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Mon Mar 20 09:45:41 2006 UTC (18 years, 2 months ago) by
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HEAD
(Module): Weights can have a decimal point as for
English (a comma might work with a correct LC_NUMERIC environment,
otherwise the weight is truncated).
Modification of warning when the covariates values are not 0 or
1.
Version 0.98g
1: /* $Id: imach.c,v 1.122 2006/03/20 09:45:41 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.122 2006/03/20 09:45:41 brouard
5: (Module): Weights can have a decimal point as for
6: English (a comma might work with a correct LC_NUMERIC environment,
7: otherwise the weight is truncated).
8: Modification of warning when the covariates values are not 0 or
9: 1.
10: Version 0.98g
11:
12: Revision 1.121 2006/03/16 17:45:01 lievre
13: * imach.c (Module): Comments concerning covariates added
14:
15: * imach.c (Module): refinements in the computation of lli if
16: status=-2 in order to have more reliable computation if stepm is
17: not 1 month. Version 0.98f
18:
19: Revision 1.120 2006/03/16 15:10:38 lievre
20: (Module): refinements in the computation of lli if
21: status=-2 in order to have more reliable computation if stepm is
22: not 1 month. Version 0.98f
23:
24: Revision 1.119 2006/03/15 17:42:26 brouard
25: (Module): Bug if status = -2, the loglikelihood was
26: computed as likelihood omitting the logarithm. Version O.98e
27:
28: Revision 1.118 2006/03/14 18:20:07 brouard
29: (Module): varevsij Comments added explaining the second
30: table of variances if popbased=1 .
31: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
32: (Module): Function pstamp added
33: (Module): Version 0.98d
34:
35: Revision 1.117 2006/03/14 17:16:22 brouard
36: (Module): varevsij Comments added explaining the second
37: table of variances if popbased=1 .
38: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
39: (Module): Function pstamp added
40: (Module): Version 0.98d
41:
42: Revision 1.116 2006/03/06 10:29:27 brouard
43: (Module): Variance-covariance wrong links and
44: varian-covariance of ej. is needed (Saito).
45:
46: Revision 1.115 2006/02/27 12:17:45 brouard
47: (Module): One freematrix added in mlikeli! 0.98c
48:
49: Revision 1.114 2006/02/26 12:57:58 brouard
50: (Module): Some improvements in processing parameter
51: filename with strsep.
52:
53: Revision 1.113 2006/02/24 14:20:24 brouard
54: (Module): Memory leaks checks with valgrind and:
55: datafile was not closed, some imatrix were not freed and on matrix
56: allocation too.
57:
58: Revision 1.112 2006/01/30 09:55:26 brouard
59: (Module): Back to gnuplot.exe instead of wgnuplot.exe
60:
61: Revision 1.111 2006/01/25 20:38:18 brouard
62: (Module): Lots of cleaning and bugs added (Gompertz)
63: (Module): Comments can be added in data file. Missing date values
64: can be a simple dot '.'.
65:
66: Revision 1.110 2006/01/25 00:51:50 brouard
67: (Module): Lots of cleaning and bugs added (Gompertz)
68:
69: Revision 1.109 2006/01/24 19:37:15 brouard
70: (Module): Comments (lines starting with a #) are allowed in data.
71:
72: Revision 1.108 2006/01/19 18:05:42 lievre
73: Gnuplot problem appeared...
74: To be fixed
75:
76: Revision 1.107 2006/01/19 16:20:37 brouard
77: Test existence of gnuplot in imach path
78:
79: Revision 1.106 2006/01/19 13:24:36 brouard
80: Some cleaning and links added in html output
81:
82: Revision 1.105 2006/01/05 20:23:19 lievre
83: *** empty log message ***
84:
85: Revision 1.104 2005/09/30 16:11:43 lievre
86: (Module): sump fixed, loop imx fixed, and simplifications.
87: (Module): If the status is missing at the last wave but we know
88: that the person is alive, then we can code his/her status as -2
89: (instead of missing=-1 in earlier versions) and his/her
90: contributions to the likelihood is 1 - Prob of dying from last
91: health status (= 1-p13= p11+p12 in the easiest case of somebody in
92: the healthy state at last known wave). Version is 0.98
93:
94: Revision 1.103 2005/09/30 15:54:49 lievre
95: (Module): sump fixed, loop imx fixed, and simplifications.
96:
97: Revision 1.102 2004/09/15 17:31:30 brouard
98: Add the possibility to read data file including tab characters.
99:
100: Revision 1.101 2004/09/15 10:38:38 brouard
101: Fix on curr_time
102:
103: Revision 1.100 2004/07/12 18:29:06 brouard
104: Add version for Mac OS X. Just define UNIX in Makefile
105:
106: Revision 1.99 2004/06/05 08:57:40 brouard
107: *** empty log message ***
108:
109: Revision 1.98 2004/05/16 15:05:56 brouard
110: New version 0.97 . First attempt to estimate force of mortality
111: directly from the data i.e. without the need of knowing the health
112: state at each age, but using a Gompertz model: log u =a + b*age .
113: This is the basic analysis of mortality and should be done before any
114: other analysis, in order to test if the mortality estimated from the
115: cross-longitudinal survey is different from the mortality estimated
116: from other sources like vital statistic data.
117:
118: The same imach parameter file can be used but the option for mle should be -3.
119:
120: Agnès, who wrote this part of the code, tried to keep most of the
121: former routines in order to include the new code within the former code.
122:
123: The output is very simple: only an estimate of the intercept and of
124: the slope with 95% confident intervals.
125:
126: Current limitations:
127: A) Even if you enter covariates, i.e. with the
128: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
129: B) There is no computation of Life Expectancy nor Life Table.
130:
131: Revision 1.97 2004/02/20 13:25:42 lievre
132: Version 0.96d. Population forecasting command line is (temporarily)
133: suppressed.
134:
135: Revision 1.96 2003/07/15 15:38:55 brouard
136: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
137: rewritten within the same printf. Workaround: many printfs.
138:
139: Revision 1.95 2003/07/08 07:54:34 brouard
140: * imach.c (Repository):
141: (Repository): Using imachwizard code to output a more meaningful covariance
142: matrix (cov(a12,c31) instead of numbers.
143:
144: Revision 1.94 2003/06/27 13:00:02 brouard
145: Just cleaning
146:
147: Revision 1.93 2003/06/25 16:33:55 brouard
148: (Module): On windows (cygwin) function asctime_r doesn't
149: exist so I changed back to asctime which exists.
150: (Module): Version 0.96b
151:
152: Revision 1.92 2003/06/25 16:30:45 brouard
153: (Module): On windows (cygwin) function asctime_r doesn't
154: exist so I changed back to asctime which exists.
155:
156: Revision 1.91 2003/06/25 15:30:29 brouard
157: * imach.c (Repository): Duplicated warning errors corrected.
158: (Repository): Elapsed time after each iteration is now output. It
159: helps to forecast when convergence will be reached. Elapsed time
160: is stamped in powell. We created a new html file for the graphs
161: concerning matrix of covariance. It has extension -cov.htm.
162:
163: Revision 1.90 2003/06/24 12:34:15 brouard
164: (Module): Some bugs corrected for windows. Also, when
165: mle=-1 a template is output in file "or"mypar.txt with the design
166: of the covariance matrix to be input.
167:
168: Revision 1.89 2003/06/24 12:30:52 brouard
169: (Module): Some bugs corrected for windows. Also, when
170: mle=-1 a template is output in file "or"mypar.txt with the design
171: of the covariance matrix to be input.
172:
173: Revision 1.88 2003/06/23 17:54:56 brouard
174: * 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.
175:
176: Revision 1.87 2003/06/18 12:26:01 brouard
177: Version 0.96
178:
179: Revision 1.86 2003/06/17 20:04:08 brouard
180: (Module): Change position of html and gnuplot routines and added
181: routine fileappend.
182:
183: Revision 1.85 2003/06/17 13:12:43 brouard
184: * imach.c (Repository): Check when date of death was earlier that
185: current date of interview. It may happen when the death was just
186: prior to the death. In this case, dh was negative and likelihood
187: was wrong (infinity). We still send an "Error" but patch by
188: assuming that the date of death was just one stepm after the
189: interview.
190: (Repository): Because some people have very long ID (first column)
191: we changed int to long in num[] and we added a new lvector for
192: memory allocation. But we also truncated to 8 characters (left
193: truncation)
194: (Repository): No more line truncation errors.
195:
196: Revision 1.84 2003/06/13 21:44:43 brouard
197: * imach.c (Repository): Replace "freqsummary" at a correct
198: place. It differs from routine "prevalence" which may be called
199: many times. Probs is memory consuming and must be used with
200: parcimony.
201: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
202:
203: Revision 1.83 2003/06/10 13:39:11 lievre
204: *** empty log message ***
205:
206: Revision 1.82 2003/06/05 15:57:20 brouard
207: Add log in imach.c and fullversion number is now printed.
208:
209: */
210: /*
211: Interpolated Markov Chain
212:
213: Short summary of the programme:
214:
215: This program computes Healthy Life Expectancies from
216: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
217: first survey ("cross") where individuals from different ages are
218: interviewed on their health status or degree of disability (in the
219: case of a health survey which is our main interest) -2- at least a
220: second wave of interviews ("longitudinal") which measure each change
221: (if any) in individual health status. Health expectancies are
222: computed from the time spent in each health state according to a
223: model. More health states you consider, more time is necessary to reach the
224: Maximum Likelihood of the parameters involved in the model. The
225: simplest model is the multinomial logistic model where pij is the
226: probability to be observed in state j at the second wave
227: conditional to be observed in state i at the first wave. Therefore
228: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
229: 'age' is age and 'sex' is a covariate. If you want to have a more
230: complex model than "constant and age", you should modify the program
231: where the markup *Covariates have to be included here again* invites
232: you to do it. More covariates you add, slower the
233: convergence.
234:
235: The advantage of this computer programme, compared to a simple
236: multinomial logistic model, is clear when the delay between waves is not
237: identical for each individual. Also, if a individual missed an
238: intermediate interview, the information is lost, but taken into
239: account using an interpolation or extrapolation.
240:
241: hPijx is the probability to be observed in state i at age x+h
242: conditional to the observed state i at age x. The delay 'h' can be
243: split into an exact number (nh*stepm) of unobserved intermediate
244: states. This elementary transition (by month, quarter,
245: semester or year) is modelled as a multinomial logistic. The hPx
246: matrix is simply the matrix product of nh*stepm elementary matrices
247: and the contribution of each individual to the likelihood is simply
248: hPijx.
249:
250: Also this programme outputs the covariance matrix of the parameters but also
251: of the life expectancies. It also computes the period (stable) prevalence.
252:
253: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
254: Institut national d'études démographiques, Paris.
255: This software have been partly granted by Euro-REVES, a concerted action
256: from the European Union.
257: It is copyrighted identically to a GNU software product, ie programme and
258: software can be distributed freely for non commercial use. Latest version
259: can be accessed at http://euroreves.ined.fr/imach .
260:
261: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
262: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
263:
264: **********************************************************************/
265: /*
266: main
267: read parameterfile
268: read datafile
269: concatwav
270: freqsummary
271: if (mle >= 1)
272: mlikeli
273: print results files
274: if mle==1
275: computes hessian
276: read end of parameter file: agemin, agemax, bage, fage, estepm
277: begin-prev-date,...
278: open gnuplot file
279: open html file
280: period (stable) prevalence
281: for age prevalim()
282: h Pij x
283: variance of p varprob
284: forecasting if prevfcast==1 prevforecast call prevalence()
285: health expectancies
286: Variance-covariance of DFLE
287: prevalence()
288: movingaverage()
289: varevsij()
290: if popbased==1 varevsij(,popbased)
291: total life expectancies
292: Variance of period (stable) prevalence
293: end
294: */
295:
296:
297:
298:
299: #include <math.h>
300: #include <stdio.h>
301: #include <stdlib.h>
302: #include <string.h>
303: #include <unistd.h>
304:
305: #include <limits.h>
306: #include <sys/types.h>
307: #include <sys/stat.h>
308: #include <errno.h>
309: extern int errno;
310:
311: /* #include <sys/time.h> */
312: #include <time.h>
313: #include "timeval.h"
314:
315: /* #include <libintl.h> */
316: /* #define _(String) gettext (String) */
317:
318: #define MAXLINE 256
319:
320: #define GNUPLOTPROGRAM "gnuplot"
321: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
322: #define FILENAMELENGTH 132
323:
324: #define GLOCK_ERROR_NOPATH -1 /* empty path */
325: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
326:
327: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
328: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
329:
330: #define NINTERVMAX 8
331: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
332: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
333: #define NCOVMAX 8 /* Maximum number of covariates */
334: #define MAXN 20000
335: #define YEARM 12. /* Number of months per year */
336: #define AGESUP 130
337: #define AGEBASE 40
338: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
339: #ifdef UNIX
340: #define DIRSEPARATOR '/'
341: #define CHARSEPARATOR "/"
342: #define ODIRSEPARATOR '\\'
343: #else
344: #define DIRSEPARATOR '\\'
345: #define CHARSEPARATOR "\\"
346: #define ODIRSEPARATOR '/'
347: #endif
348:
349: /* $Id: imach.c,v 1.122 2006/03/20 09:45:41 brouard Exp $ */
350: /* $State: Exp $ */
351:
352: char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
353: char fullversion[]="$Revision: 1.122 $ $Date: 2006/03/20 09:45:41 $";
354: char strstart[80];
355: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
356: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
357: int nvar;
358: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
359: int npar=NPARMAX;
360: int nlstate=2; /* Number of live states */
361: int ndeath=1; /* Number of dead states */
362: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
363: int popbased=0;
364:
365: int *wav; /* Number of waves for this individuual 0 is possible */
366: int maxwav; /* Maxim number of waves */
367: int jmin, jmax; /* min, max spacing between 2 waves */
368: int ijmin, ijmax; /* Individuals having jmin and jmax */
369: int gipmx, gsw; /* Global variables on the number of contributions
370: to the likelihood and the sum of weights (done by funcone)*/
371: int mle, weightopt;
372: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
373: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
374: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
375: * wave mi and wave mi+1 is not an exact multiple of stepm. */
376: double jmean; /* Mean space between 2 waves */
377: double **oldm, **newm, **savm; /* Working pointers to matrices */
378: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
379: FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
380: FILE *ficlog, *ficrespow;
381: int globpr; /* Global variable for printing or not */
382: double fretone; /* Only one call to likelihood */
383: long ipmx; /* Number of contributions */
384: double sw; /* Sum of weights */
385: char filerespow[FILENAMELENGTH];
386: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
387: FILE *ficresilk;
388: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
389: FILE *ficresprobmorprev;
390: FILE *fichtm, *fichtmcov; /* Html File */
391: FILE *ficreseij;
392: char filerese[FILENAMELENGTH];
393: FILE *ficresstdeij;
394: char fileresstde[FILENAMELENGTH];
395: FILE *ficrescveij;
396: char filerescve[FILENAMELENGTH];
397: FILE *ficresvij;
398: char fileresv[FILENAMELENGTH];
399: FILE *ficresvpl;
400: char fileresvpl[FILENAMELENGTH];
401: char title[MAXLINE];
402: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
403: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
404: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
405: char command[FILENAMELENGTH];
406: int outcmd=0;
407:
408: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
409:
410: char filelog[FILENAMELENGTH]; /* Log file */
411: char filerest[FILENAMELENGTH];
412: char fileregp[FILENAMELENGTH];
413: char popfile[FILENAMELENGTH];
414:
415: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
416:
417: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
418: struct timezone tzp;
419: extern int gettimeofday();
420: struct tm tmg, tm, tmf, *gmtime(), *localtime();
421: long time_value;
422: extern long time();
423: char strcurr[80], strfor[80];
424:
425: char *endptr;
426: long lval;
427: double dval;
428:
429: #define NR_END 1
430: #define FREE_ARG char*
431: #define FTOL 1.0e-10
432:
433: #define NRANSI
434: #define ITMAX 200
435:
436: #define TOL 2.0e-4
437:
438: #define CGOLD 0.3819660
439: #define ZEPS 1.0e-10
440: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
441:
442: #define GOLD 1.618034
443: #define GLIMIT 100.0
444: #define TINY 1.0e-20
445:
446: static double maxarg1,maxarg2;
447: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
448: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
449:
450: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
451: #define rint(a) floor(a+0.5)
452:
453: static double sqrarg;
454: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
455: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
456: int agegomp= AGEGOMP;
457:
458: int imx;
459: int stepm=1;
460: /* Stepm, step in month: minimum step interpolation*/
461:
462: int estepm;
463: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
464:
465: int m,nb;
466: long *num;
467: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
468: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
469: double **pmmij, ***probs;
470: double *ageexmed,*agecens;
471: double dateintmean=0;
472:
473: double *weight;
474: int **s; /* Status */
475: double *agedc, **covar, idx;
476: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
477: double *lsurv, *lpop, *tpop;
478:
479: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
480: double ftolhess; /* Tolerance for computing hessian */
481:
482: /**************** split *************************/
483: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
484: {
485: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
486: the name of the file (name), its extension only (ext) and its first part of the name (finame)
487: */
488: char *ss; /* pointer */
489: int l1, l2; /* length counters */
490:
491: l1 = strlen(path ); /* length of path */
492: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
493: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
494: if ( ss == NULL ) { /* no directory, so determine current directory */
495: strcpy( name, path ); /* we got the fullname name because no directory */
496: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
497: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
498: /* get current working directory */
499: /* extern char* getcwd ( char *buf , int len);*/
500: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
501: return( GLOCK_ERROR_GETCWD );
502: }
503: /* got dirc from getcwd*/
504: printf(" DIRC = %s \n",dirc);
505: } else { /* strip direcotry from path */
506: ss++; /* after this, the filename */
507: l2 = strlen( ss ); /* length of filename */
508: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
509: strcpy( name, ss ); /* save file name */
510: strncpy( dirc, path, l1 - l2 ); /* now the directory */
511: dirc[l1-l2] = 0; /* add zero */
512: printf(" DIRC2 = %s \n",dirc);
513: }
514: /* We add a separator at the end of dirc if not exists */
515: l1 = strlen( dirc ); /* length of directory */
516: if( dirc[l1-1] != DIRSEPARATOR ){
517: dirc[l1] = DIRSEPARATOR;
518: dirc[l1+1] = 0;
519: printf(" DIRC3 = %s \n",dirc);
520: }
521: ss = strrchr( name, '.' ); /* find last / */
522: if (ss >0){
523: ss++;
524: strcpy(ext,ss); /* save extension */
525: l1= strlen( name);
526: l2= strlen(ss)+1;
527: strncpy( finame, name, l1-l2);
528: finame[l1-l2]= 0;
529: }
530:
531: return( 0 ); /* we're done */
532: }
533:
534:
535: /******************************************/
536:
537: void replace_back_to_slash(char *s, char*t)
538: {
539: int i;
540: int lg=0;
541: i=0;
542: lg=strlen(t);
543: for(i=0; i<= lg; i++) {
544: (s[i] = t[i]);
545: if (t[i]== '\\') s[i]='/';
546: }
547: }
548:
549: int nbocc(char *s, char occ)
550: {
551: int i,j=0;
552: int lg=20;
553: i=0;
554: lg=strlen(s);
555: for(i=0; i<= lg; i++) {
556: if (s[i] == occ ) j++;
557: }
558: return j;
559: }
560:
561: void cutv(char *u,char *v, char*t, char occ)
562: {
563: /* cuts string t into u and v where u ends before first occurence of char 'occ'
564: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
565: gives u="abcedf" and v="ghi2j" */
566: int i,lg,j,p=0;
567: i=0;
568: for(j=0; j<=strlen(t)-1; j++) {
569: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
570: }
571:
572: lg=strlen(t);
573: for(j=0; j<p; j++) {
574: (u[j] = t[j]);
575: }
576: u[p]='\0';
577:
578: for(j=0; j<= lg; j++) {
579: if (j>=(p+1))(v[j-p-1] = t[j]);
580: }
581: }
582:
583: /********************** nrerror ********************/
584:
585: void nrerror(char error_text[])
586: {
587: fprintf(stderr,"ERREUR ...\n");
588: fprintf(stderr,"%s\n",error_text);
589: exit(EXIT_FAILURE);
590: }
591: /*********************** vector *******************/
592: double *vector(int nl, int nh)
593: {
594: double *v;
595: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
596: if (!v) nrerror("allocation failure in vector");
597: return v-nl+NR_END;
598: }
599:
600: /************************ free vector ******************/
601: void free_vector(double*v, int nl, int nh)
602: {
603: free((FREE_ARG)(v+nl-NR_END));
604: }
605:
606: /************************ivector *******************************/
607: int *ivector(long nl,long nh)
608: {
609: int *v;
610: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
611: if (!v) nrerror("allocation failure in ivector");
612: return v-nl+NR_END;
613: }
614:
615: /******************free ivector **************************/
616: void free_ivector(int *v, long nl, long nh)
617: {
618: free((FREE_ARG)(v+nl-NR_END));
619: }
620:
621: /************************lvector *******************************/
622: long *lvector(long nl,long nh)
623: {
624: long *v;
625: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
626: if (!v) nrerror("allocation failure in ivector");
627: return v-nl+NR_END;
628: }
629:
630: /******************free lvector **************************/
631: void free_lvector(long *v, long nl, long nh)
632: {
633: free((FREE_ARG)(v+nl-NR_END));
634: }
635:
636: /******************* imatrix *******************************/
637: int **imatrix(long nrl, long nrh, long ncl, long nch)
638: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
639: {
640: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
641: int **m;
642:
643: /* allocate pointers to rows */
644: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
645: if (!m) nrerror("allocation failure 1 in matrix()");
