1: /* $Id: imach.c,v 1.164 2014/12/16 10:52:11 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.164 2014/12/16 10:52:11 brouard
5: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
6:
7: * imach.c (Module): Merging 1.61 to 1.162
8:
9: Revision 1.163 2014/12/16 10:30:11 brouard
10: * imach.c (Module): Merging 1.61 to 1.162
11:
12: Revision 1.162 2014/09/25 11:43:39 brouard
13: Summary: temporary backup 0.99!
14:
15: Revision 1.1 2014/09/16 11:06:58 brouard
16: Summary: With some code (wrong) for nlopt
17:
18: Author:
19:
20: Revision 1.161 2014/09/15 20:41:41 brouard
21: Summary: Problem with macro SQR on Intel compiler
22:
23: Revision 1.160 2014/09/02 09:24:05 brouard
24: *** empty log message ***
25:
26: Revision 1.159 2014/09/01 10:34:10 brouard
27: Summary: WIN32
28: Author: Brouard
29:
30: Revision 1.158 2014/08/27 17:11:51 brouard
31: *** empty log message ***
32:
33: Revision 1.157 2014/08/27 16:26:55 brouard
34: Summary: Preparing windows Visual studio version
35: Author: Brouard
36:
37: In order to compile on Visual studio, time.h is now correct and time_t
38: and tm struct should be used. difftime should be used but sometimes I
39: just make the differences in raw time format (time(&now).
40: Trying to suppress #ifdef LINUX
41: Add xdg-open for __linux in order to open default browser.
42:
43: Revision 1.156 2014/08/25 20:10:10 brouard
44: *** empty log message ***
45:
46: Revision 1.155 2014/08/25 18:32:34 brouard
47: Summary: New compile, minor changes
48: Author: Brouard
49:
50: Revision 1.154 2014/06/20 17:32:08 brouard
51: Summary: Outputs now all graphs of convergence to period prevalence
52:
53: Revision 1.153 2014/06/20 16:45:46 brouard
54: Summary: If 3 live state, convergence to period prevalence on same graph
55: Author: Brouard
56:
57: Revision 1.152 2014/06/18 17:54:09 brouard
58: Summary: open browser, use gnuplot on same dir than imach if not found in the path
59:
60: Revision 1.151 2014/06/18 16:43:30 brouard
61: *** empty log message ***
62:
63: Revision 1.150 2014/06/18 16:42:35 brouard
64: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
65: Author: brouard
66:
67: Revision 1.149 2014/06/18 15:51:14 brouard
68: Summary: Some fixes in parameter files errors
69: Author: Nicolas Brouard
70:
71: Revision 1.148 2014/06/17 17:38:48 brouard
72: Summary: Nothing new
73: Author: Brouard
74:
75: Just a new packaging for OS/X version 0.98nS
76:
77: Revision 1.147 2014/06/16 10:33:11 brouard
78: *** empty log message ***
79:
80: Revision 1.146 2014/06/16 10:20:28 brouard
81: Summary: Merge
82: Author: Brouard
83:
84: Merge, before building revised version.
85:
86: Revision 1.145 2014/06/10 21:23:15 brouard
87: Summary: Debugging with valgrind
88: Author: Nicolas Brouard
89:
90: Lot of changes in order to output the results with some covariates
91: After the Edimburgh REVES conference 2014, it seems mandatory to
92: improve the code.
93: No more memory valgrind error but a lot has to be done in order to
94: continue the work of splitting the code into subroutines.
95: Also, decodemodel has been improved. Tricode is still not
96: optimal. nbcode should be improved. Documentation has been added in
97: the source code.
98:
99: Revision 1.143 2014/01/26 09:45:38 brouard
100: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
101:
102: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
103: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
104:
105: Revision 1.142 2014/01/26 03:57:36 brouard
106: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
107:
108: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
109:
110: Revision 1.141 2014/01/26 02:42:01 brouard
111: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
112:
113: Revision 1.140 2011/09/02 10:37:54 brouard
114: Summary: times.h is ok with mingw32 now.
115:
116: Revision 1.139 2010/06/14 07:50:17 brouard
117: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
118: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
119:
120: Revision 1.138 2010/04/30 18:19:40 brouard
121: *** empty log message ***
122:
123: Revision 1.137 2010/04/29 18:11:38 brouard
124: (Module): Checking covariates for more complex models
125: than V1+V2. A lot of change to be done. Unstable.
126:
127: Revision 1.136 2010/04/26 20:30:53 brouard
128: (Module): merging some libgsl code. Fixing computation
129: of likelione (using inter/intrapolation if mle = 0) in order to
130: get same likelihood as if mle=1.
131: Some cleaning of code and comments added.
132:
133: Revision 1.135 2009/10/29 15:33:14 brouard
134: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
135:
136: Revision 1.134 2009/10/29 13:18:53 brouard
137: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
138:
139: Revision 1.133 2009/07/06 10:21:25 brouard
140: just nforces
141:
142: Revision 1.132 2009/07/06 08:22:05 brouard
143: Many tings
144:
145: Revision 1.131 2009/06/20 16:22:47 brouard
146: Some dimensions resccaled
147:
148: Revision 1.130 2009/05/26 06:44:34 brouard
149: (Module): Max Covariate is now set to 20 instead of 8. A
150: lot of cleaning with variables initialized to 0. Trying to make
151: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
152:
153: Revision 1.129 2007/08/31 13:49:27 lievre
154: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
155:
156: Revision 1.128 2006/06/30 13:02:05 brouard
157: (Module): Clarifications on computing e.j
158:
159: Revision 1.127 2006/04/28 18:11:50 brouard
160: (Module): Yes the sum of survivors was wrong since
161: imach-114 because nhstepm was no more computed in the age
162: loop. Now we define nhstepma in the age loop.
163: (Module): In order to speed up (in case of numerous covariates) we
164: compute health expectancies (without variances) in a first step
165: and then all the health expectancies with variances or standard
166: deviation (needs data from the Hessian matrices) which slows the
167: computation.
168: In the future we should be able to stop the program is only health
169: expectancies and graph are needed without standard deviations.
170:
171: Revision 1.126 2006/04/28 17:23:28 brouard
172: (Module): Yes the sum of survivors was wrong since
173: imach-114 because nhstepm was no more computed in the age
174: loop. Now we define nhstepma in the age loop.
175: Version 0.98h
176:
177: Revision 1.125 2006/04/04 15:20:31 lievre
178: Errors in calculation of health expectancies. Age was not initialized.
179: Forecasting file added.
180:
181: Revision 1.124 2006/03/22 17:13:53 lievre
182: Parameters are printed with %lf instead of %f (more numbers after the comma).
183: The log-likelihood is printed in the log file
184:
185: Revision 1.123 2006/03/20 10:52:43 brouard
186: * imach.c (Module): <title> changed, corresponds to .htm file
187: name. <head> headers where missing.
188:
189: * imach.c (Module): Weights can have a decimal point as for
190: English (a comma might work with a correct LC_NUMERIC environment,
191: otherwise the weight is truncated).
192: Modification of warning when the covariates values are not 0 or
193: 1.
194: Version 0.98g
195:
196: Revision 1.122 2006/03/20 09:45:41 brouard
197: (Module): Weights can have a decimal point as for
198: English (a comma might work with a correct LC_NUMERIC environment,
199: otherwise the weight is truncated).
200: Modification of warning when the covariates values are not 0 or
201: 1.
202: Version 0.98g
203:
204: Revision 1.121 2006/03/16 17:45:01 lievre
205: * imach.c (Module): Comments concerning covariates added
206:
207: * imach.c (Module): refinements in the computation of lli if
208: status=-2 in order to have more reliable computation if stepm is
209: not 1 month. Version 0.98f
210:
211: Revision 1.120 2006/03/16 15:10:38 lievre
212: (Module): refinements in the computation of lli if
213: status=-2 in order to have more reliable computation if stepm is
214: not 1 month. Version 0.98f
215:
216: Revision 1.119 2006/03/15 17:42:26 brouard
217: (Module): Bug if status = -2, the loglikelihood was
218: computed as likelihood omitting the logarithm. Version O.98e
219:
220: Revision 1.118 2006/03/14 18:20:07 brouard
221: (Module): varevsij Comments added explaining the second
222: table of variances if popbased=1 .
223: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
224: (Module): Function pstamp added
225: (Module): Version 0.98d
226:
227: Revision 1.117 2006/03/14 17:16:22 brouard
228: (Module): varevsij Comments added explaining the second
229: table of variances if popbased=1 .
230: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
231: (Module): Function pstamp added
232: (Module): Version 0.98d
233:
234: Revision 1.116 2006/03/06 10:29:27 brouard
235: (Module): Variance-covariance wrong links and
236: varian-covariance of ej. is needed (Saito).
237:
238: Revision 1.115 2006/02/27 12:17:45 brouard
239: (Module): One freematrix added in mlikeli! 0.98c
240:
241: Revision 1.114 2006/02/26 12:57:58 brouard
242: (Module): Some improvements in processing parameter
243: filename with strsep.
244:
245: Revision 1.113 2006/02/24 14:20:24 brouard
246: (Module): Memory leaks checks with valgrind and:
247: datafile was not closed, some imatrix were not freed and on matrix
248: allocation too.
249:
250: Revision 1.112 2006/01/30 09:55:26 brouard
251: (Module): Back to gnuplot.exe instead of wgnuplot.exe
252:
253: Revision 1.111 2006/01/25 20:38:18 brouard
254: (Module): Lots of cleaning and bugs added (Gompertz)
255: (Module): Comments can be added in data file. Missing date values
256: can be a simple dot '.'.
257:
258: Revision 1.110 2006/01/25 00:51:50 brouard
259: (Module): Lots of cleaning and bugs added (Gompertz)
260:
261: Revision 1.109 2006/01/24 19:37:15 brouard
262: (Module): Comments (lines starting with a #) are allowed in data.
263:
264: Revision 1.108 2006/01/19 18:05:42 lievre
265: Gnuplot problem appeared...
266: To be fixed
267:
268: Revision 1.107 2006/01/19 16:20:37 brouard
269: Test existence of gnuplot in imach path
270:
271: Revision 1.106 2006/01/19 13:24:36 brouard
272: Some cleaning and links added in html output
273:
274: Revision 1.105 2006/01/05 20:23:19 lievre
275: *** empty log message ***
276:
277: Revision 1.104 2005/09/30 16:11:43 lievre
278: (Module): sump fixed, loop imx fixed, and simplifications.
279: (Module): If the status is missing at the last wave but we know
280: that the person is alive, then we can code his/her status as -2
281: (instead of missing=-1 in earlier versions) and his/her
282: contributions to the likelihood is 1 - Prob of dying from last
283: health status (= 1-p13= p11+p12 in the easiest case of somebody in
284: the healthy state at last known wave). Version is 0.98
285:
286: Revision 1.103 2005/09/30 15:54:49 lievre
287: (Module): sump fixed, loop imx fixed, and simplifications.
288:
289: Revision 1.102 2004/09/15 17:31:30 brouard
290: Add the possibility to read data file including tab characters.
291:
292: Revision 1.101 2004/09/15 10:38:38 brouard
293: Fix on curr_time
294:
295: Revision 1.100 2004/07/12 18:29:06 brouard
296: Add version for Mac OS X. Just define UNIX in Makefile
297:
298: Revision 1.99 2004/06/05 08:57:40 brouard
299: *** empty log message ***
300:
301: Revision 1.98 2004/05/16 15:05:56 brouard
302: New version 0.97 . First attempt to estimate force of mortality
303: directly from the data i.e. without the need of knowing the health
304: state at each age, but using a Gompertz model: log u =a + b*age .
305: This is the basic analysis of mortality and should be done before any
306: other analysis, in order to test if the mortality estimated from the
307: cross-longitudinal survey is different from the mortality estimated
308: from other sources like vital statistic data.
309:
310: The same imach parameter file can be used but the option for mle should be -3.
311:
312: Agnès, who wrote this part of the code, tried to keep most of the
313: former routines in order to include the new code within the former code.
314:
315: The output is very simple: only an estimate of the intercept and of
316: the slope with 95% confident intervals.
317:
318: Current limitations:
319: A) Even if you enter covariates, i.e. with the
320: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
321: B) There is no computation of Life Expectancy nor Life Table.
322:
323: Revision 1.97 2004/02/20 13:25:42 lievre
324: Version 0.96d. Population forecasting command line is (temporarily)
325: suppressed.
326:
327: Revision 1.96 2003/07/15 15:38:55 brouard
328: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
329: rewritten within the same printf. Workaround: many printfs.
330:
331: Revision 1.95 2003/07/08 07:54:34 brouard
332: * imach.c (Repository):
333: (Repository): Using imachwizard code to output a more meaningful covariance
334: matrix (cov(a12,c31) instead of numbers.
335:
336: Revision 1.94 2003/06/27 13:00:02 brouard
337: Just cleaning
338:
339: Revision 1.93 2003/06/25 16:33:55 brouard
340: (Module): On windows (cygwin) function asctime_r doesn't
341: exist so I changed back to asctime which exists.
342: (Module): Version 0.96b
343:
344: Revision 1.92 2003/06/25 16:30:45 brouard
345: (Module): On windows (cygwin) function asctime_r doesn't
346: exist so I changed back to asctime which exists.
347:
348: Revision 1.91 2003/06/25 15:30:29 brouard
349: * imach.c (Repository): Duplicated warning errors corrected.
350: (Repository): Elapsed time after each iteration is now output. It
351: helps to forecast when convergence will be reached. Elapsed time
352: is stamped in powell. We created a new html file for the graphs
353: concerning matrix of covariance. It has extension -cov.htm.
354:
355: Revision 1.90 2003/06/24 12:34:15 brouard
356: (Module): Some bugs corrected for windows. Also, when
357: mle=-1 a template is output in file "or"mypar.txt with the design
358: of the covariance matrix to be input.
359:
360: Revision 1.89 2003/06/24 12:30:52 brouard
361: (Module): Some bugs corrected for windows. Also, when
362: mle=-1 a template is output in file "or"mypar.txt with the design
363: of the covariance matrix to be input.
364:
365: Revision 1.88 2003/06/23 17:54:56 brouard
366: * 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.
367:
368: Revision 1.87 2003/06/18 12:26:01 brouard
369: Version 0.96
370:
371: Revision 1.86 2003/06/17 20:04:08 brouard
372: (Module): Change position of html and gnuplot routines and added
373: routine fileappend.
374:
375: Revision 1.85 2003/06/17 13:12:43 brouard
376: * imach.c (Repository): Check when date of death was earlier that
377: current date of interview. It may happen when the death was just
378: prior to the death. In this case, dh was negative and likelihood
379: was wrong (infinity). We still send an "Error" but patch by
380: assuming that the date of death was just one stepm after the
381: interview.
382: (Repository): Because some people have very long ID (first column)
383: we changed int to long in num[] and we added a new lvector for
384: memory allocation. But we also truncated to 8 characters (left
385: truncation)
386: (Repository): No more line truncation errors.
387:
388: Revision 1.84 2003/06/13 21:44:43 brouard
389: * imach.c (Repository): Replace "freqsummary" at a correct
390: place. It differs from routine "prevalence" which may be called
391: many times. Probs is memory consuming and must be used with
392: parcimony.
393: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
394:
395: Revision 1.83 2003/06/10 13:39:11 lievre
396: *** empty log message ***
397:
398: Revision 1.82 2003/06/05 15:57:20 brouard
399: Add log in imach.c and fullversion number is now printed.
400:
401: */
402: /*
403: Interpolated Markov Chain
404:
405: Short summary of the programme:
406:
407: This program computes Healthy Life Expectancies from
408: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
409: first survey ("cross") where individuals from different ages are
410: interviewed on their health status or degree of disability (in the
411: case of a health survey which is our main interest) -2- at least a
412: second wave of interviews ("longitudinal") which measure each change
413: (if any) in individual health status. Health expectancies are
414: computed from the time spent in each health state according to a
415: model. More health states you consider, more time is necessary to reach the
416: Maximum Likelihood of the parameters involved in the model. The
417: simplest model is the multinomial logistic model where pij is the
418: probability to be observed in state j at the second wave
419: conditional to be observed in state i at the first wave. Therefore
420: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
421: 'age' is age and 'sex' is a covariate. If you want to have a more
422: complex model than "constant and age", you should modify the program
423: where the markup *Covariates have to be included here again* invites
424: you to do it. More covariates you add, slower the
425: convergence.
426:
427: The advantage of this computer programme, compared to a simple
428: multinomial logistic model, is clear when the delay between waves is not
429: identical for each individual. Also, if a individual missed an
430: intermediate interview, the information is lost, but taken into
431: account using an interpolation or extrapolation.
432:
433: hPijx is the probability to be observed in state i at age x+h
434: conditional to the observed state i at age x. The delay 'h' can be
435: split into an exact number (nh*stepm) of unobserved intermediate
436: states. This elementary transition (by month, quarter,
437: semester or year) is modelled as a multinomial logistic. The hPx
438: matrix is simply the matrix product of nh*stepm elementary matrices
439: and the contribution of each individual to the likelihood is simply
440: hPijx.
441:
442: Also this programme outputs the covariance matrix of the parameters but also
443: of the life expectancies. It also computes the period (stable) prevalence.
444:
445: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
446: Institut national d'études démographiques, Paris.
447: This software have been partly granted by Euro-REVES, a concerted action
448: from the European Union.
449: It is copyrighted identically to a GNU software product, ie programme and
450: software can be distributed freely for non commercial use. Latest version
451: can be accessed at http://euroreves.ined.fr/imach .
452:
453: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
454: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
455:
456: **********************************************************************/
457: /*
458: main
459: read parameterfile
460: read datafile
461: concatwav
462: freqsummary
463: if (mle >= 1)
464: mlikeli
465: print results files
466: if mle==1
467: computes hessian
468: read end of parameter file: agemin, agemax, bage, fage, estepm
469: begin-prev-date,...
470: open gnuplot file
471: open html file
472: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
473: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
474: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
475: freexexit2 possible for memory heap.
476:
477: h Pij x | pij_nom ficrestpij
478: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
479: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
480: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
481:
482: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
483: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
484: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
485: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
486: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
487:
488: forecasting if prevfcast==1 prevforecast call prevalence()
489: health expectancies
490: Variance-covariance of DFLE
491: prevalence()
492: movingaverage()
493: varevsij()
494: if popbased==1 varevsij(,popbased)
495: total life expectancies
496: Variance of period (stable) prevalence
497: end
498: */
499:
500:
501:
502:
503: #include <math.h>
504: #include <stdio.h>
505: #include <stdlib.h>
506: #include <string.h>
507:
508: #ifdef _WIN32
509: #include <io.h>
510: #else
511: #include <unistd.h>
512: #endif
513:
514: #include <limits.h>
515: #include <sys/types.h>
516: #include <sys/stat.h>
517: #include <errno.h>
518: /* extern int errno; */
519:
520: /* #ifdef LINUX */
521: /* #include <time.h> */
522: /* #include "timeval.h" */
523: /* #else */
524: /* #include <sys/time.h> */
525: /* #endif */
526:
527: #include <time.h>
528:
529: #ifdef GSL
530: #include <gsl/gsl_errno.h>
531: #include <gsl/gsl_multimin.h>
532: #endif
533:
534: #ifdef NLOPT
535: #include <nlopt.h>
536: typedef struct {
537: double (* function)(double [] );
538: } myfunc_data ;
539: #endif
540:
541: /* #include <libintl.h> */
542: /* #define _(String) gettext (String) */
543:
544: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
545:
546: #define GNUPLOTPROGRAM "gnuplot"
547: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
548: #define FILENAMELENGTH 132
549:
550: #define GLOCK_ERROR_NOPATH -1 /* empty path */
551: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
552:
553: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
554: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
555:
556: #define NINTERVMAX 8
557: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
558: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
559: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
560: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
561: #define MAXN 20000
562: #define YEARM 12. /**< Number of months per year */
563: #define AGESUP 130
564: #define AGEBASE 40
565: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
566: #ifdef _WIN32
567: #define DIRSEPARATOR '\\'
568: #define CHARSEPARATOR "\\"
569: #define ODIRSEPARATOR '/'
570: #else
571: #define DIRSEPARATOR '/'
572: #define CHARSEPARATOR "/"
573: #define ODIRSEPARATOR '\\'
574: #endif
575:
576: /* $Id: imach.c,v 1.164 2014/12/16 10:52:11 brouard Exp $ */
577: /* $State: Exp $ */
578:
579: char version[]="Imach version 0.99, September 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
580: char fullversion[]="$Revision: 1.164 $ $Date: 2014/12/16 10:52:11 $";
581: char strstart[80];
582: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
583: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
584: int nvar=0, nforce=0; /* Number of variables, number of forces */
585: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
586: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
587: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
588: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
589: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
590: int cptcovprodnoage=0; /**< Number of covariate products without age */
591: int cptcoveff=0; /* Total number of covariates to vary for printing results */
592: int cptcov=0; /* Working variable */
593: int npar=NPARMAX;
594: int nlstate=2; /* Number of live states */
595: int ndeath=1; /* Number of dead states */
596: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
597: int popbased=0;
598:
599: int *wav; /* Number of waves for this individuual 0 is possible */
600: int maxwav=0; /* Maxim number of waves */
601: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
602: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
603: int gipmx=0, gsw=0; /* Global variables on the number of contributions
604: to the likelihood and the sum of weights (done by funcone)*/
605: int mle=1, weightopt=0;
606: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
607: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
608: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
609: * wave mi and wave mi+1 is not an exact multiple of stepm. */
610: int countcallfunc=0; /* Count the number of calls to func */
611: double jmean=1; /* Mean space between 2 waves */
612: double **matprod2(); /* test */
613: double **oldm, **newm, **savm; /* Working pointers to matrices */
614: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
615: /*FILE *fic ; */ /* Used in readdata only */
616: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
617: FILE *ficlog, *ficrespow;
618: int globpr=0; /* Global variable for printing or not */
619: double fretone; /* Only one call to likelihood */
620: long ipmx=0; /* Number of contributions */
621: double sw; /* Sum of weights */
622: char filerespow[FILENAMELENGTH];
623: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
624: FILE *ficresilk;
625: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
626: FILE *ficresprobmorprev;
627: FILE *fichtm, *fichtmcov; /* Html File */
628: FILE *ficreseij;
629: char filerese[FILENAMELENGTH];
630: FILE *ficresstdeij;
631: char fileresstde[FILENAMELENGTH];
632: FILE *ficrescveij;
633: char filerescve[FILENAMELENGTH];
634: FILE *ficresvij;
635: char fileresv[FILENAMELENGTH];
636: FILE *ficresvpl;
637: char fileresvpl[FILENAMELENGTH];
638: char title[MAXLINE];
639: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
640: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
641: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
642: char command[FILENAMELENGTH];
643: int outcmd=0;
644:
645: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
646:
647: char filelog[FILENAMELENGTH]; /* Log file */
648: char filerest[FILENAMELENGTH];
649: char fileregp[FILENAMELENGTH];
650: char popfile[FILENAMELENGTH];
651:
652: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
653:
654: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
655: /* struct timezone tzp; */
656: /* extern int gettimeofday(); */
657: struct tm tml, *gmtime(), *localtime();
658:
659: extern time_t time();
660:
661: struct tm start_time, end_time, curr_time, last_time, forecast_time;
662: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
663: struct tm tm;
664:
665: char strcurr[80], strfor[80];
666:
667: char *endptr;
668: long lval;
669: double dval;
670:
671: #define NR_END 1
672: #define FREE_ARG char*
673: #define FTOL 1.0e-10
674:
675: #define NRANSI
676: #define ITMAX 200
677:
678: #define TOL 2.0e-4
679:
680: #define CGOLD 0.3819660
681: #define ZEPS 1.0e-10
682: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
683:
684: #define GOLD 1.618034
685: #define GLIMIT 100.0
686: #define TINY 1.0e-20
687:
688: static double maxarg1,maxarg2;
689: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
690: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
691:
692: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
693: #define rint(a) floor(a+0.5)
694:
695: static double sqrarg;
696: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
697: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
698: int agegomp= AGEGOMP;
699:
700: int imx;
701: int stepm=1;
702: /* Stepm, step in month: minimum step interpolation*/
703:
704: int estepm;
705: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
706:
707: int m,nb;
708: long *num;
709: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
710: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
711: double **pmmij, ***probs;
712: double *ageexmed,*agecens;
713: double dateintmean=0;
714:
715: double *weight;
716: int **s; /* Status */
717: double *agedc;
718: double **covar; /**< covar[j,i], value of jth covariate for individual i,
719: * covar=matrix(0,NCOVMAX,1,n);
720: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
721: double idx;
722: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
723: int *Ndum; /** Freq of modality (tricode */
724: int **codtab; /**< codtab=imatrix(1,100,1,10); */
725: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
726: double *lsurv, *lpop, *tpop;
727:
728: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
729: double ftolhess; /**< Tolerance for computing hessian */
730:
731: /**************** split *************************/
732: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
733: {
734: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
735: the name of the file (name), its extension only (ext) and its first part of the name (finame)
736: */
737: char *ss; /* pointer */
738: int l1, l2; /* length counters */
739:
740: l1 = strlen(path ); /* length of path */
741: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
742: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
743: if ( ss == NULL ) { /* no directory, so determine current directory */
744: strcpy( name, path ); /* we got the fullname name because no directory */
745: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
746: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
747: /* get current working directory */
748: /* extern char* getcwd ( char *buf , int len);*/
749: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
750: return( GLOCK_ERROR_GETCWD );
751: }
752: /* got dirc from getcwd*/
753: printf(" DIRC = %s \n",dirc);
754: } else { /* strip direcotry from path */
755: ss++; /* after this, the filename */
756: l2 = strlen( ss ); /* length of filename */
757: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
758: strcpy( name, ss ); /* save file name */
759: strncpy( dirc, path, l1 - l2 ); /* now the directory */
760: dirc[l1-l2] = 0; /* add zero */
761: printf(" DIRC2 = %s \n",dirc);
762: }
763: /* We add a separator at the end of dirc if not exists */
764: l1 = strlen( dirc ); /* length of directory */
765: if( dirc[l1-1] != DIRSEPARATOR ){
766: dirc[l1] = DIRSEPARATOR;
767: dirc[l1+1] = 0;
768: printf(" DIRC3 = %s \n",dirc);
769: }
770: ss = strrchr( name, '.' ); /* find last / */
771: if (ss >0){
772: ss++;
773: strcpy(ext,ss); /* save extension */
774: l1= strlen( name);
775: l2= strlen(ss)+1;
776: strncpy( finame, name, l1-l2);
777: finame[l1-l2]= 0;
778: }
779:
780: return( 0 ); /* we're done */
781: }
782:
783:
784: /******************************************/
785:
786: void replace_back_to_slash(char *s, char*t)
787: {
788: int i;
789: int lg=0;
790: i=0;
791: lg=strlen(t);
792: for(i=0; i<= lg; i++) {
793: (s[i] = t[i]);
794: if (t[i]== '\\') s[i]='/';
795: }
796: }
797:
798: char *trimbb(char *out, char *in)
799: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
800: char *s;
801: s=out;
802: while (*in != '\0'){
803: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
804: in++;
805: }
806: *out++ = *in++;
807: }
808: *out='\0';
809: return s;
810: }
811:
812: char *cutl(char *blocc, char *alocc, char *in, char occ)
813: {
814: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
815: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
816: gives blocc="abcdef2ghi" and alocc="j".
