169 brouard 1807:
1.126 brouard 1808: int i, ii,j,k;
1809: double min, max, maxmin, maxmax,sumnew=0.;
1.145 brouard 1810: /* double **matprod2(); */ /* test */
1.131 brouard 1811: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1812: double **newm;
1813: double agefin, delaymax=50 ; /* Max number of years to converge */
1.169 brouard 1814:
1.126 brouard 1815: for (ii=1;ii<=nlstate+ndeath;ii++)
1816: for (j=1;j<=nlstate+ndeath;j++){
1817: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1818: }
1.169 brouard 1819:
1820: cov[1]=1.;
1821:
1822: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.126 brouard 1823: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1824: newm=savm;
1825: /* Covariates have to be included here again */
1.138 brouard 1826: cov[2]=agefin;
1.187 brouard 1827: if(nagesqr==1)
1828: cov[3]= agefin*agefin;;
1.138 brouard 1829: for (k=1; k<=cptcovn;k++) {
1.187 brouard 1830: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.145 brouard 1831: /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
1.138 brouard 1832: }
1.186 brouard 1833: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.187 brouard 1834: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
1.186 brouard 1835: for (k=1; k<=cptcovprod;k++) /* Useless */
1.187 brouard 1836: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1.138 brouard 1837:
1838: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1839: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1840: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 1841: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1842: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 1843: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 1844:
1.126 brouard 1845: savm=oldm;
1846: oldm=newm;
1847: maxmax=0.;
1848: for(j=1;j<=nlstate;j++){
1849: min=1.;
1850: max=0.;
1851: for(i=1; i<=nlstate; i++) {
1852: sumnew=0;
1853: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1854: prlim[i][j]= newm[i][j]/(1-sumnew);
1.145 brouard 1855: /*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 1856: max=FMAX(max,prlim[i][j]);
1857: min=FMIN(min,prlim[i][j]);
1858: }
1859: maxmin=max-min;
1860: maxmax=FMAX(maxmax,maxmin);
1.169 brouard 1861: } /* j loop */
1.126 brouard 1862: if(maxmax < ftolpl){
1863: return prlim;
1864: }
1.169 brouard 1865: } /* age loop */
1866: return prlim; /* should not reach here */
1.126 brouard 1867: }
1868:
1869: /*************** transition probabilities ***************/
1870:
1871: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1872: {
1.138 brouard 1873: /* According to parameters values stored in x and the covariate's values stored in cov,
1874: computes the probability to be observed in state j being in state i by appying the
1875: model to the ncovmodel covariates (including constant and age).
1876: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1877: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1878: ncth covariate in the global vector x is given by the formula:
1879: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1880: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1881: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1882: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1883: Outputs ps[i][j] the probability to be observed in j being in j according to
1884: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1885: */
1886: double s1, lnpijopii;
1.126 brouard 1887: /*double t34;*/
1.164 brouard 1888: int i,j, nc, ii, jj;
1.126 brouard 1889:
1890: for(i=1; i<= nlstate; i++){
1891: for(j=1; j<i;j++){
1.138 brouard 1892: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1893: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1894: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1895: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1896: }
1.138 brouard 1897: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1898: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1899: }
1900: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 1901: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1902: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1903: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1904: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 1905: }
1.138 brouard 1906: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 1907: }
1908: }
1909:
1910: for(i=1; i<= nlstate; i++){
1911: s1=0;
1.131 brouard 1912: for(j=1; j<i; j++){
1.138 brouard 1913: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1914: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1915: }
1916: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 1917: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1918: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1919: }
1.138 brouard 1920: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 1921: ps[i][i]=1./(s1+1.);
1.138 brouard 1922: /* Computing other pijs */
1.126 brouard 1923: for(j=1; j<i; j++)
1924: ps[i][j]= exp(ps[i][j])*ps[i][i];
1925: for(j=i+1; j<=nlstate+ndeath; j++)
1926: ps[i][j]= exp(ps[i][j])*ps[i][i];
1927: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1928: } /* end i */
1929:
1930: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1931: for(jj=1; jj<= nlstate+ndeath; jj++){
1932: ps[ii][jj]=0;
1933: ps[ii][ii]=1;
1934: }
1935: }
1936:
1.145 brouard 1937:
1938: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1939: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1940: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1941: /* } */
1942: /* printf("\n "); */
1943: /* } */
1944: /* printf("\n ");printf("%lf ",cov[2]);*/
1945: /*
1.126 brouard 1946: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1947: goto end;*/
1948: return ps;
1949: }
1950:
1951: /**************** Product of 2 matrices ******************/
1952:
1.145 brouard 1953: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 1954: {
1955: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1956: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1957: /* in, b, out are matrice of pointers which should have been initialized
1958: before: only the contents of out is modified. The function returns
1959: a pointer to pointers identical to out */
1.145 brouard 1960: int i, j, k;
1.126 brouard 1961: for(i=nrl; i<= nrh; i++)
1.145 brouard 1962: for(k=ncolol; k<=ncoloh; k++){
1963: out[i][k]=0.;
1964: for(j=ncl; j<=nch; j++)
1965: out[i][k] +=in[i][j]*b[j][k];
1966: }
1.126 brouard 1967: return out;
1968: }
1969:
1970:
1971: /************* Higher Matrix Product ***************/
1972:
1973: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1974: {
1975: /* Computes the transition matrix starting at age 'age' over
1976: 'nhstepm*hstepm*stepm' months (i.e. until
1977: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1978: nhstepm*hstepm matrices.
1979: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1980: (typically every 2 years instead of every month which is too big
1981: for the memory).
1982: Model is determined by parameters x and covariates have to be
1983: included manually here.
1984:
1985: */
1986:
1987: int i, j, d, h, k;
1.131 brouard 1988: double **out, cov[NCOVMAX+1];
1.126 brouard 1989: double **newm;
1.187 brouard 1990: double agexact;
1.126 brouard 1991:
1992: /* Hstepm could be zero and should return the unit matrix */
1993: for (i=1;i<=nlstate+ndeath;i++)
1994: for (j=1;j<=nlstate+ndeath;j++){
1995: oldm[i][j]=(i==j ? 1.0 : 0.0);
1996: po[i][j][0]=(i==j ? 1.0 : 0.0);
1997: }
1998: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1999: for(h=1; h <=nhstepm; h++){
2000: for(d=1; d <=hstepm; d++){
2001: newm=savm;
2002: /* Covariates have to be included here again */
2003: cov[1]=1.;
1.187 brouard 2004: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
2005: cov[2]=agexact;
2006: if(nagesqr==1)
2007: cov[3]= agexact*agexact;
1.131 brouard 2008: for (k=1; k<=cptcovn;k++)
1.187 brouard 2009: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.186 brouard 2010: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
2011: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.187 brouard 2012: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
1.145 brouard 2013: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.187 brouard 2014: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1.126 brouard 2015:
2016:
2017: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2018: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2019: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2020: pmij(pmmij,cov,ncovmodel,x,nlstate));
2021: savm=oldm;
2022: oldm=newm;
2023: }
2024: for(i=1; i<=nlstate+ndeath; i++)
2025: for(j=1;j<=nlstate+ndeath;j++) {
2026: po[i][j][h]=newm[i][j];
1.128 brouard 2027: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2028: }
1.128 brouard 2029: /*printf("h=%d ",h);*/
1.126 brouard 2030: } /* end h */
1.128 brouard 2031: /* printf("\n H=%d \n",h); */
1.126 brouard 2032: return po;
2033: }
2034:
1.162 brouard 2035: #ifdef NLOPT
2036: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2037: double fret;
2038: double *xt;
2039: int j;
2040: myfunc_data *d2 = (myfunc_data *) pd;
2041: /* xt = (p1-1); */
2042: xt=vector(1,n);
2043: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2044:
2045: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2046: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2047: printf("Function = %.12lf ",fret);
2048: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2049: printf("\n");
2050: free_vector(xt,1,n);
2051: return fret;
2052: }
2053: #endif
1.126 brouard 2054:
2055: /*************** log-likelihood *************/
2056: double func( double *x)
2057: {
2058: int i, ii, j, k, mi, d, kk;
1.131 brouard 2059: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2060: double **out;
2061: double sw; /* Sum of weights */
2062: double lli; /* Individual log likelihood */
2063: int s1, s2;
2064: double bbh, survp;
2065: long ipmx;
1.187 brouard 2066: double agexact;
1.126 brouard 2067: /*extern weight */
2068: /* We are differentiating ll according to initial status */
2069: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2070: /*for(i=1;i<imx;i++)
2071: printf(" %d\n",s[4][i]);
2072: */
1.162 brouard 2073:
2074: ++countcallfunc;
2075:
1.126 brouard 2076: cov[1]=1.;
2077:
2078: for(k=1; k<=nlstate; k++) ll[k]=0.;
2079:
2080: if(mle==1){
2081: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2082: /* Computes the values of the ncovmodel covariates of the model
2083: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2084: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2085: to be observed in j being in i according to the model.
2086: */
1.145 brouard 2087: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 brouard 2088: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2089: }
1.137 brouard 2090: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2091: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2092: has been calculated etc */
1.126 brouard 2093: for(mi=1; mi<= wav[i]-1; mi++){
2094: for (ii=1;ii<=nlstate+ndeath;ii++)
2095: for (j=1;j<=nlstate+ndeath;j++){
2096: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2097: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2098: }
2099: for(d=0; d<dh[mi][i]; d++){
2100: newm=savm;
1.187 brouard 2101: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2102: cov[2]=agexact;
2103: if(nagesqr==1)
2104: cov[3]= agexact*agexact;
1.126 brouard 2105: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2106: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2107: }
2108: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2109: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2110: savm=oldm;
2111: oldm=newm;
2112: } /* end mult */
2113:
2114: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2115: /* But now since version 0.9 we anticipate for bias at large stepm.
2116: * If stepm is larger than one month (smallest stepm) and if the exact delay
2117: * (in months) between two waves is not a multiple of stepm, we rounded to
2118: * the nearest (and in case of equal distance, to the lowest) interval but now
2119: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2120: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2121: * probability in order to take into account the bias as a fraction of the way
2122: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2123: * -stepm/2 to stepm/2 .
2124: * For stepm=1 the results are the same as for previous versions of Imach.
2125: * For stepm > 1 the results are less biased than in previous versions.
2126: */
2127: s1=s[mw[mi][i]][i];
2128: s2=s[mw[mi+1][i]][i];
2129: bbh=(double)bh[mi][i]/(double)stepm;
2130: /* bias bh is positive if real duration
2131: * is higher than the multiple of stepm and negative otherwise.
2132: */
2133: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2134: if( s2 > nlstate){
2135: /* i.e. if s2 is a death state and if the date of death is known
2136: then the contribution to the likelihood is the probability to
2137: die between last step unit time and current step unit time,
2138: which is also equal to probability to die before dh
2139: minus probability to die before dh-stepm .
2140: In version up to 0.92 likelihood was computed
2141: as if date of death was unknown. Death was treated as any other
2142: health state: the date of the interview describes the actual state
2143: and not the date of a change in health state. The former idea was
2144: to consider that at each interview the state was recorded
2145: (healthy, disable or death) and IMaCh was corrected; but when we
2146: introduced the exact date of death then we should have modified
2147: the contribution of an exact death to the likelihood. This new
2148: contribution is smaller and very dependent of the step unit
2149: stepm. It is no more the probability to die between last interview
2150: and month of death but the probability to survive from last
2151: interview up to one month before death multiplied by the
2152: probability to die within a month. Thanks to Chris
2153: Jackson for correcting this bug. Former versions increased
2154: mortality artificially. The bad side is that we add another loop
2155: which slows down the processing. The difference can be up to 10%
2156: lower mortality.
2157: */
1.183 brouard 2158: /* If, at the beginning of the maximization mostly, the
2159: cumulative probability or probability to be dead is
2160: constant (ie = 1) over time d, the difference is equal to
2161: 0. out[s1][3] = savm[s1][3]: probability, being at state
2162: s1 at precedent wave, to be dead a month before current
2163: wave is equal to probability, being at state s1 at
2164: precedent wave, to be dead at mont of the current
2165: wave. Then the observed probability (that this person died)
2166: is null according to current estimated parameter. In fact,
2167: it should be very low but not zero otherwise the log go to
2168: infinity.
2169: */
2170: /* #ifdef INFINITYORIGINAL */
2171: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2172: /* #else */
2173: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2174: /* lli=log(mytinydouble); */
2175: /* else */
2176: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2177: /* #endif */
2178: lli=log(out[s1][s2] - savm[s1][s2]);
1.126 brouard 2179:
2180: } else if (s2==-2) {
2181: for (j=1,survp=0. ; j<=nlstate; j++)
2182: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2183: /*survp += out[s1][j]; */
2184: lli= log(survp);
2185: }
2186:
2187: else if (s2==-4) {
2188: for (j=3,survp=0. ; j<=nlstate; j++)
2189: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2190: lli= log(survp);
2191: }
2192:
2193: else if (s2==-5) {
2194: for (j=1,survp=0. ; j<=2; j++)
2195: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2196: lli= log(survp);
2197: }
2198:
2199: else{
2200: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2201: /* 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 */
2202: }
2203: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2204: /*if(lli ==000.0)*/
2205: /*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); */
2206: ipmx +=1;
2207: sw += weight[i];
2208: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2209: /* if (lli < log(mytinydouble)){ */
2210: /* 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); */
2211: /* 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]); */
2212: /* } */
1.126 brouard 2213: } /* end of wave */
2214: } /* end of individual */
2215: } else if(mle==2){
2216: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2217: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2218: for(mi=1; mi<= wav[i]-1; mi++){
2219: for (ii=1;ii<=nlstate+ndeath;ii++)
2220: for (j=1;j<=nlstate+ndeath;j++){
2221: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2222: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2223: }
2224: for(d=0; d<=dh[mi][i]; d++){
2225: newm=savm;
1.187 brouard 2226: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2227: cov[2]=agexact;
2228: if(nagesqr==1)
2229: cov[3]= agexact*agexact;
1.126 brouard 2230: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2231: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2232: }
2233: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2234: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2235: savm=oldm;
2236: oldm=newm;
2237: } /* end mult */
2238:
2239: s1=s[mw[mi][i]][i];
2240: s2=s[mw[mi+1][i]][i];
2241: bbh=(double)bh[mi][i]/(double)stepm;
2242: 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 */
2243: ipmx +=1;
2244: sw += weight[i];
2245: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2246: } /* end of wave */
2247: } /* end of individual */
2248: } else if(mle==3){ /* exponential inter-extrapolation */
2249: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2250: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2251: for(mi=1; mi<= wav[i]-1; mi++){
2252: for (ii=1;ii<=nlstate+ndeath;ii++)
2253: for (j=1;j<=nlstate+ndeath;j++){
2254: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2255: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2256: }
2257: for(d=0; d<dh[mi][i]; d++){
2258: newm=savm;
1.187 brouard 2259: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2260: cov[2]=agexact;
2261: if(nagesqr==1)
2262: cov[3]= agexact*agexact;
1.126 brouard 2263: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2264: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2265: }
2266: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2267: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2268: savm=oldm;
2269: oldm=newm;
2270: } /* end mult */
2271:
2272: s1=s[mw[mi][i]][i];
2273: s2=s[mw[mi+1][i]][i];
2274: bbh=(double)bh[mi][i]/(double)stepm;
2275: 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 */
2276: ipmx +=1;
2277: sw += weight[i];
2278: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2279: } /* end of wave */
2280: } /* end of individual */
2281: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2282: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2283: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2284: for(mi=1; mi<= wav[i]-1; mi++){
2285: for (ii=1;ii<=nlstate+ndeath;ii++)
2286: for (j=1;j<=nlstate+ndeath;j++){
2287: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2288: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2289: }
2290: for(d=0; d<dh[mi][i]; d++){
2291: newm=savm;
1.187 brouard 2292: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2293: cov[2]=agexact;
2294: if(nagesqr==1)
2295: cov[3]= agexact*agexact;
1.126 brouard 2296: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2297: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2298: }
2299:
2300: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2301: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2302: savm=oldm;
2303: oldm=newm;
2304: } /* end mult */
2305:
2306: s1=s[mw[mi][i]][i];
2307: s2=s[mw[mi+1][i]][i];
2308: if( s2 > nlstate){
2309: lli=log(out[s1][s2] - savm[s1][s2]);
2310: }else{
2311: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2312: }
2313: ipmx +=1;
2314: sw += weight[i];
2315: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2316: /* 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]); */
2317: } /* end of wave */
2318: } /* end of individual */
2319: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2320: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2321: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2322: for(mi=1; mi<= wav[i]-1; mi++){
2323: for (ii=1;ii<=nlstate+ndeath;ii++)
2324: for (j=1;j<=nlstate+ndeath;j++){
2325: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2326: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2327: }
2328: for(d=0; d<dh[mi][i]; d++){
2329: newm=savm;
1.187 brouard 2330: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2331: cov[2]=agexact;
2332: if(nagesqr==1)
2333: cov[3]= agexact*agexact;
1.126 brouard 2334: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2335: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2336: }
2337:
2338: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2339: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2340: savm=oldm;
2341: oldm=newm;
2342: } /* end mult */
2343:
2344: s1=s[mw[mi][i]][i];
2345: s2=s[mw[mi+1][i]][i];
2346: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2347: ipmx +=1;
2348: sw += weight[i];
2349: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2350: /*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]);*/
2351: } /* end of wave */
2352: } /* end of individual */
2353: } /* End of if */
2354: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2355: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2356: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2357: return -l;
2358: }
2359:
2360: /*************** log-likelihood *************/
2361: double funcone( double *x)
2362: {
2363: /* Same as likeli but slower because of a lot of printf and if */
2364: int i, ii, j, k, mi, d, kk;
1.131 brouard 2365: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2366: double **out;
2367: double lli; /* Individual log likelihood */
2368: double llt;
2369: int s1, s2;
2370: double bbh, survp;
1.187 brouard 2371: double agexact;
1.126 brouard 2372: /*extern weight */
2373: /* We are differentiating ll according to initial status */
2374: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2375: /*for(i=1;i<imx;i++)
2376: printf(" %d\n",s[4][i]);
2377: */
2378: cov[1]=1.;
2379:
2380: for(k=1; k<=nlstate; k++) ll[k]=0.;
2381:
2382: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2383: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2384: for(mi=1; mi<= wav[i]-1; mi++){
2385: for (ii=1;ii<=nlstate+ndeath;ii++)
2386: for (j=1;j<=nlstate+ndeath;j++){
2387: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2388: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2389: }
2390: for(d=0; d<dh[mi][i]; d++){
2391: newm=savm;
1.187 brouard 2392: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2393: cov[2]=agexact;
2394: if(nagesqr==1)
2395: cov[3]= agexact*agexact;
1.126 brouard 2396: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2397: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2398: }
1.187 brouard 2399:
1.145 brouard 2400: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2401: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2402: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2403: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2404: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2405: savm=oldm;
2406: oldm=newm;
2407: } /* end mult */
2408:
2409: s1=s[mw[mi][i]][i];
2410: s2=s[mw[mi+1][i]][i];
2411: bbh=(double)bh[mi][i]/(double)stepm;
2412: /* bias is positive if real duration
2413: * is higher than the multiple of stepm and negative otherwise.
2414: */
2415: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2416: lli=log(out[s1][s2] - savm[s1][s2]);
2417: } else if (s2==-2) {
2418: for (j=1,survp=0. ; j<=nlstate; j++)
2419: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2420: lli= log(survp);
2421: }else if (mle==1){
2422: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2423: } else if(mle==2){
2424: 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 */
2425: } else if(mle==3){ /* exponential inter-extrapolation */
2426: 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 */
2427: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2428: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2429: } else{ /* mle=0 back to 1 */
2430: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2431: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2432: } /* End of if */
2433: ipmx +=1;
2434: sw += weight[i];
2435: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2436: /*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 2437: if(globpr){
1.141 brouard 2438: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1.126 brouard 2439: %11.6f %11.6f %11.6f ", \
2440: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2441: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2442: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2443: llt +=ll[k]*gipmx/gsw;
2444: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2445: }
2446: fprintf(ficresilk," %10.6f\n", -llt);
2447: }
2448: } /* end of wave */
2449: } /* end of individual */
2450: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2451: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2452: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2453: if(globpr==0){ /* First time we count the contributions and weights */
2454: gipmx=ipmx;
2455: gsw=sw;
2456: }
2457: return -l;
2458: }
2459:
2460:
2461: /*************** function likelione ***********/
2462: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2463: {
2464: /* This routine should help understanding what is done with
2465: the selection of individuals/waves and
2466: to check the exact contribution to the likelihood.
2467: Plotting could be done.
