1: /* $Id: imach.c,v 1.113 2006/02/24 14:20:24 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.113 2006/02/24 14:20:24 brouard
5: (Module): Memory leaks checks with valgrind and:
6: datafile was not closed, some imatrix were not freed and on matrix
7: allocation too.
8:
9: Revision 1.112 2006/01/30 09:55:26 brouard
10: (Module): Back to gnuplot.exe instead of wgnuplot.exe
11:
12: Revision 1.111 2006/01/25 20:38:18 brouard
13: (Module): Lots of cleaning and bugs added (Gompertz)
14: (Module): Comments can be added in data file. Missing date values
15: can be a simple dot '.'.
16:
17: Revision 1.110 2006/01/25 00:51:50 brouard
18: (Module): Lots of cleaning and bugs added (Gompertz)
19:
20: Revision 1.109 2006/01/24 19:37:15 brouard
21: (Module): Comments (lines starting with a #) are allowed in data.
22:
23: Revision 1.108 2006/01/19 18:05:42 lievre
24: Gnuplot problem appeared...
25: To be fixed
26:
27: Revision 1.107 2006/01/19 16:20:37 brouard
28: Test existence of gnuplot in imach path
29:
30: Revision 1.106 2006/01/19 13:24:36 brouard
31: Some cleaning and links added in html output
32:
33: Revision 1.105 2006/01/05 20:23:19 lievre
34: *** empty log message ***
35:
36: Revision 1.104 2005/09/30 16:11:43 lievre
37: (Module): sump fixed, loop imx fixed, and simplifications.
38: (Module): If the status is missing at the last wave but we know
39: that the person is alive, then we can code his/her status as -2
40: (instead of missing=-1 in earlier versions) and his/her
41: contributions to the likelihood is 1 - Prob of dying from last
42: health status (= 1-p13= p11+p12 in the easiest case of somebody in
43: the healthy state at last known wave). Version is 0.98
44:
45: Revision 1.103 2005/09/30 15:54:49 lievre
46: (Module): sump fixed, loop imx fixed, and simplifications.
47:
48: Revision 1.102 2004/09/15 17:31:30 brouard
49: Add the possibility to read data file including tab characters.
50:
51: Revision 1.101 2004/09/15 10:38:38 brouard
52: Fix on curr_time
53:
54: Revision 1.100 2004/07/12 18:29:06 brouard
55: Add version for Mac OS X. Just define UNIX in Makefile
56:
57: Revision 1.99 2004/06/05 08:57:40 brouard
58: *** empty log message ***
59:
60: Revision 1.98 2004/05/16 15:05:56 brouard
61: New version 0.97 . First attempt to estimate force of mortality
62: directly from the data i.e. without the need of knowing the health
63: state at each age, but using a Gompertz model: log u =a + b*age .
64: This is the basic analysis of mortality and should be done before any
65: other analysis, in order to test if the mortality estimated from the
66: cross-longitudinal survey is different from the mortality estimated
67: from other sources like vital statistic data.
68:
69: The same imach parameter file can be used but the option for mle should be -3.
70:
71: Agnès, who wrote this part of the code, tried to keep most of the
72: former routines in order to include the new code within the former code.
73:
74: The output is very simple: only an estimate of the intercept and of
75: the slope with 95% confident intervals.
76:
77: Current limitations:
78: A) Even if you enter covariates, i.e. with the
79: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
80: B) There is no computation of Life Expectancy nor Life Table.
81:
82: Revision 1.97 2004/02/20 13:25:42 lievre
83: Version 0.96d. Population forecasting command line is (temporarily)
84: suppressed.
85:
86: Revision 1.96 2003/07/15 15:38:55 brouard
87: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
88: rewritten within the same printf. Workaround: many printfs.
89:
90: Revision 1.95 2003/07/08 07:54:34 brouard
91: * imach.c (Repository):
92: (Repository): Using imachwizard code to output a more meaningful covariance
93: matrix (cov(a12,c31) instead of numbers.
94:
95: Revision 1.94 2003/06/27 13:00:02 brouard
96: Just cleaning
97:
98: Revision 1.93 2003/06/25 16:33:55 brouard
99: (Module): On windows (cygwin) function asctime_r doesn't
100: exist so I changed back to asctime which exists.
101: (Module): Version 0.96b
102:
103: Revision 1.92 2003/06/25 16:30:45 brouard
104: (Module): On windows (cygwin) function asctime_r doesn't
105: exist so I changed back to asctime which exists.
106:
107: Revision 1.91 2003/06/25 15:30:29 brouard
108: * imach.c (Repository): Duplicated warning errors corrected.