817: If occ is not found blocc is null and alocc is equal to in. Returns blocc
818: */
819: char *s, *t;
820: t=in;s=in;
821: while ((*in != occ) && (*in != '\0')){
822: *alocc++ = *in++;
823: }
824: if( *in == occ){
825: *(alocc)='\0';
826: s=++in;
827: }
828:
829: if (s == t) {/* occ not found */
830: *(alocc-(in-s))='\0';
831: in=s;
832: }
833: while ( *in != '\0'){
834: *blocc++ = *in++;
835: }
836:
837: *blocc='\0';
838: return t;
839: }
840: char *cutv(char *blocc, char *alocc, char *in, char occ)
841: {
842: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
843: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
844: gives blocc="abcdef2ghi" and alocc="j".
845: If occ is not found blocc is null and alocc is equal to in. Returns alocc
846: */
847: char *s, *t;
848: t=in;s=in;
849: while (*in != '\0'){
850: while( *in == occ){
851: *blocc++ = *in++;
852: s=in;
853: }
854: *blocc++ = *in++;
855: }
856: if (s == t) /* occ not found */
857: *(blocc-(in-s))='\0';
858: else
859: *(blocc-(in-s)-1)='\0';
860: in=s;
861: while ( *in != '\0'){
862: *alocc++ = *in++;
863: }
864:
865: *alocc='\0';
866: return s;
867: }
868:
869: int nbocc(char *s, char occ)
870: {
871: int i,j=0;
872: int lg=20;
873: i=0;
874: lg=strlen(s);
875: for(i=0; i<= lg; i++) {
876: if (s[i] == occ ) j++;
877: }
878: return j;
879: }
880:
881: /* void cutv(char *u,char *v, char*t, char occ) */
882: /* { */
883: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
884: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
885: /* gives u="abcdef2ghi" and v="j" *\/ */
886: /* int i,lg,j,p=0; */
887: /* i=0; */
888: /* lg=strlen(t); */
889: /* for(j=0; j<=lg-1; j++) { */
890: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
891: /* } */
892:
893: /* for(j=0; j<p; j++) { */
894: /* (u[j] = t[j]); */
895: /* } */
896: /* u[p]='\0'; */
897:
898: /* for(j=0; j<= lg; j++) { */
899: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
900: /* } */
901: /* } */
902:
903: #ifdef _WIN32
904: char * strsep(char **pp, const char *delim)
905: {
906: char *p, *q;
907:
908: if ((p = *pp) == NULL)
909: return 0;
910: if ((q = strpbrk (p, delim)) != NULL)
911: {
912: *pp = q + 1;
913: *q = '\0';
914: }
915: else
916: *pp = 0;
917: return p;
918: }
919: #endif
920:
921: /********************** nrerror ********************/
922:
923: void nrerror(char error_text[])
924: {
925: fprintf(stderr,"ERREUR ...\n");
926: fprintf(stderr,"%s\n",error_text);
927: exit(EXIT_FAILURE);
928: }
929: /*********************** vector *******************/
930: double *vector(int nl, int nh)
931: {
932: double *v;
933: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
934: if (!v) nrerror("allocation failure in vector");
935: return v-nl+NR_END;
936: }
937:
938: /************************ free vector ******************/
939: void free_vector(double*v, int nl, int nh)
940: {
941: free((FREE_ARG)(v+nl-NR_END));
942: }
943:
944: /************************ivector *******************************/
945: int *ivector(long nl,long nh)
946: {
947: int *v;
948: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
949: if (!v) nrerror("allocation failure in ivector");
950: return v-nl+NR_END;
951: }
952:
953: /******************free ivector **************************/
954: void free_ivector(int *v, long nl, long nh)
955: {
956: free((FREE_ARG)(v+nl-NR_END));
957: }
958:
959: /************************lvector *******************************/
960: long *lvector(long nl,long nh)
961: {
962: long *v;
963: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
964: if (!v) nrerror("allocation failure in ivector");
965: return v-nl+NR_END;
966: }
967:
968: /******************free lvector **************************/
969: void free_lvector(long *v, long nl, long nh)
970: {
971: free((FREE_ARG)(v+nl-NR_END));
972: }
973:
974: /******************* imatrix *******************************/
975: int **imatrix(long nrl, long nrh, long ncl, long nch)
976: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
977: {
978: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
979: int **m;
980:
981: /* allocate pointers to rows */
982: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
983: if (!m) nrerror("allocation failure 1 in matrix()");
984: m += NR_END;
985: m -= nrl;
986:
987:
988: /* allocate rows and set pointers to them */
989: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
990: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
991: m[nrl] += NR_END;
992: m[nrl] -= ncl;
993:
994: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
995:
996: /* return pointer to array of pointers to rows */
997: return m;
998: }
999:
1000: /****************** free_imatrix *************************/
1001: void free_imatrix(m,nrl,nrh,ncl,nch)
1002: int **m;
1003: long nch,ncl,nrh,nrl;
1004: /* free an int matrix allocated by imatrix() */
1005: {
1006: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1007: free((FREE_ARG) (m+nrl-NR_END));
1008: }
1009:
1010: /******************* matrix *******************************/
1011: double **matrix(long nrl, long nrh, long ncl, long nch)
1012: {
1013: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1014: double **m;
1015:
1016: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1017: if (!m) nrerror("allocation failure 1 in matrix()");
1018: m += NR_END;
1019: m -= nrl;
1020:
1021: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1022: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1023: m[nrl] += NR_END;
1024: m[nrl] -= ncl;
1025:
1026: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1027: return m;
1028: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1029: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1030: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1031: */
1032: }
1033:
1034: /*************************free matrix ************************/
1035: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1036: {
1037: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1038: free((FREE_ARG)(m+nrl-NR_END));
1039: }
1040:
1041: /******************* ma3x *******************************/
1042: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1043: {
1044: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1045: double ***m;
1046:
1047: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1048: if (!m) nrerror("allocation failure 1 in matrix()");
1049: m += NR_END;
1050: m -= nrl;
1051:
1052: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1053: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1054: m[nrl] += NR_END;
1055: m[nrl] -= ncl;
1056:
1057: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1058:
1059: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1060: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1061: m[nrl][ncl] += NR_END;
1062: m[nrl][ncl] -= nll;
1063: for (j=ncl+1; j<=nch; j++)
1064: m[nrl][j]=m[nrl][j-1]+nlay;
1065:
1066: for (i=nrl+1; i<=nrh; i++) {
1067: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1068: for (j=ncl+1; j<=nch; j++)
1069: m[i][j]=m[i][j-1]+nlay;
1070: }
1071: return m;
1072: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1073: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1074: */
1075: }
1076:
1077: /*************************free ma3x ************************/
1078: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1079: {
1080: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1081: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1082: free((FREE_ARG)(m+nrl-NR_END));
1083: }
1084:
1085: /*************** function subdirf ***********/
1086: char *subdirf(char fileres[])
1087: {
1088: /* Caution optionfilefiname is hidden */
1089: strcpy(tmpout,optionfilefiname);
1090: strcat(tmpout,"/"); /* Add to the right */
1091: strcat(tmpout,fileres);
1092: return tmpout;
1093: }
1094:
1095: /*************** function subdirf2 ***********/
1096: char *subdirf2(char fileres[], char *preop)
1097: {
1098:
1099: /* Caution optionfilefiname is hidden */
1100: strcpy(tmpout,optionfilefiname);
1101: strcat(tmpout,"/");
1102: strcat(tmpout,preop);
1103: strcat(tmpout,fileres);
1104: return tmpout;
1105: }
1106:
1107: /*************** function subdirf3 ***********/
1108: char *subdirf3(char fileres[], char *preop, char *preop2)
1109: {
1110:
1111: /* Caution optionfilefiname is hidden */
1112: strcpy(tmpout,optionfilefiname);
1113: strcat(tmpout,"/");
1114: strcat(tmpout,preop);
1115: strcat(tmpout,preop2);
1116: strcat(tmpout,fileres);
1117: return tmpout;
1118: }
1119:
1120: char *asc_diff_time(long time_sec, char ascdiff[])
1121: {
1122: long sec_left, days, hours, minutes;
1123: days = (time_sec) / (60*60*24);
1124: sec_left = (time_sec) % (60*60*24);
1125: hours = (sec_left) / (60*60) ;
1126: sec_left = (sec_left) %(60*60);
1127: minutes = (sec_left) /60;
1128: sec_left = (sec_left) % (60);
1129: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1130: return ascdiff;
1131: }
1132:
1133: /***************** f1dim *************************/
1134: extern int ncom;
1135: extern double *pcom,*xicom;
1136: extern double (*nrfunc)(double []);
1137:
1138: double f1dim(double x)
1139: {
1140: int j;
1141: double f;
1142: double *xt;
1143:
1144: xt=vector(1,ncom);
1145: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1146: f=(*nrfunc)(xt);
1147: free_vector(xt,1,ncom);
1148: return f;
1149: }
1150:
1151: /*****************brent *************************/
1152: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1153: {
1154: int iter;
1155: double a,b,d,etemp;
1156: double fu=0,fv,fw,fx;
1157: double ftemp=0.;
1158: double p,q,r,tol1,tol2,u,v,w,x,xm;
1159: double e=0.0;
1160:
1161: a=(ax < cx ? ax : cx);
1162: b=(ax > cx ? ax : cx);
1163: x=w=v=bx;
1164: fw=fv=fx=(*f)(x);
1165: for (iter=1;iter<=ITMAX;iter++) {
1166: xm=0.5*(a+b);
1167: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1168: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1169: printf(".");fflush(stdout);
1170: fprintf(ficlog,".");fflush(ficlog);
1171: #ifdef DEBUGBRENT
1172: 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);
1173: 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);
1174: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1175: #endif
1176: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1177: *xmin=x;
1178: return fx;
1179: }
1180: ftemp=fu;
1181: if (fabs(e) > tol1) {
1182: r=(x-w)*(fx-fv);
1183: q=(x-v)*(fx-fw);
1184: p=(x-v)*q-(x-w)*r;
1185: q=2.0*(q-r);
1186: if (q > 0.0) p = -p;
1187: q=fabs(q);
1188: etemp=e;
1189: e=d;
1190: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1191: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1192: else {
1193: d=p/q;
1194: u=x+d;
1195: if (u-a < tol2 || b-u < tol2)
1196: d=SIGN(tol1,xm-x);
1197: }
1198: } else {
1199: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1200: }
1201: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1202: fu=(*f)(u);
1203: if (fu <= fx) {
1204: if (u >= x) a=x; else b=x;
1205: SHFT(v,w,x,u)
1206: SHFT(fv,fw,fx,fu)
1207: } else {
1208: if (u < x) a=u; else b=u;
1209: if (fu <= fw || w == x) {
1210: v=w;
1211: w=u;
1212: fv=fw;
1213: fw=fu;
1214: } else if (fu <= fv || v == x || v == w) {
1215: v=u;
1216: fv=fu;
1217: }
1218: }
1219: }
1220: nrerror("Too many iterations in brent");
1221: *xmin=x;
1222: return fx;
1223: }
1224:
1225: /****************** mnbrak ***********************/
1226:
1227: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1228: double (*func)(double))
1229: {
1230: double ulim,u,r,q, dum;
1231: double fu;
1232:
1233: *fa=(*func)(*ax);
1234: *fb=(*func)(*bx);
1235: if (*fb > *fa) {
1236: SHFT(dum,*ax,*bx,dum)
1237: SHFT(dum,*fb,*fa,dum)
1238: }
1239: *cx=(*bx)+GOLD*(*bx-*ax);
1240: *fc=(*func)(*cx);
1241: while (*fb > *fc) { /* Declining fa, fb, fc */
1242: r=(*bx-*ax)*(*fb-*fc);
1243: q=(*bx-*cx)*(*fb-*fa);
1244: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1245: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1246: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
1247: if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
1248: fu=(*func)(u);
1249: #ifdef DEBUG
1250: /* f(x)=A(x-u)**2+f(u) */
1251: double A, fparabu;
1252: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1253: fparabu= *fa - A*(*ax-u)*(*ax-u);
1254: 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);
1255: 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);
1256: #endif
1257: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1258: fu=(*func)(u);
1259: if (fu < *fc) {
1260: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1261: SHFT(*fb,*fc,fu,(*func)(u))
1262: }
1263: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1264: u=ulim;
1265: fu=(*func)(u);
1266: } else {
1267: u=(*cx)+GOLD*(*cx-*bx);
1268: fu=(*func)(u);
1269: }
1270: SHFT(*ax,*bx,*cx,u)
1271: SHFT(*fa,*fb,*fc,fu)
1272: }
1273: }
1274:
1275: /*************** linmin ************************/
1276: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1277: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1278: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1279: the value of func at the returned location p . This is actually all accomplished by calling the
1280: routines mnbrak and brent .*/
1281: int ncom;
1282: double *pcom,*xicom;
1283: double (*nrfunc)(double []);
1284:
1285: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1286: {
1287: double brent(double ax, double bx, double cx,
1288: double (*f)(double), double tol, double *xmin);
1289: double f1dim(double x);
1290: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1291: double *fc, double (*func)(double));
1292: int j;
1293: double xx,xmin,bx,ax;
1294: double fx,fb,fa;
1295:
1296: ncom=n;
1297: pcom=vector(1,n);
1298: xicom=vector(1,n);
1299: nrfunc=func;
1300: for (j=1;j<=n;j++) {
1301: pcom[j]=p[j];
1302: xicom[j]=xi[j];
1303: }
1304: ax=0.0;
1305: xx=1.0;
1306: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
1307: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
1308: #ifdef DEBUG
1309: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1310: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1311: #endif
1312: for (j=1;j<=n;j++) {
1313: xi[j] *= xmin;
1314: p[j] += xi[j];
1315: }
1316: free_vector(xicom,1,n);
1317: free_vector(pcom,1,n);
1318: }
1319:
1320:
1321: /*************** powell ************************/
1322: /*
1323: Minimization of a function func of n variables. Input consists of an initial starting point
1324: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1325: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1326: such that failure to decrease by more than this amount on one iteration signals doneness. On
1327: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1328: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1329: */
1330: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1331: double (*func)(double []))
1332: {
1333: void linmin(double p[], double xi[], int n, double *fret,
1334: double (*func)(double []));
1335: int i,ibig,j;
1336: double del,t,*pt,*ptt,*xit;
1337: double fp,fptt;
1338: double *xits;
1339: int niterf, itmp;
1340:
1341: pt=vector(1,n);
1342: ptt=vector(1,n);
1343: xit=vector(1,n);
1344: xits=vector(1,n);
1345: *fret=(*func)(p);
1346: for (j=1;j<=n;j++) pt[j]=p[j];
1347: rcurr_time = time(NULL);
1348: for (*iter=1;;++(*iter)) {
1349: fp=(*fret);
1350: ibig=0;
1351: del=0.0;
1352: rlast_time=rcurr_time;
1353: /* (void) gettimeofday(&curr_time,&tzp); */
1354: rcurr_time = time(NULL);
1355: curr_time = *localtime(&rcurr_time);
1356: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1357: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1358: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1359: for (i=1;i<=n;i++) {
1360: printf(" %d %.12f",i, p[i]);
1361: fprintf(ficlog," %d %.12lf",i, p[i]);
1362: fprintf(ficrespow," %.12lf", p[i]);
1363: }
1364: printf("\n");
1365: fprintf(ficlog,"\n");
1366: fprintf(ficrespow,"\n");fflush(ficrespow);
1367: if(*iter <=3){
1368: tml = *localtime(&rcurr_time);
1369: strcpy(strcurr,asctime(&tml));
1370: rforecast_time=rcurr_time;
1371: itmp = strlen(strcurr);
1372: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1373: strcurr[itmp-1]='\0';
1374: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1375: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1376: for(niterf=10;niterf<=30;niterf+=10){
1377: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1378: forecast_time = *localtime(&rforecast_time);
1379: strcpy(strfor,asctime(&forecast_time));
1380: itmp = strlen(strfor);
1381: if(strfor[itmp-1]=='\n')
1382: strfor[itmp-1]='\0';
1383: 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);
1384: 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);
1385: }
1386: }
1387: for (i=1;i<=n;i++) {
1388: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1389: fptt=(*fret);
1390: #ifdef DEBUG
1391: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1392: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1393: #endif
1394: printf("%d",i);fflush(stdout);
1395: fprintf(ficlog,"%d",i);fflush(ficlog);
1396: linmin(p,xit,n,fret,func);
1397: if (fabs(fptt-(*fret)) > del) {
1398: del=fabs(fptt-(*fret));
1399: ibig=i;
1400: }
1401: #ifdef DEBUG
1402: printf("%d %.12e",i,(*fret));
1403: fprintf(ficlog,"%d %.12e",i,(*fret));
1404: for (j=1;j<=n;j++) {
1405: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1406: printf(" x(%d)=%.12e",j,xit[j]);
1407: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1408: }
1409: for(j=1;j<=n;j++) {
1410: printf(" p(%d)=%.12e",j,p[j]);
1411: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1412: }
1413: printf("\n");
1414: fprintf(ficlog,"\n");
1415: #endif
1416: } /* end i */
1417: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1418: #ifdef DEBUG
1419: int k[2],l;
1420: k[0]=1;
1421: k[1]=-1;
1422: printf("Max: %.12e",(*func)(p));
1423: fprintf(ficlog,"Max: %.12e",(*func)(p));
1424: for (j=1;j<=n;j++) {
1425: printf(" %.12e",p[j]);
1426: fprintf(ficlog," %.12e",p[j]);
1427: }
1428: printf("\n");
1429: fprintf(ficlog,"\n");
1430: for(l=0;l<=1;l++) {
1431: for (j=1;j<=n;j++) {
1432: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1433: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1434: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1435: }
1436: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1437: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1438: }
1439: #endif
1440:
1441:
1442: free_vector(xit,1,n);
1443: free_vector(xits,1,n);
1444: free_vector(ptt,1,n);
1445: free_vector(pt,1,n);
1446: return;
1447: }
1448: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1449: for (j=1;j<=n;j++) { /* Computes an extrapolated point */
1450: ptt[j]=2.0*p[j]-pt[j];
1451: xit[j]=p[j]-pt[j];
1452: pt[j]=p[j];
1453: }
1454: fptt=(*func)(ptt);
1455: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1456: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1457: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1458: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1459: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1460: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1461: /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
1462: /* Thus we compare delta(2h) with observed f1-f3 */
1463: /* or best gain on one ancient line 'del' with total */
1464: /* gain f1-f2 = f1 - f2 - 'del' with del */
1465: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1466:
1467: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
1468: t= t- del*SQR(fp-fptt);
1469: printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
1470: fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
1471: #ifdef DEBUG
1472: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1473: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1474: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1475: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1476: 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);
1477: 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);
1478: #endif
1479: if (t < 0.0) { /* Then we use it for last direction */
1480: linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
1481: for (j=1;j<=n;j++) {
1482: xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
1483: xi[j][n]=xit[j]; /* and nth direction by the extrapolated */
1484: }
1485: printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1486: fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);
1487:
1488: #ifdef DEBUG
1489: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1490: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1491: for(j=1;j<=n;j++){
1492: printf(" %.12e",xit[j]);
1493: fprintf(ficlog," %.12e",xit[j]);
1494: }
1495: printf("\n");
1496: fprintf(ficlog,"\n");
1497: #endif
1498: } /* end of t negative */
1499: } /* end if (fptt < fp) */
1500: }
1501: }
1502:
1503: /**** Prevalence limit (stable or period prevalence) ****************/
1504:
1505: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1506: {
1507: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1508: matrix by transitions matrix until convergence is reached */
1509:
1510: int i, ii,j,k;
1511: double min, max, maxmin, maxmax,sumnew=0.;
1512: /* double **matprod2(); */ /* test */
1513: double **out, cov[NCOVMAX+1], **pmij();
1514: double **newm;
1515: double agefin, delaymax=50 ; /* Max number of years to converge */
1516:
1517: for (ii=1;ii<=nlstate+ndeath;ii++)
1518: for (j=1;j<=nlstate+ndeath;j++){
1519: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1520: }
1521:
1522: cov[1]=1.;
1523:
1524: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1525: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1526: newm=savm;
1527: /* Covariates have to be included here again */
1528: cov[2]=agefin;
1529:
1530: for (k=1; k<=cptcovn;k++) {
1531: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1532: /*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]]);*/
1533: }
1534: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1535: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
1536: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
1537:
1538: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1539: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1540: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1541: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1542: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1543: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1544:
1545: savm=oldm;
1546: oldm=newm;
1547: maxmax=0.;
1548: for(j=1;j<=nlstate;j++){
1549: min=1.;
1550: max=0.;
1551: for(i=1; i<=nlstate; i++) {
1552: sumnew=0;
1553: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1554: prlim[i][j]= newm[i][j]/(1-sumnew);
1555: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1556: max=FMAX(max,prlim[i][j]);
1557: min=FMIN(min,prlim[i][j]);
1558: }
1559: maxmin=max-min;
1560: maxmax=FMAX(maxmax,maxmin);
1561: }
1562: if(maxmax < ftolpl){
1563: return prlim;
1564: }
1565: }
1566: }
1567:
1568: /*************** transition probabilities ***************/
1569:
1570: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1571: {
1572: /* According to parameters values stored in x and the covariate's values stored in cov,
1573: computes the probability to be observed in state j being in state i by appying the
1574: model to the ncovmodel covariates (including constant and age).
1575: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1576: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1577: ncth covariate in the global vector x is given by the formula:
1578: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1579: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1580: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1581: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1582: Outputs ps[i][j] the probability to be observed in j being in j according to
1583: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1584: */
1585: double s1, lnpijopii;
1586: /*double t34;*/
1587: int i,j, nc, ii, jj;
1588:
1589: for(i=1; i<= nlstate; i++){
1590: for(j=1; j<i;j++){
1591: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1592: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1593: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1594: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1595: }
1596: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1597: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1598: }
1599: for(j=i+1; j<=nlstate+ndeath;j++){
1600: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1601: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1602: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1603: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1604: }
1605: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1606: }
1607: }
1608:
1609: for(i=1; i<= nlstate; i++){
1610: s1=0;
1611: for(j=1; j<i; j++){
1612: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1613: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1614: }
1615: for(j=i+1; j<=nlstate+ndeath; j++){
1616: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1617: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1618: }
1619: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1620: ps[i][i]=1./(s1+1.);
1621: /* Computing other pijs */
1622: for(j=1; j<i; j++)
1623: ps[i][j]= exp(ps[i][j])*ps[i][i];
1624: for(j=i+1; j<=nlstate+ndeath; j++)
1625: ps[i][j]= exp(ps[i][j])*ps[i][i];
1626: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1627: } /* end i */
1628:
1629: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1630: for(jj=1; jj<= nlstate+ndeath; jj++){
1631: ps[ii][jj]=0;
1632: ps[ii][ii]=1;
1633: }
1634: }
1635:
1636:
1637: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1638: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1639: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1640: /* } */
1641: /* printf("\n "); */
1642: /* } */
1643: /* printf("\n ");printf("%lf ",cov[2]);*/
1644: /*
1645: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1646: goto end;*/
1647: return ps;
1648: }
1649:
1650: /**************** Product of 2 matrices ******************/
1651:
1652: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1653: {
1654: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1655: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1656: /* in, b, out are matrice of pointers which should have been initialized
1657: before: only the contents of out is modified. The function returns
1658: a pointer to pointers identical to out */
1659: int i, j, k;
1660: for(i=nrl; i<= nrh; i++)
1661: for(k=ncolol; k<=ncoloh; k++){
1662: out[i][k]=0.;
1663: for(j=ncl; j<=nch; j++)
1664: out[i][k] +=in[i][j]*b[j][k];
1665: }
1666: return out;
1667: }
1668:
1669:
1670: /************* Higher Matrix Product ***************/
1671:
1672: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1673: {
1674: /* Computes the transition matrix starting at age 'age' over
1675: 'nhstepm*hstepm*stepm' months (i.e. until
1676: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1677: nhstepm*hstepm matrices.