2468: */
2469: int k;
2470:
2471: if(*globpri !=0){ /* Just counts and sums, no printings */
2472: strcpy(fileresilk,"ilk");
2473: strcat(fileresilk,fileres);
2474: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2475: printf("Problem with resultfile: %s\n", fileresilk);
2476: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2477: }
2478: 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");
2479: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2480: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2481: for(k=1; k<=nlstate; k++)
2482: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2483: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2484: }
2485:
2486: *fretone=(*funcone)(p);
2487: if(*globpri !=0){
2488: fclose(ficresilk);
2489: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2490: fflush(fichtm);
2491: }
2492: return;
2493: }
2494:
2495:
2496: /*********** Maximum Likelihood Estimation ***************/
2497:
2498: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2499: {
1.165 brouard 2500: int i,j, iter=0;
1.126 brouard 2501: double **xi;
2502: double fret;
2503: double fretone; /* Only one call to likelihood */
2504: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2505:
2506: #ifdef NLOPT
2507: int creturn;
2508: nlopt_opt opt;
2509: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2510: double *lb;
2511: double minf; /* the minimum objective value, upon return */
2512: double * p1; /* Shifted parameters from 0 instead of 1 */
2513: myfunc_data dinst, *d = &dinst;
2514: #endif
2515:
2516:
1.126 brouard 2517: xi=matrix(1,npar,1,npar);
2518: for (i=1;i<=npar;i++)
2519: for (j=1;j<=npar;j++)
2520: xi[i][j]=(i==j ? 1.0 : 0.0);
2521: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2522: strcpy(filerespow,"pow");
2523: strcat(filerespow,fileres);
2524: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2525: printf("Problem with resultfile: %s\n", filerespow);
2526: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2527: }
2528: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2529: for (i=1;i<=nlstate;i++)
2530: for(j=1;j<=nlstate+ndeath;j++)
2531: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2532: fprintf(ficrespow,"\n");
1.162 brouard 2533: #ifdef POWELL
1.126 brouard 2534: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2535: #endif
1.126 brouard 2536:
1.162 brouard 2537: #ifdef NLOPT
2538: #ifdef NEWUOA
2539: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2540: #else
2541: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2542: #endif
2543: lb=vector(0,npar-1);
2544: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2545: nlopt_set_lower_bounds(opt, lb);
2546: nlopt_set_initial_step1(opt, 0.1);
2547:
2548: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2549: d->function = func;
2550: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2551: nlopt_set_min_objective(opt, myfunc, d);
2552: nlopt_set_xtol_rel(opt, ftol);
2553: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2554: printf("nlopt failed! %d\n",creturn);
2555: }
2556: else {
2557: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2558: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2559: iter=1; /* not equal */
2560: }
2561: nlopt_destroy(opt);
2562: #endif
1.126 brouard 2563: free_matrix(xi,1,npar,1,npar);
2564: fclose(ficrespow);
1.180 brouard 2565: printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2566: fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2567: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2568:
2569: }
2570:
2571: /**** Computes Hessian and covariance matrix ***/
2572: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2573: {
2574: double **a,**y,*x,pd;
2575: double **hess;
1.164 brouard 2576: int i, j;
1.126 brouard 2577: int *indx;
2578:
2579: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2580: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2581: void lubksb(double **a, int npar, int *indx, double b[]) ;
2582: void ludcmp(double **a, int npar, int *indx, double *d) ;
2583: double gompertz(double p[]);
2584: hess=matrix(1,npar,1,npar);
2585:
2586: printf("\nCalculation of the hessian matrix. Wait...\n");
2587: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2588: for (i=1;i<=npar;i++){
2589: printf("%d",i);fflush(stdout);
2590: fprintf(ficlog,"%d",i);fflush(ficlog);
2591:
2592: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2593:
2594: /* printf(" %f ",p[i]);
2595: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2596: }
2597:
2598: for (i=1;i<=npar;i++) {
2599: for (j=1;j<=npar;j++) {
2600: if (j>i) {
2601: printf(".%d%d",i,j);fflush(stdout);
2602: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2603: hess[i][j]=hessij(p,delti,i,j,func,npar);
2604:
2605: hess[j][i]=hess[i][j];
2606: /*printf(" %lf ",hess[i][j]);*/
2607: }
2608: }
2609: }
2610: printf("\n");
2611: fprintf(ficlog,"\n");
2612:
2613: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2614: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2615:
2616: a=matrix(1,npar,1,npar);
2617: y=matrix(1,npar,1,npar);
2618: x=vector(1,npar);
2619: indx=ivector(1,npar);
2620: for (i=1;i<=npar;i++)
2621: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2622: ludcmp(a,npar,indx,&pd);
2623:
2624: for (j=1;j<=npar;j++) {
2625: for (i=1;i<=npar;i++) x[i]=0;
2626: x[j]=1;
2627: lubksb(a,npar,indx,x);
2628: for (i=1;i<=npar;i++){
2629: matcov[i][j]=x[i];
2630: }
2631: }
2632:
2633: printf("\n#Hessian matrix#\n");
2634: fprintf(ficlog,"\n#Hessian matrix#\n");
2635: for (i=1;i<=npar;i++) {
2636: for (j=1;j<=npar;j++) {
2637: printf("%.3e ",hess[i][j]);
2638: fprintf(ficlog,"%.3e ",hess[i][j]);
2639: }
2640: printf("\n");
2641: fprintf(ficlog,"\n");
2642: }
2643:
2644: /* Recompute Inverse */
2645: for (i=1;i<=npar;i++)
2646: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2647: ludcmp(a,npar,indx,&pd);
2648:
2649: /* printf("\n#Hessian matrix recomputed#\n");
2650:
2651: for (j=1;j<=npar;j++) {
2652: for (i=1;i<=npar;i++) x[i]=0;
2653: x[j]=1;
2654: lubksb(a,npar,indx,x);
2655: for (i=1;i<=npar;i++){
2656: y[i][j]=x[i];
2657: printf("%.3e ",y[i][j]);
2658: fprintf(ficlog,"%.3e ",y[i][j]);
2659: }
2660: printf("\n");
2661: fprintf(ficlog,"\n");
2662: }
2663: */
2664:
2665: free_matrix(a,1,npar,1,npar);
2666: free_matrix(y,1,npar,1,npar);
2667: free_vector(x,1,npar);
2668: free_ivector(indx,1,npar);
2669: free_matrix(hess,1,npar,1,npar);
2670:
2671:
2672: }
2673:
2674: /*************** hessian matrix ****************/
2675: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2676: {
2677: int i;
2678: int l=1, lmax=20;
2679: double k1,k2;
1.132 brouard 2680: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2681: double res;
2682: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2683: double fx;
2684: int k=0,kmax=10;
2685: double l1;
2686:
2687: fx=func(x);
2688: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2689: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2690: l1=pow(10,l);
2691: delts=delt;
2692: for(k=1 ; k <kmax; k=k+1){
2693: delt = delta*(l1*k);
2694: p2[theta]=x[theta] +delt;
1.145 brouard 2695: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2696: p2[theta]=x[theta]-delt;
2697: k2=func(p2)-fx;
2698: /*res= (k1-2.0*fx+k2)/delt/delt; */
2699: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2700:
1.132 brouard 2701: #ifdef DEBUGHESS
1.126 brouard 2702: 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);
2703: 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);
2704: #endif
2705: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2706: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2707: k=kmax;
2708: }
2709: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 2710: k=kmax; l=lmax*10;
1.126 brouard 2711: }
2712: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2713: delts=delt;
2714: }
2715: }
2716: }
2717: delti[theta]=delts;
2718: return res;
2719:
2720: }
2721:
2722: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2723: {
2724: int i;
1.164 brouard 2725: int l=1, lmax=20;
1.126 brouard 2726: double k1,k2,k3,k4,res,fx;
1.132 brouard 2727: double p2[MAXPARM+1];
1.126 brouard 2728: int k;
2729:
2730: fx=func(x);
2731: for (k=1; k<=2; k++) {
2732: for (i=1;i<=npar;i++) p2[i]=x[i];
2733: p2[thetai]=x[thetai]+delti[thetai]/k;
2734: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2735: k1=func(p2)-fx;
2736:
2737: p2[thetai]=x[thetai]+delti[thetai]/k;
2738: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2739: k2=func(p2)-fx;
2740:
2741: p2[thetai]=x[thetai]-delti[thetai]/k;
2742: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2743: k3=func(p2)-fx;
2744:
2745: p2[thetai]=x[thetai]-delti[thetai]/k;
2746: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2747: k4=func(p2)-fx;
2748: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2749: #ifdef DEBUG
2750: 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);
2751: 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);
2752: #endif
2753: }
2754: return res;
2755: }
2756:
2757: /************** Inverse of matrix **************/
2758: void ludcmp(double **a, int n, int *indx, double *d)
2759: {
2760: int i,imax,j,k;
2761: double big,dum,sum,temp;
2762: double *vv;
2763:
2764: vv=vector(1,n);
2765: *d=1.0;
2766: for (i=1;i<=n;i++) {
2767: big=0.0;
2768: for (j=1;j<=n;j++)
2769: if ((temp=fabs(a[i][j])) > big) big=temp;
2770: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2771: vv[i]=1.0/big;
2772: }
2773: for (j=1;j<=n;j++) {
2774: for (i=1;i<j;i++) {
2775: sum=a[i][j];
2776: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2777: a[i][j]=sum;
2778: }
2779: big=0.0;
2780: for (i=j;i<=n;i++) {
2781: sum=a[i][j];
2782: for (k=1;k<j;k++)
2783: sum -= a[i][k]*a[k][j];
2784: a[i][j]=sum;
2785: if ( (dum=vv[i]*fabs(sum)) >= big) {
2786: big=dum;
2787: imax=i;
2788: }
2789: }
2790: if (j != imax) {
2791: for (k=1;k<=n;k++) {
2792: dum=a[imax][k];
2793: a[imax][k]=a[j][k];
2794: a[j][k]=dum;
2795: }
2796: *d = -(*d);
2797: vv[imax]=vv[j];
2798: }
2799: indx[j]=imax;
2800: if (a[j][j] == 0.0) a[j][j]=TINY;
2801: if (j != n) {
2802: dum=1.0/(a[j][j]);
2803: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2804: }
2805: }
2806: free_vector(vv,1,n); /* Doesn't work */
2807: ;
2808: }
2809:
2810: void lubksb(double **a, int n, int *indx, double b[])
2811: {
2812: int i,ii=0,ip,j;
2813: double sum;
2814:
2815: for (i=1;i<=n;i++) {
2816: ip=indx[i];
2817: sum=b[ip];
2818: b[ip]=b[i];
2819: if (ii)
2820: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2821: else if (sum) ii=i;
2822: b[i]=sum;
2823: }
2824: for (i=n;i>=1;i--) {
2825: sum=b[i];
2826: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2827: b[i]=sum/a[i][i];
2828: }
2829: }
2830:
2831: void pstamp(FILE *fichier)
2832: {
2833: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2834: }
2835:
2836: /************ Frequencies ********************/
2837: 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[])
2838: { /* Some frequencies */
2839:
1.164 brouard 2840: int i, m, jk, j1, bool, z1,j;
1.126 brouard 2841: int first;
2842: double ***freq; /* Frequencies */
2843: double *pp, **prop;
2844: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2845: char fileresp[FILENAMELENGTH];
2846:
2847: pp=vector(1,nlstate);
2848: prop=matrix(1,nlstate,iagemin,iagemax+3);
2849: strcpy(fileresp,"p");
2850: strcat(fileresp,fileres);
2851: if((ficresp=fopen(fileresp,"w"))==NULL) {
2852: printf("Problem with prevalence resultfile: %s\n", fileresp);
2853: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2854: exit(0);
2855: }
2856: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2857: j1=0;
2858:
2859: j=cptcoveff;
2860: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2861:
2862: first=1;
2863:
1.169 brouard 2864: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2865: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2866: /* j1++; */
1.145 brouard 2867: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 2868: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2869: scanf("%d", i);*/
2870: for (i=-5; i<=nlstate+ndeath; i++)
2871: for (jk=-5; jk<=nlstate+ndeath; jk++)
2872: for(m=iagemin; m <= iagemax+3; m++)
2873: freq[i][jk][m]=0;
1.143 brouard 2874:
2875: for (i=1; i<=nlstate; i++)
2876: for(m=iagemin; m <= iagemax+3; m++)
2877: prop[i][m]=0;
1.126 brouard 2878:
2879: dateintsum=0;
2880: k2cpt=0;
2881: for (i=1; i<=imx; i++) {
2882: bool=1;
1.144 brouard 2883: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2884: for (z1=1; z1<=cptcoveff; z1++)
2885: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
1.145 brouard 2886: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 2887: bool=0;
1.145 brouard 2888: /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",
2889: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2890: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
1.144 brouard 2891: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2892: }
1.126 brouard 2893: }
1.144 brouard 2894:
1.126 brouard 2895: if (bool==1){
2896: for(m=firstpass; m<=lastpass; m++){
2897: k2=anint[m][i]+(mint[m][i]/12.);
2898: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2899: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2900: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2901: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2902: if (m<lastpass) {
2903: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2904: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2905: }
2906:
2907: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2908: dateintsum=dateintsum+k2;
2909: k2cpt++;
2910: }
2911: /*}*/
2912: }
2913: }
1.145 brouard 2914: } /* end i */
1.126 brouard 2915:
2916: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2917: pstamp(ficresp);
2918: if (cptcovn>0) {
2919: fprintf(ficresp, "\n#********** Variable ");
2920: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2921: fprintf(ficresp, "**********\n#");
1.143 brouard 2922: fprintf(ficlog, "\n#********** Variable ");
2923: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2924: fprintf(ficlog, "**********\n#");
1.126 brouard 2925: }
2926: for(i=1; i<=nlstate;i++)
2927: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2928: fprintf(ficresp, "\n");
2929:
2930: for(i=iagemin; i <= iagemax+3; i++){
2931: if(i==iagemax+3){
2932: fprintf(ficlog,"Total");
2933: }else{
2934: if(first==1){
2935: first=0;
2936: printf("See log file for details...\n");
2937: }
2938: fprintf(ficlog,"Age %d", i);
2939: }
2940: for(jk=1; jk <=nlstate ; jk++){
2941: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2942: pp[jk] += freq[jk][m][i];
2943: }
2944: for(jk=1; jk <=nlstate ; jk++){
2945: for(m=-1, pos=0; m <=0 ; m++)
2946: pos += freq[jk][m][i];
2947: if(pp[jk]>=1.e-10){
2948: if(first==1){
1.132 brouard 2949: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 2950: }
2951: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2952: }else{
2953: if(first==1)
2954: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2955: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2956: }
2957: }
2958:
2959: for(jk=1; jk <=nlstate ; jk++){
2960: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2961: pp[jk] += freq[jk][m][i];
2962: }
2963: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2964: pos += pp[jk];
2965: posprop += prop[jk][i];
2966: }
2967: for(jk=1; jk <=nlstate ; jk++){
2968: if(pos>=1.e-5){
2969: if(first==1)
2970: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2971: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2972: }else{
2973: if(first==1)
2974: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2975: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2976: }
2977: if( i <= iagemax){
2978: if(pos>=1.e-5){
2979: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2980: /*probs[i][jk][j1]= pp[jk]/pos;*/
2981: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2982: }
2983: else
2984: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2985: }
2986: }
2987:
2988: for(jk=-1; jk <=nlstate+ndeath; jk++)
2989: for(m=-1; m <=nlstate+ndeath; m++)
2990: if(freq[jk][m][i] !=0 ) {
2991: if(first==1)
2992: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2993: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2994: }
2995: if(i <= iagemax)
2996: fprintf(ficresp,"\n");
2997: if(first==1)
2998: printf("Others in log...\n");
2999: fprintf(ficlog,"\n");
3000: }
1.145 brouard 3001: /*}*/
1.126 brouard 3002: }
3003: dateintmean=dateintsum/k2cpt;
3004:
3005: fclose(ficresp);
3006: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
3007: free_vector(pp,1,nlstate);
3008: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
3009: /* End of Freq */
3010: }
3011:
3012: /************ Prevalence ********************/
3013: 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)
3014: {
3015: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3016: in each health status at the date of interview (if between dateprev1 and dateprev2).
3017: We still use firstpass and lastpass as another selection.
3018: */
3019:
1.164 brouard 3020: int i, m, jk, j1, bool, z1,j;
3021:
3022: double **prop;
3023: double posprop;
1.126 brouard 3024: double y2; /* in fractional years */
3025: int iagemin, iagemax;
1.145 brouard 3026: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 3027:
3028: iagemin= (int) agemin;
3029: iagemax= (int) agemax;
3030: /*pp=vector(1,nlstate);*/
3031: prop=matrix(1,nlstate,iagemin,iagemax+3);
3032: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3033: j1=0;
3034:
1.145 brouard 3035: /*j=cptcoveff;*/
1.126 brouard 3036: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3037:
1.145 brouard 3038: first=1;
3039: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
3040: /*for(i1=1; i1<=ncodemax[k1];i1++){
3041: j1++;*/
1.126 brouard 3042:
3043: for (i=1; i<=nlstate; i++)
3044: for(m=iagemin; m <= iagemax+3; m++)
3045: prop[i][m]=0.0;
3046:
3047: for (i=1; i<=imx; i++) { /* Each individual */
3048: bool=1;
3049: if (cptcovn>0) {
3050: for (z1=1; z1<=cptcoveff; z1++)
3051: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
3052: bool=0;
3053: }
3054: if (bool==1) {
3055: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
3056: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3057: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3058: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3059: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3060: 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);
3061: if (s[m][i]>0 && s[m][i]<=nlstate) {
3062: /*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]]);*/
3063: prop[s[m][i]][(int)agev[m][i]] += weight[i];
3064: prop[s[m][i]][iagemax+3] += weight[i];
3065: }
3066: }
3067: } /* end selection of waves */
3068: }
3069: }
3070: for(i=iagemin; i <= iagemax+3; i++){
3071: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3072: posprop += prop[jk][i];
3073: }
1.145 brouard 3074:
1.126 brouard 3075: for(jk=1; jk <=nlstate ; jk++){
3076: if( i <= iagemax){
3077: if(posprop>=1.e-5){
3078: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 3079: } else{
3080: if(first==1){
3081: first=0;
3082: 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]);
3083: }
3084: }
1.126 brouard 3085: }
3086: }/* end jk */
3087: }/* end i */
1.145 brouard 3088: /*} *//* end i1 */
3089: } /* end j1 */
1.126 brouard 3090:
3091: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3092: /*free_vector(pp,1,nlstate);*/
3093: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3094: } /* End of prevalence */
3095:
3096: /************* Waves Concatenation ***************/
3097:
3098: 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)
3099: {
3100: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3101: Death is a valid wave (if date is known).
3102: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3103: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3104: and mw[mi+1][i]. dh depends on stepm.
3105: */
3106:
3107: int i, mi, m;
3108: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3109: double sum=0., jmean=0.;*/
3110: int first;
3111: int j, k=0,jk, ju, jl;
3112: double sum=0.;
3113: first=0;
1.164 brouard 3114: jmin=100000;
1.126 brouard 3115: jmax=-1;
3116: jmean=0.;
3117: for(i=1; i<=imx; i++){
3118: mi=0;
3119: m=firstpass;
3120: while(s[m][i] <= nlstate){
3121: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
3122: mw[++mi][i]=m;
3123: if(m >=lastpass)
3124: break;
3125: else
3126: m++;
3127: }/* end while */
3128: if (s[m][i] > nlstate){
3129: mi++; /* Death is another wave */
3130: /* if(mi==0) never been interviewed correctly before death */
3131: /* Only death is a correct wave */
3132: mw[mi][i]=m;
3133: }
3134:
3135: wav[i]=mi;
3136: if(mi==0){
3137: nbwarn++;
3138: if(first==0){
3139: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3140: first=1;
3141: }
3142: if(first==1){
3143: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3144: }
3145: } /* end mi==0 */
3146: } /* End individuals */
3147:
3148: for(i=1; i<=imx; i++){
3149: for(mi=1; mi<wav[i];mi++){
3150: if (stepm <=0)
3151: dh[mi][i]=1;
3152: else{
3153: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3154: if (agedc[i] < 2*AGESUP) {
3155: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3156: if(j==0) j=1; /* Survives at least one month after exam */
3157: else if(j<0){
3158: nberr++;
3159: 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]);
3160: j=1; /* Temporary Dangerous patch */
3161: 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);
3162: 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]);
3163: 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);
3164: }
3165: k=k+1;
3166: if (j >= jmax){
3167: jmax=j;
3168: ijmax=i;
3169: }
3170: if (j <= jmin){
3171: jmin=j;
3172: ijmin=i;
3173: }
3174: sum=sum+j;
3175: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3176: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3177: }
3178: }
3179: else{
3180: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3181: /* 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]); */
3182:
3183: k=k+1;
3184: if (j >= jmax) {
3185: jmax=j;
3186: ijmax=i;
3187: }
3188: else if (j <= jmin){
3189: jmin=j;
3190: ijmin=i;
3191: }
3192: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3193: /*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]);*/
3194: if(j<0){
3195: nberr++;
3196: 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]);
3197: 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]);
3198: }
3199: sum=sum+j;
3200: }
3201: jk= j/stepm;
3202: jl= j -jk*stepm;
3203: ju= j -(jk+1)*stepm;
3204: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3205: if(jl==0){
3206: dh[mi][i]=jk;
3207: bh[mi][i]=0;
3208: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 3209: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 3210: dh[mi][i]=jk+1;
3211: bh[mi][i]=ju;
3212: }
3213: }else{
3214: if(jl <= -ju){
3215: dh[mi][i]=jk;
3216: bh[mi][i]=jl; /* bias is positive if real duration
3217: * is higher than the multiple of stepm and negative otherwise.
3218: */
3219: }
3220: else{
3221: dh[mi][i]=jk+1;
3222: bh[mi][i]=ju;
3223: }
3224: if(dh[mi][i]==0){
3225: dh[mi][i]=1; /* At least one step */
3226: bh[mi][i]=ju; /* At least one step */
3227: /* 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);*/
3228: }
3229: } /* end if mle */
3230: }
3231: } /* end wave */
3232: }
3233: jmean=sum/k;
3234: 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 3235: 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 3236: }
3237:
3238: /*********** Tricode ****************************/
1.145 brouard 3239: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 3240: {
1.144 brouard 3241: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3242: /* 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 3243: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 3244: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 3245: * nbcode[Tvar[j]][1]=
1.144 brouard 3246: */
1.130 brouard 3247:
1.145 brouard 3248: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 3249: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 3250: int cptcode=0; /* Modality max of covariates j */
3251: int modmincovj=0; /* Modality min of covariates j */
3252:
3253:
1.126 brouard 3254: cptcoveff=0;
3255:
1.145 brouard 3256: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.144 brouard 3257: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 3258:
1.145 brouard 3259: /* Loop on covariates without age and products */
1.186 brouard 3260: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
3261: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.136 brouard 3262: modality of this covariate Vj*/
1.145 brouard 3263: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3264: * If product of Vn*Vm, still boolean *:
3265: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3266: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3267: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 3268: modality of the nth covariate of individual i. */
1.145 brouard 3269: if (ij > modmaxcovj)
3270: modmaxcovj=ij;
3271: else if (ij < modmincovj)
3272: modmincovj=ij;
3273: if ((ij < -1) && (ij > NCOVMAX)){
3274: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3275: exit(1);
3276: }else
1.136 brouard 3277: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 3278: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 3279: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 3280: /* getting the maximum value of the modality of the covariate
3281: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3282: female is 1, then modmaxcovj=1.*/
1.187 brouard 3283: } /* end for loop on individuals */
1.145 brouard 3284: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
3285: cptcode=modmaxcovj;
1.137 brouard 3286: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 3287: /*for (i=0; i<=cptcode; i++) {*/
3288: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
1.187 brouard 3289: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], i, Ndum[i]);
1.145 brouard 3290: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
3291: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
3292: }
3293: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3294: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3295: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3296:
1.136 brouard 3297: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 3298: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3299: 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 3300: modmincovj=3; modmaxcovj = 7;
1.186 brouard 3301: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3302: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3303: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 3304: nbcode[Tvar[j]][ij]=k;
3305: nbcode[Tvar[j]][1]=0;
3306: nbcode[Tvar[j]][2]=1;
3307: nbcode[Tvar[j]][3]=2;
3308: */
3309: ij=1; /* ij is similar to i but can jumps over null modalities */
3310: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
3311: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
3312: /*recode from 0 */
1.131 brouard 3313: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
1.186 brouard 3314: nbcode[Tvar[j]][ij]=k; /* stores the modality k in an array nbcode.