646: m += NR_END;
647: m -= nrl;
648:
649:
650: /* allocate rows and set pointers to them */
651: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
652: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
653: m[nrl] += NR_END;
654: m[nrl] -= ncl;
655:
656: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
657:
658: /* return pointer to array of pointers to rows */
659: return m;
660: }
661:
662: /****************** free_imatrix *************************/
663: void free_imatrix(m,nrl,nrh,ncl,nch)
664: int **m;
665: long nch,ncl,nrh,nrl;
666: /* free an int matrix allocated by imatrix() */
667: {
668: free((FREE_ARG) (m[nrl]+ncl-NR_END));
669: free((FREE_ARG) (m+nrl-NR_END));
670: }
671:
672: /******************* matrix *******************************/
673: double **matrix(long nrl, long nrh, long ncl, long nch)
674: {
675: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
676: double **m;
677:
678: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
679: if (!m) nrerror("allocation failure 1 in matrix()");
680: m += NR_END;
681: m -= nrl;
682:
683: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
684: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
685: m[nrl] += NR_END;
686: m[nrl] -= ncl;
687:
688: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
689: return m;
690: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
691: */
692: }
693:
694: /*************************free matrix ************************/
695: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
696: {
697: free((FREE_ARG)(m[nrl]+ncl-NR_END));
698: free((FREE_ARG)(m+nrl-NR_END));
699: }
700:
701: /******************* ma3x *******************************/
702: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
703: {
704: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
705: double ***m;
706:
707: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
708: if (!m) nrerror("allocation failure 1 in matrix()");
709: m += NR_END;
710: m -= nrl;
711:
712: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
713: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
714: m[nrl] += NR_END;
715: m[nrl] -= ncl;
716:
717: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
718:
719: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
720: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
721: m[nrl][ncl] += NR_END;
722: m[nrl][ncl] -= nll;
723: for (j=ncl+1; j<=nch; j++)
724: m[nrl][j]=m[nrl][j-1]+nlay;
725:
726: for (i=nrl+1; i<=nrh; i++) {
727: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
728: for (j=ncl+1; j<=nch; j++)
729: m[i][j]=m[i][j-1]+nlay;
730: }
731: return m;
732: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
733: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
734: */
735: }
736:
737: /*************************free ma3x ************************/
738: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
739: {
740: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
741: free((FREE_ARG)(m[nrl]+ncl-NR_END));
742: free((FREE_ARG)(m+nrl-NR_END));
743: }
744:
745: /*************** function subdirf ***********/
746: char *subdirf(char fileres[])
747: {
748: /* Caution optionfilefiname is hidden */
749: strcpy(tmpout,optionfilefiname);
750: strcat(tmpout,"/"); /* Add to the right */
751: strcat(tmpout,fileres);
752: return tmpout;
753: }
754:
755: /*************** function subdirf2 ***********/
756: char *subdirf2(char fileres[], char *preop)
757: {
758:
759: /* Caution optionfilefiname is hidden */
760: strcpy(tmpout,optionfilefiname);
761: strcat(tmpout,"/");
762: strcat(tmpout,preop);
763: strcat(tmpout,fileres);
764: return tmpout;
765: }
766:
767: /*************** function subdirf3 ***********/
768: char *subdirf3(char fileres[], char *preop, char *preop2)
769: {
770:
771: /* Caution optionfilefiname is hidden */
772: strcpy(tmpout,optionfilefiname);
773: strcat(tmpout,"/");
774: strcat(tmpout,preop);
775: strcat(tmpout,preop2);
776: strcat(tmpout,fileres);
777: return tmpout;
778: }
779:
780: /***************** f1dim *************************/
781: extern int ncom;
782: extern double *pcom,*xicom;
783: extern double (*nrfunc)(double []);
784:
785: double f1dim(double x)
786: {
787: int j;
788: double f;
789: double *xt;
790:
791: xt=vector(1,ncom);
792: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
793: f=(*nrfunc)(xt);
794: free_vector(xt,1,ncom);
795: return f;
796: }
797:
798: /*****************brent *************************/
799: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
800: {
801: int iter;
802: double a,b,d,etemp;
803: double fu,fv,fw,fx;
804: double ftemp;
805: double p,q,r,tol1,tol2,u,v,w,x,xm;
806: double e=0.0;
807:
808: a=(ax < cx ? ax : cx);
809: b=(ax > cx ? ax : cx);
810: x=w=v=bx;
811: fw=fv=fx=(*f)(x);
812: for (iter=1;iter<=ITMAX;iter++) {
813: xm=0.5*(a+b);
814: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
815: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
816: printf(".");fflush(stdout);
817: fprintf(ficlog,".");fflush(ficlog);
818: #ifdef DEBUG
819: 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);
820: 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);
821: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
822: #endif
823: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
824: *xmin=x;
825: return fx;
826: }
827: ftemp=fu;
828: if (fabs(e) > tol1) {
829: r=(x-w)*(fx-fv);
830: q=(x-v)*(fx-fw);
831: p=(x-v)*q-(x-w)*r;
832: q=2.0*(q-r);
833: if (q > 0.0) p = -p;
834: q=fabs(q);
835: etemp=e;
836: e=d;
837: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
838: d=CGOLD*(e=(x >= xm ? a-x : b-x));
839: else {
840: d=p/q;
841: u=x+d;
842: if (u-a < tol2 || b-u < tol2)
843: d=SIGN(tol1,xm-x);
844: }
845: } else {
846: d=CGOLD*(e=(x >= xm ? a-x : b-x));
847: }
848: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
849: fu=(*f)(u);
850: if (fu <= fx) {
851: if (u >= x) a=x; else b=x;
852: SHFT(v,w,x,u)
853: SHFT(fv,fw,fx,fu)
854: } else {
855: if (u < x) a=u; else b=u;
856: if (fu <= fw || w == x) {
857: v=w;
858: w=u;
859: fv=fw;
860: fw=fu;
861: } else if (fu <= fv || v == x || v == w) {
862: v=u;
863: fv=fu;
864: }
865: }
866: }
867: nrerror("Too many iterations in brent");
868: *xmin=x;
869: return fx;
870: }
871:
872: /****************** mnbrak ***********************/
873:
874: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
875: double (*func)(double))
876: {
877: double ulim,u,r,q, dum;
878: double fu;
879:
880: *fa=(*func)(*ax);
881: *fb=(*func)(*bx);
882: if (*fb > *fa) {
883: SHFT(dum,*ax,*bx,dum)
884: SHFT(dum,*fb,*fa,dum)
885: }
886: *cx=(*bx)+GOLD*(*bx-*ax);
887: *fc=(*func)(*cx);
888: while (*fb > *fc) {
889: r=(*bx-*ax)*(*fb-*fc);
890: q=(*bx-*cx)*(*fb-*fa);
891: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
892: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
893: ulim=(*bx)+GLIMIT*(*cx-*bx);
894: if ((*bx-u)*(u-*cx) > 0.0) {
895: fu=(*func)(u);
896: } else if ((*cx-u)*(u-ulim) > 0.0) {
897: fu=(*func)(u);
898: if (fu < *fc) {
899: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
900: SHFT(*fb,*fc,fu,(*func)(u))
901: }
902: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
903: u=ulim;
904: fu=(*func)(u);
905: } else {
906: u=(*cx)+GOLD*(*cx-*bx);
907: fu=(*func)(u);
908: }
909: SHFT(*ax,*bx,*cx,u)
910: SHFT(*fa,*fb,*fc,fu)
911: }
912: }
913:
914: /*************** linmin ************************/
915:
916: int ncom;
917: double *pcom,*xicom;
918: double (*nrfunc)(double []);
919:
920: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
921: {
922: double brent(double ax, double bx, double cx,
923: double (*f)(double), double tol, double *xmin);
924: double f1dim(double x);
925: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
926: double *fc, double (*func)(double));
927: int j;
928: double xx,xmin,bx,ax;
929: double fx,fb,fa;
930:
931: ncom=n;
932: pcom=vector(1,n);
933: xicom=vector(1,n);
934: nrfunc=func;
935: for (j=1;j<=n;j++) {
936: pcom[j]=p[j];
937: xicom[j]=xi[j];
938: }
939: ax=0.0;
940: xx=1.0;
941: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
942: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
943: #ifdef DEBUG
944: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
945: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
946: #endif
947: for (j=1;j<=n;j++) {
948: xi[j] *= xmin;
949: p[j] += xi[j];
950: }
951: free_vector(xicom,1,n);
952: free_vector(pcom,1,n);
953: }
954:
955: char *asc_diff_time(long time_sec, char ascdiff[])
956: {
957: long sec_left, days, hours, minutes;
958: days = (time_sec) / (60*60*24);
959: sec_left = (time_sec) % (60*60*24);
960: hours = (sec_left) / (60*60) ;
961: sec_left = (sec_left) %(60*60);
962: minutes = (sec_left) /60;
963: sec_left = (sec_left) % (60);
964: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
965: return ascdiff;
966: }
967:
968: /*************** powell ************************/
969: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
970: double (*func)(double []))
971: {
972: void linmin(double p[], double xi[], int n, double *fret,
973: double (*func)(double []));
974: int i,ibig,j;
975: double del,t,*pt,*ptt,*xit;
976: double fp,fptt;
977: double *xits;
978: int niterf, itmp;
979:
980: pt=vector(1,n);
981: ptt=vector(1,n);
982: xit=vector(1,n);
983: xits=vector(1,n);
984: *fret=(*func)(p);
985: for (j=1;j<=n;j++) pt[j]=p[j];
986: for (*iter=1;;++(*iter)) {
987: fp=(*fret);
988: ibig=0;
989: del=0.0;
990: last_time=curr_time;
991: (void) gettimeofday(&curr_time,&tzp);
992: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
993: /* fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
994: fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
995: */
996: for (i=1;i<=n;i++) {
997: printf(" %d %.12f",i, p[i]);
998: fprintf(ficlog," %d %.12lf",i, p[i]);
999: fprintf(ficrespow," %.12lf", p[i]);
1000: }
1001: printf("\n");
1002: fprintf(ficlog,"\n");
1003: fprintf(ficrespow,"\n");fflush(ficrespow);
1004: if(*iter <=3){
1005: tm = *localtime(&curr_time.tv_sec);
1006: strcpy(strcurr,asctime(&tm));
1007: /* asctime_r(&tm,strcurr); */
1008: forecast_time=curr_time;
1009: itmp = strlen(strcurr);
1010: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1011: strcurr[itmp-1]='\0';
1012: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1013: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1014: for(niterf=10;niterf<=30;niterf+=10){
1015: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
1016: tmf = *localtime(&forecast_time.tv_sec);
1017: /* asctime_r(&tmf,strfor); */
1018: strcpy(strfor,asctime(&tmf));
1019: itmp = strlen(strfor);
1020: if(strfor[itmp-1]=='\n')
1021: strfor[itmp-1]='\0';
1022: 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(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
1023: 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(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
1024: }
1025: }
1026: for (i=1;i<=n;i++) {
1027: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1028: fptt=(*fret);
1029: #ifdef DEBUG
1030: printf("fret=%lf \n",*fret);
1031: fprintf(ficlog,"fret=%lf \n",*fret);
1032: #endif
1033: printf("%d",i);fflush(stdout);
1034: fprintf(ficlog,"%d",i);fflush(ficlog);
1035: linmin(p,xit,n,fret,func);
1036: if (fabs(fptt-(*fret)) > del) {
1037: del=fabs(fptt-(*fret));
1038: ibig=i;
1039: }
1040: #ifdef DEBUG
1041: printf("%d %.12e",i,(*fret));
1042: fprintf(ficlog,"%d %.12e",i,(*fret));
1043: for (j=1;j<=n;j++) {
1044: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1045: printf(" x(%d)=%.12e",j,xit[j]);
1046: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1047: }
1048: for(j=1;j<=n;j++) {
1049: printf(" p=%.12e",p[j]);
1050: fprintf(ficlog," p=%.12e",p[j]);
1051: }
1052: printf("\n");
1053: fprintf(ficlog,"\n");
1054: #endif
1055: }
1056: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1057: #ifdef DEBUG
1058: int k[2],l;
1059: k[0]=1;
1060: k[1]=-1;
1061: printf("Max: %.12e",(*func)(p));
1062: fprintf(ficlog,"Max: %.12e",(*func)(p));
1063: for (j=1;j<=n;j++) {
1064: printf(" %.12e",p[j]);
1065: fprintf(ficlog," %.12e",p[j]);
1066: }
1067: printf("\n");
1068: fprintf(ficlog,"\n");
1069: for(l=0;l<=1;l++) {
1070: for (j=1;j<=n;j++) {
1071: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1072: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1073: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1074: }
1075: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1076: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1077: }
1078: #endif
1079:
1080:
1081: free_vector(xit,1,n);
1082: free_vector(xits,1,n);
1083: free_vector(ptt,1,n);
1084: free_vector(pt,1,n);
1085: return;
1086: }
1087: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1088: for (j=1;j<=n;j++) {
1089: ptt[j]=2.0*p[j]-pt[j];
1090: xit[j]=p[j]-pt[j];
1091: pt[j]=p[j];
1092: }
1093: fptt=(*func)(ptt);
1094: if (fptt < fp) {
1095: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1096: if (t < 0.0) {
1097: linmin(p,xit,n,fret,func);
1098: for (j=1;j<=n;j++) {
1099: xi[j][ibig]=xi[j][n];
1100: xi[j][n]=xit[j];
1101: }
1102: #ifdef DEBUG
1103: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1104: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1105: for(j=1;j<=n;j++){
1106: printf(" %.12e",xit[j]);
1107: fprintf(ficlog," %.12e",xit[j]);
1108: }
1109: printf("\n");
1110: fprintf(ficlog,"\n");
1111: #endif
1112: }
1113: }
1114: }
1115: }
1116:
1117: /**** Prevalence limit (stable or period prevalence) ****************/
1118:
1119: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1120: {
1121: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1122: matrix by transitions matrix until convergence is reached */
1123:
1124: int i, ii,j,k;
1125: double min, max, maxmin, maxmax,sumnew=0.;
1126: double **matprod2();
1127: double **out, cov[NCOVMAX], **pmij();
1128: double **newm;
1129: double agefin, delaymax=50 ; /* Max number of years to converge */
1130:
1131: for (ii=1;ii<=nlstate+ndeath;ii++)
1132: for (j=1;j<=nlstate+ndeath;j++){
1133: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1134: }
1135:
1136: cov[1]=1.;
1137:
1138: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1139: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1140: newm=savm;
1141: /* Covariates have to be included here again */
1142: cov[2]=agefin;
1143:
1144: for (k=1; k<=cptcovn;k++) {
1145: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1146: /* printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
1147: }
1148: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1149: for (k=1; k<=cptcovprod;k++)
1150: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1151:
1152: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1153: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1154: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1155: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1156:
1157: savm=oldm;
1158: oldm=newm;
1159: maxmax=0.;
1160: for(j=1;j<=nlstate;j++){
1161: min=1.;
1162: max=0.;
1163: for(i=1; i<=nlstate; i++) {
1164: sumnew=0;
1165: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1166: prlim[i][j]= newm[i][j]/(1-sumnew);
1167: max=FMAX(max,prlim[i][j]);
1168: min=FMIN(min,prlim[i][j]);
1169: }
1170: maxmin=max-min;
1171: maxmax=FMAX(maxmax,maxmin);
1172: }
1173: if(maxmax < ftolpl){
1174: return prlim;
1175: }
1176: }
1177: }
1178:
1179: /*************** transition probabilities ***************/
1180:
1181: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1182: {
1183: double s1, s2;
1184: /*double t34;*/
1185: int i,j,j1, nc, ii, jj;
1186:
1187: for(i=1; i<= nlstate; i++){
1188: for(j=1; j<i;j++){
1189: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1190: /*s2 += param[i][j][nc]*cov[nc];*/
1191: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1192: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1193: }
1194: ps[i][j]=s2;
1195: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1196: }
1197: for(j=i+1; j<=nlstate+ndeath;j++){
1198: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1199: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1200: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1201: }
1202: ps[i][j]=s2;
1203: }
1204: }
1205: /*ps[3][2]=1;*/
1206:
1207: for(i=1; i<= nlstate; i++){
1208: s1=0;
1209: for(j=1; j<i; j++)
1210: s1+=exp(ps[i][j]);
1211: for(j=i+1; j<=nlstate+ndeath; j++)
1212: s1+=exp(ps[i][j]);
1213: ps[i][i]=1./(s1+1.);
1214: for(j=1; j<i; j++)
1215: ps[i][j]= exp(ps[i][j])*ps[i][i];
1216: for(j=i+1; j<=nlstate+ndeath; j++)
1217: ps[i][j]= exp(ps[i][j])*ps[i][i];
1218: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1219: } /* end i */
1220:
1221: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1222: for(jj=1; jj<= nlstate+ndeath; jj++){
1223: ps[ii][jj]=0;
1224: ps[ii][ii]=1;
1225: }
1226: }
1227:
1228:
1229: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1230: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1231: /* printf("ddd %lf ",ps[ii][jj]); */
1232: /* } */
1233: /* printf("\n "); */
1234: /* } */
1235: /* printf("\n ");printf("%lf ",cov[2]); */
1236: /*
1237: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1238: goto end;*/
1239: return ps;
1240: }
1241:
1242: /**************** Product of 2 matrices ******************/
1243:
1244: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1245: {
1246: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1247: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1248: /* in, b, out are matrice of pointers which should have been initialized
1249: before: only the contents of out is modified. The function returns
1250: a pointer to pointers identical to out */
1251: long i, j, k;
1252: for(i=nrl; i<= nrh; i++)
1253: for(k=ncolol; k<=ncoloh; k++)
1254: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1255: out[i][k] +=in[i][j]*b[j][k];
1256:
1257: return out;
1258: }
1259:
1260:
1261: /************* Higher Matrix Product ***************/
1262:
1263: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1264: {
1265: /* Computes the transition matrix starting at age 'age' over
1266: 'nhstepm*hstepm*stepm' months (i.e. until
1267: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1268: nhstepm*hstepm matrices.
1269: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1270: (typically every 2 years instead of every month which is too big
1271: for the memory).
1272: Model is determined by parameters x and covariates have to be
1273: included manually here.
1274:
1275: */
1276:
1277: int i, j, d, h, k;
1278: double **out, cov[NCOVMAX];
1279: double **newm;
1280:
1281: /* Hstepm could be zero and should return the unit matrix */
1282: for (i=1;i<=nlstate+ndeath;i++)
1283: for (j=1;j<=nlstate+ndeath;j++){
1284: oldm[i][j]=(i==j ? 1.0 : 0.0);
1285: po[i][j][0]=(i==j ? 1.0 : 0.0);
1286: }
1287: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1288: for(h=1; h <=nhstepm; h++){
1289: for(d=1; d <=hstepm; d++){
1290: newm=savm;
1291: /* Covariates have to be included here again */
1292: cov[1]=1.;
1293: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1294: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1295: for (k=1; k<=cptcovage;k++)
1296: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1297: for (k=1; k<=cptcovprod;k++)
1298: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1299:
1300:
1301: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1302: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1303: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1304: pmij(pmmij,cov,ncovmodel,x,nlstate));
1305: savm=oldm;
1306: oldm=newm;
1307: }
1308: for(i=1; i<=nlstate+ndeath; i++)
1309: for(j=1;j<=nlstate+ndeath;j++) {
1310: po[i][j][h]=newm[i][j];
1311: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1312: */
1313: }
1314: } /* end h */
1315: return po;
1316: }
1317:
1318:
1319: /*************** log-likelihood *************/
1320: double func( double *x)
1321: {
1322: int i, ii, j, k, mi, d, kk;
1323: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1324: double **out;
1325: double sw; /* Sum of weights */
1326: double lli; /* Individual log likelihood */
1327: int s1, s2;
1328: double bbh, survp;
1329: long ipmx;
1330: /*extern weight */
1331: /* We are differentiating ll according to initial status */
1332: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1333: /*for(i=1;i<imx;i++)
1334: printf(" %d\n",s[4][i]);
1335: */
1336: cov[1]=1.;
1337:
1338: for(k=1; k<=nlstate; k++) ll[k]=0.;
1339:
1340: if(mle==1){
1341: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1342: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1343: for(mi=1; mi<= wav[i]-1; mi++){
1344: for (ii=1;ii<=nlstate+ndeath;ii++)
1345: for (j=1;j<=nlstate+ndeath;j++){
1346: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1347: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1348: }
1349: for(d=0; d<dh[mi][i]; d++){
1350: newm=savm;
1351: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1352: for (kk=1; kk<=cptcovage;kk++) {
1353: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1354: }
1355: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1356: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1357: savm=oldm;
1358: oldm=newm;
1359: } /* end mult */
1360:
1361: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1362: /* But now since version 0.9 we anticipate for bias at large stepm.
1363: * If stepm is larger than one month (smallest stepm) and if the exact delay
1364: * (in months) between two waves is not a multiple of stepm, we rounded to
1365: * the nearest (and in case of equal distance, to the lowest) interval but now
1366: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1367: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1368: * probability in order to take into account the bias as a fraction of the way
1369: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1370: * -stepm/2 to stepm/2 .
1371: * For stepm=1 the results are the same as for previous versions of Imach.
1372: * For stepm > 1 the results are less biased than in previous versions.
1373: */
1374: s1=s[mw[mi][i]][i];
1375: s2=s[mw[mi+1][i]][i];
1376: bbh=(double)bh[mi][i]/(double)stepm;
1377: /* bias bh is positive if real duration
1378: * is higher than the multiple of stepm and negative otherwise.
1379: */
1380: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1381: if( s2 > nlstate){
1382: /* i.e. if s2 is a death state and if the date of death is known
1383: then the contribution to the likelihood is the probability to
1384: die between last step unit time and current step unit time,
1385: which is also equal to probability to die before dh
1386: minus probability to die before dh-stepm .
1387: In version up to 0.92 likelihood was computed
1388: as if date of death was unknown. Death was treated as any other
1389: health state: the date of the interview describes the actual state
1390: and not the date of a change in health state. The former idea was
1391: to consider that at each interview the state was recorded
1392: (healthy, disable or death) and IMaCh was corrected; but when we
1393: introduced the exact date of death then we should have modified
1394: the contribution of an exact death to the likelihood. This new
1395: contribution is smaller and very dependent of the step unit
1396: stepm. It is no more the probability to die between last interview
1397: and month of death but the probability to survive from last
1398: interview up to one month before death multiplied by the
1399: probability to die within a month. Thanks to Chris
1400: Jackson for correcting this bug. Former versions increased
1401: mortality artificially. The bad side is that we add another loop
1402: which slows down the processing. The difference can be up to 10%
1403: lower mortality.