1678: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1679: (typically every 2 years instead of every month which is too big
1680: for the memory).
1681: Model is determined by parameters x and covariates have to be
1682: included manually here.
1683:
1684: */
1685:
1686: int i, j, d, h, k;
1687: double **out, cov[NCOVMAX+1];
1688: double **newm;
1689:
1690: /* Hstepm could be zero and should return the unit matrix */
1691: for (i=1;i<=nlstate+ndeath;i++)
1692: for (j=1;j<=nlstate+ndeath;j++){
1693: oldm[i][j]=(i==j ? 1.0 : 0.0);
1694: po[i][j][0]=(i==j ? 1.0 : 0.0);
1695: }
1696: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1697: for(h=1; h <=nhstepm; h++){
1698: for(d=1; d <=hstepm; d++){
1699: newm=savm;
1700: /* Covariates have to be included here again */
1701: cov[1]=1.;
1702: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1703: for (k=1; k<=cptcovn;k++)
1704: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1705: for (k=1; k<=cptcovage;k++)
1706: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1707: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1708: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1709:
1710:
1711: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1712: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1713: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1714: pmij(pmmij,cov,ncovmodel,x,nlstate));
1715: savm=oldm;
1716: oldm=newm;
1717: }
1718: for(i=1; i<=nlstate+ndeath; i++)
1719: for(j=1;j<=nlstate+ndeath;j++) {
1720: po[i][j][h]=newm[i][j];
1721: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1722: }
1723: /*printf("h=%d ",h);*/
1724: } /* end h */
1725: /* printf("\n H=%d \n",h); */
1726: return po;
1727: }
1728:
1729: #ifdef NLOPT
1730: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
1731: double fret;
1732: double *xt;
1733: int j;
1734: myfunc_data *d2 = (myfunc_data *) pd;
1735: /* xt = (p1-1); */
1736: xt=vector(1,n);
1737: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
1738:
1739: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
1740: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
1741: printf("Function = %.12lf ",fret);
1742: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
1743: printf("\n");
1744: free_vector(xt,1,n);
1745: return fret;
1746: }
1747: #endif
1748:
1749: /*************** log-likelihood *************/
1750: double func( double *x)
1751: {
1752: int i, ii, j, k, mi, d, kk;
1753: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1754: double **out;
1755: double sw; /* Sum of weights */
1756: double lli; /* Individual log likelihood */
1757: int s1, s2;
1758: double bbh, survp;
1759: long ipmx;
1760: /*extern weight */
1761: /* We are differentiating ll according to initial status */
1762: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1763: /*for(i=1;i<imx;i++)
1764: printf(" %d\n",s[4][i]);
1765: */
1766:
1767: ++countcallfunc;
1768:
1769: cov[1]=1.;
1770:
1771: for(k=1; k<=nlstate; k++) ll[k]=0.;
1772:
1773: if(mle==1){
1774: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1775: /* Computes the values of the ncovmodel covariates of the model
1776: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1777: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1778: to be observed in j being in i according to the model.
1779: */
1780: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1781: cov[2+k]=covar[Tvar[k]][i];
1782: }
1783: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1784: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1785: has been calculated etc */
1786: for(mi=1; mi<= wav[i]-1; mi++){
1787: for (ii=1;ii<=nlstate+ndeath;ii++)
1788: for (j=1;j<=nlstate+ndeath;j++){
1789: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1790: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1791: }
1792: for(d=0; d<dh[mi][i]; d++){
1793: newm=savm;
1794: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1795: for (kk=1; kk<=cptcovage;kk++) {
1796: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1797: }
1798: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1799: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1800: savm=oldm;
1801: oldm=newm;
1802: } /* end mult */
1803:
1804: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1805: /* But now since version 0.9 we anticipate for bias at large stepm.
1806: * If stepm is larger than one month (smallest stepm) and if the exact delay
1807: * (in months) between two waves is not a multiple of stepm, we rounded to
1808: * the nearest (and in case of equal distance, to the lowest) interval but now
1809: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1810: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1811: * probability in order to take into account the bias as a fraction of the way
1812: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1813: * -stepm/2 to stepm/2 .
1814: * For stepm=1 the results are the same as for previous versions of Imach.
1815: * For stepm > 1 the results are less biased than in previous versions.
1816: */
1817: s1=s[mw[mi][i]][i];
1818: s2=s[mw[mi+1][i]][i];
1819: bbh=(double)bh[mi][i]/(double)stepm;
1820: /* bias bh is positive if real duration
1821: * is higher than the multiple of stepm and negative otherwise.
1822: */
1823: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1824: if( s2 > nlstate){
1825: /* i.e. if s2 is a death state and if the date of death is known
1826: then the contribution to the likelihood is the probability to
1827: die between last step unit time and current step unit time,
1828: which is also equal to probability to die before dh
1829: minus probability to die before dh-stepm .
1830: In version up to 0.92 likelihood was computed
1831: as if date of death was unknown. Death was treated as any other
1832: health state: the date of the interview describes the actual state
1833: and not the date of a change in health state. The former idea was
1834: to consider that at each interview the state was recorded
1835: (healthy, disable or death) and IMaCh was corrected; but when we
1836: introduced the exact date of death then we should have modified
1837: the contribution of an exact death to the likelihood. This new
1838: contribution is smaller and very dependent of the step unit
1839: stepm. It is no more the probability to die between last interview
1840: and month of death but the probability to survive from last
1841: interview up to one month before death multiplied by the
1842: probability to die within a month. Thanks to Chris
1843: Jackson for correcting this bug. Former versions increased
1844: mortality artificially. The bad side is that we add another loop
1845: which slows down the processing. The difference can be up to 10%
1846: lower mortality.
1847: */
1848: lli=log(out[s1][s2] - savm[s1][s2]);
1849:
1850:
1851: } else if (s2==-2) {
1852: for (j=1,survp=0. ; j<=nlstate; j++)
1853: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1854: /*survp += out[s1][j]; */
1855: lli= log(survp);
1856: }
1857:
1858: else if (s2==-4) {
1859: for (j=3,survp=0. ; j<=nlstate; j++)
1860: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1861: lli= log(survp);
1862: }
1863:
1864: else if (s2==-5) {
1865: for (j=1,survp=0. ; j<=2; j++)
1866: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1867: lli= log(survp);
1868: }
1869:
1870: else{
1871: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1872: /* 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 */
1873: }
1874: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1875: /*if(lli ==000.0)*/
1876: /*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); */
1877: ipmx +=1;
1878: sw += weight[i];
1879: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1880: } /* end of wave */
1881: } /* end of individual */
1882: } else if(mle==2){
1883: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1884: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1885: for(mi=1; mi<= wav[i]-1; mi++){
1886: for (ii=1;ii<=nlstate+ndeath;ii++)
1887: for (j=1;j<=nlstate+ndeath;j++){
1888: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1889: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1890: }
1891: for(d=0; d<=dh[mi][i]; d++){
1892: newm=savm;
1893: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1894: for (kk=1; kk<=cptcovage;kk++) {
1895: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1896: }
1897: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1898: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1899: savm=oldm;
1900: oldm=newm;
1901: } /* end mult */
1902:
1903: s1=s[mw[mi][i]][i];
1904: s2=s[mw[mi+1][i]][i];
1905: bbh=(double)bh[mi][i]/(double)stepm;
1906: 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 */
1907: ipmx +=1;
1908: sw += weight[i];
1909: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1910: } /* end of wave */
1911: } /* end of individual */
1912: } else if(mle==3){ /* exponential inter-extrapolation */
1913: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1914: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1915: for(mi=1; mi<= wav[i]-1; mi++){
1916: for (ii=1;ii<=nlstate+ndeath;ii++)
1917: for (j=1;j<=nlstate+ndeath;j++){
1918: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1919: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1920: }
1921: for(d=0; d<dh[mi][i]; d++){
1922: newm=savm;
1923: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1924: for (kk=1; kk<=cptcovage;kk++) {
1925: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1926: }
1927: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1928: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1929: savm=oldm;
1930: oldm=newm;
1931: } /* end mult */
1932:
1933: s1=s[mw[mi][i]][i];
1934: s2=s[mw[mi+1][i]][i];
1935: bbh=(double)bh[mi][i]/(double)stepm;
1936: 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 */
1937: ipmx +=1;
1938: sw += weight[i];
1939: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1940: } /* end of wave */
1941: } /* end of individual */
1942: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1943: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1944: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1945: for(mi=1; mi<= wav[i]-1; mi++){
1946: for (ii=1;ii<=nlstate+ndeath;ii++)
1947: for (j=1;j<=nlstate+ndeath;j++){
1948: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1949: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1950: }
1951: for(d=0; d<dh[mi][i]; d++){
1952: newm=savm;
1953: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1954: for (kk=1; kk<=cptcovage;kk++) {
1955: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1956: }
1957:
1958: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1959: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1960: savm=oldm;
1961: oldm=newm;
1962: } /* end mult */
1963:
1964: s1=s[mw[mi][i]][i];
1965: s2=s[mw[mi+1][i]][i];
1966: if( s2 > nlstate){
1967: lli=log(out[s1][s2] - savm[s1][s2]);
1968: }else{
1969: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1970: }
1971: ipmx +=1;
1972: sw += weight[i];
1973: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1974: /* 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]); */
1975: } /* end of wave */
1976: } /* end of individual */
1977: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1978: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1979: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1980: for(mi=1; mi<= wav[i]-1; mi++){
1981: for (ii=1;ii<=nlstate+ndeath;ii++)
1982: for (j=1;j<=nlstate+ndeath;j++){
1983: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1984: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1985: }
1986: for(d=0; d<dh[mi][i]; d++){
1987: newm=savm;
1988: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1989: for (kk=1; kk<=cptcovage;kk++) {
1990: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1991: }
1992:
1993: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1994: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1995: savm=oldm;
1996: oldm=newm;
1997: } /* end mult */
1998:
1999: s1=s[mw[mi][i]][i];
2000: s2=s[mw[mi+1][i]][i];
2001: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2002: ipmx +=1;
2003: sw += weight[i];
2004: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2005: /*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]);*/
2006: } /* end of wave */
2007: } /* end of individual */
2008: } /* End of if */
2009: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2010: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2011: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2012: return -l;
2013: }
2014:
2015: /*************** log-likelihood *************/
2016: double funcone( double *x)
2017: {
2018: /* Same as likeli but slower because of a lot of printf and if */
2019: int i, ii, j, k, mi, d, kk;
2020: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
2021: double **out;
2022: double lli; /* Individual log likelihood */
2023: double llt;
2024: int s1, s2;
2025: double bbh, survp;
2026: /*extern weight */
2027: /* We are differentiating ll according to initial status */
2028: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2029: /*for(i=1;i<imx;i++)
2030: printf(" %d\n",s[4][i]);
2031: */
2032: cov[1]=1.;
2033:
2034: for(k=1; k<=nlstate; k++) ll[k]=0.;
2035:
2036: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2037: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2038: for(mi=1; mi<= wav[i]-1; mi++){
2039: for (ii=1;ii<=nlstate+ndeath;ii++)
2040: for (j=1;j<=nlstate+ndeath;j++){
2041: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2042: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2043: }
2044: for(d=0; d<dh[mi][i]; d++){
2045: newm=savm;
2046: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2047: for (kk=1; kk<=cptcovage;kk++) {
2048: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2049: }
2050: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2051: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2052: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2053: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2054: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
2055: savm=oldm;
2056: oldm=newm;
2057: } /* end mult */
2058:
2059: s1=s[mw[mi][i]][i];
2060: s2=s[mw[mi+1][i]][i];
2061: bbh=(double)bh[mi][i]/(double)stepm;
2062: /* bias is positive if real duration
2063: * is higher than the multiple of stepm and negative otherwise.
2064: */
2065: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2066: lli=log(out[s1][s2] - savm[s1][s2]);
2067: } else if (s2==-2) {
2068: for (j=1,survp=0. ; j<=nlstate; j++)
2069: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2070: lli= log(survp);
2071: }else if (mle==1){
2072: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2073: } else if(mle==2){
2074: 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 */
2075: } else if(mle==3){ /* exponential inter-extrapolation */
2076: 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 */
2077: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2078: lli=log(out[s1][s2]); /* Original formula */
2079: } else{ /* mle=0 back to 1 */
2080: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2081: /*lli=log(out[s1][s2]); */ /* Original formula */
2082: } /* End of if */
2083: ipmx +=1;
2084: sw += weight[i];
2085: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2086: /*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]); */
2087: if(globpr){
2088: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
2089: %11.6f %11.6f %11.6f ", \
2090: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2091: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2092: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2093: llt +=ll[k]*gipmx/gsw;
2094: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2095: }
2096: fprintf(ficresilk," %10.6f\n", -llt);
2097: }
2098: } /* end of wave */
2099: } /* end of individual */
2100: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2101: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2102: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2103: if(globpr==0){ /* First time we count the contributions and weights */
2104: gipmx=ipmx;
2105: gsw=sw;
2106: }
2107: return -l;
2108: }
2109:
2110:
2111: /*************** function likelione ***********/
2112: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2113: {
2114: /* This routine should help understanding what is done with
2115: the selection of individuals/waves and
2116: to check the exact contribution to the likelihood.
2117: Plotting could be done.
2118: */
2119: int k;
2120:
2121: if(*globpri !=0){ /* Just counts and sums, no printings */
2122: strcpy(fileresilk,"ilk");
2123: strcat(fileresilk,fileres);
2124: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2125: printf("Problem with resultfile: %s\n", fileresilk);
2126: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2127: }
2128: 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");
2129: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2130: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2131: for(k=1; k<=nlstate; k++)
2132: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2133: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2134: }
2135:
2136: *fretone=(*funcone)(p);
2137: if(*globpri !=0){
2138: fclose(ficresilk);
2139: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2140: fflush(fichtm);
2141: }
2142: return;
2143: }
2144:
2145:
2146: /*********** Maximum Likelihood Estimation ***************/
2147:
2148: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2149: {
2150: int i,j, iter;
2151: double **xi;
2152: double fret;
2153: double fretone; /* Only one call to likelihood */
2154: /* char filerespow[FILENAMELENGTH];*/
2155:
2156: #ifdef NLOPT
2157: int creturn;
2158: nlopt_opt opt;
2159: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2160: double *lb;
2161: double minf; /* the minimum objective value, upon return */
2162: double * p1; /* Shifted parameters from 0 instead of 1 */
2163: myfunc_data dinst, *d = &dinst;
2164: #endif
2165:
2166:
2167: xi=matrix(1,npar,1,npar);
2168: for (i=1;i<=npar;i++)
2169: for (j=1;j<=npar;j++)
2170: xi[i][j]=(i==j ? 1.0 : 0.0);
2171: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2172: strcpy(filerespow,"pow");
2173: strcat(filerespow,fileres);
2174: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2175: printf("Problem with resultfile: %s\n", filerespow);
2176: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2177: }
2178: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2179: for (i=1;i<=nlstate;i++)
2180: for(j=1;j<=nlstate+ndeath;j++)
2181: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2182: fprintf(ficrespow,"\n");
2183: #ifdef POWELL
2184: powell(p,xi,npar,ftol,&iter,&fret,func);
2185: #endif
2186:
2187: #ifdef NLOPT
2188: #ifdef NEWUOA
2189: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2190: #else
2191: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2192: #endif
2193: lb=vector(0,npar-1);
2194: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2195: nlopt_set_lower_bounds(opt, lb);
2196: nlopt_set_initial_step1(opt, 0.1);
2197:
2198: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2199: d->function = func;
2200: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2201: nlopt_set_min_objective(opt, myfunc, d);
2202: nlopt_set_xtol_rel(opt, ftol);
2203: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2204: printf("nlopt failed! %d\n",creturn);
2205: }
2206: else {
2207: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2208: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2209: iter=1; /* not equal */
2210: }
2211: nlopt_destroy(opt);
2212: #endif
2213: free_matrix(xi,1,npar,1,npar);
2214: fclose(ficrespow);
2215: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2216: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2217: fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2218:
2219: }
2220:
2221: /**** Computes Hessian and covariance matrix ***/
2222: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2223: {
2224: double **a,**y,*x,pd;
2225: double **hess;
2226: int i, j;
2227: int *indx;
2228:
2229: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2230: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2231: void lubksb(double **a, int npar, int *indx, double b[]) ;
2232: void ludcmp(double **a, int npar, int *indx, double *d) ;
2233: double gompertz(double p[]);
2234: hess=matrix(1,npar,1,npar);
2235:
2236: printf("\nCalculation of the hessian matrix. Wait...\n");
2237: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2238: for (i=1;i<=npar;i++){
2239: printf("%d",i);fflush(stdout);
2240: fprintf(ficlog,"%d",i);fflush(ficlog);
2241:
2242: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2243:
2244: /* printf(" %f ",p[i]);
2245: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2246: }
2247:
2248: for (i=1;i<=npar;i++) {
2249: for (j=1;j<=npar;j++) {
2250: if (j>i) {
2251: printf(".%d%d",i,j);fflush(stdout);
2252: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2253: hess[i][j]=hessij(p,delti,i,j,func,npar);
2254:
2255: hess[j][i]=hess[i][j];
2256: /*printf(" %lf ",hess[i][j]);*/
2257: }
2258: }
2259: }
2260: printf("\n");
2261: fprintf(ficlog,"\n");
2262:
2263: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2264: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2265:
2266: a=matrix(1,npar,1,npar);
2267: y=matrix(1,npar,1,npar);
2268: x=vector(1,npar);
2269: indx=ivector(1,npar);
2270: for (i=1;i<=npar;i++)
2271: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2272: ludcmp(a,npar,indx,&pd);
2273:
2274: for (j=1;j<=npar;j++) {
2275: for (i=1;i<=npar;i++) x[i]=0;
2276: x[j]=1;
2277: lubksb(a,npar,indx,x);
2278: for (i=1;i<=npar;i++){
2279: matcov[i][j]=x[i];
2280: }
2281: }
2282:
2283: printf("\n#Hessian matrix#\n");
2284: fprintf(ficlog,"\n#Hessian matrix#\n");
2285: for (i=1;i<=npar;i++) {
2286: for (j=1;j<=npar;j++) {
2287: printf("%.3e ",hess[i][j]);
2288: fprintf(ficlog,"%.3e ",hess[i][j]);
2289: }
2290: printf("\n");
2291: fprintf(ficlog,"\n");
2292: }
2293:
2294: /* Recompute Inverse */
2295: for (i=1;i<=npar;i++)
2296: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2297: ludcmp(a,npar,indx,&pd);
2298:
2299: /* printf("\n#Hessian matrix recomputed#\n");
2300:
2301: for (j=1;j<=npar;j++) {
2302: for (i=1;i<=npar;i++) x[i]=0;
2303: x[j]=1;
2304: lubksb(a,npar,indx,x);
2305: for (i=1;i<=npar;i++){
2306: y[i][j]=x[i];
2307: printf("%.3e ",y[i][j]);
2308: fprintf(ficlog,"%.3e ",y[i][j]);
2309: }
2310: printf("\n");
2311: fprintf(ficlog,"\n");
2312: }
2313: */
2314:
2315: free_matrix(a,1,npar,1,npar);
2316: free_matrix(y,1,npar,1,npar);
2317: free_vector(x,1,npar);
2318: free_ivector(indx,1,npar);
2319: free_matrix(hess,1,npar,1,npar);
2320:
2321:
2322: }
2323:
2324: /*************** hessian matrix ****************/
2325: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2326: {
2327: int i;
2328: int l=1, lmax=20;
2329: double k1,k2;
2330: double p2[MAXPARM+1]; /* identical to x */
2331: double res;
2332: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2333: double fx;
2334: int k=0,kmax=10;
2335: double l1;
2336:
2337: fx=func(x);
2338: for (i=1;i<=npar;i++) p2[i]=x[i];
2339: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
2340: l1=pow(10,l);
2341: delts=delt;
2342: for(k=1 ; k <kmax; k=k+1){
2343: delt = delta*(l1*k);
2344: p2[theta]=x[theta] +delt;
2345: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
2346: p2[theta]=x[theta]-delt;
2347: k2=func(p2)-fx;
2348: /*res= (k1-2.0*fx+k2)/delt/delt; */
2349: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2350:
2351: #ifdef DEBUGHESS
2352: 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);
2353: 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);
2354: #endif
2355: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2356: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2357: k=kmax;
2358: }
2359: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2360: k=kmax; l=lmax*10;
2361: }
2362: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2363: delts=delt;
2364: }
2365: }
2366: }
2367: delti[theta]=delts;
2368: return res;
2369:
2370: }
2371:
2372: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2373: {
2374: int i;
2375: int l=1, lmax=20;
2376: double k1,k2,k3,k4,res,fx;
2377: double p2[MAXPARM+1];
2378: int k;
2379:
2380: fx=func(x);
2381: for (k=1; k<=2; k++) {
2382: for (i=1;i<=npar;i++) p2[i]=x[i];
2383: p2[thetai]=x[thetai]+delti[thetai]/k;
2384: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2385: k1=func(p2)-fx;
2386:
2387: p2[thetai]=x[thetai]+delti[thetai]/k;
2388: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2389: k2=func(p2)-fx;
2390:
2391: p2[thetai]=x[thetai]-delti[thetai]/k;
2392: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2393: k3=func(p2)-fx;
2394:
2395: p2[thetai]=x[thetai]-delti[thetai]/k;
2396: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2397: k4=func(p2)-fx;
2398: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2399: #ifdef DEBUG
2400: 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);
2401: 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);
2402: #endif
2403: }
2404: return res;
2405: }
2406:
2407: /************** Inverse of matrix **************/
2408: void ludcmp(double **a, int n, int *indx, double *d)
2409: {
2410: int i,imax,j,k;
2411: double big,dum,sum,temp;
2412: double *vv;
2413:
2414: vv=vector(1,n);
2415: *d=1.0;
2416: for (i=1;i<=n;i++) {
2417: big=0.0;
2418: for (j=1;j<=n;j++)
2419: if ((temp=fabs(a[i][j])) > big) big=temp;
2420: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2421: vv[i]=1.0/big;
2422: }
2423: for (j=1;j<=n;j++) {
2424: for (i=1;i<j;i++) {
2425: sum=a[i][j];
2426: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2427: a[i][j]=sum;
2428: }
2429: big=0.0;
2430: for (i=j;i<=n;i++) {
2431: sum=a[i][j];
2432: for (k=1;k<j;k++)
2433: sum -= a[i][k]*a[k][j];
2434: a[i][j]=sum;
2435: if ( (dum=vv[i]*fabs(sum)) >= big) {
2436: big=dum;
2437: imax=i;
2438: }
2439: }
2440: if (j != imax) {
2441: for (k=1;k<=n;k++) {
2442: dum=a[imax][k];
2443: a[imax][k]=a[j][k];
2444: a[j][k]=dum;
2445: }
2446: *d = -(*d);
2447: vv[imax]=vv[j];
2448: }
2449: indx[j]=imax;
2450: if (a[j][j] == 0.0) a[j][j]=TINY;
2451: if (j != n) {
2452: dum=1.0/(a[j][j]);
2453: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2454: }
2455: }
2456: free_vector(vv,1,n); /* Doesn't work */
2457: ;
2458: }
2459:
2460: void lubksb(double **a, int n, int *indx, double b[])
2461: {
2462: int i,ii=0,ip,j;
2463: double sum;
2464:
2465: for (i=1;i<=n;i++) {
2466: ip=indx[i];
2467: sum=b[ip];
2468: b[ip]=b[i];
2469: if (ii)
2470: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2471: else if (sum) ii=i;
2472: b[i]=sum;
2473: }
2474: for (i=n;i>=1;i--) {
2475: sum=b[i];
2476: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2477: b[i]=sum/a[i][i];
2478: }
2479: }
2480:
2481: void pstamp(FILE *fichier)
2482: {
2483: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2484: }
2485:
2486: /************ Frequencies ********************/
2487: 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[])
2488: { /* Some frequencies */
2489:
2490: int i, m, jk, j1, bool, z1,j;
2491: int first;
2492: double ***freq; /* Frequencies */
2493: double *pp, **prop;
2494: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2495: char fileresp[FILENAMELENGTH];
2496:
2497: pp=vector(1,nlstate);
2498: prop=matrix(1,nlstate,iagemin,iagemax+3);
2499: strcpy(fileresp,"p");
2500: strcat(fileresp,fileres);
2501: if((ficresp=fopen(fileresp,"w"))==NULL) {
2502: printf("Problem with prevalence resultfile: %s\n", fileresp);
2503: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2504: exit(0);
2505: }
2506: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2507: j1=0;
2508:
2509: j=cptcoveff;
2510: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2511:
2512: first=1;
2513:
2514: /* for(k1=1; k1<=j ; k1++){ /* Loop on covariates */
2515: /* for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
2516: /* j1++;
2517: */
2518: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
2519: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2520: scanf("%d", i);*/
2521: for (i=-5; i<=nlstate+ndeath; i++)
2522: for (jk=-5; jk<=nlstate+ndeath; jk++)
2523: for(m=iagemin; m <= iagemax+3; m++)
2524: freq[i][jk][m]=0;
2525:
2526: for (i=1; i<=nlstate; i++)
2527: for(m=iagemin; m <= iagemax+3; m++)
2528: prop[i][m]=0;
2529:
2530: dateintsum=0;
2531: k2cpt=0;
2532: for (i=1; i<=imx; i++) {
2533: bool=1;
2534: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2535: for (z1=1; z1<=cptcoveff; z1++)
2536: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
2537: /* Tests if the value of each of the covariates of i is equal to filter j1 */
2538: bool=0;
2539: /* 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",
2540: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2541: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
2542: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2543: }
2544: }
2545:
2546: if (bool==1){
2547: for(m=firstpass; m<=lastpass; m++){
2548: k2=anint[m][i]+(mint[m][i]/12.);
2549: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2550: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2551: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2552: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2553: if (m<lastpass) {
2554: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2555: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2556: }
2557:
2558: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2559: dateintsum=dateintsum+k2;
2560: k2cpt++;
2561: }
2562: /*}*/
2563: }
2564: }
2565: } /* end i */
2566:
2567: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2568: pstamp(ficresp);
2569: if (cptcovn>0) {
2570: fprintf(ficresp, "\n#********** Variable ");
2571: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2572: fprintf(ficresp, "**********\n#");
2573: fprintf(ficlog, "\n#********** Variable ");
2574: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2575: fprintf(ficlog, "**********\n#");
2576: }
2577: for(i=1; i<=nlstate;i++)
2578: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2579: fprintf(ficresp, "\n");
2580:
2581: for(i=iagemin; i <= iagemax+3; i++){
2582: if(i==iagemax+3){
2583: fprintf(ficlog,"Total");
2584: }else{
2585: if(first==1){
2586: first=0;
2587: printf("See log file for details...\n");
2588: }
2589: fprintf(ficlog,"Age %d", i);
2590: }
2591: for(jk=1; jk <=nlstate ; jk++){
2592: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2593: pp[jk] += freq[jk][m][i];
2594: }
2595: for(jk=1; jk <=nlstate ; jk++){
2596: for(m=-1, pos=0; m <=0 ; m++)
2597: pos += freq[jk][m][i];
2598: if(pp[jk]>=1.e-10){
2599: if(first==1){
2600: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2601: }
2602: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2603: }else{
2604: if(first==1)
2605: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2606: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2607: }
2608: }
2609:
2610: for(jk=1; jk <=nlstate ; jk++){
2611: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2612: pp[jk] += freq[jk][m][i];
2613: }
2614: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2615: pos += pp[jk];
2616: posprop += prop[jk][i];
2617: }
2618: for(jk=1; jk <=nlstate ; jk++){
2619: if(pos>=1.e-5){
2620: if(first==1)
2621: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2622: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2623: }else{
2624: if(first==1)
2625: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2626: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2627: }
2628: if( i <= iagemax){
2629: if(pos>=1.e-5){
2630: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2631: /*probs[i][jk][j1]= pp[jk]/pos;*/
2632: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2633: }
2634: else
2635: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2636: }
2637: }
2638:
2639: for(jk=-1; jk <=nlstate+ndeath; jk++)
2640: for(m=-1; m <=nlstate+ndeath; m++)
2641: if(freq[jk][m][i] !=0 ) {
2642: if(first==1)
2643: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2644: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2645: }
2646: if(i <= iagemax)
2647: fprintf(ficresp,"\n");
2648: if(first==1)
2649: printf("Others in log...\n");
2650: fprintf(ficlog,"\n");
2651: }
2652: /*}*/
2653: }
2654: dateintmean=dateintsum/k2cpt;
2655:
2656: fclose(ficresp);
2657: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2658: free_vector(pp,1,nlstate);
2659: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2660: /* End of Freq */
2661: }
2662:
2663: /************ Prevalence ********************/
2664: 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)
2665: {
2666: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2667: in each health status at the date of interview (if between dateprev1 and dateprev2).