1.131 brouard 3315: k is a modality. If we have model=V1+V1*sex
3316: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1.126 brouard 3317: ij++;
3318: }
3319: if (ij > ncodemax[j]) break;
1.137 brouard 3320: } /* end of loop on */
3321: } /* end of loop on modality */
3322: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3323:
1.145 brouard 3324: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3325:
1.187 brouard 3326: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.145 brouard 3327: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3328: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.187 brouard 3329: Ndum[ij]++; /* Might be supersed V1 + V1*age */
1.145 brouard 3330: }
1.126 brouard 3331:
3332: ij=1;
1.145 brouard 3333: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3334: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3335: if((Ndum[i]!=0) && (i<=ncovcol)){
1.145 brouard 3336: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3337: Tvaraff[ij]=i; /*For printing (unclear) */
1.126 brouard 3338: ij++;
1.145 brouard 3339: }else
3340: Tvaraff[ij]=0;
1.126 brouard 3341: }
1.131 brouard 3342: ij--;
1.144 brouard 3343: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3344:
1.126 brouard 3345: }
3346:
1.145 brouard 3347:
1.126 brouard 3348: /*********** Health Expectancies ****************/
3349:
1.127 brouard 3350: 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 3351:
3352: {
3353: /* Health expectancies, no variances */
1.164 brouard 3354: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3355: int nhstepma, nstepma; /* Decreasing with age */
3356: double age, agelim, hf;
3357: double ***p3mat;
3358: double eip;
3359:
3360: pstamp(ficreseij);
3361: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3362: fprintf(ficreseij,"# Age");
3363: for(i=1; i<=nlstate;i++){
3364: for(j=1; j<=nlstate;j++){
3365: fprintf(ficreseij," e%1d%1d ",i,j);
3366: }
3367: fprintf(ficreseij," e%1d. ",i);
3368: }
3369: fprintf(ficreseij,"\n");
3370:
3371:
3372: if(estepm < stepm){
3373: printf ("Problem %d lower than %d\n",estepm, stepm);
3374: }
3375: else hstepm=estepm;
3376: /* We compute the life expectancy from trapezoids spaced every estepm months
3377: * This is mainly to measure the difference between two models: for example
3378: * if stepm=24 months pijx are given only every 2 years and by summing them
3379: * we are calculating an estimate of the Life Expectancy assuming a linear
3380: * progression in between and thus overestimating or underestimating according
3381: * to the curvature of the survival function. If, for the same date, we
3382: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3383: * to compare the new estimate of Life expectancy with the same linear
3384: * hypothesis. A more precise result, taking into account a more precise
3385: * curvature will be obtained if estepm is as small as stepm. */
3386:
3387: /* For example we decided to compute the life expectancy with the smallest unit */
3388: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3389: nhstepm is the number of hstepm from age to agelim
3390: nstepm is the number of stepm from age to agelin.
3391: Look at hpijx to understand the reason of that which relies in memory size
3392: and note for a fixed period like estepm months */
3393: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3394: survival function given by stepm (the optimization length). Unfortunately it
3395: means that if the survival funtion is printed only each two years of age and if
3396: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3397: results. So we changed our mind and took the option of the best precision.
3398: */
3399: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3400:
3401: agelim=AGESUP;
3402: /* If stepm=6 months */
3403: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3404: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3405:
3406: /* nhstepm age range expressed in number of stepm */
3407: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3408: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3409: /* if (stepm >= YEARM) hstepm=1;*/
3410: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3411: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3412:
3413: for (age=bage; age<=fage; age ++){
3414: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3415: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3416: /* if (stepm >= YEARM) hstepm=1;*/
3417: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3418:
3419: /* If stepm=6 months */
3420: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3421: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3422:
3423: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3424:
3425: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3426:
3427: printf("%d|",(int)age);fflush(stdout);
3428: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3429:
3430: /* Computing expectancies */
3431: for(i=1; i<=nlstate;i++)
3432: for(j=1; j<=nlstate;j++)
3433: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3434: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3435:
3436: /* 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]);*/
3437:
3438: }
3439:
3440: fprintf(ficreseij,"%3.0f",age );
3441: for(i=1; i<=nlstate;i++){
3442: eip=0;
3443: for(j=1; j<=nlstate;j++){
3444: eip +=eij[i][j][(int)age];
3445: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3446: }
3447: fprintf(ficreseij,"%9.4f", eip );
3448: }
3449: fprintf(ficreseij,"\n");
3450:
3451: }
3452: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3453: printf("\n");
3454: fprintf(ficlog,"\n");
3455:
3456: }
3457:
1.127 brouard 3458: 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 3459:
3460: {
3461: /* Covariances of health expectancies eij and of total life expectancies according
3462: to initial status i, ei. .
3463: */
3464: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3465: int nhstepma, nstepma; /* Decreasing with age */
3466: double age, agelim, hf;
3467: double ***p3matp, ***p3matm, ***varhe;
3468: double **dnewm,**doldm;
3469: double *xp, *xm;
3470: double **gp, **gm;
3471: double ***gradg, ***trgradg;
3472: int theta;
3473:
3474: double eip, vip;
3475:
3476: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3477: xp=vector(1,npar);
3478: xm=vector(1,npar);
3479: dnewm=matrix(1,nlstate*nlstate,1,npar);
3480: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3481:
3482: pstamp(ficresstdeij);
3483: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3484: fprintf(ficresstdeij,"# Age");
3485: for(i=1; i<=nlstate;i++){
3486: for(j=1; j<=nlstate;j++)
3487: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3488: fprintf(ficresstdeij," e%1d. ",i);
3489: }
3490: fprintf(ficresstdeij,"\n");
3491:
3492: pstamp(ficrescveij);
3493: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3494: fprintf(ficrescveij,"# Age");
3495: for(i=1; i<=nlstate;i++)
3496: for(j=1; j<=nlstate;j++){
3497: cptj= (j-1)*nlstate+i;
3498: for(i2=1; i2<=nlstate;i2++)
3499: for(j2=1; j2<=nlstate;j2++){
3500: cptj2= (j2-1)*nlstate+i2;
3501: if(cptj2 <= cptj)
3502: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3503: }
3504: }
3505: fprintf(ficrescveij,"\n");
3506:
3507: if(estepm < stepm){
3508: printf ("Problem %d lower than %d\n",estepm, stepm);
3509: }
3510: else hstepm=estepm;
3511: /* We compute the life expectancy from trapezoids spaced every estepm months
3512: * This is mainly to measure the difference between two models: for example
3513: * if stepm=24 months pijx are given only every 2 years and by summing them
3514: * we are calculating an estimate of the Life Expectancy assuming a linear
3515: * progression in between and thus overestimating or underestimating according
3516: * to the curvature of the survival function. If, for the same date, we
3517: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3518: * to compare the new estimate of Life expectancy with the same linear
3519: * hypothesis. A more precise result, taking into account a more precise
3520: * curvature will be obtained if estepm is as small as stepm. */
3521:
3522: /* For example we decided to compute the life expectancy with the smallest unit */
3523: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3524: nhstepm is the number of hstepm from age to agelim
3525: nstepm is the number of stepm from age to agelin.
3526: Look at hpijx to understand the reason of that which relies in memory size
3527: and note for a fixed period like estepm months */
3528: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3529: survival function given by stepm (the optimization length). Unfortunately it
3530: means that if the survival funtion is printed only each two years of age and if
3531: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3532: results. So we changed our mind and took the option of the best precision.
3533: */
3534: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3535:
3536: /* If stepm=6 months */
3537: /* nhstepm age range expressed in number of stepm */
3538: agelim=AGESUP;
3539: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3540: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3541: /* if (stepm >= YEARM) hstepm=1;*/
3542: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3543:
3544: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3545: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3546: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3547: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3548: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3549: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3550:
3551: for (age=bage; age<=fage; age ++){
3552: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3553: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3554: /* if (stepm >= YEARM) hstepm=1;*/
3555: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3556:
3557: /* If stepm=6 months */
3558: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3559: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3560:
3561: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3562:
3563: /* Computing Variances of health expectancies */
3564: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3565: decrease memory allocation */
3566: for(theta=1; theta <=npar; theta++){
3567: for(i=1; i<=npar; i++){
3568: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3569: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3570: }
3571: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3572: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3573:
3574: for(j=1; j<= nlstate; j++){
3575: for(i=1; i<=nlstate; i++){
3576: for(h=0; h<=nhstepm-1; h++){
3577: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3578: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3579: }
3580: }
3581: }
3582:
3583: for(ij=1; ij<= nlstate*nlstate; ij++)
3584: for(h=0; h<=nhstepm-1; h++){
3585: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3586: }
3587: }/* End theta */
3588:
3589:
3590: for(h=0; h<=nhstepm-1; h++)
3591: for(j=1; j<=nlstate*nlstate;j++)
3592: for(theta=1; theta <=npar; theta++)
3593: trgradg[h][j][theta]=gradg[h][theta][j];
3594:
3595:
3596: for(ij=1;ij<=nlstate*nlstate;ij++)
3597: for(ji=1;ji<=nlstate*nlstate;ji++)
3598: varhe[ij][ji][(int)age] =0.;
3599:
3600: printf("%d|",(int)age);fflush(stdout);
3601: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3602: for(h=0;h<=nhstepm-1;h++){
3603: for(k=0;k<=nhstepm-1;k++){
3604: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3605: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3606: for(ij=1;ij<=nlstate*nlstate;ij++)
3607: for(ji=1;ji<=nlstate*nlstate;ji++)
3608: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3609: }
3610: }
3611:
3612: /* Computing expectancies */
3613: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3614: for(i=1; i<=nlstate;i++)
3615: for(j=1; j<=nlstate;j++)
3616: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3617: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3618:
3619: /* 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]);*/
3620:
3621: }
3622:
3623: fprintf(ficresstdeij,"%3.0f",age );
3624: for(i=1; i<=nlstate;i++){
3625: eip=0.;
3626: vip=0.;
3627: for(j=1; j<=nlstate;j++){
3628: eip += eij[i][j][(int)age];
3629: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3630: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3631: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3632: }
3633: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3634: }
3635: fprintf(ficresstdeij,"\n");
3636:
3637: fprintf(ficrescveij,"%3.0f",age );
3638: for(i=1; i<=nlstate;i++)
3639: for(j=1; j<=nlstate;j++){
3640: cptj= (j-1)*nlstate+i;
3641: for(i2=1; i2<=nlstate;i2++)
3642: for(j2=1; j2<=nlstate;j2++){
3643: cptj2= (j2-1)*nlstate+i2;
3644: if(cptj2 <= cptj)
3645: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3646: }
3647: }
3648: fprintf(ficrescveij,"\n");
3649:
3650: }
3651: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3652: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3653: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3654: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3655: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3656: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3657: printf("\n");
3658: fprintf(ficlog,"\n");
3659:
3660: free_vector(xm,1,npar);
3661: free_vector(xp,1,npar);
3662: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3663: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3664: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3665: }
3666:
3667: /************ Variance ******************/
3668: 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[])
3669: {
3670: /* Variance of health expectancies */
3671: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3672: /* double **newm;*/
1.169 brouard 3673: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3674:
3675: int movingaverage();
1.126 brouard 3676: double **dnewm,**doldm;
3677: double **dnewmp,**doldmp;
3678: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 3679: int k;
1.126 brouard 3680: double *xp;
3681: double **gp, **gm; /* for var eij */
3682: double ***gradg, ***trgradg; /*for var eij */
3683: double **gradgp, **trgradgp; /* for var p point j */
3684: double *gpp, *gmp; /* for var p point j */
3685: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3686: double ***p3mat;
3687: double age,agelim, hf;
3688: double ***mobaverage;
3689: int theta;
3690: char digit[4];
3691: char digitp[25];
3692:
3693: char fileresprobmorprev[FILENAMELENGTH];
3694:
3695: if(popbased==1){
3696: if(mobilav!=0)
3697: strcpy(digitp,"-populbased-mobilav-");
3698: else strcpy(digitp,"-populbased-nomobil-");
3699: }
3700: else
3701: strcpy(digitp,"-stablbased-");
3702:
3703: if (mobilav!=0) {
3704: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3705: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3706: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3707: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3708: }
3709: }
3710:
3711: strcpy(fileresprobmorprev,"prmorprev");
3712: sprintf(digit,"%-d",ij);
3713: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3714: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3715: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3716: strcat(fileresprobmorprev,fileres);
3717: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3718: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3719: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3720: }
3721: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3722:
3723: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3724: pstamp(ficresprobmorprev);
3725: 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);
3726: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3727: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3728: fprintf(ficresprobmorprev," p.%-d SE",j);
3729: for(i=1; i<=nlstate;i++)
3730: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3731: }
3732: fprintf(ficresprobmorprev,"\n");
3733: fprintf(ficgp,"\n# Routine varevsij");
3734: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3735: 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");
3736: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3737: /* } */
3738: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3739: pstamp(ficresvij);
3740: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3741: if(popbased==1)
1.128 brouard 3742: 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 3743: else
3744: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3745: fprintf(ficresvij,"# Age");
3746: for(i=1; i<=nlstate;i++)
3747: for(j=1; j<=nlstate;j++)
3748: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3749: fprintf(ficresvij,"\n");
3750:
3751: xp=vector(1,npar);
3752: dnewm=matrix(1,nlstate,1,npar);
3753: doldm=matrix(1,nlstate,1,nlstate);
3754: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3755: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3756:
3757: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3758: gpp=vector(nlstate+1,nlstate+ndeath);
3759: gmp=vector(nlstate+1,nlstate+ndeath);
3760: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3761:
3762: if(estepm < stepm){
3763: printf ("Problem %d lower than %d\n",estepm, stepm);
3764: }
3765: else hstepm=estepm;
3766: /* For example we decided to compute the life expectancy with the smallest unit */
3767: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3768: nhstepm is the number of hstepm from age to agelim
3769: nstepm is the number of stepm from age to agelin.
1.128 brouard 3770: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 3771: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3772: survival function given by stepm (the optimization length). Unfortunately it
3773: means that if the survival funtion is printed every two years of age and if
3774: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3775: results. So we changed our mind and took the option of the best precision.
3776: */
3777: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3778: agelim = AGESUP;
3779: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3780: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3781: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3782: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3783: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3784: gp=matrix(0,nhstepm,1,nlstate);
3785: gm=matrix(0,nhstepm,1,nlstate);
3786:
3787:
3788: for(theta=1; theta <=npar; theta++){
3789: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3790: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3791: }
3792: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3793: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3794:
3795: if (popbased==1) {
3796: if(mobilav ==0){
3797: for(i=1; i<=nlstate;i++)
3798: prlim[i][i]=probs[(int)age][i][ij];
3799: }else{ /* mobilav */
3800: for(i=1; i<=nlstate;i++)
3801: prlim[i][i]=mobaverage[(int)age][i][ij];
3802: }
3803: }
3804:
3805: for(j=1; j<= nlstate; j++){
3806: for(h=0; h<=nhstepm; h++){
3807: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3808: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3809: }
3810: }
3811: /* This for computing probability of death (h=1 means
3812: computed over hstepm matrices product = hstepm*stepm months)
3813: as a weighted average of prlim.
3814: */
3815: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3816: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3817: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3818: }
3819: /* end probability of death */
3820:
3821: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3822: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3823: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3824: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3825:
3826: if (popbased==1) {
3827: if(mobilav ==0){
3828: for(i=1; i<=nlstate;i++)
3829: prlim[i][i]=probs[(int)age][i][ij];
3830: }else{ /* mobilav */
3831: for(i=1; i<=nlstate;i++)
3832: prlim[i][i]=mobaverage[(int)age][i][ij];
3833: }
3834: }
3835:
1.128 brouard 3836: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 3837: for(h=0; h<=nhstepm; h++){
3838: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3839: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3840: }
3841: }
3842: /* This for computing probability of death (h=1 means
3843: computed over hstepm matrices product = hstepm*stepm months)
3844: as a weighted average of prlim.
3845: */
3846: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3847: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3848: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3849: }
3850: /* end probability of death */
3851:
3852: for(j=1; j<= nlstate; j++) /* vareij */
3853: for(h=0; h<=nhstepm; h++){
3854: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3855: }
3856:
3857: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3858: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3859: }
3860:
3861: } /* End theta */
3862:
3863: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3864:
3865: for(h=0; h<=nhstepm; h++) /* veij */
3866: for(j=1; j<=nlstate;j++)
3867: for(theta=1; theta <=npar; theta++)
3868: trgradg[h][j][theta]=gradg[h][theta][j];
3869:
3870: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3871: for(theta=1; theta <=npar; theta++)
3872: trgradgp[j][theta]=gradgp[theta][j];
3873:
3874:
3875: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3876: for(i=1;i<=nlstate;i++)
3877: for(j=1;j<=nlstate;j++)
3878: vareij[i][j][(int)age] =0.;
3879:
3880: for(h=0;h<=nhstepm;h++){
3881: for(k=0;k<=nhstepm;k++){
3882: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3883: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3884: for(i=1;i<=nlstate;i++)
3885: for(j=1;j<=nlstate;j++)
3886: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3887: }
3888: }
3889:
3890: /* pptj */
3891: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3892: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3893: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3894: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3895: varppt[j][i]=doldmp[j][i];
3896: /* end ppptj */
3897: /* x centered again */
3898: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3899: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3900:
3901: if (popbased==1) {
3902: if(mobilav ==0){
3903: for(i=1; i<=nlstate;i++)
3904: prlim[i][i]=probs[(int)age][i][ij];
3905: }else{ /* mobilav */
3906: for(i=1; i<=nlstate;i++)
3907: prlim[i][i]=mobaverage[(int)age][i][ij];
3908: }
3909: }
3910:
3911: /* This for computing probability of death (h=1 means
3912: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3913: as a weighted average of prlim.