1404: */
1405: lli=log(out[s1][s2] - savm[s1][s2]);
1406:
1407:
1408: } else if (s2==-2) {
1409: for (j=1,survp=0. ; j<=nlstate; j++)
1410: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1411: /*survp += out[s1][j]; */
1412: lli= log(survp);
1413: }
1414:
1415: else if (s2==-4) {
1416: for (j=3,survp=0. ; j<=nlstate; j++)
1417: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1418: lli= log(survp);
1419: }
1420:
1421: else if (s2==-5) {
1422: for (j=1,survp=0. ; j<=2; j++)
1423: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1424: lli= log(survp);
1425: }
1426:
1427: else{
1428: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1429: /* 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 */
1430: }
1431: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1432: /*if(lli ==000.0)*/
1433: /*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); */
1434: ipmx +=1;
1435: sw += weight[i];
1436: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1437: } /* end of wave */
1438: } /* end of individual */
1439: } else if(mle==2){
1440: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1441: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1442: for(mi=1; mi<= wav[i]-1; mi++){
1443: for (ii=1;ii<=nlstate+ndeath;ii++)
1444: for (j=1;j<=nlstate+ndeath;j++){
1445: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1446: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1447: }
1448: for(d=0; d<=dh[mi][i]; d++){
1449: newm=savm;
1450: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1451: for (kk=1; kk<=cptcovage;kk++) {
1452: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1453: }
1454: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1455: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1456: savm=oldm;
1457: oldm=newm;
1458: } /* end mult */
1459:
1460: s1=s[mw[mi][i]][i];
1461: s2=s[mw[mi+1][i]][i];
1462: bbh=(double)bh[mi][i]/(double)stepm;
1463: 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 */
1464: ipmx +=1;
1465: sw += weight[i];
1466: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1467: } /* end of wave */
1468: } /* end of individual */
1469: } else if(mle==3){ /* exponential inter-extrapolation */
1470: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1471: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1472: for(mi=1; mi<= wav[i]-1; mi++){
1473: for (ii=1;ii<=nlstate+ndeath;ii++)
1474: for (j=1;j<=nlstate+ndeath;j++){
1475: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1476: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1477: }
1478: for(d=0; d<dh[mi][i]; d++){
1479: newm=savm;
1480: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1481: for (kk=1; kk<=cptcovage;kk++) {
1482: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1483: }
1484: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1485: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1486: savm=oldm;
1487: oldm=newm;
1488: } /* end mult */
1489:
1490: s1=s[mw[mi][i]][i];
1491: s2=s[mw[mi+1][i]][i];
1492: bbh=(double)bh[mi][i]/(double)stepm;
1493: 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 */
1494: ipmx +=1;
1495: sw += weight[i];
1496: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1497: } /* end of wave */
1498: } /* end of individual */
1499: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1500: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1501: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1502: for(mi=1; mi<= wav[i]-1; mi++){
1503: for (ii=1;ii<=nlstate+ndeath;ii++)
1504: for (j=1;j<=nlstate+ndeath;j++){
1505: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1506: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1507: }
1508: for(d=0; d<dh[mi][i]; d++){
1509: newm=savm;
1510: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1511: for (kk=1; kk<=cptcovage;kk++) {
1512: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1513: }
1514:
1515: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1516: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1517: savm=oldm;
1518: oldm=newm;
1519: } /* end mult */
1520:
1521: s1=s[mw[mi][i]][i];
1522: s2=s[mw[mi+1][i]][i];
1523: if( s2 > nlstate){
1524: lli=log(out[s1][s2] - savm[s1][s2]);
1525: }else{
1526: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1527: }
1528: ipmx +=1;
1529: sw += weight[i];
1530: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1531: /* 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]); */
1532: } /* end of wave */
1533: } /* end of individual */
1534: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1535: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1536: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1537: for(mi=1; mi<= wav[i]-1; mi++){
1538: for (ii=1;ii<=nlstate+ndeath;ii++)
1539: for (j=1;j<=nlstate+ndeath;j++){
1540: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1541: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1542: }
1543: for(d=0; d<dh[mi][i]; d++){
1544: newm=savm;
1545: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1546: for (kk=1; kk<=cptcovage;kk++) {
1547: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1548: }
1549:
1550: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1551: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1552: savm=oldm;
1553: oldm=newm;
1554: } /* end mult */
1555:
1556: s1=s[mw[mi][i]][i];
1557: s2=s[mw[mi+1][i]][i];
1558: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1559: ipmx +=1;
1560: sw += weight[i];
1561: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1562: /*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]);*/
1563: } /* end of wave */
1564: } /* end of individual */
1565: } /* End of if */
1566: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1567: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1568: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1569: return -l;
1570: }
1571:
1572: /*************** log-likelihood *************/
1573: double funcone( double *x)
1574: {
1575: /* Same as likeli but slower because of a lot of printf and if */
1576: int i, ii, j, k, mi, d, kk;
1577: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1578: double **out;
1579: double lli; /* Individual log likelihood */
1580: double llt;
1581: int s1, s2;
1582: double bbh, survp;
1583: /*extern weight */
1584: /* We are differentiating ll according to initial status */
1585: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1586: /*for(i=1;i<imx;i++)
1587: printf(" %d\n",s[4][i]);
1588: */
1589: cov[1]=1.;
1590:
1591: for(k=1; k<=nlstate; k++) ll[k]=0.;
1592:
1593: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1594: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1595: for(mi=1; mi<= wav[i]-1; mi++){
1596: for (ii=1;ii<=nlstate+ndeath;ii++)
1597: for (j=1;j<=nlstate+ndeath;j++){
1598: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1599: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1600: }
1601: for(d=0; d<dh[mi][i]; d++){
1602: newm=savm;
1603: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1604: for (kk=1; kk<=cptcovage;kk++) {
1605: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1606: }
1607: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1608: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1609: savm=oldm;
1610: oldm=newm;
1611: } /* end mult */
1612:
1613: s1=s[mw[mi][i]][i];
1614: s2=s[mw[mi+1][i]][i];
1615: bbh=(double)bh[mi][i]/(double)stepm;
1616: /* bias is positive if real duration
1617: * is higher than the multiple of stepm and negative otherwise.
1618: */
1619: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1620: lli=log(out[s1][s2] - savm[s1][s2]);
1621: } else if (s2==-2) {
1622: for (j=1,survp=0. ; j<=nlstate; j++)
1623: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1624: lli= log(survp);
1625: }else if (mle==1){
1626: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1627: } else if(mle==2){
1628: 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 */
1629: } else if(mle==3){ /* exponential inter-extrapolation */
1630: 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 */
1631: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1632: lli=log(out[s1][s2]); /* Original formula */
1633: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1634: lli=log(out[s1][s2]); /* Original formula */
1635: } /* End of if */
1636: ipmx +=1;
1637: sw += weight[i];
1638: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1639: /* 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]); */
1640: if(globpr){
1641: fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1642: %11.6f %11.6f %11.6f ", \
1643: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1644: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1645: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1646: llt +=ll[k]*gipmx/gsw;
1647: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1648: }
1649: fprintf(ficresilk," %10.6f\n", -llt);
1650: }
1651: } /* end of wave */
1652: } /* end of individual */
1653: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1654: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1655: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1656: if(globpr==0){ /* First time we count the contributions and weights */
1657: gipmx=ipmx;
1658: gsw=sw;
1659: }
1660: return -l;
1661: }
1662:
1663:
1664: /*************** function likelione ***********/
1665: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1666: {
1667: /* This routine should help understanding what is done with
1668: the selection of individuals/waves and
1669: to check the exact contribution to the likelihood.
1670: Plotting could be done.
1671: */
1672: int k;
1673:
1674: if(*globpri !=0){ /* Just counts and sums, no printings */
1675: strcpy(fileresilk,"ilk");
1676: strcat(fileresilk,fileres);
1677: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1678: printf("Problem with resultfile: %s\n", fileresilk);
1679: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1680: }
1681: 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");
1682: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1683: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1684: for(k=1; k<=nlstate; k++)
1685: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1686: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1687: }
1688:
1689: *fretone=(*funcone)(p);
1690: if(*globpri !=0){
1691: fclose(ficresilk);
1692: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1693: fflush(fichtm);
1694: }
1695: return;
1696: }
1697:
1698:
1699: /*********** Maximum Likelihood Estimation ***************/
1700:
1701: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1702: {
1703: int i,j, iter;
1704: double **xi;
1705: double fret;
1706: double fretone; /* Only one call to likelihood */
1707: /* char filerespow[FILENAMELENGTH];*/
1708: xi=matrix(1,npar,1,npar);
1709: for (i=1;i<=npar;i++)
1710: for (j=1;j<=npar;j++)
1711: xi[i][j]=(i==j ? 1.0 : 0.0);
1712: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1713: strcpy(filerespow,"pow");
1714: strcat(filerespow,fileres);
1715: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1716: printf("Problem with resultfile: %s\n", filerespow);
1717: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1718: }
1719: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1720: for (i=1;i<=nlstate;i++)
1721: for(j=1;j<=nlstate+ndeath;j++)
1722: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1723: fprintf(ficrespow,"\n");
1724:
1725: powell(p,xi,npar,ftol,&iter,&fret,func);
1726:
1727: free_matrix(xi,1,npar,1,npar);
1728: fclose(ficrespow);
1729: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1730: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1731: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1732:
1733: }
1734:
1735: /**** Computes Hessian and covariance matrix ***/
1736: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1737: {
1738: double **a,**y,*x,pd;
1739: double **hess;
1740: int i, j,jk;
1741: int *indx;
1742:
1743: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1744: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1745: void lubksb(double **a, int npar, int *indx, double b[]) ;
1746: void ludcmp(double **a, int npar, int *indx, double *d) ;
1747: double gompertz(double p[]);
1748: hess=matrix(1,npar,1,npar);
1749:
1750: printf("\nCalculation of the hessian matrix. Wait...\n");
1751: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1752: for (i=1;i<=npar;i++){
1753: printf("%d",i);fflush(stdout);
1754: fprintf(ficlog,"%d",i);fflush(ficlog);
1755:
1756: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1757:
1758: /* printf(" %f ",p[i]);
1759: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1760: }
1761:
1762: for (i=1;i<=npar;i++) {
1763: for (j=1;j<=npar;j++) {
1764: if (j>i) {
1765: printf(".%d%d",i,j);fflush(stdout);
1766: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1767: hess[i][j]=hessij(p,delti,i,j,func,npar);
1768:
1769: hess[j][i]=hess[i][j];
1770: /*printf(" %lf ",hess[i][j]);*/
1771: }
1772: }
1773: }
1774: printf("\n");
1775: fprintf(ficlog,"\n");
1776:
1777: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1778: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1779:
1780: a=matrix(1,npar,1,npar);
1781: y=matrix(1,npar,1,npar);
1782: x=vector(1,npar);
1783: indx=ivector(1,npar);
1784: for (i=1;i<=npar;i++)
1785: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1786: ludcmp(a,npar,indx,&pd);
1787:
1788: for (j=1;j<=npar;j++) {
1789: for (i=1;i<=npar;i++) x[i]=0;
1790: x[j]=1;
1791: lubksb(a,npar,indx,x);
1792: for (i=1;i<=npar;i++){
1793: matcov[i][j]=x[i];
1794: }
1795: }
1796:
1797: printf("\n#Hessian matrix#\n");
1798: fprintf(ficlog,"\n#Hessian matrix#\n");
1799: for (i=1;i<=npar;i++) {
1800: for (j=1;j<=npar;j++) {
1801: printf("%.3e ",hess[i][j]);
1802: fprintf(ficlog,"%.3e ",hess[i][j]);
1803: }
1804: printf("\n");
1805: fprintf(ficlog,"\n");
1806: }
1807:
1808: /* Recompute Inverse */
1809: for (i=1;i<=npar;i++)
1810: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1811: ludcmp(a,npar,indx,&pd);
1812:
1813: /* printf("\n#Hessian matrix recomputed#\n");
1814:
1815: for (j=1;j<=npar;j++) {
1816: for (i=1;i<=npar;i++) x[i]=0;
1817: x[j]=1;
1818: lubksb(a,npar,indx,x);
1819: for (i=1;i<=npar;i++){
1820: y[i][j]=x[i];
1821: printf("%.3e ",y[i][j]);
1822: fprintf(ficlog,"%.3e ",y[i][j]);
1823: }
1824: printf("\n");
1825: fprintf(ficlog,"\n");
1826: }
1827: */
1828:
1829: free_matrix(a,1,npar,1,npar);
1830: free_matrix(y,1,npar,1,npar);
1831: free_vector(x,1,npar);
1832: free_ivector(indx,1,npar);
1833: free_matrix(hess,1,npar,1,npar);
1834:
1835:
1836: }
1837:
1838: /*************** hessian matrix ****************/
1839: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1840: {
1841: int i;
1842: int l=1, lmax=20;
1843: double k1,k2;
1844: double p2[NPARMAX+1];
1845: double res;
1846: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1847: double fx;
1848: int k=0,kmax=10;
1849: double l1;
1850:
1851: fx=func(x);
1852: for (i=1;i<=npar;i++) p2[i]=x[i];
1853: for(l=0 ; l <=lmax; l++){
1854: l1=pow(10,l);
1855: delts=delt;
1856: for(k=1 ; k <kmax; k=k+1){
1857: delt = delta*(l1*k);
1858: p2[theta]=x[theta] +delt;
1859: k1=func(p2)-fx;
1860: p2[theta]=x[theta]-delt;
1861: k2=func(p2)-fx;
1862: /*res= (k1-2.0*fx+k2)/delt/delt; */
1863: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1864:
1865: #ifdef DEBUG
1866: 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);
1867: 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);
1868: #endif
1869: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1870: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1871: k=kmax;
1872: }
1873: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1874: k=kmax; l=lmax*10.;
1875: }
1876: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1877: delts=delt;
1878: }
1879: }
1880: }
1881: delti[theta]=delts;
1882: return res;
1883:
1884: }
1885:
1886: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1887: {
1888: int i;
1889: int l=1, l1, lmax=20;
1890: double k1,k2,k3,k4,res,fx;
1891: double p2[NPARMAX+1];
1892: int k;
1893:
1894: fx=func(x);
1895: for (k=1; k<=2; k++) {
1896: for (i=1;i<=npar;i++) p2[i]=x[i];
1897: p2[thetai]=x[thetai]+delti[thetai]/k;
1898: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1899: k1=func(p2)-fx;
1900:
1901: p2[thetai]=x[thetai]+delti[thetai]/k;
1902: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1903: k2=func(p2)-fx;
1904:
1905: p2[thetai]=x[thetai]-delti[thetai]/k;
1906: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1907: k3=func(p2)-fx;
1908:
1909: p2[thetai]=x[thetai]-delti[thetai]/k;
1910: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1911: k4=func(p2)-fx;
1912: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1913: #ifdef DEBUG
1914: 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);
1915: 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);
1916: #endif
1917: }
1918: return res;
1919: }
1920:
1921: /************** Inverse of matrix **************/
1922: void ludcmp(double **a, int n, int *indx, double *d)
1923: {
1924: int i,imax,j,k;
1925: double big,dum,sum,temp;
1926: double *vv;
1927:
1928: vv=vector(1,n);
1929: *d=1.0;
1930: for (i=1;i<=n;i++) {
1931: big=0.0;
1932: for (j=1;j<=n;j++)
1933: if ((temp=fabs(a[i][j])) > big) big=temp;
1934: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1935: vv[i]=1.0/big;
1936: }
1937: for (j=1;j<=n;j++) {
1938: for (i=1;i<j;i++) {
1939: sum=a[i][j];
1940: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1941: a[i][j]=sum;
1942: }
1943: big=0.0;
1944: for (i=j;i<=n;i++) {
1945: sum=a[i][j];
1946: for (k=1;k<j;k++)
1947: sum -= a[i][k]*a[k][j];
1948: a[i][j]=sum;
1949: if ( (dum=vv[i]*fabs(sum)) >= big) {
1950: big=dum;
1951: imax=i;
1952: }
1953: }
1954: if (j != imax) {
1955: for (k=1;k<=n;k++) {
1956: dum=a[imax][k];
1957: a[imax][k]=a[j][k];
1958: a[j][k]=dum;
1959: }
1960: *d = -(*d);
1961: vv[imax]=vv[j];
1962: }
1963: indx[j]=imax;
1964: if (a[j][j] == 0.0) a[j][j]=TINY;
1965: if (j != n) {
1966: dum=1.0/(a[j][j]);
1967: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1968: }
1969: }
1970: free_vector(vv,1,n); /* Doesn't work */
1971: ;
1972: }
1973:
1974: void lubksb(double **a, int n, int *indx, double b[])
1975: {
1976: int i,ii=0,ip,j;
1977: double sum;
1978:
1979: for (i=1;i<=n;i++) {
1980: ip=indx[i];
1981: sum=b[ip];
1982: b[ip]=b[i];
1983: if (ii)
1984: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1985: else if (sum) ii=i;
1986: b[i]=sum;
1987: }
1988: for (i=n;i>=1;i--) {
1989: sum=b[i];
1990: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1991: b[i]=sum/a[i][i];
1992: }
1993: }
1994:
1995: void pstamp(FILE *fichier)
1996: {
1997: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
1998: }
1999:
2000: /************ Frequencies ********************/
2001: 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[])
2002: { /* Some frequencies */
2003:
2004: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
2005: int first;
2006: double ***freq; /* Frequencies */
2007: double *pp, **prop;
2008: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2009: char fileresp[FILENAMELENGTH];
2010:
2011: pp=vector(1,nlstate);
2012: prop=matrix(1,nlstate,iagemin,iagemax+3);
2013: strcpy(fileresp,"p");
2014: strcat(fileresp,fileres);
2015: if((ficresp=fopen(fileresp,"w"))==NULL) {
2016: printf("Problem with prevalence resultfile: %s\n", fileresp);
2017: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2018: exit(0);
2019: }
2020: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2021: j1=0;
2022:
2023: j=cptcoveff;
2024: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2025:
2026: first=1;
2027:
2028: for(k1=1; k1<=j;k1++){
2029: for(i1=1; i1<=ncodemax[k1];i1++){
2030: j1++;
2031: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2032: scanf("%d", i);*/
2033: for (i=-5; i<=nlstate+ndeath; i++)
2034: for (jk=-5; jk<=nlstate+ndeath; jk++)
2035: for(m=iagemin; m <= iagemax+3; m++)
2036: freq[i][jk][m]=0;
2037:
2038: for (i=1; i<=nlstate; i++)
2039: for(m=iagemin; m <= iagemax+3; m++)
2040: prop[i][m]=0;
2041:
2042: dateintsum=0;
2043: k2cpt=0;
2044: for (i=1; i<=imx; i++) {
2045: bool=1;
2046: if (cptcovn>0) {
2047: for (z1=1; z1<=cptcoveff; z1++)
2048: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2049: bool=0;
2050: }
2051: if (bool==1){
2052: for(m=firstpass; m<=lastpass; m++){
2053: k2=anint[m][i]+(mint[m][i]/12.);
2054: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2055: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2056: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2057: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2058: if (m<lastpass) {
2059: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2060: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2061: }
2062:
2063: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2064: dateintsum=dateintsum+k2;
2065: k2cpt++;
2066: }
2067: /*}*/
2068: }
2069: }
2070: }
2071:
2072: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2073: pstamp(ficresp);
2074: if (cptcovn>0) {
2075: fprintf(ficresp, "\n#********** Variable ");
2076: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2077: fprintf(ficresp, "**********\n#");
2078: }
2079: for(i=1; i<=nlstate;i++)
2080: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2081: fprintf(ficresp, "\n");
2082:
2083: for(i=iagemin; i <= iagemax+3; i++){
2084: if(i==iagemax+3){
2085: fprintf(ficlog,"Total");
2086: }else{
2087: if(first==1){
2088: first=0;
2089: printf("See log file for details...\n");
2090: }
2091: fprintf(ficlog,"Age %d", i);
2092: }
2093: for(jk=1; jk <=nlstate ; jk++){
2094: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2095: pp[jk] += freq[jk][m][i];
2096: }
2097: for(jk=1; jk <=nlstate ; jk++){
2098: for(m=-1, pos=0; m <=0 ; m++)
2099: pos += freq[jk][m][i];
2100: if(pp[jk]>=1.e-10){
2101: if(first==1){
2102: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2103: }
2104: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2105: }else{
2106: if(first==1)
2107: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2108: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2109: }
2110: }
2111:
2112: for(jk=1; jk <=nlstate ; jk++){
2113: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2114: pp[jk] += freq[jk][m][i];
2115: }
2116: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2117: pos += pp[jk];
2118: posprop += prop[jk][i];
2119: }
2120: for(jk=1; jk <=nlstate ; jk++){
2121: if(pos>=1.e-5){
2122: if(first==1)
2123: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2124: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2125: }else{
2126: if(first==1)
2127: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2128: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2129: }
2130: if( i <= iagemax){
2131: if(pos>=1.e-5){
2132: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2133: /*probs[i][jk][j1]= pp[jk]/pos;*/
2134: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2135: }
2136: else
2137: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2138: }
2139: }
2140:
2141: for(jk=-1; jk <=nlstate+ndeath; jk++)
2142: for(m=-1; m <=nlstate+ndeath; m++)
2143: if(freq[jk][m][i] !=0 ) {
2144: if(first==1)
2145: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2146: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2147: }
2148: if(i <= iagemax)
2149: fprintf(ficresp,"\n");
2150: if(first==1)
2151: printf("Others in log...\n");
2152: fprintf(ficlog,"\n");
2153: }
2154: }
2155: }
2156: dateintmean=dateintsum/k2cpt;
2157:
2158: fclose(ficresp);
2159: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2160: free_vector(pp,1,nlstate);
2161: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2162: /* End of Freq */
2163: }
2164:
2165: /************ Prevalence ********************/
2166: 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)
2167: {
2168: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2169: in each health status at the date of interview (if between dateprev1 and dateprev2).
2170: We still use firstpass and lastpass as another selection.