2668: We still use firstpass and lastpass as another selection.
2669: */
2670:
2671: int i, m, jk, j1, bool, z1,j;
2672:
2673: double **prop;
2674: double posprop;
2675: double y2; /* in fractional years */
2676: int iagemin, iagemax;
2677: int first; /** to stop verbosity which is redirected to log file */
2678:
2679: iagemin= (int) agemin;
2680: iagemax= (int) agemax;
2681: /*pp=vector(1,nlstate);*/
2682: prop=matrix(1,nlstate,iagemin,iagemax+3);
2683: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2684: j1=0;
2685:
2686: /*j=cptcoveff;*/
2687: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2688:
2689: first=1;
2690: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2691: /*for(i1=1; i1<=ncodemax[k1];i1++){
2692: j1++;*/
2693:
2694: for (i=1; i<=nlstate; i++)
2695: for(m=iagemin; m <= iagemax+3; m++)
2696: prop[i][m]=0.0;
2697:
2698: for (i=1; i<=imx; i++) { /* Each individual */
2699: bool=1;
2700: if (cptcovn>0) {
2701: for (z1=1; z1<=cptcoveff; z1++)
2702: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2703: bool=0;
2704: }
2705: if (bool==1) {
2706: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2707: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2708: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2709: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2710: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2711: 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);
2712: if (s[m][i]>0 && s[m][i]<=nlstate) {
2713: /*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]]);*/
2714: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2715: prop[s[m][i]][iagemax+3] += weight[i];
2716: }
2717: }
2718: } /* end selection of waves */
2719: }
2720: }
2721: for(i=iagemin; i <= iagemax+3; i++){
2722: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2723: posprop += prop[jk][i];
2724: }
2725:
2726: for(jk=1; jk <=nlstate ; jk++){
2727: if( i <= iagemax){
2728: if(posprop>=1.e-5){
2729: probs[i][jk][j1]= prop[jk][i]/posprop;
2730: } else{
2731: if(first==1){
2732: first=0;
2733: 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]);
2734: }
2735: }
2736: }
2737: }/* end jk */
2738: }/* end i */
2739: /*} *//* end i1 */
2740: } /* end j1 */
2741:
2742: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2743: /*free_vector(pp,1,nlstate);*/
2744: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2745: } /* End of prevalence */
2746:
2747: /************* Waves Concatenation ***************/
2748:
2749: 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)
2750: {
2751: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2752: Death is a valid wave (if date is known).
2753: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2754: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2755: and mw[mi+1][i]. dh depends on stepm.
2756: */
2757:
2758: int i, mi, m;
2759: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2760: double sum=0., jmean=0.;*/
2761: int first;
2762: int j, k=0,jk, ju, jl;
2763: double sum=0.;
2764: first=0;
2765: jmin=100000;
2766: jmax=-1;
2767: jmean=0.;
2768: for(i=1; i<=imx; i++){
2769: mi=0;
2770: m=firstpass;
2771: while(s[m][i] <= nlstate){
2772: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2773: mw[++mi][i]=m;
2774: if(m >=lastpass)
2775: break;
2776: else
2777: m++;
2778: }/* end while */
2779: if (s[m][i] > nlstate){
2780: mi++; /* Death is another wave */
2781: /* if(mi==0) never been interviewed correctly before death */
2782: /* Only death is a correct wave */
2783: mw[mi][i]=m;
2784: }
2785:
2786: wav[i]=mi;
2787: if(mi==0){
2788: nbwarn++;
2789: if(first==0){
2790: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2791: first=1;
2792: }
2793: if(first==1){
2794: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2795: }
2796: } /* end mi==0 */
2797: } /* End individuals */
2798:
2799: for(i=1; i<=imx; i++){
2800: for(mi=1; mi<wav[i];mi++){
2801: if (stepm <=0)
2802: dh[mi][i]=1;
2803: else{
2804: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2805: if (agedc[i] < 2*AGESUP) {
2806: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2807: if(j==0) j=1; /* Survives at least one month after exam */
2808: else if(j<0){
2809: nberr++;
2810: 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]);
2811: j=1; /* Temporary Dangerous patch */
2812: 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);
2813: 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]);
2814: 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);
2815: }
2816: k=k+1;
2817: if (j >= jmax){
2818: jmax=j;
2819: ijmax=i;
2820: }
2821: if (j <= jmin){
2822: jmin=j;
2823: ijmin=i;
2824: }
2825: sum=sum+j;
2826: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2827: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2828: }
2829: }
2830: else{
2831: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2832: /* 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]); */
2833:
2834: k=k+1;
2835: if (j >= jmax) {
2836: jmax=j;
2837: ijmax=i;
2838: }
2839: else if (j <= jmin){
2840: jmin=j;
2841: ijmin=i;
2842: }
2843: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2844: /*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]);*/
2845: if(j<0){
2846: nberr++;
2847: 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]);
2848: 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]);
2849: }
2850: sum=sum+j;
2851: }
2852: jk= j/stepm;
2853: jl= j -jk*stepm;
2854: ju= j -(jk+1)*stepm;
2855: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2856: if(jl==0){
2857: dh[mi][i]=jk;
2858: bh[mi][i]=0;
2859: }else{ /* We want a negative bias in order to only have interpolation ie
2860: * to avoid the price of an extra matrix product in likelihood */
2861: dh[mi][i]=jk+1;
2862: bh[mi][i]=ju;
2863: }
2864: }else{
2865: if(jl <= -ju){
2866: dh[mi][i]=jk;
2867: bh[mi][i]=jl; /* bias is positive if real duration
2868: * is higher than the multiple of stepm and negative otherwise.
2869: */
2870: }
2871: else{
2872: dh[mi][i]=jk+1;
2873: bh[mi][i]=ju;
2874: }
2875: if(dh[mi][i]==0){
2876: dh[mi][i]=1; /* At least one step */
2877: bh[mi][i]=ju; /* At least one step */
2878: /* 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);*/
2879: }
2880: } /* end if mle */
2881: }
2882: } /* end wave */
2883: }
2884: jmean=sum/k;
2885: 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);
2886: 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);
2887: }
2888:
2889: /*********** Tricode ****************************/
2890: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
2891: {
2892: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
2893: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
2894: /* Boring subroutine which should only output nbcode[Tvar[j]][k]
2895: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
2896: /* nbcode[Tvar[j]][1]=
2897: */
2898:
2899: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
2900: int modmaxcovj=0; /* Modality max of covariates j */
2901: int cptcode=0; /* Modality max of covariates j */
2902: int modmincovj=0; /* Modality min of covariates j */
2903:
2904:
2905: cptcoveff=0;
2906:
2907: for (k=-1; k < maxncov; k++) Ndum[k]=0;
2908: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
2909:
2910: /* Loop on covariates without age and products */
2911: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
2912: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
2913: modality of this covariate Vj*/
2914: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
2915: * If product of Vn*Vm, still boolean *:
2916: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
2917: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
2918: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
2919: modality of the nth covariate of individual i. */
2920: if (ij > modmaxcovj)
2921: modmaxcovj=ij;
2922: else if (ij < modmincovj)
2923: modmincovj=ij;
2924: if ((ij < -1) && (ij > NCOVMAX)){
2925: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
2926: exit(1);
2927: }else
2928: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
2929: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
2930: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2931: /* getting the maximum value of the modality of the covariate
2932: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2933: female is 1, then modmaxcovj=1.*/
2934: }
2935: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
2936: cptcode=modmaxcovj;
2937: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
2938: /*for (i=0; i<=cptcode; i++) {*/
2939: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
2940: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
2941: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
2942: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
2943: }
2944: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
2945: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
2946: } /* Ndum[-1] number of undefined modalities */
2947:
2948: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
2949: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
2950: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
2951: modmincovj=3; modmaxcovj = 7;
2952: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
2953: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
2954: variables V1_1 and V1_2.
2955: nbcode[Tvar[j]][ij]=k;
2956: nbcode[Tvar[j]][1]=0;
2957: nbcode[Tvar[j]][2]=1;
2958: nbcode[Tvar[j]][3]=2;
2959: */
2960: ij=1; /* ij is similar to i but can jumps over null modalities */
2961: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
2962: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
2963: /*recode from 0 */
2964: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
2965: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
2966: k is a modality. If we have model=V1+V1*sex
2967: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
2968: ij++;
2969: }
2970: if (ij > ncodemax[j]) break;
2971: } /* end of loop on */
2972: } /* end of loop on modality */
2973: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
2974:
2975: for (k=-1; k< maxncov; k++) Ndum[k]=0;
2976:
2977: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
2978: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2979: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
2980: Ndum[ij]++;
2981: }
2982:
2983: ij=1;
2984: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
2985: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
2986: if((Ndum[i]!=0) && (i<=ncovcol)){
2987: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
2988: Tvaraff[ij]=i; /*For printing (unclear) */
2989: ij++;
2990: }else
2991: Tvaraff[ij]=0;
2992: }
2993: ij--;
2994: cptcoveff=ij; /*Number of total covariates*/
2995:
2996: }
2997:
2998:
2999: /*********** Health Expectancies ****************/
3000:
3001: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
3002:
3003: {
3004: /* Health expectancies, no variances */
3005: int i, j, nhstepm, hstepm, h, nstepm;
3006: int nhstepma, nstepma; /* Decreasing with age */
3007: double age, agelim, hf;
3008: double ***p3mat;
3009: double eip;
3010:
3011: pstamp(ficreseij);
3012: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3013: fprintf(ficreseij,"# Age");
3014: for(i=1; i<=nlstate;i++){
3015: for(j=1; j<=nlstate;j++){
3016: fprintf(ficreseij," e%1d%1d ",i,j);
3017: }
3018: fprintf(ficreseij," e%1d. ",i);
3019: }
3020: fprintf(ficreseij,"\n");
3021:
3022:
3023: if(estepm < stepm){
3024: printf ("Problem %d lower than %d\n",estepm, stepm);
3025: }
3026: else hstepm=estepm;
3027: /* We compute the life expectancy from trapezoids spaced every estepm months
3028: * This is mainly to measure the difference between two models: for example
3029: * if stepm=24 months pijx are given only every 2 years and by summing them
3030: * we are calculating an estimate of the Life Expectancy assuming a linear
3031: * progression in between and thus overestimating or underestimating according
3032: * to the curvature of the survival function. If, for the same date, we
3033: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3034: * to compare the new estimate of Life expectancy with the same linear
3035: * hypothesis. A more precise result, taking into account a more precise
3036: * curvature will be obtained if estepm is as small as stepm. */
3037:
3038: /* For example we decided to compute the life expectancy with the smallest unit */
3039: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3040: nhstepm is the number of hstepm from age to agelim
3041: nstepm is the number of stepm from age to agelin.
3042: Look at hpijx to understand the reason of that which relies in memory size
3043: and note for a fixed period like estepm months */
3044: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3045: survival function given by stepm (the optimization length). Unfortunately it
3046: means that if the survival funtion is printed only each two years of age and if
3047: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3048: results. So we changed our mind and took the option of the best precision.
3049: */
3050: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3051:
3052: agelim=AGESUP;
3053: /* If stepm=6 months */
3054: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3055: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3056:
3057: /* nhstepm age range expressed in number of stepm */
3058: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3059: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3060: /* if (stepm >= YEARM) hstepm=1;*/
3061: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3062: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3063:
3064: for (age=bage; age<=fage; age ++){
3065: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3066: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3067: /* if (stepm >= YEARM) hstepm=1;*/
3068: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3069:
3070: /* If stepm=6 months */
3071: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3072: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3073:
3074: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3075:
3076: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3077:
3078: printf("%d|",(int)age);fflush(stdout);
3079: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3080:
3081: /* Computing expectancies */
3082: for(i=1; i<=nlstate;i++)
3083: for(j=1; j<=nlstate;j++)
3084: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3085: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3086:
3087: /* 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]);*/
3088:
3089: }
3090:
3091: fprintf(ficreseij,"%3.0f",age );
3092: for(i=1; i<=nlstate;i++){
3093: eip=0;
3094: for(j=1; j<=nlstate;j++){
3095: eip +=eij[i][j][(int)age];
3096: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3097: }
3098: fprintf(ficreseij,"%9.4f", eip );
3099: }
3100: fprintf(ficreseij,"\n");
3101:
3102: }
3103: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3104: printf("\n");
3105: fprintf(ficlog,"\n");
3106:
3107: }
3108:
3109: 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[] )
3110:
3111: {
3112: /* Covariances of health expectancies eij and of total life expectancies according
3113: to initial status i, ei. .
3114: */
3115: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3116: int nhstepma, nstepma; /* Decreasing with age */
3117: double age, agelim, hf;
3118: double ***p3matp, ***p3matm, ***varhe;
3119: double **dnewm,**doldm;
3120: double *xp, *xm;
3121: double **gp, **gm;
3122: double ***gradg, ***trgradg;
3123: int theta;
3124:
3125: double eip, vip;
3126:
3127: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3128: xp=vector(1,npar);
3129: xm=vector(1,npar);
3130: dnewm=matrix(1,nlstate*nlstate,1,npar);
3131: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3132:
3133: pstamp(ficresstdeij);
3134: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3135: fprintf(ficresstdeij,"# Age");
3136: for(i=1; i<=nlstate;i++){
3137: for(j=1; j<=nlstate;j++)
3138: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3139: fprintf(ficresstdeij," e%1d. ",i);
3140: }
3141: fprintf(ficresstdeij,"\n");
3142:
3143: pstamp(ficrescveij);
3144: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3145: fprintf(ficrescveij,"# Age");
3146: for(i=1; i<=nlstate;i++)
3147: for(j=1; j<=nlstate;j++){
3148: cptj= (j-1)*nlstate+i;
3149: for(i2=1; i2<=nlstate;i2++)
3150: for(j2=1; j2<=nlstate;j2++){
3151: cptj2= (j2-1)*nlstate+i2;
3152: if(cptj2 <= cptj)
3153: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3154: }
3155: }
3156: fprintf(ficrescveij,"\n");
3157:
3158: if(estepm < stepm){
3159: printf ("Problem %d lower than %d\n",estepm, stepm);
3160: }
3161: else hstepm=estepm;
3162: /* We compute the life expectancy from trapezoids spaced every estepm months
3163: * This is mainly to measure the difference between two models: for example
3164: * if stepm=24 months pijx are given only every 2 years and by summing them
3165: * we are calculating an estimate of the Life Expectancy assuming a linear
3166: * progression in between and thus overestimating or underestimating according
3167: * to the curvature of the survival function. If, for the same date, we
3168: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3169: * to compare the new estimate of Life expectancy with the same linear
3170: * hypothesis. A more precise result, taking into account a more precise
3171: * curvature will be obtained if estepm is as small as stepm. */
3172:
3173: /* For example we decided to compute the life expectancy with the smallest unit */
3174: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3175: nhstepm is the number of hstepm from age to agelim
3176: nstepm is the number of stepm from age to agelin.
3177: Look at hpijx to understand the reason of that which relies in memory size
3178: and note for a fixed period like estepm months */
3179: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3180: survival function given by stepm (the optimization length). Unfortunately it
3181: means that if the survival funtion is printed only each two years of age and if
3182: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3183: results. So we changed our mind and took the option of the best precision.
3184: */
3185: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3186:
3187: /* If stepm=6 months */
3188: /* nhstepm age range expressed in number of stepm */
3189: agelim=AGESUP;
3190: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3191: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3192: /* if (stepm >= YEARM) hstepm=1;*/
3193: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3194:
3195: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3196: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3197: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3198: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3199: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3200: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3201:
3202: for (age=bage; age<=fage; age ++){
3203: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3204: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3205: /* if (stepm >= YEARM) hstepm=1;*/
3206: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3207:
3208: /* If stepm=6 months */
3209: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3210: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3211:
3212: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3213:
3214: /* Computing Variances of health expectancies */
3215: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3216: decrease memory allocation */
3217: for(theta=1; theta <=npar; theta++){
3218: for(i=1; i<=npar; i++){
3219: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3220: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3221: }
3222: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3223: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3224:
3225: for(j=1; j<= nlstate; j++){
3226: for(i=1; i<=nlstate; i++){
3227: for(h=0; h<=nhstepm-1; h++){
3228: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3229: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3230: }
3231: }
3232: }
3233:
3234: for(ij=1; ij<= nlstate*nlstate; ij++)
3235: for(h=0; h<=nhstepm-1; h++){
3236: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3237: }
3238: }/* End theta */
3239:
3240:
3241: for(h=0; h<=nhstepm-1; h++)
3242: for(j=1; j<=nlstate*nlstate;j++)
3243: for(theta=1; theta <=npar; theta++)
3244: trgradg[h][j][theta]=gradg[h][theta][j];
3245:
3246:
3247: for(ij=1;ij<=nlstate*nlstate;ij++)
3248: for(ji=1;ji<=nlstate*nlstate;ji++)
3249: varhe[ij][ji][(int)age] =0.;
3250:
3251: printf("%d|",(int)age);fflush(stdout);
3252: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3253: for(h=0;h<=nhstepm-1;h++){
3254: for(k=0;k<=nhstepm-1;k++){
3255: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3256: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3257: for(ij=1;ij<=nlstate*nlstate;ij++)
3258: for(ji=1;ji<=nlstate*nlstate;ji++)
3259: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3260: }
3261: }
3262:
3263: /* Computing expectancies */
3264: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3265: for(i=1; i<=nlstate;i++)
3266: for(j=1; j<=nlstate;j++)
3267: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3268: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3269:
3270: /* 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]);*/
3271:
3272: }
3273:
3274: fprintf(ficresstdeij,"%3.0f",age );
3275: for(i=1; i<=nlstate;i++){
3276: eip=0.;
3277: vip=0.;
3278: for(j=1; j<=nlstate;j++){
3279: eip += eij[i][j][(int)age];
3280: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3281: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3282: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3283: }
3284: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3285: }
3286: fprintf(ficresstdeij,"\n");
3287:
3288: fprintf(ficrescveij,"%3.0f",age );
3289: for(i=1; i<=nlstate;i++)
3290: for(j=1; j<=nlstate;j++){
3291: cptj= (j-1)*nlstate+i;
3292: for(i2=1; i2<=nlstate;i2++)
3293: for(j2=1; j2<=nlstate;j2++){
3294: cptj2= (j2-1)*nlstate+i2;
3295: if(cptj2 <= cptj)
3296: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3297: }
3298: }
3299: fprintf(ficrescveij,"\n");
3300:
3301: }
3302: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3303: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3304: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3305: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3306: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3307: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3308: printf("\n");
3309: fprintf(ficlog,"\n");
3310:
3311: free_vector(xm,1,npar);
3312: free_vector(xp,1,npar);
3313: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3314: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3315: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3316: }
3317:
3318: /************ Variance ******************/
3319: 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[])
3320: {
3321: /* Variance of health expectancies */
3322: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3323: /* double **newm;*/
3324: double **dnewm,**doldm;
3325: double **dnewmp,**doldmp;
3326: int i, j, nhstepm, hstepm, h, nstepm ;
3327: int k;
3328: double *xp;
3329: double **gp, **gm; /* for var eij */
3330: double ***gradg, ***trgradg; /*for var eij */
3331: double **gradgp, **trgradgp; /* for var p point j */
3332: double *gpp, *gmp; /* for var p point j */
3333: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3334: double ***p3mat;
3335: double age,agelim, hf;
3336: double ***mobaverage;
3337: int theta;
3338: char digit[4];
3339: char digitp[25];
3340:
3341: char fileresprobmorprev[FILENAMELENGTH];
3342:
3343: if(popbased==1){
3344: if(mobilav!=0)
3345: strcpy(digitp,"-populbased-mobilav-");
3346: else strcpy(digitp,"-populbased-nomobil-");
3347: }
3348: else
3349: strcpy(digitp,"-stablbased-");
3350:
3351: if (mobilav!=0) {
3352: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3353: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3354: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3355: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3356: }
3357: }
3358:
3359: strcpy(fileresprobmorprev,"prmorprev");
3360: sprintf(digit,"%-d",ij);
3361: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3362: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3363: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3364: strcat(fileresprobmorprev,fileres);
3365: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3366: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3367: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3368: }
3369: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3370:
3371: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3372: pstamp(ficresprobmorprev);
3373: 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);
3374: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3375: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3376: fprintf(ficresprobmorprev," p.%-d SE",j);
3377: for(i=1; i<=nlstate;i++)
3378: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3379: }
3380: fprintf(ficresprobmorprev,"\n");
3381: fprintf(ficgp,"\n# Routine varevsij");
3382: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3383: 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");
3384: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3385: /* } */
3386: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3387: pstamp(ficresvij);
3388: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3389: if(popbased==1)
3390: 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);
3391: else
3392: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3393: fprintf(ficresvij,"# Age");
3394: for(i=1; i<=nlstate;i++)
3395: for(j=1; j<=nlstate;j++)
3396: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3397: fprintf(ficresvij,"\n");
3398:
3399: xp=vector(1,npar);
3400: dnewm=matrix(1,nlstate,1,npar);
3401: doldm=matrix(1,nlstate,1,nlstate);
3402: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3403: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3404:
3405: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3406: gpp=vector(nlstate+1,nlstate+ndeath);
3407: gmp=vector(nlstate+1,nlstate+ndeath);
3408: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3409:
3410: if(estepm < stepm){
3411: printf ("Problem %d lower than %d\n",estepm, stepm);
3412: }
3413: else hstepm=estepm;
3414: /* For example we decided to compute the life expectancy with the smallest unit */
3415: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3416: nhstepm is the number of hstepm from age to agelim
3417: nstepm is the number of stepm from age to agelin.