3914: */
3915: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3916: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3917: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3918: }
3919: /* end probability of death */
3920:
3921: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3922: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3923: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3924: for(i=1; i<=nlstate;i++){
3925: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3926: }
3927: }
3928: fprintf(ficresprobmorprev,"\n");
3929:
3930: fprintf(ficresvij,"%.0f ",age );
3931: for(i=1; i<=nlstate;i++)
3932: for(j=1; j<=nlstate;j++){
3933: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3934: }
3935: fprintf(ficresvij,"\n");
3936: free_matrix(gp,0,nhstepm,1,nlstate);
3937: free_matrix(gm,0,nhstepm,1,nlstate);
3938: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3939: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3940: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3941: } /* End age */
3942: free_vector(gpp,nlstate+1,nlstate+ndeath);
3943: free_vector(gmp,nlstate+1,nlstate+ndeath);
3944: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3945: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.145 brouard 3946: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
1.126 brouard 3947: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 3948: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.126 brouard 3949: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3950: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3951: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 3952: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 3953: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 3954: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 3955: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3956: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3957: /* 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.png\"> <br>\n", stepm,YEARM,digitp,digit);
3958: */
3959: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3960: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3961:
3962: free_vector(xp,1,npar);
3963: free_matrix(doldm,1,nlstate,1,nlstate);
3964: free_matrix(dnewm,1,nlstate,1,npar);
3965: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3966: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3967: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3968: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3969: fclose(ficresprobmorprev);
3970: fflush(ficgp);
3971: fflush(fichtm);
3972: } /* end varevsij */
3973:
3974: /************ Variance of prevlim ******************/
3975: 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[])
3976: {
3977: /* Variance of prevalence limit */
3978: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 3979:
1.126 brouard 3980: double **dnewm,**doldm;
3981: int i, j, nhstepm, hstepm;
3982: double *xp;
3983: double *gp, *gm;
3984: double **gradg, **trgradg;
3985: double age,agelim;
3986: int theta;
3987:
3988: pstamp(ficresvpl);
3989: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3990: fprintf(ficresvpl,"# Age");
3991: for(i=1; i<=nlstate;i++)
3992: fprintf(ficresvpl," %1d-%1d",i,i);
3993: fprintf(ficresvpl,"\n");
3994:
3995: xp=vector(1,npar);
3996: dnewm=matrix(1,nlstate,1,npar);
3997: doldm=matrix(1,nlstate,1,nlstate);
3998:
3999: hstepm=1*YEARM; /* Every year of age */
4000: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
4001: agelim = AGESUP;
4002: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4003: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4004: if (stepm >= YEARM) hstepm=1;
4005: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4006: gradg=matrix(1,npar,1,nlstate);
4007: gp=vector(1,nlstate);
4008: gm=vector(1,nlstate);
4009:
4010: for(theta=1; theta <=npar; theta++){
4011: for(i=1; i<=npar; i++){ /* Computes gradient */
4012: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4013: }
4014: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4015: for(i=1;i<=nlstate;i++)
4016: gp[i] = prlim[i][i];
4017:
4018: for(i=1; i<=npar; i++) /* Computes gradient */
4019: xp[i] = x[i] - (i==theta ?delti[theta]:0);
4020: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4021: for(i=1;i<=nlstate;i++)
4022: gm[i] = prlim[i][i];
4023:
4024: for(i=1;i<=nlstate;i++)
4025: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
4026: } /* End theta */
4027:
4028: trgradg =matrix(1,nlstate,1,npar);
4029:
4030: for(j=1; j<=nlstate;j++)
4031: for(theta=1; theta <=npar; theta++)
4032: trgradg[j][theta]=gradg[theta][j];
4033:
4034: for(i=1;i<=nlstate;i++)
4035: varpl[i][(int)age] =0.;
4036: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4037: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4038: for(i=1;i<=nlstate;i++)
4039: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4040:
4041: fprintf(ficresvpl,"%.0f ",age );
4042: for(i=1; i<=nlstate;i++)
4043: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4044: fprintf(ficresvpl,"\n");
4045: free_vector(gp,1,nlstate);
4046: free_vector(gm,1,nlstate);
4047: free_matrix(gradg,1,npar,1,nlstate);
4048: free_matrix(trgradg,1,nlstate,1,npar);
4049: } /* End age */
4050:
4051: free_vector(xp,1,npar);
4052: free_matrix(doldm,1,nlstate,1,npar);
4053: free_matrix(dnewm,1,nlstate,1,nlstate);
4054:
4055: }
4056:
4057: /************ Variance of one-step probabilities ******************/
4058: 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[])
4059: {
1.164 brouard 4060: int i, j=0, k1, l1, tj;
1.126 brouard 4061: int k2, l2, j1, z1;
1.164 brouard 4062: int k=0, l;
1.145 brouard 4063: int first=1, first1, first2;
1.126 brouard 4064: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4065: double **dnewm,**doldm;
4066: double *xp;
4067: double *gp, *gm;
4068: double **gradg, **trgradg;
4069: double **mu;
1.164 brouard 4070: double age, cov[NCOVMAX+1];
1.126 brouard 4071: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4072: int theta;
4073: char fileresprob[FILENAMELENGTH];
4074: char fileresprobcov[FILENAMELENGTH];
4075: char fileresprobcor[FILENAMELENGTH];
4076: double ***varpij;
4077:
4078: strcpy(fileresprob,"prob");
4079: strcat(fileresprob,fileres);
4080: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4081: printf("Problem with resultfile: %s\n", fileresprob);
4082: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4083: }
4084: strcpy(fileresprobcov,"probcov");
4085: strcat(fileresprobcov,fileres);
4086: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4087: printf("Problem with resultfile: %s\n", fileresprobcov);
4088: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4089: }
4090: strcpy(fileresprobcor,"probcor");
4091: strcat(fileresprobcor,fileres);
4092: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4093: printf("Problem with resultfile: %s\n", fileresprobcor);
4094: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4095: }
4096: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4097: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4098: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4099: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4100: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4101: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4102: pstamp(ficresprob);
4103: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4104: fprintf(ficresprob,"# Age");
4105: pstamp(ficresprobcov);
4106: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4107: fprintf(ficresprobcov,"# Age");
4108: pstamp(ficresprobcor);
4109: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4110: fprintf(ficresprobcor,"# Age");
4111:
4112:
4113: for(i=1; i<=nlstate;i++)
4114: for(j=1; j<=(nlstate+ndeath);j++){
4115: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4116: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4117: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4118: }
4119: /* fprintf(ficresprob,"\n");
4120: fprintf(ficresprobcov,"\n");
4121: fprintf(ficresprobcor,"\n");
4122: */
1.131 brouard 4123: xp=vector(1,npar);
1.126 brouard 4124: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4125: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4126: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4127: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4128: first=1;
4129: fprintf(ficgp,"\n# Routine varprob");
4130: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4131: fprintf(fichtm,"\n");
4132:
4133: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
4134: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
4135: file %s<br>\n",optionfilehtmcov);
4136: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
4137: and drawn. It helps understanding how is the covariance between two incidences.\
4138: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4139: 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. \
4140: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4141: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4142: standard deviations wide on each axis. <br>\
4143: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4144: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4145: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4146:
4147: cov[1]=1;
1.145 brouard 4148: /* tj=cptcoveff; */
4149: tj = (int) pow(2,cptcoveff);
1.126 brouard 4150: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4151: j1=0;
1.145 brouard 4152: for(j1=1; j1<=tj;j1++){
4153: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4154: /*j1++;*/
1.126 brouard 4155: if (cptcovn>0) {
4156: fprintf(ficresprob, "\n#********** Variable ");
4157: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4158: fprintf(ficresprob, "**********\n#\n");
4159: fprintf(ficresprobcov, "\n#********** Variable ");
4160: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4161: fprintf(ficresprobcov, "**********\n#\n");
4162:
4163: fprintf(ficgp, "\n#********** Variable ");
4164: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4165: fprintf(ficgp, "**********\n#\n");
4166:
4167:
4168: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
4169: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4170: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4171:
4172: fprintf(ficresprobcor, "\n#********** Variable ");
4173: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4174: fprintf(ficresprobcor, "**********\n#");
4175: }
4176:
1.145 brouard 4177: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4178: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4179: gp=vector(1,(nlstate)*(nlstate+ndeath));
4180: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 4181: for (age=bage; age<=fage; age ++){
4182: cov[2]=age;
1.187 brouard 4183: if(nagesqr==1)
4184: cov[3]= age*age;
1.126 brouard 4185: for (k=1; k<=cptcovn;k++) {
1.187 brouard 4186: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
1.145 brouard 4187: * 1 1 1 1 1
4188: * 2 2 1 1 1
4189: * 3 1 2 1 1
4190: */
4191: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 4192: }
1.186 brouard 4193: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
4194: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
1.126 brouard 4195: for (k=1; k<=cptcovprod;k++)
1.187 brouard 4196: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1.126 brouard 4197:
4198:
4199: for(theta=1; theta <=npar; theta++){
4200: for(i=1; i<=npar; i++)
4201: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4202:
4203: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4204:
4205: k=0;
4206: for(i=1; i<= (nlstate); i++){
4207: for(j=1; j<=(nlstate+ndeath);j++){
4208: k=k+1;
4209: gp[k]=pmmij[i][j];
4210: }
4211: }
4212:
4213: for(i=1; i<=npar; i++)
4214: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4215:
4216: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4217: k=0;
4218: for(i=1; i<=(nlstate); i++){
4219: for(j=1; j<=(nlstate+ndeath);j++){
4220: k=k+1;
4221: gm[k]=pmmij[i][j];
4222: }
4223: }
4224:
4225: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4226: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4227: }
4228:
4229: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4230: for(theta=1; theta <=npar; theta++)
4231: trgradg[j][theta]=gradg[theta][j];
4232:
4233: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4234: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4235:
4236: pmij(pmmij,cov,ncovmodel,x,nlstate);
4237:
4238: k=0;
4239: for(i=1; i<=(nlstate); i++){
4240: for(j=1; j<=(nlstate+ndeath);j++){
4241: k=k+1;
4242: mu[k][(int) age]=pmmij[i][j];
4243: }
4244: }
4245: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4246: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4247: varpij[i][j][(int)age] = doldm[i][j];
4248:
4249: /*printf("\n%d ",(int)age);
4250: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4251: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4252: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4253: }*/
4254:
4255: fprintf(ficresprob,"\n%d ",(int)age);
4256: fprintf(ficresprobcov,"\n%d ",(int)age);
4257: fprintf(ficresprobcor,"\n%d ",(int)age);
4258:
4259: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4260: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4261: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4262: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4263: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4264: }
4265: i=0;
4266: for (k=1; k<=(nlstate);k++){
4267: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 4268: i++;
1.126 brouard 4269: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4270: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4271: for (j=1; j<=i;j++){
1.145 brouard 4272: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 4273: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4274: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4275: }
4276: }
4277: }/* end of loop for state */
4278: } /* end of loop for age */
1.145 brouard 4279: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4280: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4281: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4282: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4283:
1.126 brouard 4284: /* Confidence intervalle of pij */
4285: /*
1.131 brouard 4286: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 4287: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4288: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4289: 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);
4290: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4291: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4292: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4293: */
4294:
4295: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 4296: first1=1;first2=2;
1.126 brouard 4297: for (k2=1; k2<=(nlstate);k2++){
4298: for (l2=1; l2<=(nlstate+ndeath);l2++){
4299: if(l2==k2) continue;
4300: j=(k2-1)*(nlstate+ndeath)+l2;
4301: for (k1=1; k1<=(nlstate);k1++){
4302: for (l1=1; l1<=(nlstate+ndeath);l1++){
4303: if(l1==k1) continue;
4304: i=(k1-1)*(nlstate+ndeath)+l1;
4305: if(i<=j) continue;
4306: for (age=bage; age<=fage; age ++){
4307: if ((int)age %5==0){
4308: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4309: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4310: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4311: mu1=mu[i][(int) age]/stepm*YEARM ;
4312: mu2=mu[j][(int) age]/stepm*YEARM;
4313: c12=cv12/sqrt(v1*v2);
4314: /* Computing eigen value of matrix of covariance */
4315: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4316: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4317: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4318: if(first2==1){
4319: first1=0;
4320: 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);
4321: }
4322: 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);
4323: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4324: /* lc2=fabs(lc2); */
1.135 brouard 4325: }
4326:
1.126 brouard 4327: /* Eigen vectors */
4328: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4329: /*v21=sqrt(1.-v11*v11); *//* error */
4330: v21=(lc1-v1)/cv12*v11;
4331: v12=-v21;
4332: v22=v11;
4333: tnalp=v21/v11;
4334: if(first1==1){
4335: first1=0;
4336: 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);
4337: }
4338: 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);
4339: /*printf(fignu*/
4340: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4341: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4342: if(first==1){
4343: first=0;
4344: fprintf(ficgp,"\nset parametric;unset label");
4345: 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);
1.145 brouard 4346: fprintf(ficgp,"\nset ter png small size 320, 240");
1.126 brouard 4347: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4348: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4349: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4350: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4351: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4352: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4353: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4354: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4355: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4356: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4357: 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",\
4358: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4359: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4360: }else{
4361: first=0;
4362: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4363: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4364: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4365: 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",\
4366: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4367: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4368: }/* if first */
4369: } /* age mod 5 */
4370: } /* end loop age */
4371: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4372: first=1;
4373: } /*l12 */
4374: } /* k12 */
4375: } /*l1 */
4376: }/* k1 */
1.169 brouard 4377: /* } */ /* loop covariates */
1.126 brouard 4378: }
4379: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4380: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4381: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4382: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4383: free_vector(xp,1,npar);
4384: fclose(ficresprob);
4385: fclose(ficresprobcov);
4386: fclose(ficresprobcor);
4387: fflush(ficgp);
4388: fflush(fichtmcov);
4389: }
4390:
4391:
4392: /******************* Printing html file ***********/
4393: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4394: int lastpass, int stepm, int weightopt, char model[],\
4395: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4396: int popforecast, int estepm ,\
4397: double jprev1, double mprev1,double anprev1, \
4398: double jprev2, double mprev2,double anprev2){
4399: int jj1, k1, i1, cpt;
4400:
4401: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4402: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4403: </ul>");
4404: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4405: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4406: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4407: fprintf(fichtm,"\
4408: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4409: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4410: fprintf(fichtm,"\
4411: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4412: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4413: fprintf(fichtm,"\
1.128 brouard 4414: - (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 4415: <a href=\"%s\">%s</a> <br>\n",
4416: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4417: fprintf(fichtm,"\
4418: - Population projections by age and states: \
4419: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4420:
4421: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4422:
1.145 brouard 4423: m=pow(2,cptcoveff);
1.126 brouard 4424: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4425:
4426: jj1=0;
4427: for(k1=1; k1<=m;k1++){
4428: for(i1=1; i1<=ncodemax[k1];i1++){
4429: jj1++;
4430: if (cptcovn > 0) {
4431: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4432: for (cpt=1; cpt<=cptcoveff;cpt++)
4433: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4434: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4435: }
4436: /* Pij */
1.145 brouard 4437: 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.png\">%s%d_1.png</a><br> \
4438: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4439: /* Quasi-incidences */
4440: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.145 brouard 4441: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
4442: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4443: /* Period (stable) prevalence in each health state */
1.154 brouard 4444: for(cpt=1; cpt<=nlstate;cpt++){
1.166 brouard 4445: 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.png\">%s%d_%d.png</a><br> \
4446: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.126 brouard 4447: }
4448: for(cpt=1; cpt<=nlstate;cpt++) {
1.154 brouard 4449: 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.png\">%s%d%d.png</a> <br> \
4450: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
1.126 brouard 4451: }
4452: } /* end i1 */
4453: }/* End k1 */
4454: fprintf(fichtm,"</ul>");
4455:
4456:
4457: fprintf(fichtm,"\
4458: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4459: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4460:
4461: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4462: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4463: fprintf(fichtm,"\
4464: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4465: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4466:
4467: fprintf(fichtm,"\
4468: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4469: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4470: fprintf(fichtm,"\
4471: - 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): \
4472: <a href=\"%s\">%s</a> <br>\n</li>",
4473: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4474: fprintf(fichtm,"\
4475: - (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): \
4476: <a href=\"%s\">%s</a> <br>\n</li>",
4477: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4478: fprintf(fichtm,"\
1.128 brouard 4479: - 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 4480: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4481: fprintf(fichtm,"\
1.128 brouard 4482: - 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",
4483: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
1.126 brouard 4484: fprintf(fichtm,"\
4485: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4486: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4487:
4488: /* if(popforecast==1) fprintf(fichtm,"\n */
4489: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4490: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4491: /* <br>",fileres,fileres,fileres,fileres); */
4492: /* else */
4493: /* 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); */
4494: fflush(fichtm);
4495: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4496:
1.145 brouard 4497: m=pow(2,cptcoveff);
1.126 brouard 4498: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4499:
4500: jj1=0;
4501: for(k1=1; k1<=m;k1++){
4502: for(i1=1; i1<=ncodemax[k1];i1++){
4503: jj1++;
4504: if (cptcovn > 0) {
4505: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4506: for (cpt=1; cpt<=cptcoveff;cpt++)
4507: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4508: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4509: }
4510: for(cpt=1; cpt<=nlstate;cpt++) {
4511: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.145 brouard 4512: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4513: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.126 brouard 4514: }
4515: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4516: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4517: true period expectancies (those weighted with period prevalences are also\
4518: drawn in addition to the population based expectancies computed using\
4519: observed and cahotic prevalences: %s%d.png<br>\
1.126 brouard 4520: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4521: } /* end i1 */
4522: }/* End k1 */
4523: fprintf(fichtm,"</ul>");
4524: fflush(fichtm);
4525: }
4526:
4527: /******************* Gnuplot file **************/
4528: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4529:
4530: char dirfileres[132],optfileres[132];
1.164 brouard 4531: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.130 brouard 4532: int ng=0;
1.126 brouard 4533: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4534: /* printf("Problem with file %s",optionfilegnuplot); */
4535: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4536: /* } */
4537:
4538: /*#ifdef windows */
4539: fprintf(ficgp,"cd \"%s\" \n",pathc);
4540: /*#endif */
4541: m=pow(2,cptcoveff);
4542:
4543: strcpy(dirfileres,optionfilefiname);
4544: strcpy(optfileres,"vpl");
4545: /* 1eme*/
1.153 brouard 4546: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
1.126 brouard 4547: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 4548: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4549: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4550: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
1.126 brouard 4551: fprintf(ficgp,"set xlabel \"Age\" \n\
4552: set ylabel \"Probability\" \n\
1.145 brouard 4553: set ter png small size 320, 240\n\
1.170 brouard 4554: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4555:
4556: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4557: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4558: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4559: }
1.170 brouard 4560: 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 4561: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4562: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4563: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4564: }
1.170 brouard 4565: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4566: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4567: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4568: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4569: }
1.145 brouard 4570: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.126 brouard 4571: }
4572: }
4573: /*2 eme*/
1.153 brouard 4574: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126 brouard 4575: for (k1=1; k1<= m ; k1 ++) {
4576: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.145 brouard 4577: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
1.126 brouard 4578:
4579: for (i=1; i<= nlstate+1 ; i ++) {
4580: k=2*i;
1.170 brouard 4581: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4582: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4583: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4584: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4585: }
4586: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4587: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.170 brouard 4588: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4589: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4590: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4591: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4592: }
1.145 brouard 4593: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.170 brouard 4594: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4595: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4596: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4597: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4598: }
1.145 brouard 4599: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4600: else fprintf(ficgp,"\" t\"\" w l lt 0,");
1.126 brouard 4601: }
4602: }
4603:
4604: /*3eme*/
4605:
4606: for (k1=1; k1<= m ; k1 ++) {
4607: for (cpt=1; cpt<= nlstate ; cpt ++) {
4608: /* k=2+nlstate*(2*cpt-2); */
4609: k=2+(nlstate+1)*(cpt-1);
4610: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
1.145 brouard 4611: fprintf(ficgp,"set ter png small size 320, 240\n\
1.126 brouard 4612: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4613: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4614: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4615: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4616: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4617: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4618: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4619:
4620: */
4621: for (i=1; i< nlstate ; i ++) {
4622: 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);
4623: /* 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);*/
4624:
4625: }
4626: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4627: }
4628: }
4629:
4630: /* CV preval stable (period) */
1.153 brouard 4631: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4632: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126 brouard 4633: k=3;
1.153 brouard 4634: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.145 brouard 4635: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
1.126 brouard 4636: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.145 brouard 4637: set ter png small size 320, 240\n\
1.126 brouard 4638: unset log y\n\
1.153 brouard 4639: plot [%.f:%.f] ", ageminpar, agemaxpar);
4640: for (i=1; i<= nlstate ; i ++){
4641: if(i==1)
4642: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4643: else
4644: fprintf(ficgp,", '' ");
1.154 brouard 4645: l=(nlstate+ndeath)*(i-1)+1;
4646: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.153 brouard 4647: for (j=1; j<= (nlstate-1) ; j ++)
4648: fprintf(ficgp,"+$%d",k+l+j);
4649: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4650: } /* nlstate */
4651: fprintf(ficgp,"\n");
4652: } /* end cpt state*/
4653: } /* end covariate */
1.126 brouard 4654:
4655: /* proba elementaires */
1.187 brouard 4656: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 4657: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 4658: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 4659: for(k=1; k <=(nlstate+ndeath); k++){
4660: if (k != i) {
1.187 brouard 4661: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 4662: for(j=1; j <=ncovmodel; j++){
1.187 brouard 4663: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 4664: jk++;
4665: }
1.187 brouard 4666: fprintf(ficgp,"\n");
1.126 brouard 4667: }
4668: }
4669: }
1.187 brouard 4670: fprintf(ficgp,"##############\n#\n");
4671:
1.145 brouard 4672: /*goto avoid;*/
1.187 brouard 4673: fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n");
4674: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
4675: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
4676: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
4677: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
4678: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4679: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4680: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4681: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4682: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
4683: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4684: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
4685: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
4686: fprintf(ficgp,"#\n");
1.126 brouard 4687: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
1.187 brouard 4688: fprintf(ficgp,"# ng=%d\n",ng);
4689: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 4690: for(jk=1; jk <=m; jk++) {
1.187 brouard 4691: fprintf(ficgp,"# jk=%d\n",jk);
1.145 brouard 4692: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.126 brouard 4693: if (ng==2)
4694: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4695: else
4696: fprintf(ficgp,"\nset title \"Probability\"\n");
1.145 brouard 4697: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 4698: i=1;
4699: for(k2=1; k2<=nlstate; k2++) {
4700: k3=i;
4701: for(k=1; k<=(nlstate+ndeath); k++) {
4702: if (k != k2){
4703: if(ng==2)
1.187 brouard 4704: if(nagesqr==0)
4705: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4706: else /* nagesqr =1 */
4707: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
1.126 brouard 4708: else
1.187 brouard 4709: if(nagesqr==0)
4710: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4711: else /* nagesqr =1 */
4712: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
1.141 brouard 4713: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 brouard 4714: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.186 brouard 4715: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
1.187 brouard 4716: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
1.186 brouard 4717: ij++;
4718: }
4719: else
1.187 brouard 4720: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
1.126 brouard 4721: }
4722: fprintf(ficgp,")/(1");
4723:
1.187 brouard 4724: for(k1=1; k1 <=nlstate; k1++){
4725: if(nagesqr==0)
4726: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4727: else /* nagesqr =1 */
4728: 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);
4729:
1.126 brouard 4730: ij=1;
1.187 brouard 4731: for(j=3; j <=ncovmodel-nagesqr; j++){
1.186 brouard 4732: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
1.187 brouard 4733: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
1.186 brouard 4734: ij++;
4735: }
4736: else
1.187 brouard 4737: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
1.126 brouard 4738: }
4739: fprintf(ficgp,")");
4740: }
4741: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4742: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4743: i=i+ncovmodel;
4744: }
4745: } /* end k */
4746: } /* end k2 */
4747: } /* end jk */
4748: } /* end ng */
1.164 brouard 4749: /* avoid: */
1.126 brouard 4750: fflush(ficgp);
4751: } /* end gnuplot */
4752:
4753:
4754: /*************** Moving average **************/
4755: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4756:
4757: int i, cpt, cptcod;
4758: int modcovmax =1;
4759: int mobilavrange, mob;
4760: double age;
4761:
4762: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4763: a covariate has 2 modalities */
4764: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4765:
4766: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4767: if(mobilav==1) mobilavrange=5; /* default */
4768: else mobilavrange=mobilav;
4769: for (age=bage; age<=fage; age++)
4770: for (i=1; i<=nlstate;i++)
4771: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4772: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4773: /* We keep the original values on the extreme ages bage, fage and for
4774: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4775: we use a 5 terms etc. until the borders are no more concerned.
4776: */
4777: for (mob=3;mob <=mobilavrange;mob=mob+2){
4778: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4779: for (i=1; i<=nlstate;i++){
4780: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4781: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4782: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4783: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4784: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4785: }
4786: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4787: }
4788: }
4789: }/* end age */
4790: }/* end mob */
4791: }else return -1;
4792: return 0;
4793: }/* End movingaverage */
4794:
4795:
4796: /************** Forecasting ******************/
1.169 brouard 4797: 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 4798: /* proj1, year, month, day of starting projection
4799: agemin, agemax range of age
4800: dateprev1 dateprev2 range of dates during which prevalence is computed
4801: anproj2 year of en of projection (same day and month as proj1).