2171: */
2172:
2173: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
2174: double ***freq; /* Frequencies */
2175: double *pp, **prop;
2176: double pos,posprop;
2177: double y2; /* in fractional years */
2178: int iagemin, iagemax;
2179:
2180: iagemin= (int) agemin;
2181: iagemax= (int) agemax;
2182: /*pp=vector(1,nlstate);*/
2183: prop=matrix(1,nlstate,iagemin,iagemax+3);
2184: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2185: j1=0;
2186:
2187: j=cptcoveff;
2188: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2189:
2190: for(k1=1; k1<=j;k1++){
2191: for(i1=1; i1<=ncodemax[k1];i1++){
2192: j1++;
2193:
2194: for (i=1; i<=nlstate; i++)
2195: for(m=iagemin; m <= iagemax+3; m++)
2196: prop[i][m]=0.0;
2197:
2198: for (i=1; i<=imx; i++) { /* Each individual */
2199: bool=1;
2200: if (cptcovn>0) {
2201: for (z1=1; z1<=cptcoveff; z1++)
2202: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2203: bool=0;
2204: }
2205: if (bool==1) {
2206: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2207: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2208: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2209: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2210: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2211: 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);
2212: if (s[m][i]>0 && s[m][i]<=nlstate) {
2213: /*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]]);*/
2214: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2215: prop[s[m][i]][iagemax+3] += weight[i];
2216: }
2217: }
2218: } /* end selection of waves */
2219: }
2220: }
2221: for(i=iagemin; i <= iagemax+3; i++){
2222:
2223: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2224: posprop += prop[jk][i];
2225: }
2226:
2227: for(jk=1; jk <=nlstate ; jk++){
2228: if( i <= iagemax){
2229: if(posprop>=1.e-5){
2230: probs[i][jk][j1]= prop[jk][i]/posprop;
2231: }
2232: }
2233: }/* end jk */
2234: }/* end i */
2235: } /* end i1 */
2236: } /* end k1 */
2237:
2238: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2239: /*free_vector(pp,1,nlstate);*/
2240: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2241: } /* End of prevalence */
2242:
2243: /************* Waves Concatenation ***************/
2244:
2245: 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)
2246: {
2247: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2248: Death is a valid wave (if date is known).
2249: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2250: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2251: and mw[mi+1][i]. dh depends on stepm.
2252: */
2253:
2254: int i, mi, m;
2255: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2256: double sum=0., jmean=0.;*/
2257: int first;
2258: int j, k=0,jk, ju, jl;
2259: double sum=0.;
2260: first=0;
2261: jmin=1e+5;
2262: jmax=-1;
2263: jmean=0.;
2264: for(i=1; i<=imx; i++){
2265: mi=0;
2266: m=firstpass;
2267: while(s[m][i] <= nlstate){
2268: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2269: mw[++mi][i]=m;
2270: if(m >=lastpass)
2271: break;
2272: else
2273: m++;
2274: }/* end while */
2275: if (s[m][i] > nlstate){
2276: mi++; /* Death is another wave */
2277: /* if(mi==0) never been interviewed correctly before death */
2278: /* Only death is a correct wave */
2279: mw[mi][i]=m;
2280: }
2281:
2282: wav[i]=mi;
2283: if(mi==0){
2284: nbwarn++;
2285: if(first==0){
2286: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2287: first=1;
2288: }
2289: if(first==1){
2290: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2291: }
2292: } /* end mi==0 */
2293: } /* End individuals */
2294:
2295: for(i=1; i<=imx; i++){
2296: for(mi=1; mi<wav[i];mi++){
2297: if (stepm <=0)
2298: dh[mi][i]=1;
2299: else{
2300: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2301: if (agedc[i] < 2*AGESUP) {
2302: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2303: if(j==0) j=1; /* Survives at least one month after exam */
2304: else if(j<0){
2305: nberr++;
2306: 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]);
2307: j=1; /* Temporary Dangerous patch */
2308: 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);
2309: 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]);
2310: 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);
2311: }
2312: k=k+1;
2313: if (j >= jmax){
2314: jmax=j;
2315: ijmax=i;
2316: }
2317: if (j <= jmin){
2318: jmin=j;
2319: ijmin=i;
2320: }
2321: sum=sum+j;
2322: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2323: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2324: }
2325: }
2326: else{
2327: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2328: /* 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]); */
2329:
2330: k=k+1;
2331: if (j >= jmax) {
2332: jmax=j;
2333: ijmax=i;
2334: }
2335: else if (j <= jmin){
2336: jmin=j;
2337: ijmin=i;
2338: }
2339: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2340: /*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]);*/
2341: if(j<0){
2342: nberr++;
2343: 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]);
2344: 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]);
2345: }
2346: sum=sum+j;
2347: }
2348: jk= j/stepm;
2349: jl= j -jk*stepm;
2350: ju= j -(jk+1)*stepm;
2351: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2352: if(jl==0){
2353: dh[mi][i]=jk;
2354: bh[mi][i]=0;
2355: }else{ /* We want a negative bias in order to only have interpolation ie
2356: * at the price of an extra matrix product in likelihood */
2357: dh[mi][i]=jk+1;
2358: bh[mi][i]=ju;
2359: }
2360: }else{
2361: if(jl <= -ju){
2362: dh[mi][i]=jk;
2363: bh[mi][i]=jl; /* bias is positive if real duration
2364: * is higher than the multiple of stepm and negative otherwise.
2365: */
2366: }
2367: else{
2368: dh[mi][i]=jk+1;
2369: bh[mi][i]=ju;
2370: }
2371: if(dh[mi][i]==0){
2372: dh[mi][i]=1; /* At least one step */
2373: bh[mi][i]=ju; /* At least one step */
2374: /* 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);*/
2375: }
2376: } /* end if mle */
2377: }
2378: } /* end wave */
2379: }
2380: jmean=sum/k;
2381: 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);
2382: fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
2383: }
2384:
2385: /*********** Tricode ****************************/
2386: void tricode(int *Tvar, int **nbcode, int imx)
2387: {
2388:
2389: int Ndum[20],ij=1, k, j, i, maxncov=19;
2390: int cptcode=0;
2391: cptcoveff=0;
2392:
2393: for (k=0; k<maxncov; k++) Ndum[k]=0;
2394: for (k=1; k<=7; k++) ncodemax[k]=0;
2395:
2396: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
2397: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2398: modality*/
2399: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2400: Ndum[ij]++; /*store the modality */
2401: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2402: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2403: Tvar[j]. If V=sex and male is 0 and
2404: female is 1, then cptcode=1.*/
2405: }
2406:
2407: for (i=0; i<=cptcode; i++) {
2408: if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
2409: }
2410:
2411: ij=1;
2412: for (i=1; i<=ncodemax[j]; i++) {
2413: for (k=0; k<= maxncov; k++) {
2414: if (Ndum[k] != 0) {
2415: nbcode[Tvar[j]][ij]=k;
2416: /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
2417:
2418: ij++;
2419: }
2420: if (ij > ncodemax[j]) break;
2421: }
2422: }
2423: }
2424:
2425: for (k=0; k< maxncov; k++) Ndum[k]=0;
2426:
2427: for (i=1; i<=ncovmodel-2; i++) {
2428: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2429: ij=Tvar[i];
2430: Ndum[ij]++;
2431: }
2432:
2433: ij=1;
2434: for (i=1; i<= maxncov; i++) {
2435: if((Ndum[i]!=0) && (i<=ncovcol)){
2436: Tvaraff[ij]=i; /*For printing */
2437: ij++;
2438: }
2439: }
2440:
2441: cptcoveff=ij-1; /*Number of simple covariates*/
2442: }
2443:
2444: /*********** Health Expectancies ****************/
2445:
2446: void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
2447:
2448: {
2449: /* Health expectancies, no variances */
2450: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
2451: double age, agelim, hf;
2452: double ***p3mat;
2453: double eip;
2454:
2455: pstamp(ficreseij);
2456: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
2457: fprintf(ficreseij,"# Age");
2458: for(i=1; i<=nlstate;i++){
2459: for(j=1; j<=nlstate;j++){
2460: fprintf(ficreseij," e%1d%1d ",i,j);
2461: }
2462: fprintf(ficreseij," e%1d. ",i);
2463: }
2464: fprintf(ficreseij,"\n");
2465:
2466:
2467: if(estepm < stepm){
2468: printf ("Problem %d lower than %d\n",estepm, stepm);
2469: }
2470: else hstepm=estepm;
2471: /* We compute the life expectancy from trapezoids spaced every estepm months
2472: * This is mainly to measure the difference between two models: for example
2473: * if stepm=24 months pijx are given only every 2 years and by summing them
2474: * we are calculating an estimate of the Life Expectancy assuming a linear
2475: * progression in between and thus overestimating or underestimating according
2476: * to the curvature of the survival function. If, for the same date, we
2477: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2478: * to compare the new estimate of Life expectancy with the same linear
2479: * hypothesis. A more precise result, taking into account a more precise
2480: * curvature will be obtained if estepm is as small as stepm. */
2481:
2482: /* For example we decided to compute the life expectancy with the smallest unit */
2483: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2484: nhstepm is the number of hstepm from age to agelim
2485: nstepm is the number of stepm from age to agelin.
2486: Look at hpijx to understand the reason of that which relies in memory size
2487: and note for a fixed period like estepm months */
2488: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2489: survival function given by stepm (the optimization length). Unfortunately it
2490: means that if the survival funtion is printed only each two years of age and if
2491: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2492: results. So we changed our mind and took the option of the best precision.
2493: */
2494: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2495:
2496: agelim=AGESUP;
2497: /* nhstepm age range expressed in number of stepm */
2498: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2499: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2500: /* if (stepm >= YEARM) hstepm=1;*/
2501: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2502: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2503:
2504: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2505: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2506: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2507:
2508: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2509:
2510: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2511:
2512: printf("%d|",(int)age);fflush(stdout);
2513: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2514:
2515: /* Computing expectancies */
2516: for(i=1; i<=nlstate;i++)
2517: for(j=1; j<=nlstate;j++)
2518: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2519: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2520:
2521: /* 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]);*/
2522:
2523: }
2524:
2525: fprintf(ficreseij,"%3.0f",age );
2526: for(i=1; i<=nlstate;i++){
2527: eip=0;
2528: for(j=1; j<=nlstate;j++){
2529: eip +=eij[i][j][(int)age];
2530: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
2531: }
2532: fprintf(ficreseij,"%9.4f", eip );
2533: }
2534: fprintf(ficreseij,"\n");
2535:
2536: }
2537: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2538: printf("\n");
2539: fprintf(ficlog,"\n");
2540:
2541: }
2542:
2543: void cvevsij(char fileres[], 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[] )
2544:
2545: {
2546: /* Covariances of health expectancies eij and of total life expectancies according
2547: to initial status i, ei. .
2548: */
2549: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
2550: double age, agelim, hf;
2551: double ***p3matp, ***p3matm, ***varhe;
2552: double **dnewm,**doldm;
2553: double *xp, *xm;
2554: double **gp, **gm;
2555: double ***gradg, ***trgradg;
2556: int theta;
2557:
2558: double eip, vip;
2559:
2560: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2561: xp=vector(1,npar);
2562: xm=vector(1,npar);
2563: dnewm=matrix(1,nlstate*nlstate,1,npar);
2564: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2565:
2566: pstamp(ficresstdeij);
2567: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
2568: fprintf(ficresstdeij,"# Age");
2569: for(i=1; i<=nlstate;i++){
2570: for(j=1; j<=nlstate;j++)
2571: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
2572: fprintf(ficresstdeij," e%1d. ",i);
2573: }
2574: fprintf(ficresstdeij,"\n");
2575:
2576: pstamp(ficrescveij);
2577: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
2578: fprintf(ficrescveij,"# Age");
2579: for(i=1; i<=nlstate;i++)
2580: for(j=1; j<=nlstate;j++){
2581: cptj= (j-1)*nlstate+i;
2582: for(i2=1; i2<=nlstate;i2++)
2583: for(j2=1; j2<=nlstate;j2++){
2584: cptj2= (j2-1)*nlstate+i2;
2585: if(cptj2 <= cptj)
2586: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
2587: }
2588: }
2589: fprintf(ficrescveij,"\n");
2590:
2591: if(estepm < stepm){
2592: printf ("Problem %d lower than %d\n",estepm, stepm);
2593: }
2594: else hstepm=estepm;
2595: /* We compute the life expectancy from trapezoids spaced every estepm months
2596: * This is mainly to measure the difference between two models: for example
2597: * if stepm=24 months pijx are given only every 2 years and by summing them
2598: * we are calculating an estimate of the Life Expectancy assuming a linear
2599: * progression in between and thus overestimating or underestimating according
2600: * to the curvature of the survival function. If, for the same date, we
2601: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2602: * to compare the new estimate of Life expectancy with the same linear
2603: * hypothesis. A more precise result, taking into account a more precise
2604: * curvature will be obtained if estepm is as small as stepm. */
2605:
2606: /* For example we decided to compute the life expectancy with the smallest unit */
2607: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2608: nhstepm is the number of hstepm from age to agelim
2609: nstepm is the number of stepm from age to agelin.
2610: Look at hpijx to understand the reason of that which relies in memory size
2611: and note for a fixed period like estepm months */
2612: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2613: survival function given by stepm (the optimization length). Unfortunately it
2614: means that if the survival funtion is printed only each two years of age and if
2615: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2616: results. So we changed our mind and took the option of the best precision.
2617: */
2618: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2619:
2620: /* If stepm=6 months */
2621: /* nhstepm age range expressed in number of stepm */
2622: agelim=AGESUP;
2623: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2624: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2625: /* if (stepm >= YEARM) hstepm=1;*/
2626: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2627:
2628: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2629: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2630: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2631: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2632: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2633: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2634:
2635: for (age=bage; age<=fage; age ++){
2636:
2637: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2638: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2639:
2640: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2641:
2642: /* Computing Variances of health expectancies */
2643: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
2644: decrease memory allocation */
2645: for(theta=1; theta <=npar; theta++){
2646: for(i=1; i<=npar; i++){
2647: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2648: xm[i] = x[i] - (i==theta ?delti[theta]:0);
2649: }
2650: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
2651: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
2652:
2653: for(j=1; j<= nlstate; j++){
2654: for(i=1; i<=nlstate; i++){
2655: for(h=0; h<=nhstepm-1; h++){
2656: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
2657: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
2658: }
2659: }
2660: }
2661:
2662: for(ij=1; ij<= nlstate*nlstate; ij++)
2663: for(h=0; h<=nhstepm-1; h++){
2664: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
2665: }
2666: }/* End theta */
2667:
2668:
2669: for(h=0; h<=nhstepm-1; h++)
2670: for(j=1; j<=nlstate*nlstate;j++)
2671: for(theta=1; theta <=npar; theta++)
2672: trgradg[h][j][theta]=gradg[h][theta][j];
2673:
2674:
2675: for(ij=1;ij<=nlstate*nlstate;ij++)
2676: for(ji=1;ji<=nlstate*nlstate;ji++)
2677: varhe[ij][ji][(int)age] =0.;
2678:
2679: printf("%d|",(int)age);fflush(stdout);
2680: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2681: for(h=0;h<=nhstepm-1;h++){
2682: for(k=0;k<=nhstepm-1;k++){
2683: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2684: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2685: for(ij=1;ij<=nlstate*nlstate;ij++)
2686: for(ji=1;ji<=nlstate*nlstate;ji++)
2687: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
2688: }
2689: }
2690: /* Computing expectancies */
2691: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2692: for(i=1; i<=nlstate;i++)
2693: for(j=1; j<=nlstate;j++)
2694: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2695: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
2696:
2697: /* 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]);*/
2698:
2699: }
2700:
2701: fprintf(ficresstdeij,"%3.0f",age );
2702: for(i=1; i<=nlstate;i++){
2703: eip=0.;
2704: vip=0.;
2705: for(j=1; j<=nlstate;j++){
2706: eip += eij[i][j][(int)age];
2707: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
2708: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
2709: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
2710: }
2711: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
2712: }
2713: fprintf(ficresstdeij,"\n");
2714:
2715: fprintf(ficrescveij,"%3.0f",age );
2716: for(i=1; i<=nlstate;i++)
2717: for(j=1; j<=nlstate;j++){
2718: cptj= (j-1)*nlstate+i;
2719: for(i2=1; i2<=nlstate;i2++)
2720: for(j2=1; j2<=nlstate;j2++){
2721: cptj2= (j2-1)*nlstate+i2;
2722: if(cptj2 <= cptj)
2723: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
2724: }
2725: }
2726: fprintf(ficrescveij,"\n");
2727:
2728: }
2729: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2730: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2731: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2732: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2733: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2734: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2735: printf("\n");
2736: fprintf(ficlog,"\n");
2737:
2738: free_vector(xm,1,npar);
2739: free_vector(xp,1,npar);
2740: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2741: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2742: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2743: }
2744:
2745: /************ Variance ******************/
2746: 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[])
2747: {
2748: /* Variance of health expectancies */
2749: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2750: /* double **newm;*/
2751: double **dnewm,**doldm;
2752: double **dnewmp,**doldmp;
2753: int i, j, nhstepm, hstepm, h, nstepm ;
2754: int k, cptcode;
2755: double *xp;
2756: double **gp, **gm; /* for var eij */
2757: double ***gradg, ***trgradg; /*for var eij */
2758: double **gradgp, **trgradgp; /* for var p point j */
2759: double *gpp, *gmp; /* for var p point j */
2760: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2761: double ***p3mat;
2762: double age,agelim, hf;
2763: double ***mobaverage;
2764: int theta;
2765: char digit[4];
2766: char digitp[25];
2767:
2768: char fileresprobmorprev[FILENAMELENGTH];
2769:
2770: if(popbased==1){
2771: if(mobilav!=0)
2772: strcpy(digitp,"-populbased-mobilav-");
2773: else strcpy(digitp,"-populbased-nomobil-");
2774: }
2775: else
2776: strcpy(digitp,"-stablbased-");
2777:
2778: if (mobilav!=0) {
2779: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2780: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2781: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2782: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2783: }
2784: }
2785:
2786: strcpy(fileresprobmorprev,"prmorprev");
2787: sprintf(digit,"%-d",ij);
2788: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2789: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2790: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2791: strcat(fileresprobmorprev,fileres);
2792: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2793: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2794: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2795: }
2796: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2797:
2798: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2799: pstamp(ficresprobmorprev);
2800: 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);
2801: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2802: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2803: fprintf(ficresprobmorprev," p.%-d SE",j);
2804: for(i=1; i<=nlstate;i++)
2805: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2806: }
2807: fprintf(ficresprobmorprev,"\n");
2808: fprintf(ficgp,"\n# Routine varevsij");
2809: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
2810: 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");
2811: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2812: /* } */
2813: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2814: pstamp(ficresvij);
2815: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
2816: if(popbased==1)
2817: fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
2818: else
2819: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
2820: fprintf(ficresvij,"# Age");
2821: for(i=1; i<=nlstate;i++)
2822: for(j=1; j<=nlstate;j++)
2823: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
2824: fprintf(ficresvij,"\n");
2825:
2826: xp=vector(1,npar);
2827: dnewm=matrix(1,nlstate,1,npar);
2828: doldm=matrix(1,nlstate,1,nlstate);
2829: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2830: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2831:
2832: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2833: gpp=vector(nlstate+1,nlstate+ndeath);
2834: gmp=vector(nlstate+1,nlstate+ndeath);
2835: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2836:
2837: if(estepm < stepm){
2838: printf ("Problem %d lower than %d\n",estepm, stepm);
2839: }
2840: else hstepm=estepm;
2841: /* For example we decided to compute the life expectancy with the smallest unit */
2842: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2843: nhstepm is the number of hstepm from age to agelim
2844: nstepm is the number of stepm from age to agelin.
2845: Look at hpijx to understand the reason of that which relies in memory size
2846: and note for a fixed period like k years */
2847: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2848: survival function given by stepm (the optimization length). Unfortunately it
2849: means that if the survival funtion is printed every two years of age and if
2850: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2851: results. So we changed our mind and took the option of the best precision.
2852: */
2853: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2854: agelim = AGESUP;
2855: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2856: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2857: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2858: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2859: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2860: gp=matrix(0,nhstepm,1,nlstate);
2861: gm=matrix(0,nhstepm,1,nlstate);
2862:
2863:
2864: for(theta=1; theta <=npar; theta++){
2865: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2866: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2867: }
2868: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2869: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2870:
2871: if (popbased==1) {
2872: if(mobilav ==0){
2873: for(i=1; i<=nlstate;i++)
2874: prlim[i][i]=probs[(int)age][i][ij];
2875: }else{ /* mobilav */
2876: for(i=1; i<=nlstate;i++)
2877: prlim[i][i]=mobaverage[(int)age][i][ij];
2878: }
2879: }
2880:
2881: for(j=1; j<= nlstate; j++){
2882: for(h=0; h<=nhstepm; h++){
2883: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2884: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2885: }
2886: }
2887: /* This for computing probability of death (h=1 means
2888: computed over hstepm matrices product = hstepm*stepm months)
2889: as a weighted average of prlim.
2890: */
2891: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2892: for(i=1,gpp[j]=0.; i<= nlstate; i++)
2893: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2894: }
2895: /* end probability of death */
2896:
2897: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
2898: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2899: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2900: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2901:
2902: if (popbased==1) {
2903: if(mobilav ==0){
2904: for(i=1; i<=nlstate;i++)
2905: prlim[i][i]=probs[(int)age][i][ij];
2906: }else{ /* mobilav */
2907: for(i=1; i<=nlstate;i++)
2908: prlim[i][i]=mobaverage[(int)age][i][ij];
2909: }
2910: }
2911:
2912: for(j=1; j<= nlstate; j++){
2913: for(h=0; h<=nhstepm; h++){
2914: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2915: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2916: }
2917: }
2918: /* This for computing probability of death (h=1 means
2919: computed over hstepm matrices product = hstepm*stepm months)
2920: as a weighted average of prlim.