3418: Look at function hpijx to understand why (it is linked to memory size questions) */
3419: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3420: survival function given by stepm (the optimization length). Unfortunately it
3421: means that if the survival funtion is printed every two years of age and if
3422: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3423: results. So we changed our mind and took the option of the best precision.
3424: */
3425: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3426: agelim = AGESUP;
3427: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3428: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3429: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3430: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3431: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3432: gp=matrix(0,nhstepm,1,nlstate);
3433: gm=matrix(0,nhstepm,1,nlstate);
3434:
3435:
3436: for(theta=1; theta <=npar; theta++){
3437: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3438: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3439: }
3440: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3441: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3442:
3443: if (popbased==1) {
3444: if(mobilav ==0){
3445: for(i=1; i<=nlstate;i++)
3446: prlim[i][i]=probs[(int)age][i][ij];
3447: }else{ /* mobilav */
3448: for(i=1; i<=nlstate;i++)
3449: prlim[i][i]=mobaverage[(int)age][i][ij];
3450: }
3451: }
3452:
3453: for(j=1; j<= nlstate; j++){
3454: for(h=0; h<=nhstepm; h++){
3455: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3456: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3457: }
3458: }
3459: /* This for computing probability of death (h=1 means
3460: computed over hstepm matrices product = hstepm*stepm months)
3461: as a weighted average of prlim.
3462: */
3463: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3464: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3465: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3466: }
3467: /* end probability of death */
3468:
3469: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3470: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3471: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3472: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3473:
3474: if (popbased==1) {
3475: if(mobilav ==0){
3476: for(i=1; i<=nlstate;i++)
3477: prlim[i][i]=probs[(int)age][i][ij];
3478: }else{ /* mobilav */
3479: for(i=1; i<=nlstate;i++)
3480: prlim[i][i]=mobaverage[(int)age][i][ij];
3481: }
3482: }
3483:
3484: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3485: for(h=0; h<=nhstepm; h++){
3486: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3487: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3488: }
3489: }
3490: /* This for computing probability of death (h=1 means
3491: computed over hstepm matrices product = hstepm*stepm months)
3492: as a weighted average of prlim.
3493: */
3494: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3495: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3496: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3497: }
3498: /* end probability of death */
3499:
3500: for(j=1; j<= nlstate; j++) /* vareij */
3501: for(h=0; h<=nhstepm; h++){
3502: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3503: }
3504:
3505: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3506: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3507: }
3508:
3509: } /* End theta */
3510:
3511: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3512:
3513: for(h=0; h<=nhstepm; h++) /* veij */
3514: for(j=1; j<=nlstate;j++)
3515: for(theta=1; theta <=npar; theta++)
3516: trgradg[h][j][theta]=gradg[h][theta][j];
3517:
3518: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3519: for(theta=1; theta <=npar; theta++)
3520: trgradgp[j][theta]=gradgp[theta][j];
3521:
3522:
3523: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3524: for(i=1;i<=nlstate;i++)
3525: for(j=1;j<=nlstate;j++)
3526: vareij[i][j][(int)age] =0.;
3527:
3528: for(h=0;h<=nhstepm;h++){
3529: for(k=0;k<=nhstepm;k++){
3530: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3531: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3532: for(i=1;i<=nlstate;i++)
3533: for(j=1;j<=nlstate;j++)
3534: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3535: }
3536: }
3537:
3538: /* pptj */
3539: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3540: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3541: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3542: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3543: varppt[j][i]=doldmp[j][i];
3544: /* end ppptj */
3545: /* x centered again */
3546: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3547: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3548:
3549: if (popbased==1) {
3550: if(mobilav ==0){
3551: for(i=1; i<=nlstate;i++)
3552: prlim[i][i]=probs[(int)age][i][ij];
3553: }else{ /* mobilav */
3554: for(i=1; i<=nlstate;i++)
3555: prlim[i][i]=mobaverage[(int)age][i][ij];
3556: }
3557: }
3558:
3559: /* This for computing probability of death (h=1 means
3560: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3561: as a weighted average of prlim.
3562: */
3563: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3564: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3565: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3566: }
3567: /* end probability of death */
3568:
3569: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3570: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3571: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3572: for(i=1; i<=nlstate;i++){
3573: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3574: }
3575: }
3576: fprintf(ficresprobmorprev,"\n");
3577:
3578: fprintf(ficresvij,"%.0f ",age );
3579: for(i=1; i<=nlstate;i++)
3580: for(j=1; j<=nlstate;j++){
3581: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3582: }
3583: fprintf(ficresvij,"\n");
3584: free_matrix(gp,0,nhstepm,1,nlstate);
3585: free_matrix(gm,0,nhstepm,1,nlstate);
3586: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3587: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3588: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3589: } /* End age */
3590: free_vector(gpp,nlstate+1,nlstate+ndeath);
3591: free_vector(gmp,nlstate+1,nlstate+ndeath);
3592: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3593: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3594: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
3595: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3596: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3597: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3598: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3599: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3600: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
3601: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
3602: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
3603: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3604: 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);
3605: /* 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);
3606: */
3607: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3608: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3609:
3610: free_vector(xp,1,npar);
3611: free_matrix(doldm,1,nlstate,1,nlstate);
3612: free_matrix(dnewm,1,nlstate,1,npar);
3613: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3614: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3615: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3616: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3617: fclose(ficresprobmorprev);
3618: fflush(ficgp);
3619: fflush(fichtm);
3620: } /* end varevsij */
3621:
3622: /************ Variance of prevlim ******************/
3623: 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[])
3624: {
3625: /* Variance of prevalence limit */
3626: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3627:
3628: double **dnewm,**doldm;
3629: int i, j, nhstepm, hstepm;
3630: double *xp;
3631: double *gp, *gm;
3632: double **gradg, **trgradg;
3633: double age,agelim;
3634: int theta;
3635:
3636: pstamp(ficresvpl);
3637: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3638: fprintf(ficresvpl,"# Age");
3639: for(i=1; i<=nlstate;i++)
3640: fprintf(ficresvpl," %1d-%1d",i,i);
3641: fprintf(ficresvpl,"\n");
3642:
3643: xp=vector(1,npar);
3644: dnewm=matrix(1,nlstate,1,npar);
3645: doldm=matrix(1,nlstate,1,nlstate);
3646:
3647: hstepm=1*YEARM; /* Every year of age */
3648: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3649: agelim = AGESUP;
3650: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3651: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3652: if (stepm >= YEARM) hstepm=1;
3653: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3654: gradg=matrix(1,npar,1,nlstate);
3655: gp=vector(1,nlstate);
3656: gm=vector(1,nlstate);
3657:
3658: for(theta=1; theta <=npar; theta++){
3659: for(i=1; i<=npar; i++){ /* Computes gradient */
3660: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3661: }
3662: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3663: for(i=1;i<=nlstate;i++)
3664: gp[i] = prlim[i][i];
3665:
3666: for(i=1; i<=npar; i++) /* Computes gradient */
3667: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3668: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3669: for(i=1;i<=nlstate;i++)
3670: gm[i] = prlim[i][i];
3671:
3672: for(i=1;i<=nlstate;i++)
3673: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3674: } /* End theta */
3675:
3676: trgradg =matrix(1,nlstate,1,npar);
3677:
3678: for(j=1; j<=nlstate;j++)
3679: for(theta=1; theta <=npar; theta++)
3680: trgradg[j][theta]=gradg[theta][j];
3681:
3682: for(i=1;i<=nlstate;i++)
3683: varpl[i][(int)age] =0.;
3684: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3685: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3686: for(i=1;i<=nlstate;i++)
3687: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3688:
3689: fprintf(ficresvpl,"%.0f ",age );
3690: for(i=1; i<=nlstate;i++)
3691: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3692: fprintf(ficresvpl,"\n");
3693: free_vector(gp,1,nlstate);
3694: free_vector(gm,1,nlstate);
3695: free_matrix(gradg,1,npar,1,nlstate);
3696: free_matrix(trgradg,1,nlstate,1,npar);
3697: } /* End age */
3698:
3699: free_vector(xp,1,npar);
3700: free_matrix(doldm,1,nlstate,1,npar);
3701: free_matrix(dnewm,1,nlstate,1,nlstate);
3702:
3703: }
3704:
3705: /************ Variance of one-step probabilities ******************/
3706: 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[])
3707: {
3708: int i, j=0, k1, l1, tj;
3709: int k2, l2, j1, z1;
3710: int k=0, l;
3711: int first=1, first1, first2;
3712: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3713: double **dnewm,**doldm;
3714: double *xp;
3715: double *gp, *gm;
3716: double **gradg, **trgradg;
3717: double **mu;
3718: double age, cov[NCOVMAX+1];
3719: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3720: int theta;
3721: char fileresprob[FILENAMELENGTH];
3722: char fileresprobcov[FILENAMELENGTH];
3723: char fileresprobcor[FILENAMELENGTH];
3724: double ***varpij;
3725:
3726: strcpy(fileresprob,"prob");
3727: strcat(fileresprob,fileres);
3728: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3729: printf("Problem with resultfile: %s\n", fileresprob);
3730: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3731: }
3732: strcpy(fileresprobcov,"probcov");
3733: strcat(fileresprobcov,fileres);
3734: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3735: printf("Problem with resultfile: %s\n", fileresprobcov);
3736: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3737: }
3738: strcpy(fileresprobcor,"probcor");
3739: strcat(fileresprobcor,fileres);
3740: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3741: printf("Problem with resultfile: %s\n", fileresprobcor);
3742: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3743: }
3744: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3745: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3746: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3747: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3748: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3749: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3750: pstamp(ficresprob);
3751: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3752: fprintf(ficresprob,"# Age");
3753: pstamp(ficresprobcov);
3754: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3755: fprintf(ficresprobcov,"# Age");
3756: pstamp(ficresprobcor);
3757: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3758: fprintf(ficresprobcor,"# Age");
3759:
3760:
3761: for(i=1; i<=nlstate;i++)
3762: for(j=1; j<=(nlstate+ndeath);j++){
3763: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3764: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3765: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3766: }
3767: /* fprintf(ficresprob,"\n");
3768: fprintf(ficresprobcov,"\n");
3769: fprintf(ficresprobcor,"\n");
3770: */
3771: xp=vector(1,npar);
3772: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3773: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3774: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3775: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3776: first=1;
3777: fprintf(ficgp,"\n# Routine varprob");
3778: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3779: fprintf(fichtm,"\n");
3780:
3781: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3782: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3783: file %s<br>\n",optionfilehtmcov);
3784: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3785: and drawn. It helps understanding how is the covariance between two incidences.\
3786: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3787: 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. \
3788: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3789: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3790: standard deviations wide on each axis. <br>\
3791: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3792: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3793: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3794:
3795: cov[1]=1;
3796: /* tj=cptcoveff; */
3797: tj = (int) pow(2,cptcoveff);
3798: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3799: j1=0;
3800: for(j1=1; j1<=tj;j1++){
3801: /*for(i1=1; i1<=ncodemax[t];i1++){ */
3802: /*j1++;*/
3803: if (cptcovn>0) {
3804: fprintf(ficresprob, "\n#********** Variable ");
3805: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3806: fprintf(ficresprob, "**********\n#\n");
3807: fprintf(ficresprobcov, "\n#********** Variable ");
3808: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3809: fprintf(ficresprobcov, "**********\n#\n");
3810:
3811: fprintf(ficgp, "\n#********** Variable ");
3812: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3813: fprintf(ficgp, "**********\n#\n");
3814:
3815:
3816: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3817: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3818: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3819:
3820: fprintf(ficresprobcor, "\n#********** Variable ");
3821: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3822: fprintf(ficresprobcor, "**********\n#");
3823: }
3824:
3825: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3826: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3827: gp=vector(1,(nlstate)*(nlstate+ndeath));
3828: gm=vector(1,(nlstate)*(nlstate+ndeath));
3829: for (age=bage; age<=fage; age ++){
3830: cov[2]=age;
3831: for (k=1; k<=cptcovn;k++) {
3832: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
3833: * 1 1 1 1 1
3834: * 2 2 1 1 1
3835: * 3 1 2 1 1
3836: */
3837: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
3838: }
3839: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3840: for (k=1; k<=cptcovprod;k++)
3841: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3842:
3843:
3844: for(theta=1; theta <=npar; theta++){
3845: for(i=1; i<=npar; i++)
3846: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3847:
3848: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3849:
3850: k=0;
3851: for(i=1; i<= (nlstate); i++){
3852: for(j=1; j<=(nlstate+ndeath);j++){
3853: k=k+1;
3854: gp[k]=pmmij[i][j];
3855: }
3856: }
3857:
3858: for(i=1; i<=npar; i++)
3859: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3860:
3861: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3862: k=0;
3863: for(i=1; i<=(nlstate); i++){
3864: for(j=1; j<=(nlstate+ndeath);j++){
3865: k=k+1;
3866: gm[k]=pmmij[i][j];
3867: }
3868: }
3869:
3870: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3871: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3872: }
3873:
3874: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3875: for(theta=1; theta <=npar; theta++)
3876: trgradg[j][theta]=gradg[theta][j];
3877:
3878: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3879: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3880:
3881: pmij(pmmij,cov,ncovmodel,x,nlstate);
3882:
3883: k=0;
3884: for(i=1; i<=(nlstate); i++){
3885: for(j=1; j<=(nlstate+ndeath);j++){
3886: k=k+1;
3887: mu[k][(int) age]=pmmij[i][j];
3888: }
3889: }
3890: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3891: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3892: varpij[i][j][(int)age] = doldm[i][j];
3893:
3894: /*printf("\n%d ",(int)age);
3895: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3896: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3897: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3898: }*/
3899:
3900: fprintf(ficresprob,"\n%d ",(int)age);
3901: fprintf(ficresprobcov,"\n%d ",(int)age);
3902: fprintf(ficresprobcor,"\n%d ",(int)age);
3903:
3904: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3905: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3906: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3907: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3908: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3909: }
3910: i=0;
3911: for (k=1; k<=(nlstate);k++){
3912: for (l=1; l<=(nlstate+ndeath);l++){
3913: i++;
3914: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3915: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3916: for (j=1; j<=i;j++){
3917: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
3918: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3919: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3920: }
3921: }
3922: }/* end of loop for state */
3923: } /* end of loop for age */
3924: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3925: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3926: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3927: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3928:
3929: /* Confidence intervalle of pij */
3930: /*
3931: fprintf(ficgp,"\nunset parametric;unset label");
3932: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3933: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3934: 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);
3935: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3936: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3937: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3938: */
3939:
3940: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3941: first1=1;first2=2;
3942: for (k2=1; k2<=(nlstate);k2++){
3943: for (l2=1; l2<=(nlstate+ndeath);l2++){
3944: if(l2==k2) continue;
3945: j=(k2-1)*(nlstate+ndeath)+l2;
3946: for (k1=1; k1<=(nlstate);k1++){
3947: for (l1=1; l1<=(nlstate+ndeath);l1++){
3948: if(l1==k1) continue;
3949: i=(k1-1)*(nlstate+ndeath)+l1;
3950: if(i<=j) continue;
3951: for (age=bage; age<=fage; age ++){
3952: if ((int)age %5==0){
3953: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3954: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3955: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3956: mu1=mu[i][(int) age]/stepm*YEARM ;
3957: mu2=mu[j][(int) age]/stepm*YEARM;
3958: c12=cv12/sqrt(v1*v2);
3959: /* Computing eigen value of matrix of covariance */
3960: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3961: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3962: if ((lc2 <0) || (lc1 <0) ){
3963: if(first2==1){
3964: first1=0;
3965: 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);
3966: }
3967: 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);
3968: /* lc1=fabs(lc1); */ /* If we want to have them positive */
3969: /* lc2=fabs(lc2); */
3970: }
3971:
3972: /* Eigen vectors */
3973: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3974: /*v21=sqrt(1.-v11*v11); *//* error */
3975: v21=(lc1-v1)/cv12*v11;
3976: v12=-v21;
3977: v22=v11;
3978: tnalp=v21/v11;
3979: if(first1==1){
3980: first1=0;
3981: 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);
3982: }
3983: 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);
3984: /*printf(fignu*/
3985: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3986: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3987: if(first==1){
3988: first=0;
3989: fprintf(ficgp,"\nset parametric;unset label");
3990: 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);
3991: fprintf(ficgp,"\nset ter png small size 320, 240");
3992: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3993: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3994: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3995: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3996: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3997: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3998: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3999: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4000: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4001: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4002: 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",\
4003: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4004: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4005: }else{
4006: first=0;
4007: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4008: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4009: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4010: 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",\
4011: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4012: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4013: }/* if first */
4014: } /* age mod 5 */
4015: } /* end loop age */
4016: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4017: first=1;
4018: } /*l12 */
4019: } /* k12 */
4020: } /*l1 */
4021: }/* k1 */
4022: /* } /* loop covariates */
4023: }
4024: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4025: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4026: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4027: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4028: free_vector(xp,1,npar);
4029: fclose(ficresprob);
4030: fclose(ficresprobcov);
4031: fclose(ficresprobcor);
4032: fflush(ficgp);
4033: fflush(fichtmcov);
4034: }
4035:
4036:
4037: /******************* Printing html file ***********/
4038: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4039: int lastpass, int stepm, int weightopt, char model[],\
4040: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4041: int popforecast, int estepm ,\
4042: double jprev1, double mprev1,double anprev1, \
4043: double jprev2, double mprev2,double anprev2){
4044: int jj1, k1, i1, cpt;
4045:
4046: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4047: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4048: </ul>");
4049: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4050: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4051: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4052: fprintf(fichtm,"\
4053: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4054: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4055: fprintf(fichtm,"\
4056: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4057: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4058: fprintf(fichtm,"\
4059: - (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): \
4060: <a href=\"%s\">%s</a> <br>\n",
4061: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4062: fprintf(fichtm,"\
4063: - Population projections by age and states: \
4064: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4065:
4066: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4067:
4068: m=pow(2,cptcoveff);
4069: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4070:
4071: jj1=0;
4072: for(k1=1; k1<=m;k1++){
4073: for(i1=1; i1<=ncodemax[k1];i1++){
4074: jj1++;
4075: if (cptcovn > 0) {
4076: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4077: for (cpt=1; cpt<=cptcoveff;cpt++)
4078: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4079: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4080: }
4081: /* Pij */
4082: 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> \
4083: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4084: /* Quasi-incidences */
4085: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
4086: 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> \
4087: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4088: /* Period (stable) prevalence in each health state */
4089: for(cpt=1; cpt<=nlstate;cpt++){
4090: fprintf(fichtm,"<br>- Convergence from cross-sectional prevalence in each state (1 to %d) to period (stable) prevalence in specific state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
4091: <img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
4092: }
4093: for(cpt=1; cpt<=nlstate;cpt++) {
4094: 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> \
4095: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
4096: }
4097: } /* end i1 */
4098: }/* End k1 */
4099: fprintf(fichtm,"</ul>");
4100:
4101:
4102: fprintf(fichtm,"\
4103: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4104: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4105:
4106: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4107: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4108: fprintf(fichtm,"\
4109: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4110: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4111:
4112: fprintf(fichtm,"\
4113: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4114: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4115: fprintf(fichtm,"\
4116: - 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): \
4117: <a href=\"%s\">%s</a> <br>\n</li>",
4118: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4119: fprintf(fichtm,"\
4120: - (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): \
4121: <a href=\"%s\">%s</a> <br>\n</li>",
4122: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4123: fprintf(fichtm,"\
4124: - 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",
4125: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4126: fprintf(fichtm,"\
4127: - 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",
4128: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
4129: fprintf(fichtm,"\
4130: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4131: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4132:
4133: /* if(popforecast==1) fprintf(fichtm,"\n */
4134: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4135: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4136: /* <br>",fileres,fileres,fileres,fileres); */
4137: /* else */
4138: /* 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); */
4139: fflush(fichtm);
4140: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4141:
4142: m=pow(2,cptcoveff);
4143: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4144:
4145: jj1=0;
4146: for(k1=1; k1<=m;k1++){
4147: for(i1=1; i1<=ncodemax[k1];i1++){
4148: jj1++;
4149: if (cptcovn > 0) {
4150: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4151: for (cpt=1; cpt<=cptcoveff;cpt++)
4152: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4153: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4154: }
4155: for(cpt=1; cpt<=nlstate;cpt++) {
4156: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
4157: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4158: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
4159: }
4160: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
4161: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4162: true period expectancies (those weighted with period prevalences are also\
4163: drawn in addition to the population based expectancies computed using\
4164: observed and cahotic prevalences: %s%d.png<br>\
4165: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4166: } /* end i1 */
4167: }/* End k1 */
4168: fprintf(fichtm,"</ul>");
4169: fflush(fichtm);
4170: }
4171:
4172: /******************* Gnuplot file **************/
4173: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4174:
4175: char dirfileres[132],optfileres[132];
4176: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
4177: int ng=0;
4178: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4179: /* printf("Problem with file %s",optionfilegnuplot); */
4180: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4181: /* } */
4182:
4183: /*#ifdef windows */
4184: fprintf(ficgp,"cd \"%s\" \n",pathc);
4185: /*#endif */
4186: m=pow(2,cptcoveff);
4187:
4188: strcpy(dirfileres,optionfilefiname);
4189: strcpy(optfileres,"vpl");
4190: /* 1eme*/
4191: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
4192: for (cpt=1; cpt<= nlstate ; cpt ++) {
4193: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4194: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4195: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
4196: fprintf(ficgp,"set xlabel \"Age\" \n\
4197: set ylabel \"Probability\" \n\
4198: set ter png small size 320, 240\n\
4199: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
4200:
4201: for (i=1; i<= nlstate ; i ++) {
4202: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4203: else fprintf(ficgp," \%%*lf (\%%*lf)");
4204: }
4205: 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);
4206: for (i=1; i<= nlstate ; i ++) {
4207: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4208: else fprintf(ficgp," \%%*lf (\%%*lf)");
4209: }
4210: fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
4211: for (i=1; i<= nlstate ; i ++) {
4212: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4213: else fprintf(ficgp," \%%*lf (\%%*lf)");
4214: }
4215: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
4216: }
4217: }
4218: /*2 eme*/
4219: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
4220: for (k1=1; k1<= m ; k1 ++) {
4221: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
4222: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
4223:
4224: for (i=1; i<= nlstate+1 ; i ++) {
4225: k=2*i;
4226: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4227: for (j=1; j<= nlstate+1 ; j ++) {
4228: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4229: else fprintf(ficgp," \%%*lf (\%%*lf)");
4230: }
4231: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4232: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
4233: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4234: for (j=1; j<= nlstate+1 ; j ++) {
4235: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4236: else fprintf(ficgp," \%%*lf (\%%*lf)");
4237: }
4238: fprintf(ficgp,"\" t\"\" w l lt 0,");
4239: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4240: for (j=1; j<= nlstate+1 ; j ++) {
4241: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4242: else fprintf(ficgp," \%%*lf (\%%*lf)");
4243: }
4244: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4245: else fprintf(ficgp,"\" t\"\" w l lt 0,");
4246: }
4247: }
4248:
4249: /*3eme*/
4250:
4251: for (k1=1; k1<= m ; k1 ++) {
4252: for (cpt=1; cpt<= nlstate ; cpt ++) {
4253: /* k=2+nlstate*(2*cpt-2); */
4254: k=2+(nlstate+1)*(cpt-1);
4255: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
4256: fprintf(ficgp,"set ter png small size 320, 240\n\
4257: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4258: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4259: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4260: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4261: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4262: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4263: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4264:
4265: */
4266: for (i=1; i< nlstate ; i ++) {
4267: 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);
4268: /* 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);*/
4269:
4270: }
4271: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4272: }
4273: }
4274:
4275: /* CV preval stable (period) */
4276: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4277: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
4278: k=3;
4279: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
4280: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
4281: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
4282: set ter png small size 320, 240\n\
4283: unset log y\n\
4284: plot [%.f:%.f] ", ageminpar, agemaxpar);
4285: for (i=1; i<= nlstate ; i ++){
4286: if(i==1)
4287: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4288: else
4289: fprintf(ficgp,", '' ");
4290: l=(nlstate+ndeath)*(i-1)+1;
4291: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
4292: for (j=1; j<= (nlstate-1) ; j ++)
4293: fprintf(ficgp,"+$%d",k+l+j);
4294: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4295: } /* nlstate */
4296: fprintf(ficgp,"\n");
4297: } /* end cpt state*/
4298: } /* end covariate */
4299:
4300: /* proba elementaires */
4301: for(i=1,jk=1; i <=nlstate; i++){
4302: for(k=1; k <=(nlstate+ndeath); k++){
4303: if (k != i) {
4304: for(j=1; j <=ncovmodel; j++){
4305: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4306: jk++;
4307: fprintf(ficgp,"\n");
4308: }
4309: }
4310: }
4311: }
4312: /*goto avoid;*/
4313: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4314: for(jk=1; jk <=m; jk++) {
4315: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
4316: if (ng==2)
4317: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4318: else
4319: fprintf(ficgp,"\nset title \"Probability\"\n");
4320: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
4321: i=1;
4322: for(k2=1; k2<=nlstate; k2++) {
4323: k3=i;
4324: for(k=1; k<=(nlstate+ndeath); k++) {
4325: if (k != k2){
4326: if(ng==2)
4327: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4328: else
4329: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4330: ij=1;/* To be checked else nbcode[0][0] wrong */
4331: for(j=3; j <=ncovmodel; j++) {
4332: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
4333: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
4334: /* ij++; */
4335: /* } */
4336: /* else */
4337: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4338: }
4339: fprintf(ficgp,")/(1");
4340:
4341: for(k1=1; k1 <=nlstate; k1++){
4342: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4343: ij=1;
4344: for(j=3; j <=ncovmodel; j++){
4345: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
4346: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
4347: /* ij++; */
4348: /* } */
4349: /* else */
4350: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4351: }
4352: fprintf(ficgp,")");
4353: }
4354: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4355: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4356: i=i+ncovmodel;
4357: }
4358: } /* end k */
4359: } /* end k2 */
4360: } /* end jk */
4361: } /* end ng */
4362: /* avoid: */
4363: fflush(ficgp);
4364: } /* end gnuplot */
4365:
4366:
4367: /*************** Moving average **************/
4368: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4369:
4370: int i, cpt, cptcod;
4371: int modcovmax =1;
4372: int mobilavrange, mob;
4373: double age;
4374:
4375: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4376: a covariate has 2 modalities */
4377: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4378:
4379: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4380: if(mobilav==1) mobilavrange=5; /* default */
4381: else mobilavrange=mobilav;
4382: for (age=bage; age<=fage; age++)
4383: for (i=1; i<=nlstate;i++)
4384: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4385: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4386: /* We keep the original values on the extreme ages bage, fage and for
4387: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4388: we use a 5 terms etc. until the borders are no more concerned.