4802: */
1.164 brouard 4803: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 4804: double agec; /* generic age */
4805: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4806: double *popeffectif,*popcount;
4807: double ***p3mat;
4808: double ***mobaverage;
4809: char fileresf[FILENAMELENGTH];
4810:
4811: agelim=AGESUP;
4812: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4813:
4814: strcpy(fileresf,"f");
4815: strcat(fileresf,fileres);
4816: if((ficresf=fopen(fileresf,"w"))==NULL) {
4817: printf("Problem with forecast resultfile: %s\n", fileresf);
4818: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4819: }
4820: printf("Computing forecasting: result on file '%s' \n", fileresf);
4821: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4822:
4823: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4824:
4825: if (mobilav!=0) {
4826: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4827: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4828: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4829: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4830: }
4831: }
4832:
4833: stepsize=(int) (stepm+YEARM-1)/YEARM;
4834: if (stepm<=12) stepsize=1;
4835: if(estepm < stepm){
4836: printf ("Problem %d lower than %d\n",estepm, stepm);
4837: }
4838: else hstepm=estepm;
4839:
4840: hstepm=hstepm/stepm;
4841: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4842: fractional in yp1 */
4843: anprojmean=yp;
4844: yp2=modf((yp1*12),&yp);
4845: mprojmean=yp;
4846: yp1=modf((yp2*30.5),&yp);
4847: jprojmean=yp;
4848: if(jprojmean==0) jprojmean=1;
4849: if(mprojmean==0) jprojmean=1;
4850:
4851: i1=cptcoveff;
4852: if (cptcovn < 1){i1=1;}
4853:
4854: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4855:
4856: fprintf(ficresf,"#****** Routine prevforecast **\n");
4857:
4858: /* if (h==(int)(YEARM*yearp)){ */
4859: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4860: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4861: k=k+1;
4862: fprintf(ficresf,"\n#******");
4863: for(j=1;j<=cptcoveff;j++) {
4864: fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4865: }
4866: fprintf(ficresf,"******\n");
4867: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4868: for(j=1; j<=nlstate+ndeath;j++){
4869: for(i=1; i<=nlstate;i++)
4870: fprintf(ficresf," p%d%d",i,j);
4871: fprintf(ficresf," p.%d",j);
4872: }
4873: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4874: fprintf(ficresf,"\n");
4875: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4876:
4877: for (agec=fage; agec>=(ageminpar-1); agec--){
4878: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4879: nhstepm = nhstepm/hstepm;
4880: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4881: oldm=oldms;savm=savms;
4882: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4883:
4884: for (h=0; h<=nhstepm; h++){
4885: if (h*hstepm/YEARM*stepm ==yearp) {
4886: fprintf(ficresf,"\n");
4887: for(j=1;j<=cptcoveff;j++)
4888: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4889: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4890: }
4891: for(j=1; j<=nlstate+ndeath;j++) {
4892: ppij=0.;
4893: for(i=1; i<=nlstate;i++) {
4894: if (mobilav==1)
4895: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4896: else {
4897: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4898: }
4899: if (h*hstepm/YEARM*stepm== yearp) {
4900: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4901: }
4902: } /* end i */
4903: if (h*hstepm/YEARM*stepm==yearp) {
4904: fprintf(ficresf," %.3f", ppij);
4905: }
4906: }/* end j */
4907: } /* end h */
4908: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4909: } /* end agec */
4910: } /* end yearp */
4911: } /* end cptcod */
4912: } /* end cptcov */
4913:
4914: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4915:
4916: fclose(ficresf);
4917: }
4918:
4919: /************** Forecasting *****not tested NB*************/
1.169 brouard 4920: 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 4921:
4922: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4923: int *popage;
4924: double calagedatem, agelim, kk1, kk2;
4925: double *popeffectif,*popcount;
4926: double ***p3mat,***tabpop,***tabpopprev;
4927: double ***mobaverage;
4928: char filerespop[FILENAMELENGTH];
4929:
4930: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4931: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4932: agelim=AGESUP;
4933: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4934:
4935: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4936:
4937:
4938: strcpy(filerespop,"pop");
4939: strcat(filerespop,fileres);
4940: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4941: printf("Problem with forecast resultfile: %s\n", filerespop);
4942: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4943: }
4944: printf("Computing forecasting: result on file '%s' \n", filerespop);
4945: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4946:
4947: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4948:
4949: if (mobilav!=0) {
4950: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4951: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4952: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4953: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4954: }
4955: }
4956:
4957: stepsize=(int) (stepm+YEARM-1)/YEARM;
4958: if (stepm<=12) stepsize=1;
4959:
4960: agelim=AGESUP;
4961:
4962: hstepm=1;
4963: hstepm=hstepm/stepm;
4964:
4965: if (popforecast==1) {
4966: if((ficpop=fopen(popfile,"r"))==NULL) {
4967: printf("Problem with population file : %s\n",popfile);exit(0);
4968: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4969: }
4970: popage=ivector(0,AGESUP);
4971: popeffectif=vector(0,AGESUP);
4972: popcount=vector(0,AGESUP);
4973:
4974: i=1;
4975: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4976:
4977: imx=i;
4978: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4979: }
4980:
4981: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4982: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4983: k=k+1;
4984: fprintf(ficrespop,"\n#******");
4985: for(j=1;j<=cptcoveff;j++) {
4986: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4987: }
4988: fprintf(ficrespop,"******\n");
4989: fprintf(ficrespop,"# Age");
4990: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4991: if (popforecast==1) fprintf(ficrespop," [Population]");
4992:
4993: for (cpt=0; cpt<=0;cpt++) {
4994: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4995:
4996: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4997: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4998: nhstepm = nhstepm/hstepm;
4999:
5000: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5001: oldm=oldms;savm=savms;
5002: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5003:
5004: for (h=0; h<=nhstepm; h++){
5005: if (h==(int) (calagedatem+YEARM*cpt)) {
5006: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5007: }
5008: for(j=1; j<=nlstate+ndeath;j++) {
5009: kk1=0.;kk2=0;
5010: for(i=1; i<=nlstate;i++) {
5011: if (mobilav==1)
5012: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
5013: else {
5014: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
5015: }
5016: }
5017: if (h==(int)(calagedatem+12*cpt)){
5018: tabpop[(int)(agedeb)][j][cptcod]=kk1;
5019: /*fprintf(ficrespop," %.3f", kk1);
5020: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
5021: }
5022: }
5023: for(i=1; i<=nlstate;i++){
5024: kk1=0.;
5025: for(j=1; j<=nlstate;j++){
5026: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5027: }
5028: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5029: }
5030:
5031: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5032: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5033: }
5034: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5035: }
5036: }
5037:
5038: /******/
5039:
5040: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5041: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5042: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5043: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5044: nhstepm = nhstepm/hstepm;
5045:
5046: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5047: oldm=oldms;savm=savms;
5048: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5049: for (h=0; h<=nhstepm; h++){
5050: if (h==(int) (calagedatem+YEARM*cpt)) {
5051: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5052: }
5053: for(j=1; j<=nlstate+ndeath;j++) {
5054: kk1=0.;kk2=0;
5055: for(i=1; i<=nlstate;i++) {
5056: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5057: }
5058: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5059: }
5060: }
5061: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5062: }
5063: }
5064: }
5065: }
5066:
5067: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5068:
5069: if (popforecast==1) {
5070: free_ivector(popage,0,AGESUP);
5071: free_vector(popeffectif,0,AGESUP);
5072: free_vector(popcount,0,AGESUP);
5073: }
5074: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5075: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5076: fclose(ficrespop);
5077: } /* End of popforecast */
5078:
5079: int fileappend(FILE *fichier, char *optionfich)
5080: {
5081: if((fichier=fopen(optionfich,"a"))==NULL) {
5082: printf("Problem with file: %s\n", optionfich);
5083: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5084: return (0);
5085: }
5086: fflush(fichier);
5087: return (1);
5088: }
5089:
5090:
5091: /**************** function prwizard **********************/
5092: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
5093: {
5094:
5095: /* Wizard to print covariance matrix template */
5096:
1.164 brouard 5097: char ca[32], cb[32];
5098: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 5099: int numlinepar;
5100:
5101: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5102: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5103: for(i=1; i <=nlstate; i++){
5104: jj=0;
5105: for(j=1; j <=nlstate+ndeath; j++){
5106: if(j==i) continue;
5107: jj++;
5108: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5109: printf("%1d%1d",i,j);
5110: fprintf(ficparo,"%1d%1d",i,j);
5111: for(k=1; k<=ncovmodel;k++){
5112: /* printf(" %lf",param[i][j][k]); */
5113: /* fprintf(ficparo," %lf",param[i][j][k]); */
5114: printf(" 0.");
5115: fprintf(ficparo," 0.");
5116: }
5117: printf("\n");
5118: fprintf(ficparo,"\n");
5119: }
5120: }
5121: printf("# Scales (for hessian or gradient estimation)\n");
5122: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
5123: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
5124: for(i=1; i <=nlstate; i++){
5125: jj=0;
5126: for(j=1; j <=nlstate+ndeath; j++){
5127: if(j==i) continue;
5128: jj++;
5129: fprintf(ficparo,"%1d%1d",i,j);
5130: printf("%1d%1d",i,j);
5131: fflush(stdout);
5132: for(k=1; k<=ncovmodel;k++){
5133: /* printf(" %le",delti3[i][j][k]); */
5134: /* fprintf(ficparo," %le",delti3[i][j][k]); */
5135: printf(" 0.");
5136: fprintf(ficparo," 0.");
5137: }
5138: numlinepar++;
5139: printf("\n");
5140: fprintf(ficparo,"\n");
5141: }
5142: }
5143: printf("# Covariance matrix\n");
5144: /* # 121 Var(a12)\n\ */
5145: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5146: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5147: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5148: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5149: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5150: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5151: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5152: fflush(stdout);
5153: fprintf(ficparo,"# Covariance matrix\n");
5154: /* # 121 Var(a12)\n\ */
5155: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5156: /* # ...\n\ */
5157: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5158:
5159: for(itimes=1;itimes<=2;itimes++){
5160: jj=0;
5161: for(i=1; i <=nlstate; i++){
5162: for(j=1; j <=nlstate+ndeath; j++){
5163: if(j==i) continue;
5164: for(k=1; k<=ncovmodel;k++){
5165: jj++;
5166: ca[0]= k+'a'-1;ca[1]='\0';
5167: if(itimes==1){
5168: printf("#%1d%1d%d",i,j,k);
5169: fprintf(ficparo,"#%1d%1d%d",i,j,k);
5170: }else{
5171: printf("%1d%1d%d",i,j,k);
5172: fprintf(ficparo,"%1d%1d%d",i,j,k);
5173: /* printf(" %.5le",matcov[i][j]); */
5174: }
5175: ll=0;
5176: for(li=1;li <=nlstate; li++){
5177: for(lj=1;lj <=nlstate+ndeath; lj++){
5178: if(lj==li) continue;
5179: for(lk=1;lk<=ncovmodel;lk++){
5180: ll++;
5181: if(ll<=jj){
5182: cb[0]= lk +'a'-1;cb[1]='\0';
5183: if(ll<jj){
5184: if(itimes==1){
5185: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5186: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5187: }else{
5188: printf(" 0.");
5189: fprintf(ficparo," 0.");
5190: }
5191: }else{
5192: if(itimes==1){
5193: printf(" Var(%s%1d%1d)",ca,i,j);
5194: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5195: }else{
5196: printf(" 0.");
5197: fprintf(ficparo," 0.");
5198: }
5199: }
5200: }
5201: } /* end lk */
5202: } /* end lj */
5203: } /* end li */
5204: printf("\n");
5205: fprintf(ficparo,"\n");
5206: numlinepar++;
5207: } /* end k*/
5208: } /*end j */
5209: } /* end i */
5210: } /* end itimes */
5211:
5212: } /* end of prwizard */
5213: /******************* Gompertz Likelihood ******************************/
5214: double gompertz(double x[])
5215: {
5216: double A,B,L=0.0,sump=0.,num=0.;
5217: int i,n=0; /* n is the size of the sample */
5218:
5219: for (i=0;i<=imx-1 ; i++) {
5220: sump=sump+weight[i];
5221: /* sump=sump+1;*/
5222: num=num+1;
5223: }
5224:
5225:
5226: /* for (i=0; i<=imx; i++)
5227: 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]);*/
5228:
5229: for (i=1;i<=imx ; i++)
5230: {
5231: if (cens[i] == 1 && wav[i]>1)
5232: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5233:
5234: if (cens[i] == 0 && wav[i]>1)
5235: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5236: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5237:
5238: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5239: if (wav[i] > 1 ) { /* ??? */
5240: L=L+A*weight[i];
5241: /* 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]);*/
5242: }
5243: }
5244:
5245: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5246:
5247: return -2*L*num/sump;
5248: }
5249:
1.136 brouard 5250: #ifdef GSL
5251: /******************* Gompertz_f Likelihood ******************************/
5252: double gompertz_f(const gsl_vector *v, void *params)
5253: {
5254: double A,B,LL=0.0,sump=0.,num=0.;
5255: double *x= (double *) v->data;
5256: int i,n=0; /* n is the size of the sample */
5257:
5258: for (i=0;i<=imx-1 ; i++) {
5259: sump=sump+weight[i];
5260: /* sump=sump+1;*/
5261: num=num+1;
5262: }
5263:
5264:
5265: /* for (i=0; i<=imx; i++)
5266: 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]);*/
5267: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5268: for (i=1;i<=imx ; i++)
5269: {
5270: if (cens[i] == 1 && wav[i]>1)
5271: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5272:
5273: if (cens[i] == 0 && wav[i]>1)
5274: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5275: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5276:
5277: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5278: if (wav[i] > 1 ) { /* ??? */
5279: LL=LL+A*weight[i];
5280: /* 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]);*/
5281: }
5282: }
5283:
5284: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5285: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5286:
5287: return -2*LL*num/sump;
5288: }
5289: #endif
5290:
1.126 brouard 5291: /******************* Printing html file ***********/
5292: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
5293: int lastpass, int stepm, int weightopt, char model[],\
5294: int imx, double p[],double **matcov,double agemortsup){
5295: int i,k;
5296:
5297: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5298: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5299: for (i=1;i<=2;i++)
5300: 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]));
5301: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
5302: fprintf(fichtm,"</ul>");
5303:
5304: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5305:
5306: 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>");
5307:
5308: for (k=agegomp;k<(agemortsup-2);k++)
5309: 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]);
5310:
5311:
5312: fflush(fichtm);
5313: }
5314:
5315: /******************* Gnuplot file **************/
5316: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
5317:
5318: char dirfileres[132],optfileres[132];
1.164 brouard 5319:
1.126 brouard 5320: int ng;
5321:
5322:
5323: /*#ifdef windows */
5324: fprintf(ficgp,"cd \"%s\" \n",pathc);
5325: /*#endif */
5326:
5327:
5328: strcpy(dirfileres,optionfilefiname);
5329: strcpy(optfileres,"vpl");
5330: fprintf(ficgp,"set out \"graphmort.png\"\n ");
5331: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.145 brouard 5332: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
5333: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 5334: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5335:
5336: }
5337:
1.136 brouard 5338: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5339: {
1.126 brouard 5340:
1.136 brouard 5341: /*-------- data file ----------*/
5342: FILE *fic;
5343: char dummy[]=" ";
1.164 brouard 5344: int i=0, j=0, n=0;
1.136 brouard 5345: int linei, month, year,iout;
5346: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 5347: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 5348: char *stratrunc;
5349: int lstra;
1.126 brouard 5350:
5351:
1.136 brouard 5352: if((fic=fopen(datafile,"r"))==NULL) {
5353: printf("Problem while opening datafile: %s\n", datafile);return 1;
5354: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
5355: }
1.126 brouard 5356:
1.136 brouard 5357: i=1;
5358: linei=0;
5359: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5360: linei=linei+1;
5361: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5362: if(line[j] == '\t')
5363: line[j] = ' ';
5364: }
5365: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5366: ;
5367: };
5368: line[j+1]=0; /* Trims blanks at end of line */
5369: if(line[0]=='#'){
5370: fprintf(ficlog,"Comment line\n%s\n",line);
5371: printf("Comment line\n%s\n",line);
5372: continue;
5373: }
5374: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 5375: strcpy(line, linetmp);
1.136 brouard 5376:
1.126 brouard 5377:
1.136 brouard 5378: for (j=maxwav;j>=1;j--){
1.137 brouard 5379: cutv(stra, strb, line, ' ');
1.136 brouard 5380: if(strb[0]=='.') { /* Missing status */
5381: lval=-1;
5382: }else{
5383: errno=0;
5384: lval=strtol(strb,&endptr,10);
5385: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5386: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5387: 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);
5388: 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 5389: return 1;
5390: }
5391: }
5392: s[j][i]=lval;
5393:
5394: strcpy(line,stra);
5395: cutv(stra, strb,line,' ');
1.169 brouard 5396: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5397: }
1.169 brouard 5398: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5399: month=99;
5400: year=9999;
5401: }else{
1.141 brouard 5402: 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);
5403: 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 5404: return 1;
5405: }
5406: anint[j][i]= (double) year;
5407: mint[j][i]= (double)month;
5408: strcpy(line,stra);
5409: } /* ENd Waves */
5410:
5411: cutv(stra, strb,line,' ');
1.169 brouard 5412: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5413: }
1.169 brouard 5414: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5415: month=99;
5416: year=9999;
5417: }else{
1.141 brouard 5418: 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);
5419: 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 5420: return 1;
5421: }
5422: andc[i]=(double) year;
5423: moisdc[i]=(double) month;
5424: strcpy(line,stra);
5425:
5426: cutv(stra, strb,line,' ');
1.169 brouard 5427: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5428: }
1.169 brouard 5429: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 5430: month=99;
5431: year=9999;
5432: }else{
1.141 brouard 5433: 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);
5434: 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 5435: return 1;
5436: }
5437: if (year==9999) {
1.141 brouard 5438: 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);
5439: 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 5440: return 1;
1.126 brouard 5441:
1.136 brouard 5442: }
5443: annais[i]=(double)(year);
5444: moisnais[i]=(double)(month);
5445: strcpy(line,stra);
5446:
5447: cutv(stra, strb,line,' ');
5448: errno=0;
5449: dval=strtod(strb,&endptr);
5450: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5451: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5452: 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 5453: fflush(ficlog);
5454: return 1;
5455: }
5456: weight[i]=dval;
5457: strcpy(line,stra);
5458:
5459: for (j=ncovcol;j>=1;j--){
5460: cutv(stra, strb,line,' ');
5461: if(strb[0]=='.') { /* Missing status */
5462: lval=-1;
5463: }else{
5464: errno=0;
5465: lval=strtol(strb,&endptr,10);
5466: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5467: 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);
5468: 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 5469: return 1;
5470: }
5471: }
5472: if(lval <-1 || lval >1){
1.141 brouard 5473: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5474: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5475: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5476: For example, for multinomial values like 1, 2 and 3,\n \
5477: build V1=0 V2=0 for the reference value (1),\n \
5478: V1=1 V2=0 for (2) \n \
5479: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5480: output of IMaCh is often meaningless.\n \
5481: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 5482: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5483: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5484: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5485: For example, for multinomial values like 1, 2 and 3,\n \
5486: build V1=0 V2=0 for the reference value (1),\n \
5487: V1=1 V2=0 for (2) \n \
5488: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5489: output of IMaCh is often meaningless.\n \
5490: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5491: return 1;
5492: }
5493: covar[j][i]=(double)(lval);
5494: strcpy(line,stra);
5495: }
5496: lstra=strlen(stra);
5497:
5498: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5499: stratrunc = &(stra[lstra-9]);
5500: num[i]=atol(stratrunc);
5501: }
5502: else
5503: num[i]=atol(stra);
5504: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5505: 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;}*/
5506:
5507: i=i+1;
5508: } /* End loop reading data */
1.126 brouard 5509:
1.136 brouard 5510: *imax=i-1; /* Number of individuals */
5511: fclose(fic);
5512:
5513: return (0);
1.164 brouard 5514: /* endread: */
1.136 brouard 5515: printf("Exiting readdata: ");
5516: fclose(fic);
5517: return (1);
1.126 brouard 5518:
5519:
5520:
1.136 brouard 5521: }
1.145 brouard 5522: void removespace(char *str) {
5523: char *p1 = str, *p2 = str;
5524: do
5525: while (*p2 == ' ')
5526: p2++;
1.169 brouard 5527: while (*p1++ == *p2++);
1.145 brouard 5528: }
5529:
5530: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 5531: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
5532: * - nagesqr = 1 if age*age in the model, otherwise 0.
5533: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
5534: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 5535: * - cptcovage number of covariates with age*products =2
5536: * - cptcovs number of simple covariates
5537: * - 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
5538: * which is a new column after the 9 (ncovcol) variables.
5539: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5540: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5541: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5542: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5543: */
1.136 brouard 5544: {
1.145 brouard 5545: int i, j, k, ks;
1.164 brouard 5546: int j1, k1, k2;
1.136 brouard 5547: char modelsav[80];
1.145 brouard 5548: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 5549: char *strpt;
1.136 brouard 5550:
1.145 brouard 5551: /*removespace(model);*/
1.136 brouard 5552: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 5553: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 5554: if (strstr(model,"AGE") !=0){
1.187 brouard 5555: printf("Error. AGE must be in lower case 'age' model=1+age+%s ",model);
5556: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s ",model);fflush(ficlog);
1.136 brouard 5557: return 1;
5558: }
1.141 brouard 5559: if (strstr(model,"v") !=0){
5560: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5561: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5562: return 1;
5563: }
1.187 brouard 5564: strcpy(modelsav,model);
5565: if ((strpt=strstr(model,"age*age")) !=0){
5566: printf(" strpt=%s, model=%s\n",strpt, model);
5567: if(strpt != model){
5568: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
5569: 'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \
5570: corresponding column of parameters.\n",model);
5571: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
5572: 'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \
5573: corresponding column of parameters.\n",model); fflush(ficlog);
5574: return 1;
5575: }
5576:
5577: nagesqr=1;
5578: if (strstr(model,"+age*age") !=0)
5579: substrchaine(modelsav, model, "+age*age");
5580: else if (strstr(model,"age*age+") !=0)
5581: substrchaine(modelsav, model, "age*age+");
5582: else
5583: substrchaine(modelsav, model, "age*age");
5584: }else
5585: nagesqr=0;
5586: if (strlen(modelsav) >1){
5587: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
5588: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
5589: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
5590: cptcovt= j+1; /* Number of total covariates in the model, not including
5591: * cst, age and age*age
5592: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
5593: /* including age products which are counted in cptcovage.