109: (Repository): Elapsed time after each iteration is now output. It
110: helps to forecast when convergence will be reached. Elapsed time
111: is stamped in powell. We created a new html file for the graphs
112: concerning matrix of covariance. It has extension -cov.htm.
113:
114: Revision 1.90 2003/06/24 12:34:15 brouard
115: (Module): Some bugs corrected for windows. Also, when
116: mle=-1 a template is output in file "or"mypar.txt with the design
117: of the covariance matrix to be input.
118:
119: Revision 1.89 2003/06/24 12:30:52 brouard
120: (Module): Some bugs corrected for windows. Also, when
121: mle=-1 a template is output in file "or"mypar.txt with the design
122: of the covariance matrix to be input.
123:
124: Revision 1.88 2003/06/23 17:54:56 brouard
125: * 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.
126:
127: Revision 1.87 2003/06/18 12:26:01 brouard
128: Version 0.96
129:
130: Revision 1.86 2003/06/17 20:04:08 brouard
131: (Module): Change position of html and gnuplot routines and added
132: routine fileappend.
133:
134: Revision 1.85 2003/06/17 13:12:43 brouard
135: * imach.c (Repository): Check when date of death was earlier that
136: current date of interview. It may happen when the death was just
137: prior to the death. In this case, dh was negative and likelihood
138: was wrong (infinity). We still send an "Error" but patch by
139: assuming that the date of death was just one stepm after the
140: interview.
141: (Repository): Because some people have very long ID (first column)
142: we changed int to long in num[] and we added a new lvector for
143: memory allocation. But we also truncated to 8 characters (left
144: truncation)
145: (Repository): No more line truncation errors.
146:
147: Revision 1.84 2003/06/13 21:44:43 brouard
148: * imach.c (Repository): Replace "freqsummary" at a correct
149: place. It differs from routine "prevalence" which may be called
150: many times. Probs is memory consuming and must be used with
151: parcimony.
152: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
153:
154: Revision 1.83 2003/06/10 13:39:11 lievre
155: *** empty log message ***
156:
157: Revision 1.82 2003/06/05 15:57:20 brouard
158: Add log in imach.c and fullversion number is now printed.
159:
160: */
161: /*
162: Interpolated Markov Chain
163:
164: Short summary of the programme:
165:
166: This program computes Healthy Life Expectancies from
167: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
168: first survey ("cross") where individuals from different ages are
169: interviewed on their health status or degree of disability (in the
170: case of a health survey which is our main interest) -2- at least a
171: second wave of interviews ("longitudinal") which measure each change
172: (if any) in individual health status. Health expectancies are
173: computed from the time spent in each health state according to a
174: model. More health states you consider, more time is necessary to reach the
175: Maximum Likelihood of the parameters involved in the model. The
176: simplest model is the multinomial logistic model where pij is the
177: probability to be observed in state j at the second wave
178: conditional to be observed in state i at the first wave. Therefore
179: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
180: 'age' is age and 'sex' is a covariate. If you want to have a more
181: complex model than "constant and age", you should modify the program
182: where the markup *Covariates have to be included here again* invites
183: you to do it. More covariates you add, slower the
184: convergence.
185:
186: The advantage of this computer programme, compared to a simple
187: multinomial logistic model, is clear when the delay between waves is not
188: identical for each individual. Also, if a individual missed an
189: intermediate interview, the information is lost, but taken into
190: account using an interpolation or extrapolation.
191:
192: hPijx is the probability to be observed in state i at age x+h
193: conditional to the observed state i at age x. The delay 'h' can be
194: split into an exact number (nh*stepm) of unobserved intermediate
195: states. This elementary transition (by month, quarter,
196: semester or year) is modelled as a multinomial logistic. The hPx
197: matrix is simply the matrix product of nh*stepm elementary matrices
198: and the contribution of each individual to the likelihood is simply
199: hPijx.
200:
201: Also this programme outputs the covariance matrix of the parameters but also
202: of the life expectancies. It also computes the stable prevalence.
203:
204: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
205: Institut national d'études démographiques, Paris.
206: This software have been partly granted by Euro-REVES, a concerted action
207: from the European Union.
208: It is copyrighted identically to a GNU software product, ie programme and
209: software can be distributed freely for non commercial use. Latest version
210: can be accessed at http://euroreves.ined.fr/imach .
211:
212: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
213: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
214:
215: **********************************************************************/
216: /*
217: main
218: read parameterfile
219: read datafile
220: concatwav
221: freqsummary
222: if (mle >= 1)
223: mlikeli
224: print results files
225: if mle==1
226: computes hessian
227: read end of parameter file: agemin, agemax, bage, fage, estepm
228: begin-prev-date,...