2921: */
2922: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2923: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2924: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2925: }
2926: /* end probability of death */
2927:
2928: for(j=1; j<= nlstate; j++) /* vareij */
2929: for(h=0; h<=nhstepm; h++){
2930: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2931: }
2932:
2933: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2934: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2935: }
2936:
2937: } /* End theta */
2938:
2939: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2940:
2941: for(h=0; h<=nhstepm; h++) /* veij */
2942: for(j=1; j<=nlstate;j++)
2943: for(theta=1; theta <=npar; theta++)
2944: trgradg[h][j][theta]=gradg[h][theta][j];
2945:
2946: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
2947: for(theta=1; theta <=npar; theta++)
2948: trgradgp[j][theta]=gradgp[theta][j];
2949:
2950:
2951: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2952: for(i=1;i<=nlstate;i++)
2953: for(j=1;j<=nlstate;j++)
2954: vareij[i][j][(int)age] =0.;
2955:
2956: for(h=0;h<=nhstepm;h++){
2957: for(k=0;k<=nhstepm;k++){
2958: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2959: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2960: for(i=1;i<=nlstate;i++)
2961: for(j=1;j<=nlstate;j++)
2962: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2963: }
2964: }
2965:
2966: /* pptj */
2967: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2968: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
2969: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2970: for(i=nlstate+1;i<=nlstate+ndeath;i++)
2971: varppt[j][i]=doldmp[j][i];
2972: /* end ppptj */
2973: /* x centered again */
2974: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2975: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2976:
2977: if (popbased==1) {
2978: if(mobilav ==0){
2979: for(i=1; i<=nlstate;i++)
2980: prlim[i][i]=probs[(int)age][i][ij];
2981: }else{ /* mobilav */
2982: for(i=1; i<=nlstate;i++)
2983: prlim[i][i]=mobaverage[(int)age][i][ij];
2984: }
2985: }
2986:
2987: /* This for computing probability of death (h=1 means
2988: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2989: as a weighted average of prlim.
2990: */
2991: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2992: for(i=1,gmp[j]=0.;i<= nlstate; i++)
2993: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2994: }
2995: /* end probability of death */
2996:
2997: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2998: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2999: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3000: for(i=1; i<=nlstate;i++){
3001: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3002: }
3003: }
3004: fprintf(ficresprobmorprev,"\n");
3005:
3006: fprintf(ficresvij,"%.0f ",age );
3007: for(i=1; i<=nlstate;i++)
3008: for(j=1; j<=nlstate;j++){
3009: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3010: }
3011: fprintf(ficresvij,"\n");
3012: free_matrix(gp,0,nhstepm,1,nlstate);
3013: free_matrix(gm,0,nhstepm,1,nlstate);
3014: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3015: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3016: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3017: } /* End age */
3018: free_vector(gpp,nlstate+1,nlstate+ndeath);
3019: free_vector(gmp,nlstate+1,nlstate+ndeath);
3020: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3021: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3022: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
3023: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3024: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3025: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3026: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3027: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3028: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
3029: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
3030: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
3031: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3032: 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);
3033: /* 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);
3034: */
3035: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3036: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3037:
3038: free_vector(xp,1,npar);
3039: free_matrix(doldm,1,nlstate,1,nlstate);
3040: free_matrix(dnewm,1,nlstate,1,npar);
3041: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3042: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3043: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3044: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3045: fclose(ficresprobmorprev);
3046: fflush(ficgp);
3047: fflush(fichtm);
3048: } /* end varevsij */
3049:
3050: /************ Variance of prevlim ******************/
3051: 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[])
3052: {
3053: /* Variance of prevalence limit */
3054: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3055: double **newm;
3056: double **dnewm,**doldm;
3057: int i, j, nhstepm, hstepm;
3058: int k, cptcode;
3059: double *xp;
3060: double *gp, *gm;
3061: double **gradg, **trgradg;
3062: double age,agelim;
3063: int theta;
3064:
3065: pstamp(ficresvpl);
3066: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3067: fprintf(ficresvpl,"# Age");
3068: for(i=1; i<=nlstate;i++)
3069: fprintf(ficresvpl," %1d-%1d",i,i);
3070: fprintf(ficresvpl,"\n");
3071:
3072: xp=vector(1,npar);
3073: dnewm=matrix(1,nlstate,1,npar);
3074: doldm=matrix(1,nlstate,1,nlstate);
3075:
3076: hstepm=1*YEARM; /* Every year of age */
3077: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3078: agelim = AGESUP;
3079: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3080: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3081: if (stepm >= YEARM) hstepm=1;
3082: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3083: gradg=matrix(1,npar,1,nlstate);
3084: gp=vector(1,nlstate);
3085: gm=vector(1,nlstate);
3086:
3087: for(theta=1; theta <=npar; theta++){
3088: for(i=1; i<=npar; i++){ /* Computes gradient */
3089: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3090: }
3091: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3092: for(i=1;i<=nlstate;i++)
3093: gp[i] = prlim[i][i];
3094:
3095: for(i=1; i<=npar; i++) /* Computes gradient */
3096: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3097: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3098: for(i=1;i<=nlstate;i++)
3099: gm[i] = prlim[i][i];
3100:
3101: for(i=1;i<=nlstate;i++)
3102: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3103: } /* End theta */
3104:
3105: trgradg =matrix(1,nlstate,1,npar);
3106:
3107: for(j=1; j<=nlstate;j++)
3108: for(theta=1; theta <=npar; theta++)
3109: trgradg[j][theta]=gradg[theta][j];
3110:
3111: for(i=1;i<=nlstate;i++)
3112: varpl[i][(int)age] =0.;
3113: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3114: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3115: for(i=1;i<=nlstate;i++)
3116: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3117:
3118: fprintf(ficresvpl,"%.0f ",age );
3119: for(i=1; i<=nlstate;i++)
3120: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3121: fprintf(ficresvpl,"\n");
3122: free_vector(gp,1,nlstate);
3123: free_vector(gm,1,nlstate);
3124: free_matrix(gradg,1,npar,1,nlstate);
3125: free_matrix(trgradg,1,nlstate,1,npar);
3126: } /* End age */
3127:
3128: free_vector(xp,1,npar);
3129: free_matrix(doldm,1,nlstate,1,npar);
3130: free_matrix(dnewm,1,nlstate,1,nlstate);
3131:
3132: }
3133:
3134: /************ Variance of one-step probabilities ******************/
3135: 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[])
3136: {
3137: int i, j=0, i1, k1, l1, t, tj;
3138: int k2, l2, j1, z1;
3139: int k=0,l, cptcode;
3140: int first=1, first1;
3141: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3142: double **dnewm,**doldm;
3143: double *xp;
3144: double *gp, *gm;
3145: double **gradg, **trgradg;
3146: double **mu;
3147: double age,agelim, cov[NCOVMAX];
3148: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3149: int theta;
3150: char fileresprob[FILENAMELENGTH];
3151: char fileresprobcov[FILENAMELENGTH];
3152: char fileresprobcor[FILENAMELENGTH];
3153:
3154: double ***varpij;
3155:
3156: strcpy(fileresprob,"prob");
3157: strcat(fileresprob,fileres);
3158: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3159: printf("Problem with resultfile: %s\n", fileresprob);
3160: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3161: }
3162: strcpy(fileresprobcov,"probcov");
3163: strcat(fileresprobcov,fileres);
3164: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3165: printf("Problem with resultfile: %s\n", fileresprobcov);
3166: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3167: }
3168: strcpy(fileresprobcor,"probcor");
3169: strcat(fileresprobcor,fileres);
3170: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3171: printf("Problem with resultfile: %s\n", fileresprobcor);
3172: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3173: }
3174: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3175: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3176: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3177: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3178: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3179: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3180: pstamp(ficresprob);
3181: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3182: fprintf(ficresprob,"# Age");
3183: pstamp(ficresprobcov);
3184: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3185: fprintf(ficresprobcov,"# Age");
3186: pstamp(ficresprobcor);
3187: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3188: fprintf(ficresprobcor,"# Age");
3189:
3190:
3191: for(i=1; i<=nlstate;i++)
3192: for(j=1; j<=(nlstate+ndeath);j++){
3193: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3194: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3195: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3196: }
3197: /* fprintf(ficresprob,"\n");
3198: fprintf(ficresprobcov,"\n");
3199: fprintf(ficresprobcor,"\n");
3200: */
3201: xp=vector(1,npar);
3202: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3203: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3204: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3205: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3206: first=1;
3207: fprintf(ficgp,"\n# Routine varprob");
3208: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3209: fprintf(fichtm,"\n");
3210:
3211: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3212: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3213: file %s<br>\n",optionfilehtmcov);
3214: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3215: and drawn. It helps understanding how is the covariance between two incidences.\
3216: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3217: 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. \
3218: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3219: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3220: standard deviations wide on each axis. <br>\
3221: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3222: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3223: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3224:
3225: cov[1]=1;
3226: tj=cptcoveff;
3227: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3228: j1=0;
3229: for(t=1; t<=tj;t++){
3230: for(i1=1; i1<=ncodemax[t];i1++){
3231: j1++;
3232: if (cptcovn>0) {
3233: fprintf(ficresprob, "\n#********** Variable ");
3234: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3235: fprintf(ficresprob, "**********\n#\n");
3236: fprintf(ficresprobcov, "\n#********** Variable ");
3237: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3238: fprintf(ficresprobcov, "**********\n#\n");
3239:
3240: fprintf(ficgp, "\n#********** Variable ");
3241: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3242: fprintf(ficgp, "**********\n#\n");
3243:
3244:
3245: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3246: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3247: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3248:
3249: fprintf(ficresprobcor, "\n#********** Variable ");
3250: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3251: fprintf(ficresprobcor, "**********\n#");
3252: }
3253:
3254: for (age=bage; age<=fage; age ++){
3255: cov[2]=age;
3256: for (k=1; k<=cptcovn;k++) {
3257: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3258: }
3259: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3260: for (k=1; k<=cptcovprod;k++)
3261: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3262:
3263: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3264: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3265: gp=vector(1,(nlstate)*(nlstate+ndeath));
3266: gm=vector(1,(nlstate)*(nlstate+ndeath));
3267:
3268: for(theta=1; theta <=npar; theta++){
3269: for(i=1; i<=npar; i++)
3270: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3271:
3272: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3273:
3274: k=0;
3275: for(i=1; i<= (nlstate); i++){
3276: for(j=1; j<=(nlstate+ndeath);j++){
3277: k=k+1;
3278: gp[k]=pmmij[i][j];
3279: }
3280: }
3281:
3282: for(i=1; i<=npar; i++)
3283: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3284:
3285: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3286: k=0;
3287: for(i=1; i<=(nlstate); i++){
3288: for(j=1; j<=(nlstate+ndeath);j++){
3289: k=k+1;
3290: gm[k]=pmmij[i][j];
3291: }
3292: }
3293:
3294: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3295: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3296: }
3297:
3298: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3299: for(theta=1; theta <=npar; theta++)
3300: trgradg[j][theta]=gradg[theta][j];
3301:
3302: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3303: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3304: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3305: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3306: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3307: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3308:
3309: pmij(pmmij,cov,ncovmodel,x,nlstate);
3310:
3311: k=0;
3312: for(i=1; i<=(nlstate); i++){
3313: for(j=1; j<=(nlstate+ndeath);j++){
3314: k=k+1;
3315: mu[k][(int) age]=pmmij[i][j];
3316: }
3317: }
3318: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3319: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3320: varpij[i][j][(int)age] = doldm[i][j];
3321:
3322: /*printf("\n%d ",(int)age);
3323: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3324: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3325: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3326: }*/
3327:
3328: fprintf(ficresprob,"\n%d ",(int)age);
3329: fprintf(ficresprobcov,"\n%d ",(int)age);
3330: fprintf(ficresprobcor,"\n%d ",(int)age);
3331:
3332: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3333: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3334: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3335: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3336: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3337: }
3338: i=0;
3339: for (k=1; k<=(nlstate);k++){
3340: for (l=1; l<=(nlstate+ndeath);l++){
3341: i=i++;
3342: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3343: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3344: for (j=1; j<=i;j++){
3345: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3346: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3347: }
3348: }
3349: }/* end of loop for state */
3350: } /* end of loop for age */
3351:
3352: /* Confidence intervalle of pij */
3353: /*
3354: fprintf(ficgp,"\nset noparametric;unset label");
3355: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3356: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3357: 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);
3358: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3359: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3360: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3361: */
3362:
3363: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3364: first1=1;
3365: for (k2=1; k2<=(nlstate);k2++){
3366: for (l2=1; l2<=(nlstate+ndeath);l2++){
3367: if(l2==k2) continue;
3368: j=(k2-1)*(nlstate+ndeath)+l2;
3369: for (k1=1; k1<=(nlstate);k1++){
3370: for (l1=1; l1<=(nlstate+ndeath);l1++){
3371: if(l1==k1) continue;
3372: i=(k1-1)*(nlstate+ndeath)+l1;
3373: if(i<=j) continue;
3374: for (age=bage; age<=fage; age ++){
3375: if ((int)age %5==0){
3376: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3377: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3378: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3379: mu1=mu[i][(int) age]/stepm*YEARM ;
3380: mu2=mu[j][(int) age]/stepm*YEARM;
3381: c12=cv12/sqrt(v1*v2);
3382: /* Computing eigen value of matrix of covariance */
3383: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3384: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3385: /* Eigen vectors */
3386: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3387: /*v21=sqrt(1.-v11*v11); *//* error */
3388: v21=(lc1-v1)/cv12*v11;
3389: v12=-v21;
3390: v22=v11;
3391: tnalp=v21/v11;
3392: if(first1==1){
3393: first1=0;
3394: 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);
3395: }
3396: 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);
3397: /*printf(fignu*/
3398: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3399: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3400: if(first==1){
3401: first=0;
3402: fprintf(ficgp,"\nset parametric;unset label");
3403: 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);
3404: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3405: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3406: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3407: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3408: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3409: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3410: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3411: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3412: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3413: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3414: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3415: 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",\
3416: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3417: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3418: }else{
3419: first=0;
3420: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3421: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3422: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3423: 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",\
3424: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3425: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3426: }/* if first */
3427: } /* age mod 5 */
3428: } /* end loop age */
3429: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3430: first=1;
3431: } /*l12 */
3432: } /* k12 */
3433: } /*l1 */
3434: }/* k1 */
3435: } /* loop covariates */
3436: }
3437: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3438: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3439: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3440: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
3441: free_vector(xp,1,npar);
3442: fclose(ficresprob);
3443: fclose(ficresprobcov);
3444: fclose(ficresprobcor);
3445: fflush(ficgp);
3446: fflush(fichtmcov);
3447: }
3448:
3449:
3450: /******************* Printing html file ***********/
3451: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3452: int lastpass, int stepm, int weightopt, char model[],\
3453: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3454: int popforecast, int estepm ,\
3455: double jprev1, double mprev1,double anprev1, \
3456: double jprev2, double mprev2,double anprev2){
3457: int jj1, k1, i1, cpt;
3458:
3459: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3460: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3461: </ul>");
3462: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3463: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3464: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3465: fprintf(fichtm,"\
3466: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3467: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3468: fprintf(fichtm,"\
3469: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3470: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3471: fprintf(fichtm,"\
3472: - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age: ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
3473: <a href=\"%s\">%s</a> <br>\n</li>",
3474: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3475:
3476:
3477: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3478:
3479: m=cptcoveff;
3480: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3481:
3482: jj1=0;
3483: for(k1=1; k1<=m;k1++){
3484: for(i1=1; i1<=ncodemax[k1];i1++){
3485: jj1++;
3486: if (cptcovn > 0) {
3487: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3488: for (cpt=1; cpt<=cptcoveff;cpt++)
3489: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3490: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3491: }
3492: /* Pij */
3493: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
3494: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3495: /* Quasi-incidences */
3496: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3497: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
3498: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3499: /* Period (stable) prevalence in each health state */
3500: for(cpt=1; cpt<nlstate;cpt++){
3501: fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
3502: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3503: }
3504: for(cpt=1; cpt<=nlstate;cpt++) {
3505: fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
3506: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3507: }
3508: } /* end i1 */
3509: }/* End k1 */
3510: fprintf(fichtm,"</ul>");
3511:
3512:
3513: fprintf(fichtm,"\
3514: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3515: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3516:
3517: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3518: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3519: fprintf(fichtm,"\
3520: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3521: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3522:
3523: fprintf(fichtm,"\
3524: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3525: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3526: fprintf(fichtm,"\
3527: - 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): \
3528: <a href=\"%s\">%s</a> <br>\n</li>",
3529: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
3530: fprintf(fichtm,"\
3531: - (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): \
3532: <a href=\"%s\">%s</a> <br>\n</li>",
3533: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
3534: fprintf(fichtm,"\
3535: - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij 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",
3536: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3537: fprintf(fichtm,"\
3538: - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
3539: subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3540: fprintf(fichtm,"\
3541: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
3542: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3543:
3544: /* if(popforecast==1) fprintf(fichtm,"\n */
3545: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3546: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3547: /* <br>",fileres,fileres,fileres,fileres); */
3548: /* else */
3549: /* 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); */
3550: fflush(fichtm);
3551: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3552:
3553: m=cptcoveff;
3554: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3555:
3556: jj1=0;
3557: for(k1=1; k1<=m;k1++){
3558: for(i1=1; i1<=ncodemax[k1];i1++){
3559: jj1++;
3560: if (cptcovn > 0) {
3561: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3562: for (cpt=1; cpt<=cptcoveff;cpt++)
3563: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3564: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3565: }
3566: for(cpt=1; cpt<=nlstate;cpt++) {
3567: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3568: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
3569: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3570: }
3571: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3572: health expectancies in states (1) and (2): %s%d.png<br>\
3573: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3574: } /* end i1 */
3575: }/* End k1 */
3576: fprintf(fichtm,"</ul>");
3577: fflush(fichtm);
3578: }
3579:
3580: /******************* Gnuplot file **************/
3581: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3582:
3583: char dirfileres[132],optfileres[132];
3584: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3585: int ng;
3586: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3587: /* printf("Problem with file %s",optionfilegnuplot); */
3588: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3589: /* } */
3590:
3591: /*#ifdef windows */
3592: fprintf(ficgp,"cd \"%s\" \n",pathc);
3593: /*#endif */
3594: m=pow(2,cptcoveff);
3595:
3596: strcpy(dirfileres,optionfilefiname);
3597: strcpy(optfileres,"vpl");
3598: /* 1eme*/
3599: for (cpt=1; cpt<= nlstate ; cpt ++) {
3600: for (k1=1; k1<= m ; k1 ++) {
3601: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3602: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3603: fprintf(ficgp,"set xlabel \"Age\" \n\
3604: set ylabel \"Probability\" \n\
3605: set ter png small\n\
3606: set size 0.65,0.65\n\
3607: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3608:
3609: for (i=1; i<= nlstate ; i ++) {
3610: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3611: else fprintf(ficgp," \%%*lf (\%%*lf)");
3612: }
3613: fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3614: for (i=1; i<= nlstate ; i ++) {
3615: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3616: else fprintf(ficgp," \%%*lf (\%%*lf)");
3617: }
3618: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3619: for (i=1; i<= nlstate ; i ++) {
3620: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3621: else fprintf(ficgp," \%%*lf (\%%*lf)");
3622: }
3623: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
3624: }
3625: }
3626: /*2 eme*/
3627:
3628: for (k1=1; k1<= m ; k1 ++) {
3629: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
3630: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3631:
3632: for (i=1; i<= nlstate+1 ; i ++) {
3633: k=2*i;
3634: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3635: for (j=1; j<= nlstate+1 ; j ++) {
3636: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3637: else fprintf(ficgp," \%%*lf (\%%*lf)");
3638: }
3639: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3640: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3641: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3642: for (j=1; j<= nlstate+1 ; j ++) {
3643: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3644: else fprintf(ficgp," \%%*lf (\%%*lf)");
3645: }
3646: fprintf(ficgp,"\" t\"\" w l 0,");
3647: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3648: for (j=1; j<= nlstate+1 ; j ++) {
3649: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3650: else fprintf(ficgp," \%%*lf (\%%*lf)");
3651: }
3652: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3653: else fprintf(ficgp,"\" t\"\" w l 0,");
3654: }
3655: }
3656:
3657: /*3eme*/
3658:
3659: for (k1=1; k1<= m ; k1 ++) {
3660: for (cpt=1; cpt<= nlstate ; cpt ++) {
3661: /* k=2+nlstate*(2*cpt-2); */
3662: k=2+(nlstate+1)*(cpt-1);
3663: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3664: fprintf(ficgp,"set ter png small\n\
3665: set size 0.65,0.65\n\
3666: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
3667: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3668: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3669: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3670: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3671: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3672: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3673:
3674: */
3675: for (i=1; i< nlstate ; i ++) {
3676: 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);
3677: /* 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);*/
3678:
3679: }
3680: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
3681: }
3682: }
3683:
3684: /* CV preval stable (period) */
3685: for (k1=1; k1<= m ; k1 ++) {
3686: for (cpt=1; cpt<=nlstate ; cpt ++) {
3687: k=3;
3688: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3689: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3690: set ter png small\nset size 0.65,0.65\n\
3691: unset log y\n\
3692: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
3693:
3694: for (i=1; i< nlstate ; i ++)
3695: fprintf(ficgp,"+$%d",k+i+1);
3696: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3697:
3698: l=3+(nlstate+ndeath)*cpt;
3699: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
3700: for (i=1; i< nlstate ; i ++) {
3701: l=3+(nlstate+ndeath)*cpt;
3702: fprintf(ficgp,"+$%d",l+i+1);
3703: }
3704: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3705: }
3706: }
3707:
3708: /* proba elementaires */
3709: for(i=1,jk=1; i <=nlstate; i++){
3710: for(k=1; k <=(nlstate+ndeath); k++){
3711: if (k != i) {
3712: for(j=1; j <=ncovmodel; j++){
3713: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3714: jk++;
3715: fprintf(ficgp,"\n");
3716: }
3717: }
3718: }
3719: }
3720:
3721: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3722: for(jk=1; jk <=m; jk++) {
3723: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
3724: if (ng==2)
3725: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3726: else
3727: fprintf(ficgp,"\nset title \"Probability\"\n");
3728: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3729: i=1;
3730: for(k2=1; k2<=nlstate; k2++) {
3731: k3=i;
3732: for(k=1; k<=(nlstate+ndeath); k++) {
3733: if (k != k2){
3734: if(ng==2)
3735: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3736: else
3737: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3738: ij=1;
3739: for(j=3; j <=ncovmodel; j++) {
3740: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3741: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3742: ij++;
3743: }
3744: else
3745: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3746: }
3747: fprintf(ficgp,")/(1");
3748:
3749: for(k1=1; k1 <=nlstate; k1++){
3750: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3751: ij=1;
3752: for(j=3; j <=ncovmodel; j++){
3753: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3754: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3755: ij++;
3756: }
3757: else
3758: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3759: }
3760: fprintf(ficgp,")");
3761: }
3762: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3763: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3764: i=i+ncovmodel;
3765: }
3766: } /* end k */
3767: } /* end k2 */
3768: } /* end jk */
3769: } /* end ng */
3770: fflush(ficgp);
3771: } /* end gnuplot */
3772:
3773:
3774: /*************** Moving average **************/
3775: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3776:
3777: int i, cpt, cptcod;
3778: int modcovmax =1;
3779: int mobilavrange, mob;
3780: double age;
3781:
3782: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3783: a covariate has 2 modalities */
3784: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3785:
3786: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3787: if(mobilav==1) mobilavrange=5; /* default */
3788: else mobilavrange=mobilav;
3789: for (age=bage; age<=fage; age++)
3790: for (i=1; i<=nlstate;i++)
3791: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3792: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3793: /* We keep the original values on the extreme ages bage, fage and for
3794: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3795: we use a 5 terms etc. until the borders are no more concerned.