5594: * but the covariates which are products must be treated
5595: * separately: ncovn=4- 2=2 (V1+V3). */
5596: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5597: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5598:
5599:
5600: /* Design
5601: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5602: * < ncovcol=8 >
5603: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5604: * k= 1 2 3 4 5 6 7 8
5605: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5606: * covar[k,i], value of kth covariate if not including age for individual i:
5607: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5608: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5609: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5610: * Tage[++cptcovage]=k
5611: * if products, new covar are created after ncovcol with k1
5612: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5613: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5614: * 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
5615: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5616: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5617: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5618: * < ncovcol=8 >
5619: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5620: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5621: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5622: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5623: * p Tprod[1]@2={ 6, 5}
5624: *p Tvard[1][1]@4= {7, 8, 5, 6}
5625: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5626: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5627: *How to reorganize?
5628: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5629: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5630: * {2, 1, 4, 8, 5, 6, 3, 7}
5631: * Struct []
5632: */
1.145 brouard 5633:
1.187 brouard 5634: /* This loop fills the array Tvar from the string 'model'.*/
5635: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5636: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5637: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5638: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5639: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5640: /* k=1 Tvar[1]=2 (from V2) */
5641: /* k=5 Tvar[5] */
5642: /* for (k=1; k<=cptcovn;k++) { */
5643: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5644: /* } */
5645: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */
5646: /*
5647: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5648: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 5649: Tvar[k]=0;
1.187 brouard 5650: cptcovage=0;
5651: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5652: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5653: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5654: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5655: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5656: /*scanf("%d",i);*/
5657: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5658: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5659: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5660: /* covar is not filled and then is empty */
5661: cptcovprod--;
5662: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5663: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
5664: cptcovage++; /* Sums the number of covariates which include age as a product */
5665: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
5666: /*printf("stre=%s ", stre);*/
5667: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5668: cptcovprod--;
5669: cutl(stre,strb,strc,'V');
5670: Tvar[k]=atoi(stre);
5671: cptcovage++;
5672: Tage[cptcovage]=k;
5673: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5674: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5675: cptcovn++;
5676: cptcovprodnoage++;k1++;
5677: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5678: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5679: because this model-covariate is a construction we invent a new column
5680: ncovcol + k1
5681: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5682: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5683: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5684: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5685: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5686: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5687: k2=k2+2;
5688: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5689: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5690: for (i=1; i<=lastobs;i++){
5691: /* Computes the new covariate which is a product of
5692: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5693: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5694: }
5695: } /* End age is not in the model */
5696: } /* End if model includes a product */
5697: else { /* no more sum */
5698: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5699: /* scanf("%d",i);*/
5700: cutl(strd,strc,strb,'V');
5701: ks++; /**< Number of simple covariates */
1.145 brouard 5702: cptcovn++;
1.187 brouard 5703: Tvar[k]=atoi(strd);
5704: }
5705: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5706: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5707: scanf("%d",i);*/
5708: } /* end of loop + on total covariates */
5709: } /* end if strlen(modelsave == 0) age*age might exist */
5710: } /* end if strlen(model == 0) */
1.136 brouard 5711:
5712: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5713: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5714:
5715: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5716: printf("cptcovprod=%d ", cptcovprod);
5717: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5718:
5719: scanf("%d ",i);*/
5720:
5721:
1.137 brouard 5722: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 5723: /*endread:*/
1.136 brouard 5724: printf("Exiting decodemodel: ");
5725: return (1);
5726: }
5727:
1.169 brouard 5728: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 5729: {
5730: int i, m;
5731:
5732: for (i=1; i<=imx; i++) {
5733: for(m=2; (m<= maxwav); m++) {
5734: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5735: anint[m][i]=9999;
5736: s[m][i]=-1;
5737: }
5738: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 5739: *nberr = *nberr + 1;
5740: 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);
5741: 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 5742: s[m][i]=-1;
5743: }
5744: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 5745: (*nberr)++;
1.136 brouard 5746: 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]);
5747: 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]);
5748: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5749: }
5750: }
5751: }
5752:
5753: for (i=1; i<=imx; i++) {
5754: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5755: for(m=firstpass; (m<= lastpass); m++){
5756: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5757: if (s[m][i] >= nlstate+1) {
1.169 brouard 5758: if(agedc[i]>0){
5759: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 5760: agev[m][i]=agedc[i];
5761: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 5762: }else {
1.136 brouard 5763: if ((int)andc[i]!=9999){
5764: nbwarn++;
5765: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5766: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5767: agev[m][i]=-1;
5768: }
5769: }
1.169 brouard 5770: } /* agedc > 0 */
1.136 brouard 5771: }
5772: else if(s[m][i] !=9){ /* Standard case, age in fractional
5773: years but with the precision of a month */
5774: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5775: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5776: agev[m][i]=1;
5777: else if(agev[m][i] < *agemin){
5778: *agemin=agev[m][i];
5779: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5780: }
5781: else if(agev[m][i] >*agemax){
5782: *agemax=agev[m][i];
1.156 brouard 5783: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 5784: }
5785: /*agev[m][i]=anint[m][i]-annais[i];*/
5786: /* agev[m][i] = age[i]+2*m;*/
5787: }
5788: else { /* =9 */
5789: agev[m][i]=1;
5790: s[m][i]=-1;
5791: }
5792: }
5793: else /*= 0 Unknown */
5794: agev[m][i]=1;
5795: }
5796:
5797: }
5798: for (i=1; i<=imx; i++) {
5799: for(m=firstpass; (m<=lastpass); m++){
5800: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 5801: (*nberr)++;
1.136 brouard 5802: 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);
5803: 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);
5804: return 1;
5805: }
5806: }
5807: }
5808:
5809: /*for (i=1; i<=imx; i++){
5810: for (m=firstpass; (m<lastpass); m++){
5811: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5812: }
5813:
5814: }*/
5815:
5816:
1.139 brouard 5817: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5818: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 5819:
5820: return (0);
1.164 brouard 5821: /* endread:*/
1.136 brouard 5822: printf("Exiting calandcheckages: ");
5823: return (1);
5824: }
5825:
1.172 brouard 5826: #if defined(_MSC_VER)
5827: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5828: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5829: //#include "stdafx.h"
5830: //#include <stdio.h>
5831: //#include <tchar.h>
5832: //#include <windows.h>
5833: //#include <iostream>
5834: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
5835:
5836: LPFN_ISWOW64PROCESS fnIsWow64Process;
5837:
5838: BOOL IsWow64()
5839: {
5840: BOOL bIsWow64 = FALSE;
5841:
5842: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
5843: // (HANDLE, PBOOL);
5844:
5845: //LPFN_ISWOW64PROCESS fnIsWow64Process;
5846:
5847: HMODULE module = GetModuleHandle(_T("kernel32"));
5848: const char funcName[] = "IsWow64Process";
5849: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
5850: GetProcAddress(module, funcName);
5851:
5852: if (NULL != fnIsWow64Process)
5853: {
5854: if (!fnIsWow64Process(GetCurrentProcess(),
5855: &bIsWow64))
5856: //throw std::exception("Unknown error");
5857: printf("Unknown error\n");
5858: }
5859: return bIsWow64 != FALSE;
5860: }
5861: #endif
1.177 brouard 5862:
1.169 brouard 5863: void syscompilerinfo()
1.167 brouard 5864: {
5865: /* #include "syscompilerinfo.h"*/
1.185 brouard 5866: /* command line Intel compiler 32bit windows, XP compatible:*/
5867: /* /GS /W3 /Gy
5868: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
5869: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
5870: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 5871: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
5872: */
5873: /* 64 bits */
1.185 brouard 5874: /*
5875: /GS /W3 /Gy
5876: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
5877: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
5878: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
5879: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
5880: /* Optimization are useless and O3 is slower than O2 */
5881: /*
5882: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
5883: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
5884: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
5885: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
5886: */
1.186 brouard 5887: /* Link is */ /* /OUT:"visual studio
1.185 brouard 5888: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
5889: /PDB:"visual studio
5890: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
5891: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
5892: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
5893: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
5894: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
5895: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
5896: uiAccess='false'"
5897: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
5898: /NOLOGO /TLBID:1
5899: */
1.177 brouard 5900: #if defined __INTEL_COMPILER
1.178 brouard 5901: #if defined(__GNUC__)
5902: struct utsname sysInfo; /* For Intel on Linux and OS/X */
5903: #endif
1.177 brouard 5904: #elif defined(__GNUC__)
1.179 brouard 5905: #ifndef __APPLE__
1.174 brouard 5906: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 5907: #endif
1.177 brouard 5908: struct utsname sysInfo;
1.178 brouard 5909: int cross = CROSS;
5910: if (cross){
5911: printf("Cross-");
5912: fprintf(ficlog, "Cross-");
5913: }
1.174 brouard 5914: #endif
5915:
1.171 brouard 5916: #include <stdint.h>
1.178 brouard 5917:
1.169 brouard 5918: printf("Compiled with:");fprintf(ficlog,"Compiled with:");
5919: #if defined(__clang__)
5920: printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
5921: #endif
5922: #if defined(__ICC) || defined(__INTEL_COMPILER)
5923: printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
5924: #endif
5925: #if defined(__GNUC__) || defined(__GNUG__)
5926: printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
5927: #endif
5928: #if defined(__HP_cc) || defined(__HP_aCC)
5929: printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
5930: #endif
5931: #if defined(__IBMC__) || defined(__IBMCPP__)
5932: printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
5933: #endif
5934: #if defined(_MSC_VER)
5935: printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
5936: #endif
5937: #if defined(__PGI)
5938: printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
5939: #endif
5940: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
5941: printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 5942: #endif
1.174 brouard 5943: printf(" for ");fprintf(ficlog," for ");
1.169 brouard 5944:
1.167 brouard 5945: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
5946: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
5947: // Windows (x64 and x86)
1.174 brouard 5948: printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 5949: #elif __unix__ // all unices, not all compilers
5950: // Unix
1.174 brouard 5951: printf("Unix ");fprintf(ficlog,"Unix ");
1.167 brouard 5952: #elif __linux__
5953: // linux
1.174 brouard 5954: printf("linux ");fprintf(ficlog,"linux ");
1.167 brouard 5955: #elif __APPLE__
1.174 brouard 5956: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
5957: printf("Mac OS ");fprintf(ficlog,"Mac OS ");
1.167 brouard 5958: #endif
5959:
5960: /* __MINGW32__ */
5961: /* __CYGWIN__ */
5962: /* __MINGW64__ */
5963: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
5964: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
5965: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
5966: /* _WIN64 // Defined for applications for Win64. */
5967: /* _M_X64 // Defined for compilations that target x64 processors. */
5968: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 5969:
1.167 brouard 5970: #if UINTPTR_MAX == 0xffffffff
1.174 brouard 5971: printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 5972: #elif UINTPTR_MAX == 0xffffffffffffffff
1.174 brouard 5973: printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 5974: #else
1.174 brouard 5975: printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 5976: #endif
5977:
1.169 brouard 5978: #if defined(__GNUC__)
5979: # if defined(__GNUC_PATCHLEVEL__)
5980: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5981: + __GNUC_MINOR__ * 100 \
5982: + __GNUC_PATCHLEVEL__)
5983: # else
5984: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5985: + __GNUC_MINOR__ * 100)
5986: # endif
1.174 brouard 5987: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
5988: fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 5989:
5990: if (uname(&sysInfo) != -1) {
5991: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5992: fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5993: }
5994: else
5995: perror("uname() error");
1.179 brouard 5996: //#ifndef __INTEL_COMPILER
5997: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 5998: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.179 brouard 5999: fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 6000: #endif
1.169 brouard 6001: #endif
1.172 brouard 6002:
6003: // void main()
6004: // {
1.169 brouard 6005: #if defined(_MSC_VER)
1.174 brouard 6006: if (IsWow64()){
1.176 brouard 6007: printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6008: fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 6009: }
6010: else{
1.176 brouard 6011: printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.178 brouard 6012: fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 6013: }
1.172 brouard 6014: // printf("\nPress Enter to continue...");
6015: // getchar();
6016: // }
6017:
1.169 brouard 6018: #endif
6019:
1.167 brouard 6020:
6021: }
1.136 brouard 6022:
1.180 brouard 6023: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
6024: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6025: int i, j, k, i1 ;
6026: double ftolpl = 1.e-10;
6027: double age, agebase, agelim;
6028:
6029: strcpy(filerespl,"pl");
6030: strcat(filerespl,fileres);
6031: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6032: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6033: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6034: }
6035: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6036: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6037: pstamp(ficrespl);
6038: fprintf(ficrespl,"# Period (stable) prevalence \n");
6039: fprintf(ficrespl,"#Age ");
6040: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6041: fprintf(ficrespl,"\n");
6042:
6043: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6044:
6045: agebase=ageminpar;
6046: agelim=agemaxpar;
6047:
6048: i1=pow(2,cptcoveff);
6049: if (cptcovn < 1){i1=1;}
6050:
6051: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6052: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6053: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6054: k=k+1;
6055: /* to clean */
6056: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
6057: fprintf(ficrespl,"\n#******");
6058: printf("\n#******");
6059: fprintf(ficlog,"\n#******");
6060: for(j=1;j<=cptcoveff;j++) {
6061: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6062: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6063: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6064: }
6065: fprintf(ficrespl,"******\n");
6066: printf("******\n");
6067: fprintf(ficlog,"******\n");
6068:
6069: fprintf(ficrespl,"#Age ");
6070: for(j=1;j<=cptcoveff;j++) {
6071: fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6072: }
6073: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6074: fprintf(ficrespl,"\n");
6075:
6076: for (age=agebase; age<=agelim; age++){
6077: /* for (age=agebase; age<=agebase; age++){ */
6078: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6079: fprintf(ficrespl,"%.0f ",age );
6080: for(j=1;j<=cptcoveff;j++)
6081: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6082: for(i=1; i<=nlstate;i++)
6083: fprintf(ficrespl," %.5f", prlim[i][i]);
6084: fprintf(ficrespl,"\n");
6085: } /* Age */
6086: /* was end of cptcod */
6087: } /* cptcov */
1.184 brouard 6088: return 0;
1.180 brouard 6089: }
6090:
6091: int hPijx(double *p, int bage, int fage){
6092: /*------------- h Pij x at various ages ------------*/
6093:
6094: int stepsize;
6095: int agelim;
6096: int hstepm;
6097: int nhstepm;
6098: int h, i, i1, j, k;
6099:
6100: double agedeb;
6101: double ***p3mat;
6102:
6103: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
6104: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6105: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
6106: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
6107: }
6108: printf("Computing pij: result on file '%s' \n", filerespij);
6109: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6110:
6111: stepsize=(int) (stepm+YEARM-1)/YEARM;
6112: /*if (stepm<=24) stepsize=2;*/
6113:
6114: agelim=AGESUP;
6115: hstepm=stepsize*YEARM; /* Every year of age */
6116: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6117:
6118: /* hstepm=1; aff par mois*/
6119: pstamp(ficrespij);
6120: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6121: i1= pow(2,cptcoveff);
1.183 brouard 6122: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
6123: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
6124: /* k=k+1; */
6125: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6126: fprintf(ficrespij,"\n#****** ");
6127: for(j=1;j<=cptcoveff;j++)
6128: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6129: fprintf(ficrespij,"******\n");
6130:
6131: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6132: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6133: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6134:
6135: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 6136:
1.183 brouard 6137: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6138: oldm=oldms;savm=savms;
6139: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6140: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6141: for(i=1; i<=nlstate;i++)
6142: for(j=1; j<=nlstate+ndeath;j++)
6143: fprintf(ficrespij," %1d-%1d",i,j);
6144: fprintf(ficrespij,"\n");
6145: for (h=0; h<=nhstepm; h++){
6146: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
6147: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 6148: for(i=1; i<=nlstate;i++)
6149: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 6150: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 6151: fprintf(ficrespij,"\n");
6152: }
1.183 brouard 6153: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6154: fprintf(ficrespij,"\n");
6155: }
1.180 brouard 6156: /*}*/
6157: }
1.184 brouard 6158: return 0;
1.180 brouard 6159: }
6160:
6161:
1.136 brouard 6162: /***********************************************/
6163: /**************** Main Program *****************/
6164: /***********************************************/
6165:
6166: int main(int argc, char *argv[])
6167: {
6168: #ifdef GSL
6169: const gsl_multimin_fminimizer_type *T;
6170: size_t iteri = 0, it;
6171: int rval = GSL_CONTINUE;
6172: int status = GSL_SUCCESS;
6173: double ssval;
6174: #endif
6175: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 6176: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
6177:
6178: int jj, ll, li, lj, lk;
1.136 brouard 6179: int numlinepar=0; /* Current linenumber of parameter file */
6180: int itimes;
6181: int NDIM=2;
6182: int vpopbased=0;
6183:
1.164 brouard 6184: char ca[32], cb[32];
1.136 brouard 6185: /* FILE *fichtm; *//* Html File */
6186: /* FILE *ficgp;*/ /*Gnuplot File */
6187: struct stat info;
1.164 brouard 6188: double agedeb;
1.136 brouard 6189: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
6190:
1.165 brouard 6191: double fret;
1.136 brouard 6192: double dum; /* Dummy variable */
6193: double ***p3mat;
6194: double ***mobaverage;
1.164 brouard 6195:
6196: char line[MAXLINE];
1.136 brouard 6197: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
6198: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 6199: char *tok, *val; /* pathtot */
1.136 brouard 6200: int firstobs=1, lastobs=10;
1.164 brouard 6201: int c, h , cpt;
6202: int jl;
6203: int i1, j1, jk, stepsize;
6204: int *tab;
1.136 brouard 6205: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
6206: int mobilav=0,popforecast=0;
6207: int hstepm, nhstepm;
6208: int agemortsup;
6209: float sumlpop=0.;
6210: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
6211: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
6212:
1.164 brouard 6213: double bage=0, fage=110, age, agelim, agebase;
1.136 brouard 6214: double ftolpl=FTOL;
6215: double **prlim;
6216: double ***param; /* Matrix of parameters */
6217: double *p;
6218: double **matcov; /* Matrix of covariance */
6219: double ***delti3; /* Scale */
6220: double *delti; /* Scale */
6221: double ***eij, ***vareij;
6222: double **varpl; /* Variances of prevalence limits by age */
6223: double *epj, vepp;
1.164 brouard 6224:
1.136 brouard 6225: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6226: double **ximort;
1.145 brouard 6227: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 6228: int *dcwave;
6229:
1.164 brouard 6230: char z[1]="c";
1.136 brouard 6231:
6232: /*char *strt;*/
6233: char strtend[80];
1.126 brouard 6234:
1.164 brouard 6235:
1.126 brouard 6236: /* setlocale (LC_ALL, ""); */
6237: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6238: /* textdomain (PACKAGE); */
6239: /* setlocale (LC_CTYPE, ""); */
6240: /* setlocale (LC_MESSAGES, ""); */
6241:
6242: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 6243: rstart_time = time(NULL);
6244: /* (void) gettimeofday(&start_time,&tzp);*/
6245: start_time = *localtime(&rstart_time);
1.126 brouard 6246: curr_time=start_time;
1.157 brouard 6247: /*tml = *localtime(&start_time.tm_sec);*/
6248: /* strcpy(strstart,asctime(&tml)); */
6249: strcpy(strstart,asctime(&start_time));
1.126 brouard 6250:
6251: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 6252: /* tp.tm_sec = tp.tm_sec +86400; */
6253: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 6254: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6255: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6256: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 6257: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 6258: /* strt=asctime(&tmg); */
6259: /* printf("Time(after) =%s",strstart); */
6260: /* (void) time (&time_value);
6261: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6262: * tm = *localtime(&time_value);
6263: * strstart=asctime(&tm);
6264: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6265: */
6266:
6267: nberr=0; /* Number of errors and warnings */