4389: */
4390: for (mob=3;mob <=mobilavrange;mob=mob+2){
4391: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4392: for (i=1; i<=nlstate;i++){
4393: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4394: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4395: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4396: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4397: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4398: }
4399: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4400: }
4401: }
4402: }/* end age */
4403: }/* end mob */
4404: }else return -1;
4405: return 0;
4406: }/* End movingaverage */
4407:
4408:
4409: /************** Forecasting ******************/
4410: 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){
4411: /* proj1, year, month, day of starting projection
4412: agemin, agemax range of age
4413: dateprev1 dateprev2 range of dates during which prevalence is computed
4414: anproj2 year of en of projection (same day and month as proj1).
4415: */
4416: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
4417: double agec; /* generic age */
4418: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4419: double *popeffectif,*popcount;
4420: double ***p3mat;
4421: double ***mobaverage;
4422: char fileresf[FILENAMELENGTH];
4423:
4424: agelim=AGESUP;
4425: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4426:
4427: strcpy(fileresf,"f");
4428: strcat(fileresf,fileres);
4429: if((ficresf=fopen(fileresf,"w"))==NULL) {
4430: printf("Problem with forecast resultfile: %s\n", fileresf);
4431: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4432: }
4433: printf("Computing forecasting: result on file '%s' \n", fileresf);
4434: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4435:
4436: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4437:
4438: if (mobilav!=0) {
4439: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4440: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4441: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4442: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4443: }
4444: }
4445:
4446: stepsize=(int) (stepm+YEARM-1)/YEARM;
4447: if (stepm<=12) stepsize=1;
4448: if(estepm < stepm){
4449: printf ("Problem %d lower than %d\n",estepm, stepm);
4450: }
4451: else hstepm=estepm;
4452:
4453: hstepm=hstepm/stepm;
4454: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4455: fractional in yp1 */
4456: anprojmean=yp;
4457: yp2=modf((yp1*12),&yp);
4458: mprojmean=yp;
4459: yp1=modf((yp2*30.5),&yp);
4460: jprojmean=yp;
4461: if(jprojmean==0) jprojmean=1;
4462: if(mprojmean==0) jprojmean=1;
4463:
4464: i1=cptcoveff;
4465: if (cptcovn < 1){i1=1;}
4466:
4467: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4468:
4469: fprintf(ficresf,"#****** Routine prevforecast **\n");
4470:
4471: /* if (h==(int)(YEARM*yearp)){ */
4472: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4473: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4474: k=k+1;
4475: fprintf(ficresf,"\n#******");
4476: for(j=1;j<=cptcoveff;j++) {
4477: 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]]);
4478: }
4479: fprintf(ficresf,"******\n");
4480: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4481: for(j=1; j<=nlstate+ndeath;j++){
4482: for(i=1; i<=nlstate;i++)
4483: fprintf(ficresf," p%d%d",i,j);
4484: fprintf(ficresf," p.%d",j);
4485: }
4486: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4487: fprintf(ficresf,"\n");
4488: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4489:
4490: for (agec=fage; agec>=(ageminpar-1); agec--){
4491: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4492: nhstepm = nhstepm/hstepm;
4493: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4494: oldm=oldms;savm=savms;
4495: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4496:
4497: for (h=0; h<=nhstepm; h++){
4498: if (h*hstepm/YEARM*stepm ==yearp) {
4499: fprintf(ficresf,"\n");
4500: for(j=1;j<=cptcoveff;j++)
4501: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4502: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4503: }
4504: for(j=1; j<=nlstate+ndeath;j++) {
4505: ppij=0.;
4506: for(i=1; i<=nlstate;i++) {
4507: if (mobilav==1)
4508: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4509: else {
4510: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4511: }
4512: if (h*hstepm/YEARM*stepm== yearp) {
4513: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4514: }
4515: } /* end i */
4516: if (h*hstepm/YEARM*stepm==yearp) {
4517: fprintf(ficresf," %.3f", ppij);
4518: }
4519: }/* end j */
4520: } /* end h */
4521: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4522: } /* end agec */
4523: } /* end yearp */
4524: } /* end cptcod */
4525: } /* end cptcov */
4526:
4527: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4528:
4529: fclose(ficresf);
4530: }
4531:
4532: /************** Forecasting *****not tested NB*************/
4533: 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){
4534:
4535: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4536: int *popage;
4537: double calagedatem, agelim, kk1, kk2;
4538: double *popeffectif,*popcount;
4539: double ***p3mat,***tabpop,***tabpopprev;
4540: double ***mobaverage;
4541: char filerespop[FILENAMELENGTH];
4542:
4543: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4544: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4545: agelim=AGESUP;
4546: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4547:
4548: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4549:
4550:
4551: strcpy(filerespop,"pop");
4552: strcat(filerespop,fileres);
4553: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4554: printf("Problem with forecast resultfile: %s\n", filerespop);
4555: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4556: }
4557: printf("Computing forecasting: result on file '%s' \n", filerespop);
4558: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4559:
4560: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4561:
4562: if (mobilav!=0) {
4563: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4564: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4565: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4566: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4567: }
4568: }
4569:
4570: stepsize=(int) (stepm+YEARM-1)/YEARM;
4571: if (stepm<=12) stepsize=1;
4572:
4573: agelim=AGESUP;
4574:
4575: hstepm=1;
4576: hstepm=hstepm/stepm;
4577:
4578: if (popforecast==1) {
4579: if((ficpop=fopen(popfile,"r"))==NULL) {
4580: printf("Problem with population file : %s\n",popfile);exit(0);
4581: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4582: }
4583: popage=ivector(0,AGESUP);
4584: popeffectif=vector(0,AGESUP);
4585: popcount=vector(0,AGESUP);
4586:
4587: i=1;
4588: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4589:
4590: imx=i;
4591: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4592: }
4593:
4594: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4595: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4596: k=k+1;
4597: fprintf(ficrespop,"\n#******");
4598: for(j=1;j<=cptcoveff;j++) {
4599: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4600: }
4601: fprintf(ficrespop,"******\n");
4602: fprintf(ficrespop,"# Age");
4603: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4604: if (popforecast==1) fprintf(ficrespop," [Population]");
4605:
4606: for (cpt=0; cpt<=0;cpt++) {
4607: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4608:
4609: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4610: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4611: nhstepm = nhstepm/hstepm;
4612:
4613: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4614: oldm=oldms;savm=savms;
4615: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4616:
4617: for (h=0; h<=nhstepm; h++){
4618: if (h==(int) (calagedatem+YEARM*cpt)) {
4619: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4620: }
4621: for(j=1; j<=nlstate+ndeath;j++) {
4622: kk1=0.;kk2=0;
4623: for(i=1; i<=nlstate;i++) {
4624: if (mobilav==1)
4625: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4626: else {
4627: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4628: }
4629: }
4630: if (h==(int)(calagedatem+12*cpt)){
4631: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4632: /*fprintf(ficrespop," %.3f", kk1);
4633: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4634: }
4635: }
4636: for(i=1; i<=nlstate;i++){
4637: kk1=0.;
4638: for(j=1; j<=nlstate;j++){
4639: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4640: }
4641: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4642: }
4643:
4644: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4645: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4646: }
4647: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4648: }
4649: }
4650:
4651: /******/
4652:
4653: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4654: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4655: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4656: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4657: nhstepm = nhstepm/hstepm;
4658:
4659: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4660: oldm=oldms;savm=savms;
4661: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4662: for (h=0; h<=nhstepm; h++){
4663: if (h==(int) (calagedatem+YEARM*cpt)) {
4664: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4665: }
4666: for(j=1; j<=nlstate+ndeath;j++) {
4667: kk1=0.;kk2=0;
4668: for(i=1; i<=nlstate;i++) {
4669: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4670: }
4671: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4672: }
4673: }
4674: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4675: }
4676: }
4677: }
4678: }
4679:
4680: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4681:
4682: if (popforecast==1) {
4683: free_ivector(popage,0,AGESUP);
4684: free_vector(popeffectif,0,AGESUP);
4685: free_vector(popcount,0,AGESUP);
4686: }
4687: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4688: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4689: fclose(ficrespop);
4690: } /* End of popforecast */
4691:
4692: int fileappend(FILE *fichier, char *optionfich)
4693: {
4694: if((fichier=fopen(optionfich,"a"))==NULL) {
4695: printf("Problem with file: %s\n", optionfich);
4696: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4697: return (0);
4698: }
4699: fflush(fichier);
4700: return (1);
4701: }
4702:
4703:
4704: /**************** function prwizard **********************/
4705: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4706: {
4707:
4708: /* Wizard to print covariance matrix template */
4709:
4710: char ca[32], cb[32];
4711: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
4712: int numlinepar;
4713:
4714: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4715: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4716: for(i=1; i <=nlstate; i++){
4717: jj=0;
4718: for(j=1; j <=nlstate+ndeath; j++){
4719: if(j==i) continue;
4720: jj++;
4721: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4722: printf("%1d%1d",i,j);
4723: fprintf(ficparo,"%1d%1d",i,j);
4724: for(k=1; k<=ncovmodel;k++){
4725: /* printf(" %lf",param[i][j][k]); */
4726: /* fprintf(ficparo," %lf",param[i][j][k]); */
4727: printf(" 0.");
4728: fprintf(ficparo," 0.");
4729: }
4730: printf("\n");
4731: fprintf(ficparo,"\n");
4732: }
4733: }
4734: printf("# Scales (for hessian or gradient estimation)\n");
4735: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4736: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4737: for(i=1; i <=nlstate; i++){
4738: jj=0;
4739: for(j=1; j <=nlstate+ndeath; j++){
4740: if(j==i) continue;
4741: jj++;
4742: fprintf(ficparo,"%1d%1d",i,j);
4743: printf("%1d%1d",i,j);
4744: fflush(stdout);
4745: for(k=1; k<=ncovmodel;k++){
4746: /* printf(" %le",delti3[i][j][k]); */
4747: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4748: printf(" 0.");
4749: fprintf(ficparo," 0.");
4750: }
4751: numlinepar++;
4752: printf("\n");
4753: fprintf(ficparo,"\n");
4754: }
4755: }
4756: printf("# Covariance matrix\n");
4757: /* # 121 Var(a12)\n\ */
4758: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4759: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4760: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4761: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4762: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4763: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4764: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4765: fflush(stdout);
4766: fprintf(ficparo,"# Covariance matrix\n");
4767: /* # 121 Var(a12)\n\ */
4768: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4769: /* # ...\n\ */
4770: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4771:
4772: for(itimes=1;itimes<=2;itimes++){
4773: jj=0;
4774: for(i=1; i <=nlstate; i++){
4775: for(j=1; j <=nlstate+ndeath; j++){
4776: if(j==i) continue;
4777: for(k=1; k<=ncovmodel;k++){
4778: jj++;
4779: ca[0]= k+'a'-1;ca[1]='\0';
4780: if(itimes==1){
4781: printf("#%1d%1d%d",i,j,k);
4782: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4783: }else{
4784: printf("%1d%1d%d",i,j,k);
4785: fprintf(ficparo,"%1d%1d%d",i,j,k);
4786: /* printf(" %.5le",matcov[i][j]); */
4787: }
4788: ll=0;
4789: for(li=1;li <=nlstate; li++){
4790: for(lj=1;lj <=nlstate+ndeath; lj++){
4791: if(lj==li) continue;
4792: for(lk=1;lk<=ncovmodel;lk++){
4793: ll++;
4794: if(ll<=jj){
4795: cb[0]= lk +'a'-1;cb[1]='\0';
4796: if(ll<jj){
4797: if(itimes==1){
4798: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4799: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4800: }else{
4801: printf(" 0.");
4802: fprintf(ficparo," 0.");
4803: }
4804: }else{
4805: if(itimes==1){
4806: printf(" Var(%s%1d%1d)",ca,i,j);
4807: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4808: }else{
4809: printf(" 0.");
4810: fprintf(ficparo," 0.");
4811: }
4812: }
4813: }
4814: } /* end lk */
4815: } /* end lj */
4816: } /* end li */
4817: printf("\n");
4818: fprintf(ficparo,"\n");
4819: numlinepar++;
4820: } /* end k*/
4821: } /*end j */
4822: } /* end i */
4823: } /* end itimes */
4824:
4825: } /* end of prwizard */
4826: /******************* Gompertz Likelihood ******************************/
4827: double gompertz(double x[])
4828: {
4829: double A,B,L=0.0,sump=0.,num=0.;
4830: int i,n=0; /* n is the size of the sample */
4831:
4832: for (i=0;i<=imx-1 ; i++) {
4833: sump=sump+weight[i];
4834: /* sump=sump+1;*/
4835: num=num+1;
4836: }
4837:
4838:
4839: /* for (i=0; i<=imx; i++)
4840: 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]);*/
4841:
4842: for (i=1;i<=imx ; i++)
4843: {
4844: if (cens[i] == 1 && wav[i]>1)
4845: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4846:
4847: if (cens[i] == 0 && wav[i]>1)
4848: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4849: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4850:
4851: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4852: if (wav[i] > 1 ) { /* ??? */
4853: L=L+A*weight[i];
4854: /* 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]);*/
4855: }
4856: }
4857:
4858: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4859:
4860: return -2*L*num/sump;
4861: }
4862:
4863: #ifdef GSL
4864: /******************* Gompertz_f Likelihood ******************************/
4865: double gompertz_f(const gsl_vector *v, void *params)
4866: {
4867: double A,B,LL=0.0,sump=0.,num=0.;
4868: double *x= (double *) v->data;
4869: int i,n=0; /* n is the size of the sample */
4870:
4871: for (i=0;i<=imx-1 ; i++) {
4872: sump=sump+weight[i];
4873: /* sump=sump+1;*/
4874: num=num+1;
4875: }
4876:
4877:
4878: /* for (i=0; i<=imx; i++)
4879: 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]);*/
4880: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4881: for (i=1;i<=imx ; i++)
4882: {
4883: if (cens[i] == 1 && wav[i]>1)
4884: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4885:
4886: if (cens[i] == 0 && wav[i]>1)
4887: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4888: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4889:
4890: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4891: if (wav[i] > 1 ) { /* ??? */
4892: LL=LL+A*weight[i];
4893: /* 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]);*/
4894: }
4895: }
4896:
4897: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4898: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4899:
4900: return -2*LL*num/sump;
4901: }
4902: #endif
4903:
4904: /******************* Printing html file ***********/
4905: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4906: int lastpass, int stepm, int weightopt, char model[],\
4907: int imx, double p[],double **matcov,double agemortsup){
4908: int i,k;
4909:
4910: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4911: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4912: for (i=1;i<=2;i++)
4913: 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]));
4914: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4915: fprintf(fichtm,"</ul>");
4916:
4917: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4918:
4919: 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>");
4920:
4921: for (k=agegomp;k<(agemortsup-2);k++)
4922: 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]);
4923:
4924:
4925: fflush(fichtm);
4926: }
4927:
4928: /******************* Gnuplot file **************/
4929: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4930:
4931: char dirfileres[132],optfileres[132];
4932:
4933: int ng;
4934:
4935:
4936: /*#ifdef windows */
4937: fprintf(ficgp,"cd \"%s\" \n",pathc);
4938: /*#endif */
4939:
4940:
4941: strcpy(dirfileres,optionfilefiname);
4942: strcpy(optfileres,"vpl");
4943: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4944: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4945: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
4946: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
4947: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4948:
4949: }
4950:
4951: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
4952: {
4953:
4954: /*-------- data file ----------*/
4955: FILE *fic;
4956: char dummy[]=" ";
4957: int i=0, j=0, n=0;
4958: int linei, month, year,iout;
4959: char line[MAXLINE], linetmp[MAXLINE];
4960: char stra[MAXLINE], strb[MAXLINE];
4961: char *stratrunc;
4962: int lstra;
4963:
4964:
4965: if((fic=fopen(datafile,"r"))==NULL) {
4966: printf("Problem while opening datafile: %s\n", datafile);return 1;
4967: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
4968: }
4969:
4970: i=1;
4971: linei=0;
4972: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4973: linei=linei+1;
4974: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4975: if(line[j] == '\t')
4976: line[j] = ' ';
4977: }
4978: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4979: ;
4980: };
4981: line[j+1]=0; /* Trims blanks at end of line */
4982: if(line[0]=='#'){
4983: fprintf(ficlog,"Comment line\n%s\n",line);
4984: printf("Comment line\n%s\n",line);
4985: continue;
4986: }
4987: trimbb(linetmp,line); /* Trims multiple blanks in line */
4988: strcpy(line, linetmp);
4989:
4990:
4991: for (j=maxwav;j>=1;j--){
4992: cutv(stra, strb, line, ' ');
4993: if(strb[0]=='.') { /* Missing status */
4994: lval=-1;
4995: }else{
4996: errno=0;
4997: lval=strtol(strb,&endptr,10);
4998: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4999: if( strb[0]=='\0' || (*endptr != '\0')){
5000: 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);
5001: 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);
5002: return 1;
5003: }
5004: }
5005: s[j][i]=lval;
5006:
5007: strcpy(line,stra);
5008: cutv(stra, strb,line,' ');
5009: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
5010: }
5011: else if(iout=sscanf(strb,"%s.",dummy) != 0){
5012: month=99;
5013: year=9999;
5014: }else{
5015: 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);
5016: 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);
5017: return 1;
5018: }
5019: anint[j][i]= (double) year;
5020: mint[j][i]= (double)month;
5021: strcpy(line,stra);
5022: } /* ENd Waves */
5023:
5024: cutv(stra, strb,line,' ');
5025: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
5026: }
5027: else if(iout=sscanf(strb,"%s.",dummy) != 0){
5028: month=99;
5029: year=9999;
5030: }else{
5031: 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);
5032: 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);
5033: return 1;
5034: }
5035: andc[i]=(double) year;
5036: moisdc[i]=(double) month;
5037: strcpy(line,stra);
5038:
5039: cutv(stra, strb,line,' ');
5040: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
5041: }
5042: else if(iout=sscanf(strb,"%s.", dummy) != 0){
5043: month=99;
5044: year=9999;
5045: }else{
5046: 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);
5047: 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);
5048: return 1;
5049: }
5050: if (year==9999) {
5051: 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);
5052: 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);
5053: return 1;
5054:
5055: }
5056: annais[i]=(double)(year);
5057: moisnais[i]=(double)(month);
5058: strcpy(line,stra);
5059:
5060: cutv(stra, strb,line,' ');
5061: errno=0;
5062: dval=strtod(strb,&endptr);
5063: if( strb[0]=='\0' || (*endptr != '\0')){
5064: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5065: 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);
5066: fflush(ficlog);
5067: return 1;
5068: }
5069: weight[i]=dval;
5070: strcpy(line,stra);
5071:
5072: for (j=ncovcol;j>=1;j--){
5073: cutv(stra, strb,line,' ');
5074: if(strb[0]=='.') { /* Missing status */
5075: lval=-1;
5076: }else{
5077: errno=0;
5078: lval=strtol(strb,&endptr,10);
5079: if( strb[0]=='\0' || (*endptr != '\0')){
5080: 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);
5081: 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);
5082: return 1;
5083: }
5084: }
5085: if(lval <-1 || lval >1){
5086: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5087: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5088: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5089: For example, for multinomial values like 1, 2 and 3,\n \
5090: build V1=0 V2=0 for the reference value (1),\n \
5091: V1=1 V2=0 for (2) \n \
5092: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5093: output of IMaCh is often meaningless.\n \
5094: Exiting.\n",lval,linei, i,line,j);
5095: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5096: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5097: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5098: For example, for multinomial values like 1, 2 and 3,\n \
5099: build V1=0 V2=0 for the reference value (1),\n \
5100: V1=1 V2=0 for (2) \n \
5101: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5102: output of IMaCh is often meaningless.\n \
5103: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5104: return 1;
5105: }
5106: covar[j][i]=(double)(lval);
5107: strcpy(line,stra);
5108: }
5109: lstra=strlen(stra);
5110:
5111: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5112: stratrunc = &(stra[lstra-9]);
5113: num[i]=atol(stratrunc);
5114: }
5115: else
5116: num[i]=atol(stra);
5117: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5118: 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;}*/
5119:
5120: i=i+1;
5121: } /* End loop reading data */
5122:
5123: *imax=i-1; /* Number of individuals */
5124: fclose(fic);
5125:
5126: return (0);
5127: /* endread: */
5128: printf("Exiting readdata: ");
5129: fclose(fic);
5130: return (1);
5131:
5132:
5133:
5134: }
5135: void removespace(char *str) {
5136: char *p1 = str, *p2 = str;
5137: do
5138: while (*p2 == ' ')
5139: p2++;
5140: while (*p1++ = *p2++);
5141: }
5142:
5143: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
5144: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
5145: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
5146: * - cptcovn or number of covariates k of the models excluding age*products =6
5147: * - cptcovage number of covariates with age*products =2
5148: * - cptcovs number of simple covariates
5149: * - 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
5150: * which is a new column after the 9 (ncovcol) variables.
5151: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5152: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5153: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5154: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5155: */
5156: {
5157: int i, j, k, ks;
5158: int j1, k1, k2;
5159: char modelsav[80];
5160: char stra[80], strb[80], strc[80], strd[80],stre[80];
5161:
5162: /*removespace(model);*/
5163: if (strlen(model) >1){ /* If there is at least 1 covariate */
5164: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5165: j=nbocc(model,'+'); /**< j=Number of '+' */
5166: j1=nbocc(model,'*'); /**< j1=Number of '*' */
5167: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
5168: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
5169: /* including age products which are counted in cptcovage.
5170: /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
5171: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5172: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5173: strcpy(modelsav,model);
5174: if (strstr(model,"AGE") !=0){
5175: printf("Error. AGE must be in lower case 'age' model=%s ",model);
5176: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
5177: return 1;
5178: }
5179: if (strstr(model,"v") !=0){
5180: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5181: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5182: return 1;
5183: }
5184:
5185: /* Design
5186: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5187: * < ncovcol=8 >
5188: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5189: * k= 1 2 3 4 5 6 7 8
5190: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5191: * covar[k,i], value of kth covariate if not including age for individual i:
5192: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5193: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5194: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5195: * Tage[++cptcovage]=k
5196: * if products, new covar are created after ncovcol with k1
5197: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5198: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5199: * 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
5200: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5201: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5202: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5203: * < ncovcol=8 >
5204: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5205: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5206: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5207: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5208: * p Tprod[1]@2={ 6, 5}
5209: *p Tvard[1][1]@4= {7, 8, 5, 6}
5210: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5211: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5212: *How to reorganize?