3796: */
3797: for (mob=3;mob <=mobilavrange;mob=mob+2){
3798: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3799: for (i=1; i<=nlstate;i++){
3800: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3801: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3802: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3803: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3804: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3805: }
3806: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3807: }
3808: }
3809: }/* end age */
3810: }/* end mob */
3811: }else return -1;
3812: return 0;
3813: }/* End movingaverage */
3814:
3815:
3816: /************** Forecasting ******************/
3817: 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){
3818: /* proj1, year, month, day of starting projection
3819: agemin, agemax range of age
3820: dateprev1 dateprev2 range of dates during which prevalence is computed
3821: anproj2 year of en of projection (same day and month as proj1).
3822: */
3823: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
3824: int *popage;
3825: double agec; /* generic age */
3826: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3827: double *popeffectif,*popcount;
3828: double ***p3mat;
3829: double ***mobaverage;
3830: char fileresf[FILENAMELENGTH];
3831:
3832: agelim=AGESUP;
3833: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3834:
3835: strcpy(fileresf,"f");
3836: strcat(fileresf,fileres);
3837: if((ficresf=fopen(fileresf,"w"))==NULL) {
3838: printf("Problem with forecast resultfile: %s\n", fileresf);
3839: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3840: }
3841: printf("Computing forecasting: result on file '%s' \n", fileresf);
3842: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3843:
3844: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3845:
3846: if (mobilav!=0) {
3847: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3848: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3849: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3850: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3851: }
3852: }
3853:
3854: stepsize=(int) (stepm+YEARM-1)/YEARM;
3855: if (stepm<=12) stepsize=1;
3856: if(estepm < stepm){
3857: printf ("Problem %d lower than %d\n",estepm, stepm);
3858: }
3859: else hstepm=estepm;
3860:
3861: hstepm=hstepm/stepm;
3862: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3863: fractional in yp1 */
3864: anprojmean=yp;
3865: yp2=modf((yp1*12),&yp);
3866: mprojmean=yp;
3867: yp1=modf((yp2*30.5),&yp);
3868: jprojmean=yp;
3869: if(jprojmean==0) jprojmean=1;
3870: if(mprojmean==0) jprojmean=1;
3871:
3872: i1=cptcoveff;
3873: if (cptcovn < 1){i1=1;}
3874:
3875: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
3876:
3877: fprintf(ficresf,"#****** Routine prevforecast **\n");
3878:
3879: /* if (h==(int)(YEARM*yearp)){ */
3880: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
3881: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3882: k=k+1;
3883: fprintf(ficresf,"\n#******");
3884: for(j=1;j<=cptcoveff;j++) {
3885: 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]]);
3886: }
3887: fprintf(ficresf,"******\n");
3888: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3889: for(j=1; j<=nlstate+ndeath;j++){
3890: for(i=1; i<=nlstate;i++)
3891: fprintf(ficresf," p%d%d",i,j);
3892: fprintf(ficresf," p.%d",j);
3893: }
3894: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
3895: fprintf(ficresf,"\n");
3896: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
3897:
3898: for (agec=fage; agec>=(ageminpar-1); agec--){
3899: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
3900: nhstepm = nhstepm/hstepm;
3901: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3902: oldm=oldms;savm=savms;
3903: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
3904:
3905: for (h=0; h<=nhstepm; h++){
3906: if (h*hstepm/YEARM*stepm ==yearp) {
3907: fprintf(ficresf,"\n");
3908: for(j=1;j<=cptcoveff;j++)
3909: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3910: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
3911: }
3912: for(j=1; j<=nlstate+ndeath;j++) {
3913: ppij=0.;
3914: for(i=1; i<=nlstate;i++) {
3915: if (mobilav==1)
3916: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
3917: else {
3918: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
3919: }
3920: if (h*hstepm/YEARM*stepm== yearp) {
3921: fprintf(ficresf," %.3f", p3mat[i][j][h]);
3922: }
3923: } /* end i */
3924: if (h*hstepm/YEARM*stepm==yearp) {
3925: fprintf(ficresf," %.3f", ppij);
3926: }
3927: }/* end j */
3928: } /* end h */
3929: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3930: } /* end agec */
3931: } /* end yearp */
3932: } /* end cptcod */
3933: } /* end cptcov */
3934:
3935: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3936:
3937: fclose(ficresf);
3938: }
3939:
3940: /************** Forecasting *****not tested NB*************/
3941: 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){
3942:
3943: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3944: int *popage;
3945: double calagedatem, agelim, kk1, kk2;
3946: double *popeffectif,*popcount;
3947: double ***p3mat,***tabpop,***tabpopprev;
3948: double ***mobaverage;
3949: char filerespop[FILENAMELENGTH];
3950:
3951: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3952: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3953: agelim=AGESUP;
3954: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
3955:
3956: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3957:
3958:
3959: strcpy(filerespop,"pop");
3960: strcat(filerespop,fileres);
3961: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3962: printf("Problem with forecast resultfile: %s\n", filerespop);
3963: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3964: }
3965: printf("Computing forecasting: result on file '%s' \n", filerespop);
3966: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3967:
3968: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3969:
3970: if (mobilav!=0) {
3971: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3972: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3973: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3974: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3975: }
3976: }
3977:
3978: stepsize=(int) (stepm+YEARM-1)/YEARM;
3979: if (stepm<=12) stepsize=1;
3980:
3981: agelim=AGESUP;
3982:
3983: hstepm=1;
3984: hstepm=hstepm/stepm;
3985:
3986: if (popforecast==1) {
3987: if((ficpop=fopen(popfile,"r"))==NULL) {
3988: printf("Problem with population file : %s\n",popfile);exit(0);
3989: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3990: }
3991: popage=ivector(0,AGESUP);
3992: popeffectif=vector(0,AGESUP);
3993: popcount=vector(0,AGESUP);
3994:
3995: i=1;
3996: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3997:
3998: imx=i;
3999: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4000: }
4001:
4002: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4003: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4004: k=k+1;
4005: fprintf(ficrespop,"\n#******");
4006: for(j=1;j<=cptcoveff;j++) {
4007: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4008: }
4009: fprintf(ficrespop,"******\n");
4010: fprintf(ficrespop,"# Age");
4011: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4012: if (popforecast==1) fprintf(ficrespop," [Population]");
4013:
4014: for (cpt=0; cpt<=0;cpt++) {
4015: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4016:
4017: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4018: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4019: nhstepm = nhstepm/hstepm;
4020:
4021: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4022: oldm=oldms;savm=savms;
4023: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4024:
4025: for (h=0; h<=nhstepm; h++){
4026: if (h==(int) (calagedatem+YEARM*cpt)) {
4027: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4028: }
4029: for(j=1; j<=nlstate+ndeath;j++) {
4030: kk1=0.;kk2=0;
4031: for(i=1; i<=nlstate;i++) {
4032: if (mobilav==1)
4033: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4034: else {
4035: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4036: }
4037: }
4038: if (h==(int)(calagedatem+12*cpt)){
4039: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4040: /*fprintf(ficrespop," %.3f", kk1);
4041: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4042: }
4043: }
4044: for(i=1; i<=nlstate;i++){
4045: kk1=0.;
4046: for(j=1; j<=nlstate;j++){
4047: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4048: }
4049: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4050: }
4051:
4052: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4053: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4054: }
4055: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4056: }
4057: }
4058:
4059: /******/
4060:
4061: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4062: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4063: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4064: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4065: nhstepm = nhstepm/hstepm;
4066:
4067: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4068: oldm=oldms;savm=savms;
4069: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4070: for (h=0; h<=nhstepm; h++){
4071: if (h==(int) (calagedatem+YEARM*cpt)) {
4072: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4073: }
4074: for(j=1; j<=nlstate+ndeath;j++) {
4075: kk1=0.;kk2=0;
4076: for(i=1; i<=nlstate;i++) {
4077: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4078: }
4079: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4080: }
4081: }
4082: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4083: }
4084: }
4085: }
4086: }
4087:
4088: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4089:
4090: if (popforecast==1) {
4091: free_ivector(popage,0,AGESUP);
4092: free_vector(popeffectif,0,AGESUP);
4093: free_vector(popcount,0,AGESUP);
4094: }
4095: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4096: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4097: fclose(ficrespop);
4098: } /* End of popforecast */
4099:
4100: int fileappend(FILE *fichier, char *optionfich)
4101: {
4102: if((fichier=fopen(optionfich,"a"))==NULL) {
4103: printf("Problem with file: %s\n", optionfich);
4104: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4105: return (0);
4106: }
4107: fflush(fichier);
4108: return (1);
4109: }
4110:
4111:
4112: /**************** function prwizard **********************/
4113: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4114: {
4115:
4116: /* Wizard to print covariance matrix template */
4117:
4118: char ca[32], cb[32], cc[32];
4119: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4120: int numlinepar;
4121:
4122: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4123: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4124: for(i=1; i <=nlstate; i++){
4125: jj=0;
4126: for(j=1; j <=nlstate+ndeath; j++){
4127: if(j==i) continue;
4128: jj++;
4129: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4130: printf("%1d%1d",i,j);
4131: fprintf(ficparo,"%1d%1d",i,j);
4132: for(k=1; k<=ncovmodel;k++){
4133: /* printf(" %lf",param[i][j][k]); */
4134: /* fprintf(ficparo," %lf",param[i][j][k]); */
4135: printf(" 0.");
4136: fprintf(ficparo," 0.");
4137: }
4138: printf("\n");
4139: fprintf(ficparo,"\n");
4140: }
4141: }
4142: printf("# Scales (for hessian or gradient estimation)\n");
4143: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4144: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4145: for(i=1; i <=nlstate; i++){
4146: jj=0;
4147: for(j=1; j <=nlstate+ndeath; j++){
4148: if(j==i) continue;
4149: jj++;
4150: fprintf(ficparo,"%1d%1d",i,j);
4151: printf("%1d%1d",i,j);
4152: fflush(stdout);
4153: for(k=1; k<=ncovmodel;k++){
4154: /* printf(" %le",delti3[i][j][k]); */
4155: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4156: printf(" 0.");
4157: fprintf(ficparo," 0.");
4158: }
4159: numlinepar++;
4160: printf("\n");
4161: fprintf(ficparo,"\n");
4162: }
4163: }
4164: printf("# Covariance matrix\n");
4165: /* # 121 Var(a12)\n\ */
4166: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4167: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4168: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4169: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4170: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4171: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4172: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4173: fflush(stdout);
4174: fprintf(ficparo,"# Covariance matrix\n");
4175: /* # 121 Var(a12)\n\ */
4176: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4177: /* # ...\n\ */
4178: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4179:
4180: for(itimes=1;itimes<=2;itimes++){
4181: jj=0;
4182: for(i=1; i <=nlstate; i++){
4183: for(j=1; j <=nlstate+ndeath; j++){
4184: if(j==i) continue;
4185: for(k=1; k<=ncovmodel;k++){
4186: jj++;
4187: ca[0]= k+'a'-1;ca[1]='\0';
4188: if(itimes==1){
4189: printf("#%1d%1d%d",i,j,k);
4190: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4191: }else{
4192: printf("%1d%1d%d",i,j,k);
4193: fprintf(ficparo,"%1d%1d%d",i,j,k);
4194: /* printf(" %.5le",matcov[i][j]); */
4195: }
4196: ll=0;
4197: for(li=1;li <=nlstate; li++){
4198: for(lj=1;lj <=nlstate+ndeath; lj++){
4199: if(lj==li) continue;
4200: for(lk=1;lk<=ncovmodel;lk++){
4201: ll++;
4202: if(ll<=jj){
4203: cb[0]= lk +'a'-1;cb[1]='\0';
4204: if(ll<jj){
4205: if(itimes==1){
4206: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4207: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4208: }else{
4209: printf(" 0.");
4210: fprintf(ficparo," 0.");
4211: }
4212: }else{
4213: if(itimes==1){
4214: printf(" Var(%s%1d%1d)",ca,i,j);
4215: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4216: }else{
4217: printf(" 0.");
4218: fprintf(ficparo," 0.");
4219: }
4220: }
4221: }
4222: } /* end lk */
4223: } /* end lj */
4224: } /* end li */
4225: printf("\n");
4226: fprintf(ficparo,"\n");
4227: numlinepar++;
4228: } /* end k*/
4229: } /*end j */
4230: } /* end i */
4231: } /* end itimes */
4232:
4233: } /* end of prwizard */
4234: /******************* Gompertz Likelihood ******************************/
4235: double gompertz(double x[])
4236: {
4237: double A,B,L=0.0,sump=0.,num=0.;
4238: int i,n=0; /* n is the size of the sample */
4239:
4240: for (i=0;i<=imx-1 ; i++) {
4241: sump=sump+weight[i];
4242: /* sump=sump+1;*/
4243: num=num+1;
4244: }
4245:
4246:
4247: /* for (i=0; i<=imx; i++)
4248: 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]);*/
4249:
4250: for (i=1;i<=imx ; i++)
4251: {
4252: if (cens[i] == 1 && wav[i]>1)
4253: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4254:
4255: if (cens[i] == 0 && wav[i]>1)
4256: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4257: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4258:
4259: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4260: if (wav[i] > 1 ) { /* ??? */
4261: L=L+A*weight[i];
4262: /* 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]);*/
4263: }
4264: }
4265:
4266: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4267:
4268: return -2*L*num/sump;
4269: }
4270:
4271: /******************* Printing html file ***********/
4272: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4273: int lastpass, int stepm, int weightopt, char model[],\
4274: int imx, double p[],double **matcov,double agemortsup){
4275: int i,k;
4276:
4277: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4278: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4279: for (i=1;i<=2;i++)
4280: 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]));
4281: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4282: fprintf(fichtm,"</ul>");
4283:
4284: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4285:
4286: 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>");
4287:
4288: for (k=agegomp;k<(agemortsup-2);k++)
4289: 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]);
4290:
4291:
4292: fflush(fichtm);
4293: }
4294:
4295: /******************* Gnuplot file **************/
4296: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4297:
4298: char dirfileres[132],optfileres[132];
4299: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4300: int ng;
4301:
4302:
4303: /*#ifdef windows */
4304: fprintf(ficgp,"cd \"%s\" \n",pathc);
4305: /*#endif */
4306:
4307:
4308: strcpy(dirfileres,optionfilefiname);
4309: strcpy(optfileres,"vpl");
4310: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4311: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4312: fprintf(ficgp, "set ter png small\n set log y\n");
4313: fprintf(ficgp, "set size 0.65,0.65\n");
4314: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4315:
4316: }
4317:
4318:
4319:
4320:
4321:
4322: /***********************************************/
4323: /**************** Main Program *****************/
4324: /***********************************************/
4325:
4326: int main(int argc, char *argv[])
4327: {
4328: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
4329: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
4330: int linei, month, year,iout;
4331: int jj, ll, li, lj, lk, imk;
4332: int numlinepar=0; /* Current linenumber of parameter file */
4333: int itimes;
4334: int NDIM=2;
4335:
4336: char ca[32], cb[32], cc[32];
4337: char dummy[]=" ";
4338: /* FILE *fichtm; *//* Html File */
4339: /* FILE *ficgp;*/ /*Gnuplot File */
4340: struct stat info;
4341: double agedeb, agefin,hf;
4342: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
4343:
4344: double fret;
4345: double **xi,tmp,delta;
4346:
4347: double dum; /* Dummy variable */
4348: double ***p3mat;
4349: double ***mobaverage;
4350: int *indx;
4351: char line[MAXLINE], linepar[MAXLINE];
4352: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
4353: char pathr[MAXLINE], pathimach[MAXLINE];
4354: char **bp, *tok, *val; /* pathtot */
4355: int firstobs=1, lastobs=10;
4356: int sdeb, sfin; /* Status at beginning and end */
4357: int c, h , cpt,l;
4358: int ju,jl, mi;
4359: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
4360: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
4361: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
4362: int mobilav=0,popforecast=0;
4363: int hstepm, nhstepm;
4364: int agemortsup;
4365: float sumlpop=0.;
4366: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
4367: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
4368:
4369: double bage, fage, age, agelim, agebase;
4370: double ftolpl=FTOL;
4371: double **prlim;
4372: double *severity;
4373: double ***param; /* Matrix of parameters */
4374: double *p;
4375: double **matcov; /* Matrix of covariance */
4376: double ***delti3; /* Scale */
4377: double *delti; /* Scale */
4378: double ***eij, ***vareij;
4379: double **varpl; /* Variances of prevalence limits by age */
4380: double *epj, vepp;
4381: double kk1, kk2;
4382: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
4383: double **ximort;
4384: char *alph[]={"a","a","b","c","d","e"}, str[4];
4385: int *dcwave;
4386:
4387: char z[1]="c", occ;
4388:
4389: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
4390: char *strt, strtend[80];
4391: char *stratrunc;
4392: int lstra;
4393:
4394: long total_usecs;
4395:
4396: /* setlocale (LC_ALL, ""); */
4397: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4398: /* textdomain (PACKAGE); */
4399: /* setlocale (LC_CTYPE, ""); */
4400: /* setlocale (LC_MESSAGES, ""); */
4401:
4402: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4403: (void) gettimeofday(&start_time,&tzp);
4404: curr_time=start_time;
4405: tm = *localtime(&start_time.tv_sec);
4406: tmg = *gmtime(&start_time.tv_sec);
4407: strcpy(strstart,asctime(&tm));
4408:
4409: /* printf("Localtime (at start)=%s",strstart); */
4410: /* tp.tv_sec = tp.tv_sec +86400; */
4411: /* tm = *localtime(&start_time.tv_sec); */
4412: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4413: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4414: /* tmg.tm_hour=tmg.tm_hour + 1; */
4415: /* tp.tv_sec = mktime(&tmg); */
4416: /* strt=asctime(&tmg); */
4417: /* printf("Time(after) =%s",strstart); */
4418: /* (void) time (&time_value);
4419: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4420: * tm = *localtime(&time_value);
4421: * strstart=asctime(&tm);
4422: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
4423: */
4424:
4425: nberr=0; /* Number of errors and warnings */
4426: nbwarn=0;
4427: getcwd(pathcd, size);
4428:
4429: printf("\n%s\n%s",version,fullversion);
4430: if(argc <=1){
4431: printf("\nEnter the parameter file name: ");
4432: fgets(pathr,FILENAMELENGTH,stdin);
4433: i=strlen(pathr);
4434: if(pathr[i-1]=='\n')
4435: pathr[i-1]='\0';
4436: for (tok = pathr; tok != NULL; ){
4437: printf("Pathr |%s|\n",pathr);
4438: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
4439: printf("val= |%s| pathr=%s\n",val,pathr);
4440: strcpy (pathtot, val);
4441: if(pathr[0] == '\0') break; /* Dirty */
4442: }
4443: }
4444: else{
4445: strcpy(pathtot,argv[1]);
4446: }
4447: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
4448: /*cygwin_split_path(pathtot,path,optionfile);
4449: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
4450: /* cutv(path,optionfile,pathtot,'\\');*/
4451:
4452: /* Split argv[0], imach program to get pathimach */
4453: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
4454: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4455: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4456: /* strcpy(pathimach,argv[0]); */
4457: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
4458: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
4459: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
4460: chdir(path); /* Can be a relative path */
4461: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
4462: printf("Current directory %s!\n",pathcd);
4463: strcpy(command,"mkdir ");
4464: strcat(command,optionfilefiname);
4465: if((outcmd=system(command)) != 0){
4466: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
4467: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
4468: /* fclose(ficlog); */
4469: /* exit(1); */
4470: }
4471: /* if((imk=mkdir(optionfilefiname))<0){ */
4472: /* perror("mkdir"); */
4473: /* } */
4474:
4475: /*-------- arguments in the command line --------*/
4476:
4477: /* Log file */
4478: strcat(filelog, optionfilefiname);
4479: strcat(filelog,".log"); /* */
4480: if((ficlog=fopen(filelog,"w"))==NULL) {
4481: printf("Problem with logfile %s\n",filelog);
4482: goto end;
4483: }
4484: fprintf(ficlog,"Log filename:%s\n",filelog);
4485: fprintf(ficlog,"\n%s\n%s",version,fullversion);
4486: fprintf(ficlog,"\nEnter the parameter file name: \n");
4487: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
4488: path=%s \n\
4489: optionfile=%s\n\
4490: optionfilext=%s\n\
4491: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
4492:
4493: printf("Local time (at start):%s",strstart);
4494: fprintf(ficlog,"Local time (at start): %s",strstart);
4495: fflush(ficlog);
4496: /* (void) gettimeofday(&curr_time,&tzp); */
4497: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
4498:
4499: /* */
4500: strcpy(fileres,"r");
4501: strcat(fileres, optionfilefiname);
4502: strcat(fileres,".txt"); /* Other files have txt extension */
4503:
4504: /*---------arguments file --------*/
4505:
4506: if((ficpar=fopen(optionfile,"r"))==NULL) {
4507: printf("Problem with optionfile %s\n",optionfile);
4508: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
4509: fflush(ficlog);
4510: goto end;
4511: }
4512:
4513:
4514:
4515: strcpy(filereso,"o");
4516: strcat(filereso,fileres);
4517: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
4518: printf("Problem with Output resultfile: %s\n", filereso);
4519: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
4520: fflush(ficlog);
4521: goto end;
4522: }
4523:
4524: /* Reads comments: lines beginning with '#' */