6268: nbwarn=0;
1.184 brouard 6269: #ifdef WIN32
6270: _getcwd(pathcd, size);
6271: #else
1.126 brouard 6272: getcwd(pathcd, size);
1.184 brouard 6273: #endif
1.126 brouard 6274:
6275: printf("\n%s\n%s",version,fullversion);
6276: if(argc <=1){
6277: printf("\nEnter the parameter file name: ");
6278: fgets(pathr,FILENAMELENGTH,stdin);
6279: i=strlen(pathr);
6280: if(pathr[i-1]=='\n')
6281: pathr[i-1]='\0';
1.156 brouard 6282: i=strlen(pathr);
6283: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
6284: pathr[i-1]='\0';
1.126 brouard 6285: for (tok = pathr; tok != NULL; ){
6286: printf("Pathr |%s|\n",pathr);
6287: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6288: printf("val= |%s| pathr=%s\n",val,pathr);
6289: strcpy (pathtot, val);
6290: if(pathr[0] == '\0') break; /* Dirty */
6291: }
6292: }
6293: else{
6294: strcpy(pathtot,argv[1]);
6295: }
6296: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6297: /*cygwin_split_path(pathtot,path,optionfile);
6298: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6299: /* cutv(path,optionfile,pathtot,'\\');*/
6300:
6301: /* Split argv[0], imach program to get pathimach */
6302: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6303: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6304: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6305: /* strcpy(pathimach,argv[0]); */
6306: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6307: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6308: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 6309: #ifdef WIN32
6310: _chdir(path); /* Can be a relative path */
6311: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
6312: #else
1.126 brouard 6313: chdir(path); /* Can be a relative path */
1.184 brouard 6314: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
6315: #endif
6316: printf("Current directory %s!\n",pathcd);
1.126 brouard 6317: strcpy(command,"mkdir ");
6318: strcat(command,optionfilefiname);
6319: if((outcmd=system(command)) != 0){
1.169 brouard 6320: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 6321: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6322: /* fclose(ficlog); */
6323: /* exit(1); */
6324: }
6325: /* if((imk=mkdir(optionfilefiname))<0){ */
6326: /* perror("mkdir"); */
6327: /* } */
6328:
6329: /*-------- arguments in the command line --------*/
6330:
1.186 brouard 6331: /* Main Log file */
1.126 brouard 6332: strcat(filelog, optionfilefiname);
6333: strcat(filelog,".log"); /* */
6334: if((ficlog=fopen(filelog,"w"))==NULL) {
6335: printf("Problem with logfile %s\n",filelog);
6336: goto end;
6337: }
6338: fprintf(ficlog,"Log filename:%s\n",filelog);
6339: fprintf(ficlog,"\n%s\n%s",version,fullversion);
6340: fprintf(ficlog,"\nEnter the parameter file name: \n");
6341: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6342: path=%s \n\
6343: optionfile=%s\n\
6344: optionfilext=%s\n\
1.156 brouard 6345: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 6346:
1.167 brouard 6347: syscompilerinfo();
6348:
1.126 brouard 6349: printf("Local time (at start):%s",strstart);
6350: fprintf(ficlog,"Local time (at start): %s",strstart);
6351: fflush(ficlog);
6352: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 6353: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 6354:
6355: /* */
6356: strcpy(fileres,"r");
6357: strcat(fileres, optionfilefiname);
6358: strcat(fileres,".txt"); /* Other files have txt extension */
6359:
1.186 brouard 6360: /* Main ---------arguments file --------*/
1.126 brouard 6361:
6362: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 6363: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6364: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 6365: fflush(ficlog);
1.149 brouard 6366: /* goto end; */
6367: exit(70);
1.126 brouard 6368: }
6369:
6370:
6371:
6372: strcpy(filereso,"o");
6373: strcat(filereso,fileres);
6374: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6375: printf("Problem with Output resultfile: %s\n", filereso);
6376: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6377: fflush(ficlog);
6378: goto end;
6379: }
6380:
6381: /* Reads comments: lines beginning with '#' */
6382: numlinepar=0;
6383: while((c=getc(ficpar))=='#' && c!= EOF){
6384: ungetc(c,ficpar);
6385: fgets(line, MAXLINE, ficpar);
6386: numlinepar++;
1.141 brouard 6387: fputs(line,stdout);
1.126 brouard 6388: fputs(line,ficparo);
6389: fputs(line,ficlog);
6390: }
6391: ungetc(c,ficpar);
6392:
1.187 brouard 6393: 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);
1.126 brouard 6394: numlinepar++;
1.187 brouard 6395: 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);
6396: if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
6397: model[strlen(model)-1]='\0';
6398: 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);
6399: 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 6400: fflush(ficlog);
1.190 ! brouard 6401: /* if(model[0]=='#'|| model[0]== '\0'){ */
! 6402: if(model[0]=='#'){
1.187 brouard 6403: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
6404: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
6405: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
6406: if(mle != -1){
6407: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
6408: exit(1);
6409: }
6410: }
1.126 brouard 6411: while((c=getc(ficpar))=='#' && c!= EOF){
6412: ungetc(c,ficpar);
6413: fgets(line, MAXLINE, ficpar);
6414: numlinepar++;
1.141 brouard 6415: fputs(line, stdout);
6416: //puts(line);
1.126 brouard 6417: fputs(line,ficparo);
6418: fputs(line,ficlog);
6419: }
6420: ungetc(c,ficpar);
6421:
6422:
1.145 brouard 6423: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 6424: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
6425: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
6426: v1+v2*age+v2*v3 makes cptcovn = 3
6427: */
6428: if (strlen(model)>1)
1.187 brouard 6429: 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 6430: else
1.187 brouard 6431: ncovmodel=2; /* Constant and age */
1.133 brouard 6432: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
6433: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 6434: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
6435: 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);
6436: 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);
6437: fflush(stdout);
6438: fclose (ficlog);
6439: goto end;
6440: }
1.126 brouard 6441: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6442: delti=delti3[1][1];
6443: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
6444: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
6445: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
6446: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6447: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6448: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6449: fclose (ficparo);
6450: fclose (ficlog);
6451: goto end;
6452: exit(0);
6453: }
1.186 brouard 6454: else if(mle==-3) { /* Main Wizard */
1.126 brouard 6455: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
6456: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6457: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6458: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6459: matcov=matrix(1,npar,1,npar);
6460: }
6461: else{
1.145 brouard 6462: /* Read guessed parameters */
1.126 brouard 6463: /* Reads comments: lines beginning with '#' */
6464: while((c=getc(ficpar))=='#' && c!= EOF){
6465: ungetc(c,ficpar);
6466: fgets(line, MAXLINE, ficpar);
6467: numlinepar++;
1.141 brouard 6468: fputs(line,stdout);
1.126 brouard 6469: fputs(line,ficparo);
6470: fputs(line,ficlog);
6471: }
6472: ungetc(c,ficpar);
6473:
6474: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6475: for(i=1; i <=nlstate; i++){
6476: j=0;
6477: for(jj=1; jj <=nlstate+ndeath; jj++){
6478: if(jj==i) continue;
6479: j++;
6480: fscanf(ficpar,"%1d%1d",&i1,&j1);
6481: if ((i1 != i) && (j1 != j)){
6482: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
6483: It might be a problem of design; if ncovcol and the model are correct\n \
6484: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
6485: exit(1);
6486: }
6487: fprintf(ficparo,"%1d%1d",i1,j1);
6488: if(mle==1)
6489: printf("%1d%1d",i,j);
6490: fprintf(ficlog,"%1d%1d",i,j);
6491: for(k=1; k<=ncovmodel;k++){
6492: fscanf(ficpar," %lf",¶m[i][j][k]);
6493: if(mle==1){
6494: printf(" %lf",param[i][j][k]);
6495: fprintf(ficlog," %lf",param[i][j][k]);
6496: }
6497: else
6498: fprintf(ficlog," %lf",param[i][j][k]);
6499: fprintf(ficparo," %lf",param[i][j][k]);
6500: }
6501: fscanf(ficpar,"\n");
6502: numlinepar++;
6503: if(mle==1)
6504: printf("\n");
6505: fprintf(ficlog,"\n");
6506: fprintf(ficparo,"\n");
6507: }
6508: }
6509: fflush(ficlog);
6510:
1.145 brouard 6511: /* Reads scales values */
1.126 brouard 6512: p=param[1][1];
6513:
6514: /* Reads comments: lines beginning with '#' */
6515: while((c=getc(ficpar))=='#' && c!= EOF){
6516: ungetc(c,ficpar);
6517: fgets(line, MAXLINE, ficpar);
6518: numlinepar++;
1.141 brouard 6519: fputs(line,stdout);
1.126 brouard 6520: fputs(line,ficparo);
6521: fputs(line,ficlog);
6522: }
6523: ungetc(c,ficpar);
6524:
6525: for(i=1; i <=nlstate; i++){
6526: for(j=1; j <=nlstate+ndeath-1; j++){
6527: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 6528: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 6529: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
6530: exit(1);
6531: }
6532: printf("%1d%1d",i,j);
6533: fprintf(ficparo,"%1d%1d",i1,j1);
6534: fprintf(ficlog,"%1d%1d",i1,j1);
6535: for(k=1; k<=ncovmodel;k++){
6536: fscanf(ficpar,"%le",&delti3[i][j][k]);
6537: printf(" %le",delti3[i][j][k]);
6538: fprintf(ficparo," %le",delti3[i][j][k]);
6539: fprintf(ficlog," %le",delti3[i][j][k]);
6540: }
6541: fscanf(ficpar,"\n");
6542: numlinepar++;
6543: printf("\n");
6544: fprintf(ficparo,"\n");
6545: fprintf(ficlog,"\n");
6546: }
6547: }
6548: fflush(ficlog);
6549:
1.145 brouard 6550: /* Reads covariance matrix */
1.126 brouard 6551: delti=delti3[1][1];
6552:
6553:
6554: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
6555:
6556: /* Reads comments: lines beginning with '#' */
6557: while((c=getc(ficpar))=='#' && c!= EOF){
6558: ungetc(c,ficpar);
6559: fgets(line, MAXLINE, ficpar);
6560: numlinepar++;
1.141 brouard 6561: fputs(line,stdout);
1.126 brouard 6562: fputs(line,ficparo);
6563: fputs(line,ficlog);
6564: }
6565: ungetc(c,ficpar);
6566:
6567: matcov=matrix(1,npar,1,npar);
1.131 brouard 6568: for(i=1; i <=npar; i++)
6569: for(j=1; j <=npar; j++) matcov[i][j]=0.;
6570:
1.126 brouard 6571: for(i=1; i <=npar; i++){
1.145 brouard 6572: fscanf(ficpar,"%s",str);
1.126 brouard 6573: if(mle==1)
6574: printf("%s",str);
6575: fprintf(ficlog,"%s",str);
6576: fprintf(ficparo,"%s",str);
6577: for(j=1; j <=i; j++){
6578: fscanf(ficpar," %le",&matcov[i][j]);
6579: if(mle==1){
6580: printf(" %.5le",matcov[i][j]);
6581: }
6582: fprintf(ficlog," %.5le",matcov[i][j]);
6583: fprintf(ficparo," %.5le",matcov[i][j]);
6584: }
6585: fscanf(ficpar,"\n");
6586: numlinepar++;
6587: if(mle==1)
6588: printf("\n");
6589: fprintf(ficlog,"\n");
6590: fprintf(ficparo,"\n");
6591: }
6592: for(i=1; i <=npar; i++)
6593: for(j=i+1;j<=npar;j++)
6594: matcov[i][j]=matcov[j][i];
6595:
6596: if(mle==1)
6597: printf("\n");
6598: fprintf(ficlog,"\n");
6599:
6600: fflush(ficlog);
6601:
6602: /*-------- Rewriting parameter file ----------*/
6603: strcpy(rfileres,"r"); /* "Rparameterfile */
6604: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
6605: strcat(rfileres,"."); /* */
6606: strcat(rfileres,optionfilext); /* Other files have txt extension */
6607: if((ficres =fopen(rfileres,"w"))==NULL) {
6608: printf("Problem writing new parameter file: %s\n", fileres);goto end;
6609: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
6610: }
6611: fprintf(ficres,"#%s\n",version);
6612: } /* End of mle != -3 */
6613:
1.186 brouard 6614: /* Main data
6615: */
1.126 brouard 6616: n= lastobs;
6617: num=lvector(1,n);
6618: moisnais=vector(1,n);
6619: annais=vector(1,n);
6620: moisdc=vector(1,n);
6621: andc=vector(1,n);
6622: agedc=vector(1,n);
6623: cod=ivector(1,n);
6624: weight=vector(1,n);
6625: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
6626: mint=matrix(1,maxwav,1,n);
6627: anint=matrix(1,maxwav,1,n);
1.131 brouard 6628: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 6629: tab=ivector(1,NCOVMAX);
1.144 brouard 6630: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.126 brouard 6631:
1.136 brouard 6632: /* Reads data from file datafile */
6633: if (readdata(datafile, firstobs, lastobs, &imx)==1)
6634: goto end;
6635:
6636: /* Calculation of the number of parameters from char model */
1.137 brouard 6637: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
6638: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
6639: k=3 V4 Tvar[k=3]= 4 (from V4)
6640: k=2 V1 Tvar[k=2]= 1 (from V1)
6641: k=1 Tvar[1]=2 (from V2)
6642: */
6643: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6644: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6645: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6646: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6647: */
6648: /* For model-covariate k tells which data-covariate to use but
6649: because this model-covariate is a construction we invent a new column
6650: ncovcol + k1
6651: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6652: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 6653: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 6654: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6655: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6656: */
1.145 brouard 6657: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6658: 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 6659: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6660: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 6661: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 6662: 4 covariates (3 plus signs)
6663: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6664: */
1.136 brouard 6665:
1.186 brouard 6666: /* Main decodemodel */
6667:
1.187 brouard 6668:
1.136 brouard 6669: if(decodemodel(model, lastobs) == 1)
6670: goto end;
6671:
1.137 brouard 6672: if((double)(lastobs-imx)/(double)imx > 1.10){
6673: nbwarn++;
6674: 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);
6675: 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);
6676: }
1.136 brouard 6677: /* if(mle==1){*/
1.137 brouard 6678: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6679: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 6680: }
6681:
6682: /*-calculation of age at interview from date of interview and age at death -*/
6683: agev=matrix(1,maxwav,1,imx);
6684:
6685: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6686: goto end;
6687:
1.126 brouard 6688:
1.136 brouard 6689: agegomp=(int)agemin;
6690: free_vector(moisnais,1,n);
6691: free_vector(annais,1,n);
1.126 brouard 6692: /* free_matrix(mint,1,maxwav,1,n);
6693: free_matrix(anint,1,maxwav,1,n);*/
6694: free_vector(moisdc,1,n);
6695: free_vector(andc,1,n);
1.145 brouard 6696: /* */
6697:
1.126 brouard 6698: wav=ivector(1,imx);
6699: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6700: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6701: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6702:
6703: /* Concatenates waves */
6704: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 6705: /* */
6706:
1.126 brouard 6707: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6708:
6709: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6710: ncodemax[1]=1;
1.145 brouard 6711: Ndum =ivector(-1,NCOVMAX);
1.187 brouard 6712: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
1.145 brouard 6713: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.186 brouard 6714: /* Nbcode gives the value of the lth modality of jth covariate, in
6715: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
6716: /* 1 to ncodemax[j] is the maximum value of this jth covariate */
1.145 brouard 6717:
6718: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6719: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
1.186 brouard 6720: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.145 brouard 6721: h=0;
6722:
6723:
6724: /*if (cptcovn > 0) */
1.126 brouard 6725:
1.145 brouard 6726:
1.126 brouard 6727: m=pow(2,cptcoveff);
6728:
1.131 brouard 6729: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
1.143 brouard 6730: 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 */
6731: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6732: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
1.126 brouard 6733: h++;
1.141 brouard 6734: if (h>m)
1.136 brouard 6735: h=1;
1.144 brouard 6736: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.186 brouard 6737: * For k=4 covariates, h goes from 1 to 2**k
6738: * codtabm(h,k)= 1 & (h-1) >> (k-1) ;
6739: * h\k 1 2 3 4
1.143 brouard 6740: *______________________________
6741: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6742: * 2 2 1 1 1
6743: * 3 i=2 1 2 1 1
6744: * 4 2 2 1 1
6745: * 5 i=3 1 i=2 1 2 1
6746: * 6 2 1 2 1
6747: * 7 i=4 1 2 2 1
6748: * 8 2 2 2 1
6749: * 9 i=5 1 i=3 1 i=2 1 1
6750: * 10 2 1 1 1
6751: * 11 i=6 1 2 1 1
6752: * 12 2 2 1 1
6753: * 13 i=7 1 i=4 1 2 1
6754: * 14 2 1 2 1
6755: * 15 i=8 1 2 2 1
6756: * 16 2 2 2 1
6757: */
1.141 brouard 6758: codtab[h][k]=j;
1.186 brouard 6759: /* codtab[12][3]=1; */
1.145 brouard 6760: /*codtab[h][Tvar[k]]=j;*/
1.130 brouard 6761: 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]]);
1.126 brouard 6762: }
6763: }
6764: }
6765: }
6766: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6767: codtab[1][2]=1;codtab[2][2]=2; */
6768: /* for(i=1; i <=m ;i++){
6769: for(k=1; k <=cptcovn; k++){
1.131 brouard 6770: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
1.126 brouard 6771: }
6772: printf("\n");
6773: }
6774: scanf("%d",i);*/
1.145 brouard 6775:
6776: free_ivector(Ndum,-1,NCOVMAX);
6777:
6778:
1.126 brouard 6779:
1.186 brouard 6780: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 6781: strcpy(optionfilegnuplot,optionfilefiname);
6782: if(mle==-3)
6783: strcat(optionfilegnuplot,"-mort");
6784: strcat(optionfilegnuplot,".gp");
6785:
6786: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6787: printf("Problem with file %s",optionfilegnuplot);
6788: }
6789: else{
6790: fprintf(ficgp,"\n# %s\n", version);
6791: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 6792: //fprintf(ficgp,"set missing 'NaNq'\n");
6793: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 6794: }
6795: /* fclose(ficgp);*/
1.186 brouard 6796:
6797:
6798: /* Initialisation of --------- index.htm --------*/
1.126 brouard 6799:
6800: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6801: if(mle==-3)
6802: strcat(optionfilehtm,"-mort");
6803: strcat(optionfilehtm,".htm");
6804: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 6805: printf("Problem with %s \n",optionfilehtm);
6806: exit(0);
1.126 brouard 6807: }
6808:
6809: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6810: strcat(optionfilehtmcov,"-cov.htm");
6811: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6812: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6813: }
6814: else{
6815: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6816: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6817: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6818: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6819: }
6820:
6821: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6822: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6823: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6824: \n\
6825: <hr size=\"2\" color=\"#EC5E5E\">\
6826: <ul><li><h4>Parameter files</h4>\n\
6827: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6828: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6829: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6830: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6831: - Date and time at start: %s</ul>\n",\
6832: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6833: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6834: fileres,fileres,\
6835: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6836: fflush(fichtm);
6837:
6838: strcpy(pathr,path);
6839: strcat(pathr,optionfilefiname);
1.184 brouard 6840: #ifdef WIN32
6841: _chdir(optionfilefiname); /* Move to directory named optionfile */
6842: #else
1.126 brouard 6843: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 6844: #endif
6845:
1.126 brouard 6846:
6847: /* Calculates basic frequencies. Computes observed prevalence at single age
6848: and prints on file fileres'p'. */
6849: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6850:
6851: fprintf(fichtm,"\n");
6852: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6853: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6854: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6855: imx,agemin,agemax,jmin,jmax,jmean);
6856: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6857: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6858: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6859: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6860: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6861:
6862:
6863: /* For Powell, parameters are in a vector p[] starting at p[1]
6864: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6865: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6866:
6867: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 6868: /* For mortality only */
1.126 brouard 6869: if (mle==-3){
1.136 brouard 6870: ximort=matrix(1,NDIM,1,NDIM);
1.186 brouard 6871: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 6872: cens=ivector(1,n);
6873: ageexmed=vector(1,n);
6874: agecens=vector(1,n);
6875: dcwave=ivector(1,n);
6876:
6877: for (i=1; i<=imx; i++){
6878: dcwave[i]=-1;
6879: for (m=firstpass; m<=lastpass; m++)
6880: if (s[m][i]>nlstate) {
6881: dcwave[i]=m;
6882: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6883: break;
6884: }
6885: }
6886:
6887: for (i=1; i<=imx; i++) {
6888: if (wav[i]>0){
6889: ageexmed[i]=agev[mw[1][i]][i];
6890: j=wav[i];
6891: agecens[i]=1.;
6892:
6893: if (ageexmed[i]> 1 && wav[i] > 0){
6894: agecens[i]=agev[mw[j][i]][i];
6895: cens[i]= 1;
6896: }else if (ageexmed[i]< 1)
6897: cens[i]= -1;
6898: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6899: cens[i]=0 ;
6900: }
6901: else cens[i]=-1;
6902: }
6903:
6904: for (i=1;i<=NDIM;i++) {
6905: for (j=1;j<=NDIM;j++)
6906: ximort[i][j]=(i == j ? 1.0 : 0.0);
6907: }
6908:
1.145 brouard 6909: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 6910: /*printf("%lf %lf", p[1], p[2]);*/
6911:
6912:
1.136 brouard 6913: #ifdef GSL
6914: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 6915: #else
1.126 brouard 6916: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 6917: #endif
1.126 brouard 6918: strcpy(filerespow,"pow-mort");
6919: strcat(filerespow,fileres);
6920: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6921: printf("Problem with resultfile: %s\n", filerespow);
6922: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6923: }
1.136 brouard 6924: #ifdef GSL
6925: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 6926: #else
1.126 brouard 6927: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 6928: #endif
1.126 brouard 6929: /* for (i=1;i<=nlstate;i++)
6930: for(j=1;j<=nlstate+ndeath;j++)
6931: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6932: */
6933: fprintf(ficrespow,"\n");
1.136 brouard 6934: #ifdef GSL
6935: /* gsl starts here */
6936: T = gsl_multimin_fminimizer_nmsimplex;
6937: gsl_multimin_fminimizer *sfm = NULL;
6938: gsl_vector *ss, *x;
6939: gsl_multimin_function minex_func;
6940:
6941: /* Initial vertex size vector */
6942: ss = gsl_vector_alloc (NDIM);
6943:
6944: if (ss == NULL){
6945: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6946: }
6947: /* Set all step sizes to 1 */
6948: gsl_vector_set_all (ss, 0.001);
6949:
6950: /* Starting point */
1.126 brouard 6951:
1.136 brouard 6952: x = gsl_vector_alloc (NDIM);
6953:
6954: if (x == NULL){
6955: gsl_vector_free(ss);
6956: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6957: }
6958:
6959: /* Initialize method and iterate */
6960: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 6961: /* gsl_vector_set(x, 0, 0.0268); */
6962: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 6963: gsl_vector_set(x, 0, p[1]);
6964: gsl_vector_set(x, 1, p[2]);
6965:
6966: minex_func.f = &gompertz_f;
6967: minex_func.n = NDIM;
6968: minex_func.params = (void *)&p; /* ??? */
6969:
6970: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6971: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6972:
6973: printf("Iterations beginning .....\n\n");
6974: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6975:
6976: iteri=0;
6977: while (rval == GSL_CONTINUE){
6978: iteri++;
6979: status = gsl_multimin_fminimizer_iterate(sfm);
6980:
6981: if (status) printf("error: %s\n", gsl_strerror (status));
6982: fflush(0);
6983:
6984: if (status)
6985: break;
6986:
6987: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6988: ssval = gsl_multimin_fminimizer_size (sfm);
6989:
6990: if (rval == GSL_SUCCESS)
6991: printf ("converged to a local maximum at\n");
6992:
6993: printf("%5d ", iteri);
6994: for (it = 0; it < NDIM; it++){
6995: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6996: }