5213: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5214: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5215: * {2, 1, 4, 8, 5, 6, 3, 7}
5216: * Struct []
5217: */
5218:
5219: /* This loop fills the array Tvar from the string 'model'.*/
5220: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5221: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5222: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5223: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5224: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5225: /* k=1 Tvar[1]=2 (from V2) */
5226: /* k=5 Tvar[5] */
5227: /* for (k=1; k<=cptcovn;k++) { */
5228: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5229: /* } */
5230: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5231: /*
5232: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5233: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5234: Tvar[k]=0;
5235: cptcovage=0;
5236: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5237: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5238: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5239: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5240: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5241: /*scanf("%d",i);*/
5242: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5243: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5244: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5245: /* covar is not filled and then is empty */
5246: cptcovprod--;
5247: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5248: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
5249: cptcovage++; /* Sums the number of covariates which include age as a product */
5250: Tage[cptcovage]=k; /* Tage[1] = 4 */
5251: /*printf("stre=%s ", stre);*/
5252: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5253: cptcovprod--;
5254: cutl(stre,strb,strc,'V');
5255: Tvar[k]=atoi(stre);
5256: cptcovage++;
5257: Tage[cptcovage]=k;
5258: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5259: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5260: cptcovn++;
5261: cptcovprodnoage++;k1++;
5262: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5263: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5264: because this model-covariate is a construction we invent a new column
5265: ncovcol + k1
5266: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5267: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5268: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5269: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5270: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5271: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5272: k2=k2+2;
5273: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5274: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5275: for (i=1; i<=lastobs;i++){
5276: /* Computes the new covariate which is a product of
5277: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5278: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5279: }
5280: } /* End age is not in the model */
5281: } /* End if model includes a product */
5282: else { /* no more sum */
5283: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5284: /* scanf("%d",i);*/
5285: cutl(strd,strc,strb,'V');
5286: ks++; /**< Number of simple covariates */
5287: cptcovn++;
5288: Tvar[k]=atoi(strd);
5289: }
5290: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5291: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5292: scanf("%d",i);*/
5293: } /* end of loop + */
5294: } /* end model */
5295:
5296: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5297: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5298:
5299: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5300: printf("cptcovprod=%d ", cptcovprod);
5301: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5302:
5303: scanf("%d ",i);*/
5304:
5305:
5306: return (0); /* with covar[new additional covariate if product] and Tage if age */
5307: /*endread:*/
5308: printf("Exiting decodemodel: ");
5309: return (1);
5310: }
5311:
5312: calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
5313: {
5314: int i, m;
5315:
5316: for (i=1; i<=imx; i++) {
5317: for(m=2; (m<= maxwav); m++) {
5318: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5319: anint[m][i]=9999;
5320: s[m][i]=-1;
5321: }
5322: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5323: *nberr++;
5324: 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\n",(int)moisdc[i],(int)andc[i],num[i],i);
5325: 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\n",(int)moisdc[i],(int)andc[i],num[i],i);
5326: s[m][i]=-1;
5327: }
5328: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5329: *nberr++;
5330: 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]);
5331: 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]);
5332: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5333: }
5334: }
5335: }
5336:
5337: for (i=1; i<=imx; i++) {
5338: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5339: for(m=firstpass; (m<= lastpass); m++){
5340: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5341: if (s[m][i] >= nlstate+1) {
5342: if(agedc[i]>0)
5343: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
5344: agev[m][i]=agedc[i];
5345: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5346: else {
5347: if ((int)andc[i]!=9999){
5348: nbwarn++;
5349: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5350: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5351: agev[m][i]=-1;
5352: }
5353: }
5354: }
5355: else if(s[m][i] !=9){ /* Standard case, age in fractional
5356: years but with the precision of a month */
5357: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5358: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5359: agev[m][i]=1;
5360: else if(agev[m][i] < *agemin){
5361: *agemin=agev[m][i];
5362: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5363: }
5364: else if(agev[m][i] >*agemax){
5365: *agemax=agev[m][i];
5366: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
5367: }
5368: /*agev[m][i]=anint[m][i]-annais[i];*/
5369: /* agev[m][i] = age[i]+2*m;*/
5370: }
5371: else { /* =9 */
5372: agev[m][i]=1;
5373: s[m][i]=-1;
5374: }
5375: }
5376: else /*= 0 Unknown */
5377: agev[m][i]=1;
5378: }
5379:
5380: }
5381: for (i=1; i<=imx; i++) {
5382: for(m=firstpass; (m<=lastpass); m++){
5383: if (s[m][i] > (nlstate+ndeath)) {
5384: *nberr++;
5385: 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);
5386: 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);
5387: return 1;
5388: }
5389: }
5390: }
5391:
5392: /*for (i=1; i<=imx; i++){
5393: for (m=firstpass; (m<lastpass); m++){
5394: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5395: }
5396:
5397: }*/
5398:
5399:
5400: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5401: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5402:
5403: return (0);
5404: /* endread:*/
5405: printf("Exiting calandcheckages: ");
5406: return (1);
5407: }
5408:
5409:
5410: /***********************************************/
5411: /**************** Main Program *****************/
5412: /***********************************************/
5413:
5414: int main(int argc, char *argv[])
5415: {
5416: #ifdef GSL
5417: const gsl_multimin_fminimizer_type *T;
5418: size_t iteri = 0, it;
5419: int rval = GSL_CONTINUE;
5420: int status = GSL_SUCCESS;
5421: double ssval;
5422: #endif
5423: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
5424: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
5425:
5426: int jj, ll, li, lj, lk;
5427: int numlinepar=0; /* Current linenumber of parameter file */
5428: int itimes;
5429: int NDIM=2;
5430: int vpopbased=0;
5431:
5432: char ca[32], cb[32];
5433: /* FILE *fichtm; *//* Html File */
5434: /* FILE *ficgp;*/ /*Gnuplot File */
5435: struct stat info;
5436: double agedeb;
5437: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5438:
5439:
5440: double dum; /* Dummy variable */
5441: double ***p3mat;
5442: double ***mobaverage;
5443:
5444: char line[MAXLINE];
5445: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5446: char pathr[MAXLINE], pathimach[MAXLINE];
5447: char *tok, *val; /* pathtot */
5448: int firstobs=1, lastobs=10;
5449: int c, h , cpt;
5450: int jl;
5451: int i1, j1, jk, stepsize;
5452: int *tab;
5453: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5454: int mobilav=0,popforecast=0;
5455: int hstepm, nhstepm;
5456: int agemortsup;
5457: float sumlpop=0.;
5458: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5459: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5460:
5461: double bage=0, fage=110, age, agelim, agebase;
5462: double ftolpl=FTOL;
5463: double **prlim;
5464: double ***param; /* Matrix of parameters */
5465: double *p;
5466: double **matcov; /* Matrix of covariance */
5467: double ***delti3; /* Scale */
5468: double *delti; /* Scale */
5469: double ***eij, ***vareij;
5470: double **varpl; /* Variances of prevalence limits by age */
5471: double *epj, vepp;
5472:
5473: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5474: double **ximort;
5475: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
5476: int *dcwave;
5477:
5478: char z[1]="c";
5479:
5480: /*char *strt;*/
5481: char strtend[80];
5482:
5483:
5484: /* setlocale (LC_ALL, ""); */
5485: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5486: /* textdomain (PACKAGE); */
5487: /* setlocale (LC_CTYPE, ""); */
5488: /* setlocale (LC_MESSAGES, ""); */
5489:
5490: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
5491: rstart_time = time(NULL);
5492: /* (void) gettimeofday(&start_time,&tzp);*/
5493: start_time = *localtime(&rstart_time);
5494: curr_time=start_time;
5495: /*tml = *localtime(&start_time.tm_sec);*/
5496: /* strcpy(strstart,asctime(&tml)); */
5497: strcpy(strstart,asctime(&start_time));
5498:
5499: /* printf("Localtime (at start)=%s",strstart); */
5500: /* tp.tm_sec = tp.tm_sec +86400; */
5501: /* tm = *localtime(&start_time.tm_sec); */
5502: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5503: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5504: /* tmg.tm_hour=tmg.tm_hour + 1; */
5505: /* tp.tm_sec = mktime(&tmg); */
5506: /* strt=asctime(&tmg); */
5507: /* printf("Time(after) =%s",strstart); */
5508: /* (void) time (&time_value);
5509: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5510: * tm = *localtime(&time_value);
5511: * strstart=asctime(&tm);
5512: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5513: */
5514:
5515: nberr=0; /* Number of errors and warnings */
5516: nbwarn=0;
5517: getcwd(pathcd, size);
5518:
5519: printf("\n%s\n%s",version,fullversion);
5520: if(argc <=1){
5521: printf("\nEnter the parameter file name: ");
5522: fgets(pathr,FILENAMELENGTH,stdin);
5523: i=strlen(pathr);
5524: if(pathr[i-1]=='\n')
5525: pathr[i-1]='\0';
5526: i=strlen(pathr);
5527: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
5528: pathr[i-1]='\0';
5529: for (tok = pathr; tok != NULL; ){
5530: printf("Pathr |%s|\n",pathr);
5531: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5532: printf("val= |%s| pathr=%s\n",val,pathr);
5533: strcpy (pathtot, val);
5534: if(pathr[0] == '\0') break; /* Dirty */
5535: }
5536: }
5537: else{
5538: strcpy(pathtot,argv[1]);
5539: }
5540: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5541: /*cygwin_split_path(pathtot,path,optionfile);
5542: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5543: /* cutv(path,optionfile,pathtot,'\\');*/
5544:
5545: /* Split argv[0], imach program to get pathimach */
5546: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5547: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5548: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5549: /* strcpy(pathimach,argv[0]); */
5550: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5551: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5552: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5553: chdir(path); /* Can be a relative path */
5554: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5555: printf("Current directory %s!\n",pathcd);
5556: strcpy(command,"mkdir ");
5557: strcat(command,optionfilefiname);
5558: if((outcmd=system(command)) != 0){
5559: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
5560: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5561: /* fclose(ficlog); */
5562: /* exit(1); */
5563: }
5564: /* if((imk=mkdir(optionfilefiname))<0){ */
5565: /* perror("mkdir"); */
5566: /* } */
5567:
5568: /*-------- arguments in the command line --------*/
5569:
5570: /* Log file */
5571: strcat(filelog, optionfilefiname);
5572: strcat(filelog,".log"); /* */
5573: if((ficlog=fopen(filelog,"w"))==NULL) {
5574: printf("Problem with logfile %s\n",filelog);
5575: goto end;
5576: }
5577: fprintf(ficlog,"Log filename:%s\n",filelog);
5578: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5579: fprintf(ficlog,"\nEnter the parameter file name: \n");
5580: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5581: path=%s \n\
5582: optionfile=%s\n\
5583: optionfilext=%s\n\
5584: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
5585:
5586: printf("Local time (at start):%s",strstart);
5587: fprintf(ficlog,"Local time (at start): %s",strstart);
5588: fflush(ficlog);
5589: /* (void) gettimeofday(&curr_time,&tzp); */
5590: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
5591:
5592: /* */
5593: strcpy(fileres,"r");
5594: strcat(fileres, optionfilefiname);
5595: strcat(fileres,".txt"); /* Other files have txt extension */
5596:
5597: /*---------arguments file --------*/
5598:
5599: if((ficpar=fopen(optionfile,"r"))==NULL) {
5600: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5601: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5602: fflush(ficlog);
5603: /* goto end; */
5604: exit(70);
5605: }
5606:
5607:
5608:
5609: strcpy(filereso,"o");
5610: strcat(filereso,fileres);
5611: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5612: printf("Problem with Output resultfile: %s\n", filereso);
5613: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5614: fflush(ficlog);
5615: goto end;
5616: }
5617:
5618: /* Reads comments: lines beginning with '#' */
5619: numlinepar=0;
5620: while((c=getc(ficpar))=='#' && c!= EOF){
5621: ungetc(c,ficpar);
5622: fgets(line, MAXLINE, ficpar);
5623: numlinepar++;
5624: fputs(line,stdout);
5625: fputs(line,ficparo);
5626: fputs(line,ficlog);
5627: }
5628: ungetc(c,ficpar);
5629:
5630: 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=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
5631: numlinepar++;
5632: 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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
5633: 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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
5634: 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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
5635: fflush(ficlog);
5636: while((c=getc(ficpar))=='#' && c!= EOF){
5637: ungetc(c,ficpar);
5638: fgets(line, MAXLINE, ficpar);
5639: numlinepar++;
5640: fputs(line, stdout);
5641: //puts(line);
5642: fputs(line,ficparo);
5643: fputs(line,ficlog);
5644: }
5645: ungetc(c,ficpar);
5646:
5647:
5648: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
5649: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5650: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5651: v1+v2*age+v2*v3 makes cptcovn = 3
5652: */
5653: if (strlen(model)>1)
5654: 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*/
5655: else
5656: ncovmodel=2;
5657: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
5658: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5659: npar= nforce*ncovmodel; /* Number of parameters like aij*/
5660: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5661: 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);
5662: 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);
5663: fflush(stdout);
5664: fclose (ficlog);
5665: goto end;
5666: }
5667: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5668: delti=delti3[1][1];
5669: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5670: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5671: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5672: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5673: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5674: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5675: fclose (ficparo);
5676: fclose (ficlog);
5677: goto end;
5678: exit(0);
5679: }
5680: else if(mle==-3) {
5681: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5682: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5683: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5684: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5685: matcov=matrix(1,npar,1,npar);
5686: }
5687: else{
5688: /* Read guessed parameters */
5689: /* Reads comments: lines beginning with '#' */
5690: while((c=getc(ficpar))=='#' && c!= EOF){
5691: ungetc(c,ficpar);
5692: fgets(line, MAXLINE, ficpar);
5693: numlinepar++;
5694: fputs(line,stdout);
5695: fputs(line,ficparo);
5696: fputs(line,ficlog);
5697: }
5698: ungetc(c,ficpar);
5699:
5700: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5701: for(i=1; i <=nlstate; i++){
5702: j=0;
5703: for(jj=1; jj <=nlstate+ndeath; jj++){
5704: if(jj==i) continue;
5705: j++;
5706: fscanf(ficpar,"%1d%1d",&i1,&j1);
5707: if ((i1 != i) && (j1 != j)){
5708: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5709: It might be a problem of design; if ncovcol and the model are correct\n \
5710: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5711: exit(1);
5712: }
5713: fprintf(ficparo,"%1d%1d",i1,j1);
5714: if(mle==1)
5715: printf("%1d%1d",i,j);
5716: fprintf(ficlog,"%1d%1d",i,j);
5717: for(k=1; k<=ncovmodel;k++){
5718: fscanf(ficpar," %lf",¶m[i][j][k]);
5719: if(mle==1){
5720: printf(" %lf",param[i][j][k]);
5721: fprintf(ficlog," %lf",param[i][j][k]);
5722: }
5723: else
5724: fprintf(ficlog," %lf",param[i][j][k]);
5725: fprintf(ficparo," %lf",param[i][j][k]);
5726: }
5727: fscanf(ficpar,"\n");
5728: numlinepar++;
5729: if(mle==1)
5730: printf("\n");
5731: fprintf(ficlog,"\n");
5732: fprintf(ficparo,"\n");
5733: }
5734: }
5735: fflush(ficlog);
5736:
5737: /* Reads scales values */
5738: p=param[1][1];
5739:
5740: /* Reads comments: lines beginning with '#' */
5741: while((c=getc(ficpar))=='#' && c!= EOF){
5742: ungetc(c,ficpar);
5743: fgets(line, MAXLINE, ficpar);
5744: numlinepar++;
5745: fputs(line,stdout);
5746: fputs(line,ficparo);
5747: fputs(line,ficlog);
5748: }
5749: ungetc(c,ficpar);
5750:
5751: for(i=1; i <=nlstate; i++){
5752: for(j=1; j <=nlstate+ndeath-1; j++){
5753: fscanf(ficpar,"%1d%1d",&i1,&j1);
5754: if ( (i1-i) * (j1-j) != 0){
5755: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5756: exit(1);
5757: }
5758: printf("%1d%1d",i,j);
5759: fprintf(ficparo,"%1d%1d",i1,j1);
5760: fprintf(ficlog,"%1d%1d",i1,j1);
5761: for(k=1; k<=ncovmodel;k++){
5762: fscanf(ficpar,"%le",&delti3[i][j][k]);
5763: printf(" %le",delti3[i][j][k]);
5764: fprintf(ficparo," %le",delti3[i][j][k]);
5765: fprintf(ficlog," %le",delti3[i][j][k]);
5766: }
5767: fscanf(ficpar,"\n");
5768: numlinepar++;
5769: printf("\n");
5770: fprintf(ficparo,"\n");
5771: fprintf(ficlog,"\n");
5772: }
5773: }
5774: fflush(ficlog);
5775:
5776: /* Reads covariance matrix */
5777: delti=delti3[1][1];
5778:
5779:
5780: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
5781:
5782: /* Reads comments: lines beginning with '#' */
5783: while((c=getc(ficpar))=='#' && c!= EOF){
5784: ungetc(c,ficpar);
5785: fgets(line, MAXLINE, ficpar);
5786: numlinepar++;
5787: fputs(line,stdout);
5788: fputs(line,ficparo);
5789: fputs(line,ficlog);
5790: }
5791: ungetc(c,ficpar);
5792:
5793: matcov=matrix(1,npar,1,npar);
5794: for(i=1; i <=npar; i++)
5795: for(j=1; j <=npar; j++) matcov[i][j]=0.;
5796:
5797: for(i=1; i <=npar; i++){
5798: fscanf(ficpar,"%s",str);
5799: if(mle==1)
5800: printf("%s",str);
5801: fprintf(ficlog,"%s",str);
5802: fprintf(ficparo,"%s",str);
5803: for(j=1; j <=i; j++){
5804: fscanf(ficpar," %le",&matcov[i][j]);
5805: if(mle==1){
5806: printf(" %.5le",matcov[i][j]);
5807: }
5808: fprintf(ficlog," %.5le",matcov[i][j]);
5809: fprintf(ficparo," %.5le",matcov[i][j]);
5810: }
5811: fscanf(ficpar,"\n");
5812: numlinepar++;
5813: if(mle==1)
5814: printf("\n");
5815: fprintf(ficlog,"\n");
5816: fprintf(ficparo,"\n");
5817: }
5818: for(i=1; i <=npar; i++)
5819: for(j=i+1;j<=npar;j++)
5820: matcov[i][j]=matcov[j][i];
5821:
5822: if(mle==1)
5823: printf("\n");
5824: fprintf(ficlog,"\n");
5825:
5826: fflush(ficlog);
5827:
5828: /*-------- Rewriting parameter file ----------*/
5829: strcpy(rfileres,"r"); /* "Rparameterfile */
5830: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
5831: strcat(rfileres,"."); /* */
5832: strcat(rfileres,optionfilext); /* Other files have txt extension */
5833: if((ficres =fopen(rfileres,"w"))==NULL) {
5834: printf("Problem writing new parameter file: %s\n", fileres);goto end;
5835: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
5836: }
5837: fprintf(ficres,"#%s\n",version);
5838: } /* End of mle != -3 */
5839:
5840:
5841: n= lastobs;
5842: num=lvector(1,n);
5843: moisnais=vector(1,n);
5844: annais=vector(1,n);
5845: moisdc=vector(1,n);
5846: andc=vector(1,n);
5847: agedc=vector(1,n);
5848: cod=ivector(1,n);
5849: weight=vector(1,n);
5850: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
5851: mint=matrix(1,maxwav,1,n);
5852: anint=matrix(1,maxwav,1,n);
5853: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
5854: tab=ivector(1,NCOVMAX);
5855: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
5856:
5857: /* Reads data from file datafile */
5858: if (readdata(datafile, firstobs, lastobs, &imx)==1)
5859: goto end;
5860:
5861: /* Calculation of the number of parameters from char model */
5862: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
5863: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
5864: k=3 V4 Tvar[k=3]= 4 (from V4)
5865: k=2 V1 Tvar[k=2]= 1 (from V1)
5866: k=1 Tvar[1]=2 (from V2)
5867: */
5868: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
5869: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
5870: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
5871: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
5872: */
5873: /* For model-covariate k tells which data-covariate to use but
5874: because this model-covariate is a construction we invent a new column
5875: ncovcol + k1
5876: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
5877: Tvar[3=V1*V4]=4+1 etc */
5878: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
5879: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
5880: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
5881: */
5882: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
5883: 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
5884: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
5885: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
5886: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
5887: 4 covariates (3 plus signs)
5888: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
5889: */
5890:
5891: if(decodemodel(model, lastobs) == 1)
5892: goto end;
5893:
5894: if((double)(lastobs-imx)/(double)imx > 1.10){
5895: nbwarn++;
5896: 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);
5897: 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);
5898: }
5899: /* if(mle==1){*/
5900: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
5901: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
5902: }
5903:
5904: /*-calculation of age at interview from date of interview and age at death -*/
5905: agev=matrix(1,maxwav,1,imx);
5906:
5907: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
5908: goto end;
5909:
5910:
5911: agegomp=(int)agemin;
5912: free_vector(moisnais,1,n);
5913: free_vector(annais,1,n);
5914: /* free_matrix(mint,1,maxwav,1,n);
5915: free_matrix(anint,1,maxwav,1,n);*/
5916: free_vector(moisdc,1,n);
5917: free_vector(andc,1,n);
5918: /* */
5919:
5920: wav=ivector(1,imx);
5921: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5922: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5923: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5924:
5925: /* Concatenates waves */
5926: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
5927: /* */
5928:
5929: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5930:
5931: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5932: ncodemax[1]=1;
5933: Ndum =ivector(-1,NCOVMAX);
5934: if (ncovmodel > 2)
5935: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
5936:
5937: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
5938: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
5939: h=0;
5940:
5941:
5942: /*if (cptcovn > 0) */
5943:
5944:
5945: m=pow(2,cptcoveff);
5946:
5947: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
5948: 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 */
5949: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
5950: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
5951: h++;
5952: if (h>m)
5953: h=1;
5954: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
5955: * h 1 2 3 4
5956: *______________________________
5957: * 1 i=1 1 i=1 1 i=1 1 i=1 1
5958: * 2 2 1 1 1
5959: * 3 i=2 1 2 1 1
5960: * 4 2 2 1 1
5961: * 5 i=3 1 i=2 1 2 1
5962: * 6 2 1 2 1
5963: * 7 i=4 1 2 2 1
5964: * 8 2 2 2 1
5965: * 9 i=5 1 i=3 1 i=2 1 1
5966: * 10 2 1 1 1
5967: * 11 i=6 1 2 1 1
5968: * 12 2 2 1 1
5969: * 13 i=7 1 i=4 1 2 1
5970: * 14 2 1 2 1
5971: * 15 i=8 1 2 2 1
5972: * 16 2 2 2 1
5973: */
5974: codtab[h][k]=j;
5975: /*codtab[h][Tvar[k]]=j;*/
5976: 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]]);
5977: }
5978: }
5979: }
5980: }
5981: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5982: codtab[1][2]=1;codtab[2][2]=2; */
5983: /* for(i=1; i <=m ;i++){
5984: for(k=1; k <=cptcovn; k++){
5985: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
5986: }
5987: printf("\n");
5988: }
5989: scanf("%d",i);*/
5990:
5991: free_ivector(Ndum,-1,NCOVMAX);
5992:
5993:
5994:
5995: /*------------ gnuplot -------------*/
5996: strcpy(optionfilegnuplot,optionfilefiname);
5997: if(mle==-3)
5998: strcat(optionfilegnuplot,"-mort");
5999: strcat(optionfilegnuplot,".gp");
6000:
6001: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6002: printf("Problem with file %s",optionfilegnuplot);
6003: }
6004: else{
6005: fprintf(ficgp,"\n# %s\n", version);
6006: fprintf(ficgp,"# %s\n", optionfilegnuplot);
6007: //fprintf(ficgp,"set missing 'NaNq'\n");
6008: fprintf(ficgp,"set datafile missing 'NaNq'\n");
6009: }
6010: /* fclose(ficgp);*/
6011: /*--------- index.htm --------*/
6012:
6013: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6014: if(mle==-3)
6015: strcat(optionfilehtm,"-mort");
6016: strcat(optionfilehtm,".htm");
6017: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
6018: printf("Problem with %s \n",optionfilehtm);
6019: exit(0);
6020: }
6021:
6022: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6023: strcat(optionfilehtmcov,"-cov.htm");
6024: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6025: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6026: }
6027: else{
6028: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6029: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6030: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6031: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6032: }
6033:
6034: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6035: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6036: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6037: \n\
6038: <hr size=\"2\" color=\"#EC5E5E\">\
6039: <ul><li><h4>Parameter files</h4>\n\
6040: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6041: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6042: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6043: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6044: - Date and time at start: %s</ul>\n",\
6045: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6046: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6047: fileres,fileres,\
6048: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6049: fflush(fichtm);
6050:
6051: strcpy(pathr,path);
6052: strcat(pathr,optionfilefiname);