4525: numlinepar=0;
4526: while((c=getc(ficpar))=='#' && c!= EOF){
4527: ungetc(c,ficpar);
4528: fgets(line, MAXLINE, ficpar);
4529: numlinepar++;
4530: puts(line);
4531: fputs(line,ficparo);
4532: fputs(line,ficlog);
4533: }
4534: ungetc(c,ficpar);
4535:
4536: 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);
4537: numlinepar++;
4538: 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);
4539: 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);
4540: 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);
4541: fflush(ficlog);
4542: while((c=getc(ficpar))=='#' && c!= EOF){
4543: ungetc(c,ficpar);
4544: fgets(line, MAXLINE, ficpar);
4545: numlinepar++;
4546: puts(line);
4547: fputs(line,ficparo);
4548: fputs(line,ficlog);
4549: }
4550: ungetc(c,ficpar);
4551:
4552:
4553: covar=matrix(0,NCOVMAX,1,n);
4554: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
4555: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4556:
4557: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
4558: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
4559: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4560:
4561: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4562: delti=delti3[1][1];
4563: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
4564: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4565: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4566: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4567: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4568: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4569: fclose (ficparo);
4570: fclose (ficlog);
4571: exit(0);
4572: }
4573: else if(mle==-3) {
4574: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4575: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4576: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4577: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4578: matcov=matrix(1,npar,1,npar);
4579: }
4580: else{
4581: /* Read guess parameters */
4582: /* Reads comments: lines beginning with '#' */
4583: while((c=getc(ficpar))=='#' && c!= EOF){
4584: ungetc(c,ficpar);
4585: fgets(line, MAXLINE, ficpar);
4586: numlinepar++;
4587: puts(line);
4588: fputs(line,ficparo);
4589: fputs(line,ficlog);
4590: }
4591: ungetc(c,ficpar);
4592:
4593: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4594: for(i=1; i <=nlstate; i++){
4595: j=0;
4596: for(jj=1; jj <=nlstate+ndeath; jj++){
4597: if(jj==i) continue;
4598: j++;
4599: fscanf(ficpar,"%1d%1d",&i1,&j1);
4600: if ((i1 != i) && (j1 != j)){
4601: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4602: exit(1);
4603: }
4604: fprintf(ficparo,"%1d%1d",i1,j1);
4605: if(mle==1)
4606: printf("%1d%1d",i,j);
4607: fprintf(ficlog,"%1d%1d",i,j);
4608: for(k=1; k<=ncovmodel;k++){
4609: fscanf(ficpar," %lf",¶m[i][j][k]);
4610: if(mle==1){
4611: printf(" %lf",param[i][j][k]);
4612: fprintf(ficlog," %lf",param[i][j][k]);
4613: }
4614: else
4615: fprintf(ficlog," %lf",param[i][j][k]);
4616: fprintf(ficparo," %lf",param[i][j][k]);
4617: }
4618: fscanf(ficpar,"\n");
4619: numlinepar++;
4620: if(mle==1)
4621: printf("\n");
4622: fprintf(ficlog,"\n");
4623: fprintf(ficparo,"\n");
4624: }
4625: }
4626: fflush(ficlog);
4627:
4628: p=param[1][1];
4629:
4630: /* Reads comments: lines beginning with '#' */
4631: while((c=getc(ficpar))=='#' && c!= EOF){
4632: ungetc(c,ficpar);
4633: fgets(line, MAXLINE, ficpar);
4634: numlinepar++;
4635: puts(line);
4636: fputs(line,ficparo);
4637: fputs(line,ficlog);
4638: }
4639: ungetc(c,ficpar);
4640:
4641: for(i=1; i <=nlstate; i++){
4642: for(j=1; j <=nlstate+ndeath-1; j++){
4643: fscanf(ficpar,"%1d%1d",&i1,&j1);
4644: if ((i1-i)*(j1-j)!=0){
4645: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4646: exit(1);
4647: }
4648: printf("%1d%1d",i,j);
4649: fprintf(ficparo,"%1d%1d",i1,j1);
4650: fprintf(ficlog,"%1d%1d",i1,j1);
4651: for(k=1; k<=ncovmodel;k++){
4652: fscanf(ficpar,"%le",&delti3[i][j][k]);
4653: printf(" %le",delti3[i][j][k]);
4654: fprintf(ficparo," %le",delti3[i][j][k]);
4655: fprintf(ficlog," %le",delti3[i][j][k]);
4656: }
4657: fscanf(ficpar,"\n");
4658: numlinepar++;
4659: printf("\n");
4660: fprintf(ficparo,"\n");
4661: fprintf(ficlog,"\n");
4662: }
4663: }
4664: fflush(ficlog);
4665:
4666: delti=delti3[1][1];
4667:
4668:
4669: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
4670:
4671: /* Reads comments: lines beginning with '#' */
4672: while((c=getc(ficpar))=='#' && c!= EOF){
4673: ungetc(c,ficpar);
4674: fgets(line, MAXLINE, ficpar);
4675: numlinepar++;
4676: puts(line);
4677: fputs(line,ficparo);
4678: fputs(line,ficlog);
4679: }
4680: ungetc(c,ficpar);
4681:
4682: matcov=matrix(1,npar,1,npar);
4683: for(i=1; i <=npar; i++){
4684: fscanf(ficpar,"%s",&str);
4685: if(mle==1)
4686: printf("%s",str);
4687: fprintf(ficlog,"%s",str);
4688: fprintf(ficparo,"%s",str);
4689: for(j=1; j <=i; j++){
4690: fscanf(ficpar," %le",&matcov[i][j]);
4691: if(mle==1){
4692: printf(" %.5le",matcov[i][j]);
4693: }
4694: fprintf(ficlog," %.5le",matcov[i][j]);
4695: fprintf(ficparo," %.5le",matcov[i][j]);
4696: }
4697: fscanf(ficpar,"\n");
4698: numlinepar++;
4699: if(mle==1)
4700: printf("\n");
4701: fprintf(ficlog,"\n");
4702: fprintf(ficparo,"\n");
4703: }
4704: for(i=1; i <=npar; i++)
4705: for(j=i+1;j<=npar;j++)
4706: matcov[i][j]=matcov[j][i];
4707:
4708: if(mle==1)
4709: printf("\n");
4710: fprintf(ficlog,"\n");
4711:
4712: fflush(ficlog);
4713:
4714: /*-------- Rewriting parameter file ----------*/
4715: strcpy(rfileres,"r"); /* "Rparameterfile */
4716: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4717: strcat(rfileres,"."); /* */
4718: strcat(rfileres,optionfilext); /* Other files have txt extension */
4719: if((ficres =fopen(rfileres,"w"))==NULL) {
4720: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4721: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4722: }
4723: fprintf(ficres,"#%s\n",version);
4724: } /* End of mle != -3 */
4725:
4726: /*-------- data file ----------*/
4727: if((fic=fopen(datafile,"r"))==NULL) {
4728: printf("Problem while opening datafile: %s\n", datafile);goto end;
4729: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
4730: }
4731:
4732: n= lastobs;
4733: severity = vector(1,maxwav);
4734: outcome=imatrix(1,maxwav+1,1,n);
4735: num=lvector(1,n);
4736: moisnais=vector(1,n);
4737: annais=vector(1,n);
4738: moisdc=vector(1,n);
4739: andc=vector(1,n);
4740: agedc=vector(1,n);
4741: cod=ivector(1,n);
4742: weight=vector(1,n);
4743: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4744: mint=matrix(1,maxwav,1,n);
4745: anint=matrix(1,maxwav,1,n);
4746: s=imatrix(1,maxwav+1,1,n);
4747: tab=ivector(1,NCOVMAX);
4748: ncodemax=ivector(1,8);
4749:
4750: i=1;
4751: linei=0;
4752: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4753: linei=linei+1;
4754: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4755: if(line[j] == '\t')
4756: line[j] = ' ';
4757: }
4758: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4759: ;
4760: };
4761: line[j+1]=0; /* Trims blanks at end of line */
4762: if(line[0]=='#'){
4763: fprintf(ficlog,"Comment line\n%s\n",line);
4764: printf("Comment line\n%s\n",line);
4765: continue;
4766: }
4767:
4768: for (j=maxwav;j>=1;j--){
4769: cutv(stra, strb,line,' ');
4770: errno=0;
4771: lval=strtol(strb,&endptr,10);
4772: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4773: if( strb[0]=='\0' || (*endptr != '\0')){
4774: printf("Error reading data around '%d' at line number %d %s 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);
4775: exit(1);
4776: }
4777: s[j][i]=lval;
4778:
4779: strcpy(line,stra);
4780: cutv(stra, strb,line,' ');
4781: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4782: }
4783: else if(iout=sscanf(strb,"%s.") != 0){
4784: month=99;
4785: year=9999;
4786: }else{
4787: printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
4788: exit(1);
4789: }
4790: anint[j][i]= (double) year;
4791: mint[j][i]= (double)month;
4792: strcpy(line,stra);
4793: } /* ENd Waves */
4794:
4795: cutv(stra, strb,line,' ');
4796: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4797: }
4798: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4799: month=99;
4800: year=9999;
4801: }else{
4802: printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
4803: exit(1);
4804: }
4805: andc[i]=(double) year;
4806: moisdc[i]=(double) month;
4807: strcpy(line,stra);
4808:
4809: cutv(stra, strb,line,' ');
4810: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4811: }
4812: else if(iout=sscanf(strb,"%s.") != 0){
4813: month=99;
4814: year=9999;
4815: }else{
4816: printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line,j);
4817: exit(1);
4818: }
4819: annais[i]=(double)(year);
4820: moisnais[i]=(double)(month);
4821: strcpy(line,stra);
4822:
4823: cutv(stra, strb,line,' ');
4824: errno=0;
4825: dval=strtod(strb,&endptr);
4826: if( strb[0]=='\0' || (*endptr != '\0')){
4827: printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
4828: exit(1);
4829: }
4830: weight[i]=dval;
4831: strcpy(line,stra);
4832:
4833: for (j=ncovcol;j>=1;j--){
4834: cutv(stra, strb,line,' ');
4835: errno=0;
4836: lval=strtol(strb,&endptr,10);
4837: if( strb[0]=='\0' || (*endptr != '\0')){
4838: printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1). Exiting.\n",lval, linei,i, line);
4839: exit(1);
4840: }
4841: if(lval <-1 || lval >1){
4842: printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
4843: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4844: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4845: For example, for multinomial values like 1, 2 and 3,\n \
4846: build V1=0 V2=0 for the reference value (1),\n \
4847: V1=1 V2=0 for (2) \n \
4848: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4849: output of IMaCh is often meaningless.\n \
4850: Exiting.\n",lval,linei, i,line,j);
4851: exit(1);
4852: }
4853: covar[j][i]=(double)(lval);
4854: strcpy(line,stra);
4855: }
4856: lstra=strlen(stra);
4857:
4858: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4859: stratrunc = &(stra[lstra-9]);
4860: num[i]=atol(stratrunc);
4861: }
4862: else
4863: num[i]=atol(stra);
4864: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4865: 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;}*/
4866:
4867: i=i+1;
4868: } /* End loop reading data */
4869: fclose(fic);
4870: /* printf("ii=%d", ij);
4871: scanf("%d",i);*/
4872: imx=i-1; /* Number of individuals */
4873:
4874: /* for (i=1; i<=imx; i++){
4875: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4876: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4877: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4878: }*/
4879: /* for (i=1; i<=imx; i++){
4880: if (s[4][i]==9) s[4][i]=-1;
4881: 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]));}*/
4882:
4883: /* for (i=1; i<=imx; i++) */
4884:
4885: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4886: else weight[i]=1;*/
4887:
4888: /* Calculation of the number of parameters from char model */
4889: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4890: Tprod=ivector(1,15);
4891: Tvaraff=ivector(1,15);
4892: Tvard=imatrix(1,15,1,2);
4893: Tage=ivector(1,15);
4894:
4895: if (strlen(model) >1){ /* If there is at least 1 covariate */
4896: j=0, j1=0, k1=1, k2=1;
4897: j=nbocc(model,'+'); /* j=Number of '+' */
4898: j1=nbocc(model,'*'); /* j1=Number of '*' */
4899: cptcovn=j+1;
4900: cptcovprod=j1; /*Number of products */
4901:
4902: strcpy(modelsav,model);
4903: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4904: printf("Error. Non available option model=%s ",model);
4905: fprintf(ficlog,"Error. Non available option model=%s ",model);
4906: goto end;
4907: }
4908:
4909: /* This loop fills the array Tvar from the string 'model'.*/
4910:
4911: for(i=(j+1); i>=1;i--){
4912: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
4913: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
4914: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4915: /*scanf("%d",i);*/
4916: if (strchr(strb,'*')) { /* Model includes a product */
4917: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4918: if (strcmp(strc,"age")==0) { /* Vn*age */
4919: cptcovprod--;
4920: cutv(strb,stre,strd,'V');
4921: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4922: cptcovage++;
4923: Tage[cptcovage]=i;
4924: /*printf("stre=%s ", stre);*/
4925: }
4926: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4927: cptcovprod--;
4928: cutv(strb,stre,strc,'V');
4929: Tvar[i]=atoi(stre);
4930: cptcovage++;
4931: Tage[cptcovage]=i;
4932: }
4933: else { /* Age is not in the model */
4934: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4935: Tvar[i]=ncovcol+k1;
4936: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4937: Tprod[k1]=i;
4938: Tvard[k1][1]=atoi(strc); /* m*/
4939: Tvard[k1][2]=atoi(stre); /* n */
4940: Tvar[cptcovn+k2]=Tvard[k1][1];
4941: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4942: for (k=1; k<=lastobs;k++)
4943: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4944: k1++;
4945: k2=k2+2;
4946: }
4947: }
4948: else { /* no more sum */
4949: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4950: /* scanf("%d",i);*/
4951: cutv(strd,strc,strb,'V');
4952: Tvar[i]=atoi(strc);
4953: }
4954: strcpy(modelsav,stra);
4955: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4956: scanf("%d",i);*/
4957: } /* end of loop + */
4958: } /* end model */
4959:
4960: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4961: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4962:
4963: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4964: printf("cptcovprod=%d ", cptcovprod);
4965: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
4966:
4967: scanf("%d ",i);*/
4968:
4969: /* if(mle==1){*/
4970: if (weightopt != 1) { /* Maximisation without weights*/
4971: for(i=1;i<=n;i++) weight[i]=1.0;
4972: }
4973: /*-calculation of age at interview from date of interview and age at death -*/
4974: agev=matrix(1,maxwav,1,imx);
4975:
4976: for (i=1; i<=imx; i++) {
4977: for(m=2; (m<= maxwav); m++) {
4978: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
4979: anint[m][i]=9999;
4980: s[m][i]=-1;
4981: }
4982: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
4983: nberr++;
4984: 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);
4985: 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);
4986: s[m][i]=-1;
4987: }
4988: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
4989: nberr++;
4990: 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]);
4991: 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]);
4992: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
4993: }
4994: }
4995: }
4996:
4997: for (i=1; i<=imx; i++) {
4998: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
4999: for(m=firstpass; (m<= lastpass); m++){
5000: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5001: if (s[m][i] >= nlstate+1) {
5002: if(agedc[i]>0)
5003: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
5004: agev[m][i]=agedc[i];
5005: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5006: else {
5007: if ((int)andc[i]!=9999){
5008: nbwarn++;
5009: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5010: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5011: agev[m][i]=-1;
5012: }
5013: }
5014: }
5015: else if(s[m][i] !=9){ /* Standard case, age in fractional
5016: years but with the precision of a month */
5017: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5018: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5019: agev[m][i]=1;
5020: else if(agev[m][i] <agemin){
5021: agemin=agev[m][i];
5022: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
5023: }
5024: else if(agev[m][i] >agemax){
5025: agemax=agev[m][i];
5026: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
5027: }
5028: /*agev[m][i]=anint[m][i]-annais[i];*/
5029: /* agev[m][i] = age[i]+2*m;*/
5030: }
5031: else { /* =9 */
5032: agev[m][i]=1;
5033: s[m][i]=-1;
5034: }
5035: }
5036: else /*= 0 Unknown */
5037: agev[m][i]=1;
5038: }
5039:
5040: }
5041: for (i=1; i<=imx; i++) {
5042: for(m=firstpass; (m<=lastpass); m++){
5043: if (s[m][i] > (nlstate+ndeath)) {
5044: nberr++;
5045: 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);
5046: 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);
5047: goto end;
5048: }
5049: }
5050: }
5051:
5052: /*for (i=1; i<=imx; i++){
5053: for (m=firstpass; (m<lastpass); m++){
5054: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5055: }
5056:
5057: }*/
5058:
5059:
5060: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5061: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5062:
5063: agegomp=(int)agemin;
5064: free_vector(severity,1,maxwav);
5065: free_imatrix(outcome,1,maxwav+1,1,n);
5066: free_vector(moisnais,1,n);
5067: free_vector(annais,1,n);
5068: /* free_matrix(mint,1,maxwav,1,n);
5069: free_matrix(anint,1,maxwav,1,n);*/
5070: free_vector(moisdc,1,n);
5071: free_vector(andc,1,n);
5072:
5073:
5074: wav=ivector(1,imx);
5075: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5076: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5077: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5078:
5079: /* Concatenates waves */
5080: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
5081:
5082: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5083:
5084: Tcode=ivector(1,100);
5085: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5086: ncodemax[1]=1;
5087: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
5088:
5089: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
5090: the estimations*/
5091: h=0;
5092: m=pow(2,cptcoveff);
5093:
5094: for(k=1;k<=cptcoveff; k++){
5095: for(i=1; i <=(m/pow(2,k));i++){
5096: for(j=1; j <= ncodemax[k]; j++){
5097: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
5098: h++;
5099: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
5100: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
5101: }
5102: }
5103: }
5104: }
5105: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5106: codtab[1][2]=1;codtab[2][2]=2; */
5107: /* for(i=1; i <=m ;i++){
5108: for(k=1; k <=cptcovn; k++){
5109: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
5110: }
5111: printf("\n");
5112: }
5113: scanf("%d",i);*/
5114:
5115: /*------------ gnuplot -------------*/
5116: strcpy(optionfilegnuplot,optionfilefiname);
5117: if(mle==-3)
5118: strcat(optionfilegnuplot,"-mort");
5119: strcat(optionfilegnuplot,".gp");
5120:
5121: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
5122: printf("Problem with file %s",optionfilegnuplot);
5123: }
5124: else{
5125: fprintf(ficgp,"\n# %s\n", version);
5126: fprintf(ficgp,"# %s\n", optionfilegnuplot);
5127: fprintf(ficgp,"set missing 'NaNq'\n");
5128: }
5129: /* fclose(ficgp);*/
5130: /*--------- index.htm --------*/
5131:
5132: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
5133: if(mle==-3)
5134: strcat(optionfilehtm,"-mort");
5135: strcat(optionfilehtm,".htm");
5136: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
5137: printf("Problem with %s \n",optionfilehtm), exit(0);
5138: }
5139:
5140: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
5141: strcat(optionfilehtmcov,"-cov.htm");
5142: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
5143: printf("Problem with %s \n",optionfilehtmcov), exit(0);
5144: }
5145: else{
5146: fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
5147: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5148: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
5149: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
5150: }
5151:
5152: fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
5153: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5154: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
5155: \n\
5156: <hr size=\"2\" color=\"#EC5E5E\">\
5157: <ul><li><h4>Parameter files</h4>\n\
5158: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
5159: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
5160: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
5161: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
5162: - Date and time at start: %s</ul>\n",\
5163: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
5164: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
5165: fileres,fileres,\
5166: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
5167: fflush(fichtm);
5168:
5169: strcpy(pathr,path);
5170: strcat(pathr,optionfilefiname);
5171: chdir(optionfilefiname); /* Move to directory named optionfile */
5172:
5173: /* Calculates basic frequencies. Computes observed prevalence at single age
5174: and prints on file fileres'p'. */
5175: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
5176:
5177: fprintf(fichtm,"\n");
5178: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
5179: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
5180: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
5181: imx,agemin,agemax,jmin,jmax,jmean);
5182: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5183: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5184: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5185: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5186: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
5187:
5188:
5189: /* For Powell, parameters are in a vector p[] starting at p[1]
5190: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
5191: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
5192:
5193: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
5194:
5195: if (mle==-3){
5196: ximort=matrix(1,NDIM,1,NDIM);
5197: cens=ivector(1,n);
5198: ageexmed=vector(1,n);
5199: agecens=vector(1,n);
5200: dcwave=ivector(1,n);
5201:
5202: for (i=1; i<=imx; i++){
5203: dcwave[i]=-1;
5204: for (m=firstpass; m<=lastpass; m++)
5205: if (s[m][i]>nlstate) {
5206: dcwave[i]=m;
5207: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5208: break;
5209: }
5210: }
5211:
5212: for (i=1; i<=imx; i++) {
5213: if (wav[i]>0){
5214: ageexmed[i]=agev[mw[1][i]][i];
5215: j=wav[i];
5216: agecens[i]=1.;
5217:
5218: if (ageexmed[i]> 1 && wav[i] > 0){
5219: agecens[i]=agev[mw[j][i]][i];
5220: cens[i]= 1;
5221: }else if (ageexmed[i]< 1)
5222: cens[i]= -1;
5223: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5224: cens[i]=0 ;
5225: }
5226: else cens[i]=-1;
5227: }
5228:
5229: for (i=1;i<=NDIM;i++) {
5230: for (j=1;j<=NDIM;j++)
5231: ximort[i][j]=(i == j ? 1.0 : 0.0);
5232: }
5233:
5234: p[1]=0.0268; p[NDIM]=0.083;
5235: /*printf("%lf %lf", p[1], p[2]);*/
5236:
5237:
5238: printf("Powell\n"); fprintf(ficlog,"Powell\n");
5239: strcpy(filerespow,"pow-mort");
5240: strcat(filerespow,fileres);
5241: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5242: printf("Problem with resultfile: %s\n", filerespow);
5243: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5244: }
5245: fprintf(ficrespow,"# Powell\n# iter -2*LL");
5246: /* for (i=1;i<=nlstate;i++)
5247: for(j=1;j<=nlstate+ndeath;j++)
5248: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5249: */
5250: fprintf(ficrespow,"\n");
5251:
5252: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
5253: fclose(ficrespow);
5254:
5255: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
5256:
5257: for(i=1; i <=NDIM; i++)
5258: for(j=i+1;j<=NDIM;j++)
5259: matcov[i][j]=matcov[j][i];
5260:
5261: printf("\nCovariance matrix\n ");
5262: for(i=1; i <=NDIM; i++) {
5263: for(j=1;j<=NDIM;j++){
5264: printf("%f ",matcov[i][j]);
5265: }
5266: printf("\n ");
5267: }
5268:
5269: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
5270: for (i=1;i<=NDIM;i++)
5271: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
5272:
5273: lsurv=vector(1,AGESUP);
5274: lpop=vector(1,AGESUP);
5275: tpop=vector(1,AGESUP);
5276: lsurv[agegomp]=100000;
5277:
5278: for (k=agegomp;k<=AGESUP;k++) {
5279: agemortsup=k;
5280: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
5281: }
5282:
5283: for (k=agegomp;k<agemortsup;k++)
5284: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
5285:
5286: for (k=agegomp;k<agemortsup;k++){
5287: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
5288: sumlpop=sumlpop+lpop[k];
5289: }
5290:
5291: tpop[agegomp]=sumlpop;
5292: for (k=agegomp;k<(agemortsup-3);k++){
5293: /* tpop[k+1]=2;*/
5294: tpop[k+1]=tpop[k]-lpop[k];
5295: }
5296:
5297:
5298: printf("\nAge lx qx dx Lx Tx e(x)\n");
5299: for (k=agegomp;k<(agemortsup-2);k++)
5300: 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]);
5301:
5302:
5303: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
5304: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5305:
5306: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
5307: stepm, weightopt,\
5308: model,imx,p,matcov,agemortsup);
5309:
5310: free_vector(lsurv,1,AGESUP);
5311: free_vector(lpop,1,AGESUP);
5312: free_vector(tpop,1,AGESUP);
5313: } /* Endof if mle==-3 */
5314:
5315: else{ /* For mle >=1 */
5316:
5317: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5318: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5319: for (k=1; k<=npar;k++)
5320: printf(" %d %8.5f",k,p[k]);
5321: printf("\n");
5322: globpr=1; /* to print the contributions */
5323: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5324: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5325: for (k=1; k<=npar;k++)
5326: printf(" %d %8.5f",k,p[k]);
5327: printf("\n");
5328: if(mle>=1){ /* Could be 1 or 2 */
5329: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
5330: }
5331:
5332: /*--------- results files --------------*/
5333: 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);
5334:
5335:
5336: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5337: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5338: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5339: for(i=1,jk=1; i <=nlstate; i++){
5340: for(k=1; k <=(nlstate+ndeath); k++){
5341: if (k != i) {
5342: printf("%d%d ",i,k);
5343: fprintf(ficlog,"%d%d ",i,k);
5344: fprintf(ficres,"%1d%1d ",i,k);
5345: for(j=1; j <=ncovmodel; j++){
5346: printf("%f ",p[jk]);
5347: fprintf(ficlog,"%f ",p[jk]);
5348: fprintf(ficres,"%f ",p[jk]);
5349: jk++;
5350: }
5351: printf("\n");
5352: fprintf(ficlog,"\n");
5353: fprintf(ficres,"\n");
5354: }
5355: }
5356: }
5357: if(mle!=0){
5358: /* Computing hessian and covariance matrix */
5359: ftolhess=ftol; /* Usually correct */
5360: hesscov(matcov, p, npar, delti, ftolhess, func);
5361: }
5362: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
5363: printf("# Scales (for hessian or gradient estimation)\n");
5364: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
5365: for(i=1,jk=1; i <=nlstate; i++){
5366: for(j=1; j <=nlstate+ndeath; j++){
5367: if (j!=i) {
5368: fprintf(ficres,"%1d%1d",i,j);
5369: printf("%1d%1d",i,j);
5370: fprintf(ficlog,"%1d%1d",i,j);
5371: for(k=1; k<=ncovmodel;k++){
5372: printf(" %.5e",delti[jk]);
5373: fprintf(ficlog," %.5e",delti[jk]);
5374: fprintf(ficres," %.5e",delti[jk]);
5375: jk++;
5376: }
5377: printf("\n");
5378: fprintf(ficlog,"\n");
5379: fprintf(ficres,"\n");
5380: }
5381: }
5382: }
5383:
5384: 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");
5385: if(mle>=1)
5386: 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");
5387: 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");
5388: /* # 121 Var(a12)\n\ */
5389: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5390: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5391: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5392: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5393: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5394: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5395: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5396:
5397:
5398: /* Just to have a covariance matrix which will be more understandable
5399: even is we still don't want to manage dictionary of variables
5400: */
5401: for(itimes=1;itimes<=2;itimes++){
5402: jj=0;
5403: for(i=1; i <=nlstate; i++){
5404: for(j=1; j <=nlstate+ndeath; j++){
5405: if(j==i) continue;
5406: for(k=1; k<=ncovmodel;k++){
5407: jj++;
5408: ca[0]= k+'a'-1;ca[1]='\0';
5409: if(itimes==1){
5410: if(mle>=1)
5411: printf("#%1d%1d%d",i,j,k);
5412: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5413: fprintf(ficres,"#%1d%1d%d",i,j,k);
5414: }else{
5415: if(mle>=1)
5416: printf("%1d%1d%d",i,j,k);
5417: fprintf(ficlog,"%1d%1d%d",i,j,k);
5418: fprintf(ficres,"%1d%1d%d",i,j,k);
5419: }
5420: ll=0;
5421: for(li=1;li <=nlstate; li++){
5422: for(lj=1;lj <=nlstate+ndeath; lj++){
5423: if(lj==li) continue;
5424: for(lk=1;lk<=ncovmodel;lk++){
5425: ll++;
5426: if(ll<=jj){
5427: cb[0]= lk +'a'-1;cb[1]='\0';
5428: if(ll<jj){
5429: if(itimes==1){
5430: if(mle>=1)
5431: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5432: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5433: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5434: }else{
5435: if(mle>=1)
5436: printf(" %.5e",matcov[jj][ll]);
5437: fprintf(ficlog," %.5e",matcov[jj][ll]);
5438: fprintf(ficres," %.5e",matcov[jj][ll]);
5439: }
5440: }else{
5441: if(itimes==1){
5442: if(mle>=1)
5443: printf(" Var(%s%1d%1d)",ca,i,j);
5444: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5445: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5446: }else{
5447: if(mle>=1)
5448: printf(" %.5e",matcov[jj][ll]);
5449: fprintf(ficlog," %.5e",matcov[jj][ll]);
5450: fprintf(ficres," %.5e",matcov[jj][ll]);
5451: }
5452: }
5453: }
5454: } /* end lk */
5455: } /* end lj */
5456: } /* end li */
5457: if(mle>=1)
5458: printf("\n");
5459: fprintf(ficlog,"\n");
5460: fprintf(ficres,"\n");
5461: numlinepar++;
5462: } /* end k*/
5463: } /*end j */
5464: } /* end i */
5465: } /* end itimes */
5466:
5467: fflush(ficlog);
5468: fflush(ficres);
5469:
5470: while((c=getc(ficpar))=='#' && c!= EOF){
5471: ungetc(c,ficpar);
5472: fgets(line, MAXLINE, ficpar);
5473: puts(line);
5474: fputs(line,ficparo);
5475: }
5476: ungetc(c,ficpar);
5477:
5478: estepm=0;
5479: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5480: if (estepm==0 || estepm < stepm) estepm=stepm;
5481: if (fage <= 2) {
5482: bage = ageminpar;
5483: fage = agemaxpar;
5484: }
5485:
5486: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5487: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5488: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5489:
5490: while((c=getc(ficpar))=='#' && c!= EOF){
5491: ungetc(c,ficpar);
5492: fgets(line, MAXLINE, ficpar);
5493: puts(line);
5494: fputs(line,ficparo);
5495: }
5496: ungetc(c,ficpar);
5497:
5498: 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);
5499: 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);
5500: 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);
5501: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5502: 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);
5503:
5504: while((c=getc(ficpar))=='#' && c!= EOF){
5505: ungetc(c,ficpar);
5506: fgets(line, MAXLINE, ficpar);
5507: puts(line);
5508: fputs(line,ficparo);
5509: }
5510: ungetc(c,ficpar);
5511:
5512:
5513: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5514: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5515:
5516: fscanf(ficpar,"pop_based=%d\n",&popbased);
5517: fprintf(ficparo,"pop_based=%d\n",popbased);
5518: fprintf(ficres,"pop_based=%d\n",popbased);
5519:
5520: while((c=getc(ficpar))=='#' && c!= EOF){
5521: ungetc(c,ficpar);
5522: fgets(line, MAXLINE, ficpar);
5523: puts(line);
5524: fputs(line,ficparo);
5525: }
5526: ungetc(c,ficpar);
5527:
5528: 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);
5529: 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);
5530: 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);
5531: 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);
5532: 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);
5533: /* day and month of proj2 are not used but only year anproj2.*/
5534:
5535:
5536:
5537: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5538: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5539:
5540: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
5541: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5542:
5543: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5544: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5545: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5546:
5547: /*------------ free_vector -------------*/
5548: /* chdir(path); */
5549:
5550: free_ivector(wav,1,imx);
5551: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5552: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5553: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5554: free_lvector(num,1,n);
5555: free_vector(agedc,1,n);
5556: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5557: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5558: fclose(ficparo);
5559: fclose(ficres);
5560:
5561:
5562: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
5563:
5564: strcpy(filerespl,"pl");
5565: strcat(filerespl,fileres);
5566: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5567: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5568: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5569: }
5570: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5571: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5572: pstamp(ficrespl);
5573: fprintf(ficrespl,"# Period (stable) prevalence \n");
5574: fprintf(ficrespl,"#Age ");
5575: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5576: fprintf(ficrespl,"\n");
5577:
5578: prlim=matrix(1,nlstate,1,nlstate);
5579:
5580: agebase=ageminpar;
5581: agelim=agemaxpar;
5582: ftolpl=1.e-10;
5583: i1=cptcoveff;
5584: if (cptcovn < 1){i1=1;}
5585:
5586: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5587: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5588: k=k+1;
5589: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
5590: fprintf(ficrespl,"\n#******");
5591: printf("\n#******");
5592: fprintf(ficlog,"\n#******");
5593: for(j=1;j<=cptcoveff;j++) {
5594: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5595: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5596: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5597: }
5598: fprintf(ficrespl,"******\n");
5599: printf("******\n");
5600: fprintf(ficlog,"******\n");
5601:
5602: for (age=agebase; age<=agelim; age++){
5603: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5604: fprintf(ficrespl,"%.0f ",age );
5605: for(j=1;j<=cptcoveff;j++)
5606: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5607: for(i=1; i<=nlstate;i++)
5608: fprintf(ficrespl," %.5f", prlim[i][i]);
5609: fprintf(ficrespl,"\n");
5610: }
5611: }
5612: }
5613: fclose(ficrespl);
5614:
5615: /*------------- h Pij x at various ages ------------*/
5616:
5617: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5618: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5619: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
5620: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
5621: }
5622: printf("Computing pij: result on file '%s' \n", filerespij);
5623: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
5624:
5625: stepsize=(int) (stepm+YEARM-1)/YEARM;
5626: /*if (stepm<=24) stepsize=2;*/
5627:
5628: agelim=AGESUP;
5629: hstepm=stepsize*YEARM; /* Every year of age */
5630: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
5631:
5632: /* hstepm=1; aff par mois*/
5633: pstamp(ficrespij);
5634: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5635: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5636: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5637: k=k+1;
5638: fprintf(ficrespij,"\n#****** ");
5639: for(j=1;j<=cptcoveff;j++)
5640: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5641: fprintf(ficrespij,"******\n");
5642:
5643: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5644: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5645: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5646:
5647: /* nhstepm=nhstepm*YEARM; aff par mois*/
5648:
5649: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5650: oldm=oldms;savm=savms;
5651: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5652: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
5653: for(i=1; i<=nlstate;i++)
5654: for(j=1; j<=nlstate+ndeath;j++)
5655: fprintf(ficrespij," %1d-%1d",i,j);
5656: fprintf(ficrespij,"\n");
5657: for (h=0; h<=nhstepm; h++){
5658: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
5659: for(i=1; i<=nlstate;i++)
5660: for(j=1; j<=nlstate+ndeath;j++)
5661: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
5662: fprintf(ficrespij,"\n");
5663: }
5664: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5665: fprintf(ficrespij,"\n");
5666: }
5667: }
5668: }
5669:
5670: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
5671:
5672: fclose(ficrespij);
5673:
5674: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5675: for(i=1;i<=AGESUP;i++)
5676: for(j=1;j<=NCOVMAX;j++)
5677: for(k=1;k<=NCOVMAX;k++)
5678: probs[i][j][k]=0.;
5679:
5680: /*---------- Forecasting ------------------*/
5681: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
5682: if(prevfcast==1){
5683: /* if(stepm ==1){*/
5684: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
5685: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
5686: /* } */
5687: /* else{ */
5688: /* erreur=108; */
5689: /* 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); */
5690: /* 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); */
5691: /* } */
5692: }
5693:
5694:
5695: /*---------- Health expectancies and variances ------------*/
5696:
5697: strcpy(filerest,"t");
5698: strcat(filerest,fileres);
5699: if((ficrest=fopen(filerest,"w"))==NULL) {
5700: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
5701: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
5702: }
5703: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
5704: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
5705:
5706:
5707: strcpy(filerese,"e");
5708: strcat(filerese,fileres);
5709: if((ficreseij=fopen(filerese,"w"))==NULL) {
5710: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5711: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5712: }
5713: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
5714: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
5715:
5716: strcpy(fileresstde,"stde");
5717: strcat(fileresstde,fileres);
5718: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
5719: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5720: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5721: }
5722: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5723: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5724:
5725: strcpy(filerescve,"cve");
5726: strcat(filerescve,fileres);
5727: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
5728: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5729: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5730: }
5731: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5732: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5733:
5734: strcpy(fileresv,"v");
5735: strcat(fileresv,fileres);
5736: if((ficresvij=fopen(fileresv,"w"))==NULL) {
5737: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
5738: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
5739: }
5740: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5741: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5742:
5743: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
5744: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5745: /* 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",\
5746: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
5747: */
5748:
5749: if (mobilav!=0) {
5750: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5751: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
5752: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5753: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5754: }
5755: }
5756:
5757: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5758: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5759: k=k+1;
5760: fprintf(ficrest,"\n#****** ");
5761: for(j=1;j<=cptcoveff;j++)
5762: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5763: fprintf(ficrest,"******\n");
5764:
5765: fprintf(ficreseij,"\n#****** ");
5766: fprintf(ficresstdeij,"\n#****** ");
5767: fprintf(ficrescveij,"\n#****** ");
5768: for(j=1;j<=cptcoveff;j++) {
5769: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5770: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5771: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5772: }
5773: fprintf(ficreseij,"******\n");
5774: fprintf(ficresstdeij,"******\n");
5775: fprintf(ficrescveij,"******\n");
5776:
5777: fprintf(ficresvij,"\n#****** ");
5778: for(j=1;j<=cptcoveff;j++)
5779: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5780: fprintf(ficresvij,"******\n");
5781:
5782: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5783: oldm=oldms;savm=savms;
5784: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
5785: cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
5786:
5787: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5788: oldm=oldms;savm=savms;
5789: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
5790: if(popbased==1){
5791: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
5792: }
5793:
5794: pstamp(ficrest);
5795: fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
5796: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5797: fprintf(ficrest,"\n");
5798:
5799: epj=vector(1,nlstate+1);
5800: for(age=bage; age <=fage ;age++){
5801: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5802: if (popbased==1) {
5803: if(mobilav ==0){
5804: for(i=1; i<=nlstate;i++)
5805: prlim[i][i]=probs[(int)age][i][k];
5806: }else{ /* mobilav */
5807: for(i=1; i<=nlstate;i++)
5808: prlim[i][i]=mobaverage[(int)age][i][k];
5809: }
5810: }
5811:
5812: fprintf(ficrest," %4.0f",age);
5813: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5814: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5815: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5816: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5817: }
5818: epj[nlstate+1] +=epj[j];
5819: }
5820:
5821: for(i=1, vepp=0.;i <=nlstate;i++)
5822: for(j=1;j <=nlstate;j++)
5823: vepp += vareij[i][j][(int)age];
5824: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5825: for(j=1;j <=nlstate;j++){
5826: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5827: }
5828: fprintf(ficrest,"\n");
5829: }
5830: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5831: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5832: free_vector(epj,1,nlstate+1);
5833: }
5834: }
5835: free_vector(weight,1,n);
5836: free_imatrix(Tvard,1,15,1,2);
5837: free_imatrix(s,1,maxwav+1,1,n);
5838: free_matrix(anint,1,maxwav,1,n);
5839: free_matrix(mint,1,maxwav,1,n);
5840: free_ivector(cod,1,n);
5841: free_ivector(tab,1,NCOVMAX);
5842: fclose(ficreseij);
5843: fclose(ficresstdeij);
5844: fclose(ficrescveij);
5845: fclose(ficresvij);
5846: fclose(ficrest);
5847: fclose(ficpar);
5848:
5849: /*------- Variance of period (stable) prevalence------*/
5850:
5851: strcpy(fileresvpl,"vpl");
5852: strcat(fileresvpl,fileres);
5853: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
5854: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
5855: exit(0);
5856: }
5857: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
5858:
5859: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5860: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5861: k=k+1;
5862: fprintf(ficresvpl,"\n#****** ");
5863: for(j=1;j<=cptcoveff;j++)
5864: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5865: fprintf(ficresvpl,"******\n");
5866:
5867: varpl=matrix(1,nlstate,(int) bage, (int) fage);
5868: oldm=oldms;savm=savms;
5869: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
5870: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
5871: }
5872: }
5873:
5874: fclose(ficresvpl);
5875:
5876: /*---------- End : free ----------------*/
5877: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5878: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5879:
5880: } /* mle==-3 arrives here for freeing */
5881: free_matrix(prlim,1,nlstate,1,nlstate);
5882: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
5883: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
5884: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
5885: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
5886: free_matrix(covar,0,NCOVMAX,1,n);
5887: free_matrix(matcov,1,npar,1,npar);
5888: /*free_vector(delti,1,npar);*/
5889: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5890: free_matrix(agev,1,maxwav,1,imx);
5891: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5892:
5893: free_ivector(ncodemax,1,8);
5894: free_ivector(Tvar,1,15);
5895: free_ivector(Tprod,1,15);
5896: free_ivector(Tvaraff,1,15);
5897: free_ivector(Tage,1,15);
5898: free_ivector(Tcode,1,100);
5899:
5900: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
5901: free_imatrix(codtab,1,100,1,10);
5902: fflush(fichtm);
5903: fflush(ficgp);
5904:
5905:
5906: if((nberr >0) || (nbwarn>0)){
5907: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
5908: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
5909: }else{
5910: printf("End of Imach\n");
5911: fprintf(ficlog,"End of Imach\n");
5912: }
5913: printf("See log file on %s\n",filelog);
5914: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
5915: (void) gettimeofday(&end_time,&tzp);
5916: tm = *localtime(&end_time.tv_sec);
5917: tmg = *gmtime(&end_time.tv_sec);
5918: strcpy(strtend,asctime(&tm));
5919: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
5920: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
5921: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5922:
5923: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5924: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5925: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5926: /* printf("Total time was %d uSec.\n", total_usecs);*/
5927: /* if(fileappend(fichtm,optionfilehtm)){ */
5928: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
5929: fclose(fichtm);
5930: fclose(fichtmcov);
5931: fclose(ficgp);
5932: fclose(ficlog);
5933: /*------ End -----------*/
5934:
5935:
5936: printf("Before Current directory %s!\n",pathcd);
5937: if(chdir(pathcd) != 0)
5938: printf("Can't move to directory %s!\n",path);
5939: if(getcwd(pathcd,MAXLINE) > 0)
5940: printf("Current directory %s!\n",pathcd);
5941: /*strcat(plotcmd,CHARSEPARATOR);*/
5942: sprintf(plotcmd,"gnuplot");
5943: #ifndef UNIX
5944: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
5945: #endif
5946: if(!stat(plotcmd,&info)){
5947: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
5948: if(!stat(getenv("GNUPLOTBIN"),&info)){
5949: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
5950: }else
5951: strcpy(pplotcmd,plotcmd);
5952: #ifdef UNIX
5953: strcpy(plotcmd,GNUPLOTPROGRAM);
5954: if(!stat(plotcmd,&info)){
5955: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
5956: }else
5957: strcpy(pplotcmd,plotcmd);
5958: #endif
5959: }else
5960: strcpy(pplotcmd,plotcmd);
5961:
5962: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
5963: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
5964:
5965: if((outcmd=system(plotcmd)) != 0){
5966: printf("\n Problem with gnuplot\n");
5967: }
5968: printf(" Wait...");
5969: while (z[0] != 'q') {
5970: /* chdir(path); */
5971: printf("\nType e to edit output files, g to graph again and q for exiting: ");
5972: scanf("%s",z);
5973: /* if (z[0] == 'c') system("./imach"); */
5974: if (z[0] == 'e') {
5975: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
5976: system(optionfilehtm);
5977: }
5978: else if (z[0] == 'g') system(plotcmd);
5979: else if (z[0] == 'q') exit(0);
5980: }
5981: end:
5982: while (z[0] != 'q') {
5983: printf("\nType q for exiting: ");
5984: scanf("%s",z);
5985: }
5986: }
5987:
5988:
5989:
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