6997: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6998: }
6999:
7000: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
7001:
7002: gsl_vector_free(x); /* initial values */
7003: gsl_vector_free(ss); /* inital step size */
7004: for (it=0; it<NDIM; it++){
7005: p[it+1]=gsl_vector_get(sfm->x,it);
7006: fprintf(ficrespow," %.12lf", p[it]);
7007: }
7008: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
7009: #endif
7010: #ifdef POWELL
7011: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
7012: #endif
1.126 brouard 7013: fclose(ficrespow);
7014:
7015: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
7016:
7017: for(i=1; i <=NDIM; i++)
7018: for(j=i+1;j<=NDIM;j++)
7019: matcov[i][j]=matcov[j][i];
7020:
7021: printf("\nCovariance matrix\n ");
7022: for(i=1; i <=NDIM; i++) {
7023: for(j=1;j<=NDIM;j++){
7024: printf("%f ",matcov[i][j]);
7025: }
7026: printf("\n ");
7027: }
7028:
7029: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
7030: for (i=1;i<=NDIM;i++)
7031: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
7032:
7033: lsurv=vector(1,AGESUP);
7034: lpop=vector(1,AGESUP);
7035: tpop=vector(1,AGESUP);
7036: lsurv[agegomp]=100000;
7037:
7038: for (k=agegomp;k<=AGESUP;k++) {
7039: agemortsup=k;
7040: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
7041: }
7042:
7043: for (k=agegomp;k<agemortsup;k++)
7044: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
7045:
7046: for (k=agegomp;k<agemortsup;k++){
7047: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
7048: sumlpop=sumlpop+lpop[k];
7049: }
7050:
7051: tpop[agegomp]=sumlpop;
7052: for (k=agegomp;k<(agemortsup-3);k++){
7053: /* tpop[k+1]=2;*/
7054: tpop[k+1]=tpop[k]-lpop[k];
7055: }
7056:
7057:
7058: printf("\nAge lx qx dx Lx Tx e(x)\n");
7059: for (k=agegomp;k<(agemortsup-2);k++)
7060: 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]);
7061:
7062:
7063: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
7064: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7065:
7066: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
7067: stepm, weightopt,\
7068: model,imx,p,matcov,agemortsup);
7069:
7070: free_vector(lsurv,1,AGESUP);
7071: free_vector(lpop,1,AGESUP);
7072: free_vector(tpop,1,AGESUP);
1.136 brouard 7073: #ifdef GSL
7074: free_ivector(cens,1,n);
7075: free_vector(agecens,1,n);
7076: free_ivector(dcwave,1,n);
7077: free_matrix(ximort,1,NDIM,1,NDIM);
7078: #endif
1.186 brouard 7079: } /* Endof if mle==-3 mortality only */
7080: /* Standard maximisation */
1.126 brouard 7081: else{ /* For mle >=1 */
1.132 brouard 7082: globpr=0;/* debug */
1.186 brouard 7083: /* Computes likelihood for initial parameters */
1.132 brouard 7084: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 7085: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7086: for (k=1; k<=npar;k++)
7087: printf(" %d %8.5f",k,p[k]);
7088: printf("\n");
1.186 brouard 7089: globpr=1; /* again, to print the contributions */
1.126 brouard 7090: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7091: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7092: for (k=1; k<=npar;k++)
7093: printf(" %d %8.5f",k,p[k]);
7094: printf("\n");
1.186 brouard 7095: if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
1.126 brouard 7096: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
7097: }
7098:
7099: /*--------- results files --------------*/
1.187 brouard 7100: 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 7101:
7102:
7103: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7104: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7105: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7106: for(i=1,jk=1; i <=nlstate; i++){
7107: for(k=1; k <=(nlstate+ndeath); k++){
7108: if (k != i) {
7109: printf("%d%d ",i,k);
7110: fprintf(ficlog,"%d%d ",i,k);
7111: fprintf(ficres,"%1d%1d ",i,k);
7112: for(j=1; j <=ncovmodel; j++){
1.190 ! brouard 7113: printf("%12.7f ",p[jk]);
! 7114: fprintf(ficlog,"%12.7f ",p[jk]);
! 7115: fprintf(ficres,"%12.7f ",p[jk]);
1.126 brouard 7116: jk++;
7117: }
7118: printf("\n");
7119: fprintf(ficlog,"\n");
7120: fprintf(ficres,"\n");
7121: }
7122: }
7123: }
7124: if(mle!=0){
7125: /* Computing hessian and covariance matrix */
7126: ftolhess=ftol; /* Usually correct */
7127: hesscov(matcov, p, npar, delti, ftolhess, func);
7128: }
7129: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
7130: printf("# Scales (for hessian or gradient estimation)\n");
7131: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
7132: for(i=1,jk=1; i <=nlstate; i++){
7133: for(j=1; j <=nlstate+ndeath; j++){
7134: if (j!=i) {
7135: fprintf(ficres,"%1d%1d",i,j);
7136: printf("%1d%1d",i,j);
7137: fprintf(ficlog,"%1d%1d",i,j);
7138: for(k=1; k<=ncovmodel;k++){
7139: printf(" %.5e",delti[jk]);
7140: fprintf(ficlog," %.5e",delti[jk]);
7141: fprintf(ficres," %.5e",delti[jk]);
7142: jk++;
7143: }
7144: printf("\n");
7145: fprintf(ficlog,"\n");
7146: fprintf(ficres,"\n");
7147: }
7148: }
7149: }
7150:
7151: 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");
7152: if(mle>=1)
7153: 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");
7154: 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");
7155: /* # 121 Var(a12)\n\ */
7156: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7157: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7158: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7159: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7160: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7161: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7162: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7163:
7164:
7165: /* Just to have a covariance matrix which will be more understandable
7166: even is we still don't want to manage dictionary of variables
7167: */
7168: for(itimes=1;itimes<=2;itimes++){
7169: jj=0;
7170: for(i=1; i <=nlstate; i++){
7171: for(j=1; j <=nlstate+ndeath; j++){
7172: if(j==i) continue;
7173: for(k=1; k<=ncovmodel;k++){
7174: jj++;
7175: ca[0]= k+'a'-1;ca[1]='\0';
7176: if(itimes==1){
7177: if(mle>=1)
7178: printf("#%1d%1d%d",i,j,k);
7179: fprintf(ficlog,"#%1d%1d%d",i,j,k);
7180: fprintf(ficres,"#%1d%1d%d",i,j,k);
7181: }else{
7182: if(mle>=1)
7183: printf("%1d%1d%d",i,j,k);
7184: fprintf(ficlog,"%1d%1d%d",i,j,k);
7185: fprintf(ficres,"%1d%1d%d",i,j,k);
7186: }
7187: ll=0;
7188: for(li=1;li <=nlstate; li++){
7189: for(lj=1;lj <=nlstate+ndeath; lj++){
7190: if(lj==li) continue;
7191: for(lk=1;lk<=ncovmodel;lk++){
7192: ll++;
7193: if(ll<=jj){
7194: cb[0]= lk +'a'-1;cb[1]='\0';
7195: if(ll<jj){
7196: if(itimes==1){
7197: if(mle>=1)
7198: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7199: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7200: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7201: }else{
7202: if(mle>=1)
7203: printf(" %.5e",matcov[jj][ll]);
7204: fprintf(ficlog," %.5e",matcov[jj][ll]);
7205: fprintf(ficres," %.5e",matcov[jj][ll]);
7206: }
7207: }else{
7208: if(itimes==1){
7209: if(mle>=1)
7210: printf(" Var(%s%1d%1d)",ca,i,j);
7211: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
7212: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
7213: }else{
7214: if(mle>=1)
7215: printf(" %.5e",matcov[jj][ll]);
7216: fprintf(ficlog," %.5e",matcov[jj][ll]);
7217: fprintf(ficres," %.5e",matcov[jj][ll]);
7218: }
7219: }
7220: }
7221: } /* end lk */
7222: } /* end lj */
7223: } /* end li */
7224: if(mle>=1)
7225: printf("\n");
7226: fprintf(ficlog,"\n");
7227: fprintf(ficres,"\n");
7228: numlinepar++;
7229: } /* end k*/
7230: } /*end j */
7231: } /* end i */
7232: } /* end itimes */
7233:
7234: fflush(ficlog);
7235: fflush(ficres);
7236:
7237: while((c=getc(ficpar))=='#' && c!= EOF){
7238: ungetc(c,ficpar);
7239: fgets(line, MAXLINE, ficpar);
1.141 brouard 7240: fputs(line,stdout);
1.126 brouard 7241: fputs(line,ficparo);
7242: }
7243: ungetc(c,ficpar);
7244:
7245: estepm=0;
7246: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
7247: if (estepm==0 || estepm < stepm) estepm=stepm;
7248: if (fage <= 2) {
7249: bage = ageminpar;
7250: fage = agemaxpar;
7251: }
7252:
7253: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
7254: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7255: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.186 brouard 7256:
7257: /* Other stuffs, more or less useful */
1.126 brouard 7258: while((c=getc(ficpar))=='#' && c!= EOF){
7259: ungetc(c,ficpar);
7260: fgets(line, MAXLINE, ficpar);
1.141 brouard 7261: fputs(line,stdout);
1.126 brouard 7262: fputs(line,ficparo);
7263: }
7264: ungetc(c,ficpar);
7265:
7266: 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);
7267: 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);
7268: 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);
7269: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7270: 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);
7271:
7272: while((c=getc(ficpar))=='#' && c!= EOF){
7273: ungetc(c,ficpar);
7274: fgets(line, MAXLINE, ficpar);
1.141 brouard 7275: fputs(line,stdout);
1.126 brouard 7276: fputs(line,ficparo);
7277: }
7278: ungetc(c,ficpar);
7279:
7280:
7281: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
7282: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
7283:
7284: fscanf(ficpar,"pop_based=%d\n",&popbased);
7285: fprintf(ficparo,"pop_based=%d\n",popbased);
7286: fprintf(ficres,"pop_based=%d\n",popbased);
7287:
7288: while((c=getc(ficpar))=='#' && c!= EOF){
7289: ungetc(c,ficpar);
7290: fgets(line, MAXLINE, ficpar);
1.141 brouard 7291: fputs(line,stdout);
1.126 brouard 7292: fputs(line,ficparo);
7293: }
7294: ungetc(c,ficpar);
7295:
7296: 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);
7297: 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);
7298: 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);
7299: 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);
7300: 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);
7301: /* day and month of proj2 are not used but only year anproj2.*/
7302:
7303:
7304:
1.145 brouard 7305: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
7306: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 7307:
7308: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
7309: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7310:
7311: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
7312: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
7313: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
7314:
7315: /*------------ free_vector -------------*/
7316: /* chdir(path); */
7317:
7318: free_ivector(wav,1,imx);
7319: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
7320: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
7321: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
7322: free_lvector(num,1,n);
7323: free_vector(agedc,1,n);
7324: /*free_matrix(covar,0,NCOVMAX,1,n);*/
7325: /*free_matrix(covar,1,NCOVMAX,1,n);*/
7326: fclose(ficparo);
7327: fclose(ficres);
7328:
7329:
1.186 brouard 7330: /* Other results (useful)*/
7331:
7332:
1.126 brouard 7333: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 7334: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
7335: prlim=matrix(1,nlstate,1,nlstate);
7336: prevalence_limit(p, prlim, ageminpar, agemaxpar);
1.126 brouard 7337: fclose(ficrespl);
7338:
1.145 brouard 7339: #ifdef FREEEXIT2
7340: #include "freeexit2.h"
7341: #endif
7342:
1.126 brouard 7343: /*------------- h Pij x at various ages ------------*/
1.180 brouard 7344: /*#include "hpijx.h"*/
7345: hPijx(p, bage, fage);
1.145 brouard 7346: fclose(ficrespij);
1.126 brouard 7347:
1.145 brouard 7348: /*-------------- Variance of one-step probabilities---*/
7349: k=1;
1.126 brouard 7350: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
7351:
7352:
7353: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7354: for(i=1;i<=AGESUP;i++)
7355: for(j=1;j<=NCOVMAX;j++)
7356: for(k=1;k<=NCOVMAX;k++)
7357: probs[i][j][k]=0.;
7358:
7359: /*---------- Forecasting ------------------*/
7360: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
7361: if(prevfcast==1){
7362: /* if(stepm ==1){*/
7363: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
7364: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
7365: /* } */
7366: /* else{ */
7367: /* erreur=108; */
7368: /* 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); */
7369: /* 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); */
7370: /* } */
7371: }
1.186 brouard 7372:
7373: /* ------ Other prevalence ratios------------ */
1.126 brouard 7374:
1.127 brouard 7375: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
7376:
7377: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
7378: /* 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",\
7379: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
7380: */
1.126 brouard 7381:
1.127 brouard 7382: if (mobilav!=0) {
7383: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7384: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
7385: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
7386: printf(" Error in movingaverage mobilav=%d\n",mobilav);
7387: }
1.126 brouard 7388: }
7389:
7390:
1.127 brouard 7391: /*---------- Health expectancies, no variances ------------*/
7392:
1.126 brouard 7393: strcpy(filerese,"e");
7394: strcat(filerese,fileres);
7395: if((ficreseij=fopen(filerese,"w"))==NULL) {
7396: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7397: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7398: }
7399: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
7400: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145 brouard 7401: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7402: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7403:
7404: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 7405: fprintf(ficreseij,"\n#****** ");
7406: for(j=1;j<=cptcoveff;j++) {
7407: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7408: }
7409: fprintf(ficreseij,"******\n");
7410:
7411: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7412: oldm=oldms;savm=savms;
7413: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
7414:
7415: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7416: /*}*/
1.127 brouard 7417: }
7418: fclose(ficreseij);
7419:
7420:
7421: /*---------- Health expectancies and variances ------------*/
7422:
7423:
7424: strcpy(filerest,"t");
7425: strcat(filerest,fileres);
7426: if((ficrest=fopen(filerest,"w"))==NULL) {
7427: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
7428: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
7429: }
7430: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7431: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7432:
1.126 brouard 7433:
7434: strcpy(fileresstde,"stde");
7435: strcat(fileresstde,fileres);
7436: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
7437: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7438: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7439: }
7440: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7441: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7442:
7443: strcpy(filerescve,"cve");
7444: strcat(filerescve,fileres);
7445: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
7446: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7447: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7448: }
7449: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7450: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7451:
7452: strcpy(fileresv,"v");
7453: strcat(fileresv,fileres);
7454: if((ficresvij=fopen(fileresv,"w"))==NULL) {
7455: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
7456: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
7457: }
7458: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7459: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7460:
1.145 brouard 7461: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7462: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7463:
7464: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7465: fprintf(ficrest,"\n#****** ");
1.126 brouard 7466: for(j=1;j<=cptcoveff;j++)
7467: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7468: fprintf(ficrest,"******\n");
7469:
7470: fprintf(ficresstdeij,"\n#****** ");
7471: fprintf(ficrescveij,"\n#****** ");
7472: for(j=1;j<=cptcoveff;j++) {
7473: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7474: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7475: }
7476: fprintf(ficresstdeij,"******\n");
7477: fprintf(ficrescveij,"******\n");
7478:
7479: fprintf(ficresvij,"\n#****** ");
7480: for(j=1;j<=cptcoveff;j++)
7481: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7482: fprintf(ficresvij,"******\n");
7483:
7484: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7485: oldm=oldms;savm=savms;
1.127 brouard 7486: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.145 brouard 7487: /*
7488: */
7489: /* goto endfree; */
1.126 brouard 7490:
7491: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7492: pstamp(ficrest);
1.145 brouard 7493:
7494:
1.128 brouard 7495: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.145 brouard 7496: oldm=oldms;savm=savms; /* Segmentation fault */
1.161 brouard 7497: cptcod= 0; /* To be deleted */
7498: 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 7499: 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 7500: if(vpopbased==1)
7501: 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);
7502: else
7503: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
7504: fprintf(ficrest,"# Age e.. (std) ");
7505: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
7506: fprintf(ficrest,"\n");
1.126 brouard 7507:
1.128 brouard 7508: epj=vector(1,nlstate+1);
7509: for(age=bage; age <=fage ;age++){
7510: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
7511: if (vpopbased==1) {
7512: if(mobilav ==0){
7513: for(i=1; i<=nlstate;i++)
7514: prlim[i][i]=probs[(int)age][i][k];
7515: }else{ /* mobilav */
7516: for(i=1; i<=nlstate;i++)
7517: prlim[i][i]=mobaverage[(int)age][i][k];
7518: }
1.126 brouard 7519: }
7520:
1.128 brouard 7521: fprintf(ficrest," %4.0f",age);
7522: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
7523: for(i=1, epj[j]=0.;i <=nlstate;i++) {
7524: epj[j] += prlim[i][i]*eij[i][j][(int)age];
7525: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
7526: }
7527: epj[nlstate+1] +=epj[j];
1.126 brouard 7528: }
7529:
1.128 brouard 7530: for(i=1, vepp=0.;i <=nlstate;i++)
7531: for(j=1;j <=nlstate;j++)
7532: vepp += vareij[i][j][(int)age];
7533: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
7534: for(j=1;j <=nlstate;j++){
7535: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
7536: }
7537: fprintf(ficrest,"\n");
1.126 brouard 7538: }
7539: }
7540: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7541: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7542: free_vector(epj,1,nlstate+1);
1.145 brouard 7543: /*}*/
1.126 brouard 7544: }
7545: free_vector(weight,1,n);
1.145 brouard 7546: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 7547: free_imatrix(s,1,maxwav+1,1,n);
7548: free_matrix(anint,1,maxwav,1,n);
7549: free_matrix(mint,1,maxwav,1,n);
7550: free_ivector(cod,1,n);
7551: free_ivector(tab,1,NCOVMAX);
7552: fclose(ficresstdeij);
7553: fclose(ficrescveij);
7554: fclose(ficresvij);
7555: fclose(ficrest);
7556: fclose(ficpar);
7557:
7558: /*------- Variance of period (stable) prevalence------*/
7559:
7560: strcpy(fileresvpl,"vpl");
7561: strcat(fileresvpl,fileres);
7562: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
7563: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
7564: exit(0);
7565: }
7566: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
7567:
1.145 brouard 7568: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7569: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7570:
7571: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7572: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 7573: for(j=1;j<=cptcoveff;j++)
7574: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7575: fprintf(ficresvpl,"******\n");
7576:
7577: varpl=matrix(1,nlstate,(int) bage, (int) fage);
7578: oldm=oldms;savm=savms;
7579: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
7580: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7581: /*}*/
1.126 brouard 7582: }
7583:
7584: fclose(ficresvpl);
7585:
7586: /*---------- End : free ----------------*/
7587: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7588: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7589: } /* mle==-3 arrives here for freeing */
1.164 brouard 7590: /* endfree:*/
1.141 brouard 7591: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 7592: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
7593: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
7594: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
7595: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
7596: free_matrix(covar,0,NCOVMAX,1,n);
7597: free_matrix(matcov,1,npar,1,npar);
7598: /*free_vector(delti,1,npar);*/
7599: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7600: free_matrix(agev,1,maxwav,1,imx);
7601: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7602:
1.145 brouard 7603: free_ivector(ncodemax,1,NCOVMAX);
7604: free_ivector(Tvar,1,NCOVMAX);
7605: free_ivector(Tprod,1,NCOVMAX);
7606: free_ivector(Tvaraff,1,NCOVMAX);
7607: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 7608:
7609: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
7610: free_imatrix(codtab,1,100,1,10);
7611: fflush(fichtm);
7612: fflush(ficgp);
7613:
7614:
7615: if((nberr >0) || (nbwarn>0)){
7616: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
7617: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
7618: }else{
7619: printf("End of Imach\n");
7620: fprintf(ficlog,"End of Imach\n");
7621: }
7622: printf("See log file on %s\n",filelog);
7623: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 7624: /*(void) gettimeofday(&end_time,&tzp);*/
7625: rend_time = time(NULL);
7626: end_time = *localtime(&rend_time);
7627: /* tml = *localtime(&end_time.tm_sec); */
7628: strcpy(strtend,asctime(&end_time));
1.126 brouard 7629: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
7630: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 7631: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 7632:
1.157 brouard 7633: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7634: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7635: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 7636: /* printf("Total time was %d uSec.\n", total_usecs);*/
7637: /* if(fileappend(fichtm,optionfilehtm)){ */
7638: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7639: fclose(fichtm);
7640: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7641: fclose(fichtmcov);
7642: fclose(ficgp);
7643: fclose(ficlog);
7644: /*------ End -----------*/
7645:
7646:
7647: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 7648: #ifdef WIN32
7649: if (_chdir(pathcd) != 0)
7650: printf("Can't move to directory %s!\n",path);
7651: if(_getcwd(pathcd,MAXLINE) > 0)
7652: #else
1.126 brouard 7653: if(chdir(pathcd) != 0)
1.184 brouard 7654: printf("Can't move to directory %s!\n", path);
7655: if (getcwd(pathcd, MAXLINE) > 0)
7656: #endif
1.126 brouard 7657: printf("Current directory %s!\n",pathcd);
7658: /*strcat(plotcmd,CHARSEPARATOR);*/
7659: sprintf(plotcmd,"gnuplot");
1.157 brouard 7660: #ifdef _WIN32
1.126 brouard 7661: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
7662: #endif
7663: if(!stat(plotcmd,&info)){
1.158 brouard 7664: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7665: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 7666: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 7667: }else
7668: strcpy(pplotcmd,plotcmd);
1.157 brouard 7669: #ifdef __unix
1.126 brouard 7670: strcpy(plotcmd,GNUPLOTPROGRAM);
7671: if(!stat(plotcmd,&info)){
1.158 brouard 7672: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7673: }else
7674: strcpy(pplotcmd,plotcmd);
7675: #endif
7676: }else
7677: strcpy(pplotcmd,plotcmd);
7678:
7679: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 7680: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7681:
7682: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 7683: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 7684: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 7685: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 7686: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 7687: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 7688: }
1.158 brouard 7689: printf(" Successful, please wait...");
1.126 brouard 7690: while (z[0] != 'q') {
7691: /* chdir(path); */
1.154 brouard 7692: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 7693: scanf("%s",z);
7694: /* if (z[0] == 'c') system("./imach"); */
7695: if (z[0] == 'e') {
1.158 brouard 7696: #ifdef __APPLE__
1.152 brouard 7697: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 7698: #elif __linux
7699: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 7700: #else
1.152 brouard 7701: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 7702: #endif
7703: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7704: system(pplotcmd);
1.126 brouard 7705: }
7706: else if (z[0] == 'g') system(plotcmd);
7707: else if (z[0] == 'q') exit(0);
7708: }
7709: end:
7710: while (z[0] != 'q') {
7711: printf("\nType q for exiting: ");
7712: scanf("%s",z);
7713: }
7714: }
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