6053: chdir(optionfilefiname); /* Move to directory named optionfile */
6054:
6055: /* Calculates basic frequencies. Computes observed prevalence at single age
6056: and prints on file fileres'p'. */
6057: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6058:
6059: fprintf(fichtm,"\n");
6060: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6061: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6062: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6063: imx,agemin,agemax,jmin,jmax,jmean);
6064: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6065: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6066: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6067: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6068: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6069:
6070:
6071: /* For Powell, parameters are in a vector p[] starting at p[1]
6072: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6073: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6074:
6075: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
6076:
6077: if (mle==-3){
6078: ximort=matrix(1,NDIM,1,NDIM);
6079: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
6080: cens=ivector(1,n);
6081: ageexmed=vector(1,n);
6082: agecens=vector(1,n);
6083: dcwave=ivector(1,n);
6084:
6085: for (i=1; i<=imx; i++){
6086: dcwave[i]=-1;
6087: for (m=firstpass; m<=lastpass; m++)
6088: if (s[m][i]>nlstate) {
6089: dcwave[i]=m;
6090: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6091: break;
6092: }
6093: }
6094:
6095: for (i=1; i<=imx; i++) {
6096: if (wav[i]>0){
6097: ageexmed[i]=agev[mw[1][i]][i];
6098: j=wav[i];
6099: agecens[i]=1.;
6100:
6101: if (ageexmed[i]> 1 && wav[i] > 0){
6102: agecens[i]=agev[mw[j][i]][i];
6103: cens[i]= 1;
6104: }else if (ageexmed[i]< 1)
6105: cens[i]= -1;
6106: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6107: cens[i]=0 ;
6108: }
6109: else cens[i]=-1;
6110: }
6111:
6112: for (i=1;i<=NDIM;i++) {
6113: for (j=1;j<=NDIM;j++)
6114: ximort[i][j]=(i == j ? 1.0 : 0.0);
6115: }
6116:
6117: /*p[1]=0.0268; p[NDIM]=0.083;*/
6118: /*printf("%lf %lf", p[1], p[2]);*/
6119:
6120:
6121: #ifdef GSL
6122: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
6123: #else
6124: printf("Powell\n"); fprintf(ficlog,"Powell\n");
6125: #endif
6126: strcpy(filerespow,"pow-mort");
6127: strcat(filerespow,fileres);
6128: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6129: printf("Problem with resultfile: %s\n", filerespow);
6130: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6131: }
6132: #ifdef GSL
6133: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
6134: #else
6135: fprintf(ficrespow,"# Powell\n# iter -2*LL");
6136: #endif
6137: /* for (i=1;i<=nlstate;i++)
6138: for(j=1;j<=nlstate+ndeath;j++)
6139: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6140: */
6141: fprintf(ficrespow,"\n");
6142: #ifdef GSL
6143: /* gsl starts here */
6144: T = gsl_multimin_fminimizer_nmsimplex;
6145: gsl_multimin_fminimizer *sfm = NULL;
6146: gsl_vector *ss, *x;
6147: gsl_multimin_function minex_func;
6148:
6149: /* Initial vertex size vector */
6150: ss = gsl_vector_alloc (NDIM);
6151:
6152: if (ss == NULL){
6153: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6154: }
6155: /* Set all step sizes to 1 */
6156: gsl_vector_set_all (ss, 0.001);
6157:
6158: /* Starting point */
6159:
6160: x = gsl_vector_alloc (NDIM);
6161:
6162: if (x == NULL){
6163: gsl_vector_free(ss);
6164: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6165: }
6166:
6167: /* Initialize method and iterate */
6168: /* p[1]=0.0268; p[NDIM]=0.083; */
6169: /* gsl_vector_set(x, 0, 0.0268); */
6170: /* gsl_vector_set(x, 1, 0.083); */
6171: gsl_vector_set(x, 0, p[1]);
6172: gsl_vector_set(x, 1, p[2]);
6173:
6174: minex_func.f = &gompertz_f;
6175: minex_func.n = NDIM;
6176: minex_func.params = (void *)&p; /* ??? */
6177:
6178: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6179: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6180:
6181: printf("Iterations beginning .....\n\n");
6182: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6183:
6184: iteri=0;
6185: while (rval == GSL_CONTINUE){
6186: iteri++;
6187: status = gsl_multimin_fminimizer_iterate(sfm);
6188:
6189: if (status) printf("error: %s\n", gsl_strerror (status));
6190: fflush(0);
6191:
6192: if (status)
6193: break;
6194:
6195: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6196: ssval = gsl_multimin_fminimizer_size (sfm);
6197:
6198: if (rval == GSL_SUCCESS)
6199: printf ("converged to a local maximum at\n");
6200:
6201: printf("%5d ", iteri);
6202: for (it = 0; it < NDIM; it++){
6203: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6204: }
6205: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6206: }
6207:
6208: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6209:
6210: gsl_vector_free(x); /* initial values */
6211: gsl_vector_free(ss); /* inital step size */
6212: for (it=0; it<NDIM; it++){
6213: p[it+1]=gsl_vector_get(sfm->x,it);
6214: fprintf(ficrespow," %.12lf", p[it]);
6215: }
6216: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6217: #endif
6218: #ifdef POWELL
6219: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6220: #endif
6221: fclose(ficrespow);
6222:
6223: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6224:
6225: for(i=1; i <=NDIM; i++)
6226: for(j=i+1;j<=NDIM;j++)
6227: matcov[i][j]=matcov[j][i];
6228:
6229: printf("\nCovariance matrix\n ");
6230: for(i=1; i <=NDIM; i++) {
6231: for(j=1;j<=NDIM;j++){
6232: printf("%f ",matcov[i][j]);
6233: }
6234: printf("\n ");
6235: }
6236:
6237: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6238: for (i=1;i<=NDIM;i++)
6239: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6240:
6241: lsurv=vector(1,AGESUP);
6242: lpop=vector(1,AGESUP);
6243: tpop=vector(1,AGESUP);
6244: lsurv[agegomp]=100000;
6245:
6246: for (k=agegomp;k<=AGESUP;k++) {
6247: agemortsup=k;
6248: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6249: }
6250:
6251: for (k=agegomp;k<agemortsup;k++)
6252: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6253:
6254: for (k=agegomp;k<agemortsup;k++){
6255: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6256: sumlpop=sumlpop+lpop[k];
6257: }
6258:
6259: tpop[agegomp]=sumlpop;
6260: for (k=agegomp;k<(agemortsup-3);k++){
6261: /* tpop[k+1]=2;*/
6262: tpop[k+1]=tpop[k]-lpop[k];
6263: }
6264:
6265:
6266: printf("\nAge lx qx dx Lx Tx e(x)\n");
6267: for (k=agegomp;k<(agemortsup-2);k++)
6268: 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]);
6269:
6270:
6271: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6272: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6273:
6274: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6275: stepm, weightopt,\
6276: model,imx,p,matcov,agemortsup);
6277:
6278: free_vector(lsurv,1,AGESUP);
6279: free_vector(lpop,1,AGESUP);
6280: free_vector(tpop,1,AGESUP);
6281: #ifdef GSL
6282: free_ivector(cens,1,n);
6283: free_vector(agecens,1,n);
6284: free_ivector(dcwave,1,n);
6285: free_matrix(ximort,1,NDIM,1,NDIM);
6286: #endif
6287: } /* Endof if mle==-3 */
6288:
6289: else{ /* For mle >=1 */
6290: globpr=0;/* debug */
6291: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6292: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6293: for (k=1; k<=npar;k++)
6294: printf(" %d %8.5f",k,p[k]);
6295: printf("\n");
6296: globpr=1; /* to print the contributions */
6297: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6298: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6299: for (k=1; k<=npar;k++)
6300: printf(" %d %8.5f",k,p[k]);
6301: printf("\n");
6302: if(mle>=1){ /* Could be 1 or 2 */
6303: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6304: }
6305:
6306: /*--------- results files --------------*/
6307: 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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
6308:
6309:
6310: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6311: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6312: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6313: for(i=1,jk=1; i <=nlstate; i++){
6314: for(k=1; k <=(nlstate+ndeath); k++){
6315: if (k != i) {
6316: printf("%d%d ",i,k);
6317: fprintf(ficlog,"%d%d ",i,k);
6318: fprintf(ficres,"%1d%1d ",i,k);
6319: for(j=1; j <=ncovmodel; j++){
6320: printf("%lf ",p[jk]);
6321: fprintf(ficlog,"%lf ",p[jk]);
6322: fprintf(ficres,"%lf ",p[jk]);
6323: jk++;
6324: }
6325: printf("\n");
6326: fprintf(ficlog,"\n");
6327: fprintf(ficres,"\n");
6328: }
6329: }
6330: }
6331: if(mle!=0){
6332: /* Computing hessian and covariance matrix */
6333: ftolhess=ftol; /* Usually correct */
6334: hesscov(matcov, p, npar, delti, ftolhess, func);
6335: }
6336: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6337: printf("# Scales (for hessian or gradient estimation)\n");
6338: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6339: for(i=1,jk=1; i <=nlstate; i++){
6340: for(j=1; j <=nlstate+ndeath; j++){
6341: if (j!=i) {
6342: fprintf(ficres,"%1d%1d",i,j);
6343: printf("%1d%1d",i,j);
6344: fprintf(ficlog,"%1d%1d",i,j);
6345: for(k=1; k<=ncovmodel;k++){
6346: printf(" %.5e",delti[jk]);
6347: fprintf(ficlog," %.5e",delti[jk]);
6348: fprintf(ficres," %.5e",delti[jk]);
6349: jk++;
6350: }
6351: printf("\n");
6352: fprintf(ficlog,"\n");
6353: fprintf(ficres,"\n");
6354: }
6355: }
6356: }
6357:
6358: 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");
6359: if(mle>=1)
6360: 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");
6361: 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");
6362: /* # 121 Var(a12)\n\ */
6363: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6364: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6365: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6366: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6367: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6368: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6369: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6370:
6371:
6372: /* Just to have a covariance matrix which will be more understandable
6373: even is we still don't want to manage dictionary of variables
6374: */
6375: for(itimes=1;itimes<=2;itimes++){
6376: jj=0;
6377: for(i=1; i <=nlstate; i++){
6378: for(j=1; j <=nlstate+ndeath; j++){
6379: if(j==i) continue;
6380: for(k=1; k<=ncovmodel;k++){
6381: jj++;
6382: ca[0]= k+'a'-1;ca[1]='\0';
6383: if(itimes==1){
6384: if(mle>=1)
6385: printf("#%1d%1d%d",i,j,k);
6386: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6387: fprintf(ficres,"#%1d%1d%d",i,j,k);
6388: }else{
6389: if(mle>=1)
6390: printf("%1d%1d%d",i,j,k);
6391: fprintf(ficlog,"%1d%1d%d",i,j,k);
6392: fprintf(ficres,"%1d%1d%d",i,j,k);
6393: }
6394: ll=0;
6395: for(li=1;li <=nlstate; li++){
6396: for(lj=1;lj <=nlstate+ndeath; lj++){
6397: if(lj==li) continue;
6398: for(lk=1;lk<=ncovmodel;lk++){
6399: ll++;
6400: if(ll<=jj){
6401: cb[0]= lk +'a'-1;cb[1]='\0';
6402: if(ll<jj){
6403: if(itimes==1){
6404: if(mle>=1)
6405: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6406: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6407: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6408: }else{
6409: if(mle>=1)
6410: printf(" %.5e",matcov[jj][ll]);
6411: fprintf(ficlog," %.5e",matcov[jj][ll]);
6412: fprintf(ficres," %.5e",matcov[jj][ll]);
6413: }
6414: }else{
6415: if(itimes==1){
6416: if(mle>=1)
6417: printf(" Var(%s%1d%1d)",ca,i,j);
6418: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6419: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6420: }else{
6421: if(mle>=1)
6422: printf(" %.5e",matcov[jj][ll]);
6423: fprintf(ficlog," %.5e",matcov[jj][ll]);
6424: fprintf(ficres," %.5e",matcov[jj][ll]);
6425: }
6426: }
6427: }
6428: } /* end lk */
6429: } /* end lj */
6430: } /* end li */
6431: if(mle>=1)
6432: printf("\n");
6433: fprintf(ficlog,"\n");
6434: fprintf(ficres,"\n");
6435: numlinepar++;
6436: } /* end k*/
6437: } /*end j */
6438: } /* end i */
6439: } /* end itimes */
6440:
6441: fflush(ficlog);
6442: fflush(ficres);
6443:
6444: while((c=getc(ficpar))=='#' && c!= EOF){
6445: ungetc(c,ficpar);
6446: fgets(line, MAXLINE, ficpar);
6447: fputs(line,stdout);
6448: fputs(line,ficparo);
6449: }
6450: ungetc(c,ficpar);
6451:
6452: estepm=0;
6453: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6454: if (estepm==0 || estepm < stepm) estepm=stepm;
6455: if (fage <= 2) {
6456: bage = ageminpar;
6457: fage = agemaxpar;
6458: }
6459:
6460: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6461: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6462: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6463:
6464: while((c=getc(ficpar))=='#' && c!= EOF){
6465: ungetc(c,ficpar);
6466: fgets(line, MAXLINE, ficpar);
6467: fputs(line,stdout);
6468: fputs(line,ficparo);
6469: }
6470: ungetc(c,ficpar);
6471:
6472: 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);
6473: 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);
6474: 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);
6475: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6476: 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);
6477:
6478: while((c=getc(ficpar))=='#' && c!= EOF){
6479: ungetc(c,ficpar);
6480: fgets(line, MAXLINE, ficpar);
6481: fputs(line,stdout);
6482: fputs(line,ficparo);
6483: }
6484: ungetc(c,ficpar);
6485:
6486:
6487: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6488: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6489:
6490: fscanf(ficpar,"pop_based=%d\n",&popbased);
6491: fprintf(ficparo,"pop_based=%d\n",popbased);
6492: fprintf(ficres,"pop_based=%d\n",popbased);
6493:
6494: while((c=getc(ficpar))=='#' && c!= EOF){
6495: ungetc(c,ficpar);
6496: fgets(line, MAXLINE, ficpar);
6497: fputs(line,stdout);
6498: fputs(line,ficparo);
6499: }
6500: ungetc(c,ficpar);
6501:
6502: 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);
6503: 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);
6504: 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);
6505: 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);
6506: 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);
6507: /* day and month of proj2 are not used but only year anproj2.*/
6508:
6509:
6510:
6511: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
6512: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
6513:
6514: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6515: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6516:
6517: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6518: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6519: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6520:
6521: /*------------ free_vector -------------*/
6522: /* chdir(path); */
6523:
6524: free_ivector(wav,1,imx);
6525: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6526: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6527: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6528: free_lvector(num,1,n);
6529: free_vector(agedc,1,n);
6530: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6531: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6532: fclose(ficparo);
6533: fclose(ficres);
6534:
6535:
6536: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6537: #include "prevlim.h" /* Use ficrespl, ficlog */
6538: fclose(ficrespl);
6539:
6540: #ifdef FREEEXIT2
6541: #include "freeexit2.h"
6542: #endif
6543:
6544: /*------------- h Pij x at various ages ------------*/
6545: #include "hpijx.h"
6546: fclose(ficrespij);
6547:
6548: /*-------------- Variance of one-step probabilities---*/
6549: k=1;
6550: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6551:
6552:
6553: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6554: for(i=1;i<=AGESUP;i++)
6555: for(j=1;j<=NCOVMAX;j++)
6556: for(k=1;k<=NCOVMAX;k++)
6557: probs[i][j][k]=0.;
6558:
6559: /*---------- Forecasting ------------------*/
6560: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6561: if(prevfcast==1){
6562: /* if(stepm ==1){*/
6563: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6564: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6565: /* } */
6566: /* else{ */
6567: /* erreur=108; */
6568: /* 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); */
6569: /* 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); */
6570: /* } */
6571: }
6572:
6573:
6574: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6575:
6576: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6577: /* 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",\
6578: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6579: */
6580:
6581: if (mobilav!=0) {
6582: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6583: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6584: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6585: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6586: }
6587: }
6588:
6589:
6590: /*---------- Health expectancies, no variances ------------*/
6591:
6592: strcpy(filerese,"e");
6593: strcat(filerese,fileres);
6594: if((ficreseij=fopen(filerese,"w"))==NULL) {
6595: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6596: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6597: }
6598: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6599: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
6600: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6601: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6602:
6603: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6604: fprintf(ficreseij,"\n#****** ");
6605: for(j=1;j<=cptcoveff;j++) {
6606: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6607: }
6608: fprintf(ficreseij,"******\n");
6609:
6610: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6611: oldm=oldms;savm=savms;
6612: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6613:
6614: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6615: /*}*/
6616: }
6617: fclose(ficreseij);
6618:
6619:
6620: /*---------- Health expectancies and variances ------------*/
6621:
6622:
6623: strcpy(filerest,"t");
6624: strcat(filerest,fileres);
6625: if((ficrest=fopen(filerest,"w"))==NULL) {
6626: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6627: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6628: }
6629: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6630: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6631:
6632:
6633: strcpy(fileresstde,"stde");
6634: strcat(fileresstde,fileres);
6635: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6636: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6637: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6638: }
6639: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6640: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6641:
6642: strcpy(filerescve,"cve");
6643: strcat(filerescve,fileres);
6644: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6645: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6646: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6647: }
6648: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6649: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6650:
6651: strcpy(fileresv,"v");
6652: strcat(fileresv,fileres);
6653: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6654: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6655: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6656: }
6657: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6658: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6659:
6660: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6661: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6662:
6663: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6664: fprintf(ficrest,"\n#****** ");
6665: for(j=1;j<=cptcoveff;j++)
6666: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6667: fprintf(ficrest,"******\n");
6668:
6669: fprintf(ficresstdeij,"\n#****** ");
6670: fprintf(ficrescveij,"\n#****** ");
6671: for(j=1;j<=cptcoveff;j++) {
6672: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6673: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6674: }
6675: fprintf(ficresstdeij,"******\n");
6676: fprintf(ficrescveij,"******\n");
6677:
6678: fprintf(ficresvij,"\n#****** ");
6679: for(j=1;j<=cptcoveff;j++)
6680: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6681: fprintf(ficresvij,"******\n");
6682:
6683: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6684: oldm=oldms;savm=savms;
6685: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
6686: /*
6687: */
6688: /* goto endfree; */
6689:
6690: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6691: pstamp(ficrest);
6692:
6693:
6694: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6695: oldm=oldms;savm=savms; /* Segmentation fault */
6696: cptcod= 0; /* To be deleted */
6697: 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 */
6698: 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 ");
6699: if(vpopbased==1)
6700: 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);
6701: else
6702: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6703: fprintf(ficrest,"# Age e.. (std) ");
6704: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6705: fprintf(ficrest,"\n");
6706:
6707: epj=vector(1,nlstate+1);
6708: for(age=bage; age <=fage ;age++){
6709: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6710: if (vpopbased==1) {
6711: if(mobilav ==0){
6712: for(i=1; i<=nlstate;i++)
6713: prlim[i][i]=probs[(int)age][i][k];
6714: }else{ /* mobilav */
6715: for(i=1; i<=nlstate;i++)
6716: prlim[i][i]=mobaverage[(int)age][i][k];
6717: }
6718: }
6719:
6720: fprintf(ficrest," %4.0f",age);
6721: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6722: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6723: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6724: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6725: }
6726: epj[nlstate+1] +=epj[j];
6727: }
6728:
6729: for(i=1, vepp=0.;i <=nlstate;i++)
6730: for(j=1;j <=nlstate;j++)
6731: vepp += vareij[i][j][(int)age];
6732: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6733: for(j=1;j <=nlstate;j++){
6734: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6735: }
6736: fprintf(ficrest,"\n");
6737: }
6738: }
6739: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6740: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6741: free_vector(epj,1,nlstate+1);
6742: /*}*/
6743: }
6744: free_vector(weight,1,n);
6745: free_imatrix(Tvard,1,NCOVMAX,1,2);
6746: free_imatrix(s,1,maxwav+1,1,n);
6747: free_matrix(anint,1,maxwav,1,n);
6748: free_matrix(mint,1,maxwav,1,n);
6749: free_ivector(cod,1,n);
6750: free_ivector(tab,1,NCOVMAX);
6751: fclose(ficresstdeij);
6752: fclose(ficrescveij);
6753: fclose(ficresvij);
6754: fclose(ficrest);
6755: fclose(ficpar);
6756:
6757: /*------- Variance of period (stable) prevalence------*/
6758:
6759: strcpy(fileresvpl,"vpl");
6760: strcat(fileresvpl,fileres);
6761: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6762: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6763: exit(0);
6764: }
6765: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6766:
6767: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6768: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6769:
6770: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6771: fprintf(ficresvpl,"\n#****** ");
6772: for(j=1;j<=cptcoveff;j++)
6773: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6774: fprintf(ficresvpl,"******\n");
6775:
6776: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6777: oldm=oldms;savm=savms;
6778: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6779: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
6780: /*}*/
6781: }
6782:
6783: fclose(ficresvpl);
6784:
6785: /*---------- End : free ----------------*/
6786: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6787: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6788: } /* mle==-3 arrives here for freeing */
6789: /* endfree:*/
6790: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
6791: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6792: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6793: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6794: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6795: free_matrix(covar,0,NCOVMAX,1,n);
6796: free_matrix(matcov,1,npar,1,npar);
6797: /*free_vector(delti,1,npar);*/
6798: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6799: free_matrix(agev,1,maxwav,1,imx);
6800: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6801:
6802: free_ivector(ncodemax,1,NCOVMAX);
6803: free_ivector(Tvar,1,NCOVMAX);
6804: free_ivector(Tprod,1,NCOVMAX);
6805: free_ivector(Tvaraff,1,NCOVMAX);
6806: free_ivector(Tage,1,NCOVMAX);
6807:
6808: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6809: free_imatrix(codtab,1,100,1,10);
6810: fflush(fichtm);
6811: fflush(ficgp);
6812:
6813:
6814: if((nberr >0) || (nbwarn>0)){
6815: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6816: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6817: }else{
6818: printf("End of Imach\n");
6819: fprintf(ficlog,"End of Imach\n");
6820: }
6821: printf("See log file on %s\n",filelog);
6822: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
6823: /*(void) gettimeofday(&end_time,&tzp);*/
6824: rend_time = time(NULL);
6825: end_time = *localtime(&rend_time);
6826: /* tml = *localtime(&end_time.tm_sec); */
6827: strcpy(strtend,asctime(&end_time));
6828: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6829: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
6830: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
6831:
6832: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
6833: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
6834: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
6835: /* printf("Total time was %d uSec.\n", total_usecs);*/
6836: /* if(fileappend(fichtm,optionfilehtm)){ */
6837: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6838: fclose(fichtm);
6839: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6840: fclose(fichtmcov);
6841: fclose(ficgp);
6842: fclose(ficlog);
6843: /*------ End -----------*/
6844:
6845:
6846: printf("Before Current directory %s!\n",pathcd);
6847: if(chdir(pathcd) != 0)
6848: printf("Can't move to directory %s!\n",path);
6849: if(getcwd(pathcd,MAXLINE) > 0)
6850: printf("Current directory %s!\n",pathcd);
6851: /*strcat(plotcmd,CHARSEPARATOR);*/
6852: sprintf(plotcmd,"gnuplot");
6853: #ifdef _WIN32
6854: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6855: #endif
6856: if(!stat(plotcmd,&info)){
6857: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
6858: if(!stat(getenv("GNUPLOTBIN"),&info)){
6859: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
6860: }else
6861: strcpy(pplotcmd,plotcmd);
6862: #ifdef __unix
6863: strcpy(plotcmd,GNUPLOTPROGRAM);
6864: if(!stat(plotcmd,&info)){
6865: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
6866: }else
6867: strcpy(pplotcmd,plotcmd);
6868: #endif
6869: }else
6870: strcpy(pplotcmd,plotcmd);
6871:
6872: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
6873: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
6874:
6875: if((outcmd=system(plotcmd)) != 0){
6876: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
6877: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
6878: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
6879: if((outcmd=system(plotcmd)) != 0)
6880: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
6881: }
6882: printf(" Successful, please wait...");
6883: while (z[0] != 'q') {
6884: /* chdir(path); */
6885: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
6886: scanf("%s",z);
6887: /* if (z[0] == 'c') system("./imach"); */
6888: if (z[0] == 'e') {
6889: #ifdef __APPLE__
6890: sprintf(pplotcmd, "open %s", optionfilehtm);
6891: #elif __linux
6892: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
6893: #else
6894: sprintf(pplotcmd, "%s", optionfilehtm);
6895: #endif
6896: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
6897: system(pplotcmd);
6898: }
6899: else if (z[0] == 'g') system(plotcmd);
6900: else if (z[0] == 'q') exit(0);
6901: }
6902: end:
6903: while (z[0] != 'q') {
6904: printf("\nType q for exiting: ");
6905: scanf("%s",z);
6906: }
6907: }
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