229: open gnuplot file
230: open html file
231: stable prevalence
232: for age prevalim()
233: h Pij x
234: variance of p varprob
235: forecasting if prevfcast==1 prevforecast call prevalence()
236: health expectancies
237: Variance-covariance of DFLE
238: prevalence()
239: movingaverage()
240: varevsij()
241: if popbased==1 varevsij(,popbased)
242: total life expectancies
243: Variance of stable prevalence
244: end
245: */
246:
247:
248:
249:
250: #include <math.h>
251: #include <stdio.h>
252: #include <stdlib.h>
253: #include <string.h>
254: #include <unistd.h>
255:
256: #include <limits.h>
257: #include <sys/types.h>
258: #include <sys/stat.h>
259: #include <errno.h>
260: extern int errno;
261:
262: /* #include <sys/time.h> */
263: #include <time.h>
264: #include "timeval.h"
265:
266: /* #include <libintl.h> */
267: /* #define _(String) gettext (String) */
268:
269: #define MAXLINE 256
270:
271: #define GNUPLOTPROGRAM "gnuplot"
272: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
273: #define FILENAMELENGTH 132
274:
275: #define GLOCK_ERROR_NOPATH -1 /* empty path */
276: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
277:
278: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
279: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
280:
281: #define NINTERVMAX 8
282: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
283: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
284: #define NCOVMAX 8 /* Maximum number of covariates */
285: #define MAXN 20000
286: #define YEARM 12. /* Number of months per year */
287: #define AGESUP 130
288: #define AGEBASE 40
289: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
290: #ifdef UNIX
291: #define DIRSEPARATOR '/'
292: #define CHARSEPARATOR "/"
293: #define ODIRSEPARATOR '\\'
294: #else
295: #define DIRSEPARATOR '\\'
296: #define CHARSEPARATOR "\\"
297: #define ODIRSEPARATOR '/'
298: #endif
299:
300: /* $Id: imach.c,v 1.113 2006/02/24 14:20:24 brouard Exp $ */
301: /* $State: Exp $ */
302:
303: char version[]="Imach version 0.98b, January 2006, INED-EUROREVES ";
304: char fullversion[]="$Revision: 1.113 $ $Date: 2006/02/24 14:20:24 $";
305: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
306: int nvar;
307: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
308: int npar=NPARMAX;
309: int nlstate=2; /* Number of live states */
310: int ndeath=1; /* Number of dead states */
311: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
312: int popbased=0;
313:
314: int *wav; /* Number of waves for this individuual 0 is possible */
315: int maxwav; /* Maxim number of waves */
316: int jmin, jmax; /* min, max spacing between 2 waves */
317: int ijmin, ijmax; /* Individuals having jmin and jmax */
318: int gipmx, gsw; /* Global variables on the number of contributions
319: to the likelihood and the sum of weights (done by funcone)*/
320: int mle, weightopt;
321: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
322: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
323: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
324: * wave mi and wave mi+1 is not an exact multiple of stepm. */
325: double jmean; /* Mean space between 2 waves */
326: double **oldm, **newm, **savm; /* Working pointers to matrices */
327: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
328: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
329: FILE *ficlog, *ficrespow;
330: int globpr; /* Global variable for printing or not */
331: double fretone; /* Only one call to likelihood */
332: long ipmx; /* Number of contributions */
333: double sw; /* Sum of weights */
334: char filerespow[FILENAMELENGTH];
335: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
336: FILE *ficresilk;
337: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
338: FILE *ficresprobmorprev;
339: FILE *fichtm, *fichtmcov; /* Html File */
340: FILE *ficreseij;
341: char filerese[FILENAMELENGTH];
342: FILE *ficresvij;
343: char fileresv[FILENAMELENGTH];
344: FILE *ficresvpl;
345: char fileresvpl[FILENAMELENGTH];
346: char title[MAXLINE];
347: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
348: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
349: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
350: char command[FILENAMELENGTH];
351: int outcmd=0;
352:
353: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
354:
355: char filelog[FILENAMELENGTH]; /* Log file */
356: char filerest[FILENAMELENGTH];
357: char fileregp[FILENAMELENGTH];
358: char popfile[FILENAMELENGTH];
359:
360: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
361:
362: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
363: struct timezone tzp;
364: extern int gettimeofday();
365: struct tm tmg, tm, tmf, *gmtime(), *localtime();
366: long time_value;
367: extern long time();
368: char strcurr[80], strfor[80];
369:
370: char *endptr;
371: long lval;
372:
373: #define NR_END 1
374: #define FREE_ARG char*
375: #define FTOL 1.0e-10
376:
377: #define NRANSI
378: #define ITMAX 200
379:
380: #define TOL 2.0e-4
381:
382: #define CGOLD 0.3819660
383: #define ZEPS 1.0e-10
384: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
385:
386: #define GOLD 1.618034
387: #define GLIMIT 100.0
388: #define TINY 1.0e-20
389:
390: static double maxarg1,maxarg2;
391: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
392: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
393:
394: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
395: #define rint(a) floor(a+0.5)
396:
397: static double sqrarg;
398: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
399: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
400: int agegomp= AGEGOMP;
401:
402: int imx;
403: int stepm=1;
404: /* Stepm, step in month: minimum step interpolation*/
405:
406: int estepm;
407: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
408:
409: int m,nb;
410: long *num;
411: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
412: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
413: double **pmmij, ***probs;
414: double *ageexmed,*agecens;
415: double dateintmean=0;
416:
417: double *weight;
418: int **s; /* Status */
419: double *agedc, **covar, idx;
420: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
421: double *lsurv, *lpop, *tpop;
422:
423: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
424: double ftolhess; /* Tolerance for computing hessian */
425:
426: /**************** split *************************/
427: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
428: {
429: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
430: the name of the file (name), its extension only (ext) and its first part of the name (finame)
431: */
432: char *ss; /* pointer */
433: int l1, l2; /* length counters */
434:
435: l1 = strlen(path ); /* length of path */
436: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
437: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
438: if ( ss == NULL ) { /* no directory, so determine current directory */
439: strcpy( name, path ); /* we got the fullname name because no directory */
440: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
441: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
442: /* get current working directory */
443: /* extern char* getcwd ( char *buf , int len);*/
444: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
445: return( GLOCK_ERROR_GETCWD );
446: }
447: /* got dirc from getcwd*/
448: printf(" DIRC = %s \n",dirc);
449: } else { /* strip direcotry from path */
450: ss++; /* after this, the filename */
451: l2 = strlen( ss ); /* length of filename */
452: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
453: strcpy( name, ss ); /* save file name */
454: strncpy( dirc, path, l1 - l2 ); /* now the directory */
455: dirc[l1-l2] = 0; /* add zero */
456: printf(" DIRC2 = %s \n",dirc);
457: }
458: /* We add a separator at the end of dirc if not exists */
459: l1 = strlen( dirc ); /* length of directory */
460: if( dirc[l1-1] != DIRSEPARATOR ){
461: dirc[l1] = DIRSEPARATOR;
462: dirc[l1+1] = 0;
463: printf(" DIRC3 = %s \n",dirc);
464: }
465: ss = strrchr( name, '.' ); /* find last / */
466: if (ss >0){
467: ss++;
468: strcpy(ext,ss); /* save extension */
469: l1= strlen( name);
470: l2= strlen(ss)+1;
471: strncpy( finame, name, l1-l2);
472: finame[l1-l2]= 0;
473: }
474:
475: return( 0 ); /* we're done */
476: }
477:
478:
479: /******************************************/
480:
481: void replace_back_to_slash(char *s, char*t)
482: {
483: int i;
484: int lg=0;
485: i=0;
486: lg=strlen(t);
487: for(i=0; i<= lg; i++) {
488: (s[i] = t[i]);
489: if (t[i]== '\\') s[i]='/';
490: }
491: }
492:
493: int nbocc(char *s, char occ)
494: {
495: int i,j=0;
496: int lg=20;
497: i=0;
498: lg=strlen(s);
499: for(i=0; i<= lg; i++) {
500: if (s[i] == occ ) j++;
501: }
502: return j;
503: }
504:
505: void cutv(char *u,char *v, char*t, char occ)
506: {
507: /* cuts string t into u and v where u ends before first occurence of char 'occ'
508: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
509: gives u="abcedf" and v="ghi2j" */
510: int i,lg,j,p=0;
511: i=0;
512: for(j=0; j<=strlen(t)-1; j++) {
513: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
514: }
515:
516: lg=strlen(t);
517: for(j=0; j<p; j++) {
518: (u[j] = t[j]);
519: }
520: u[p]='\0';
521:
522: for(j=0; j<= lg; j++) {
523: if (j>=(p+1))(v[j-p-1] = t[j]);
524: }
525: }
526:
527: /********************** nrerror ********************/
528:
529: void nrerror(char error_text[])
530: {
531: fprintf(stderr,"ERREUR ...\n");
532: fprintf(stderr,"%s\n",error_text);
533: exit(EXIT_FAILURE);
534: }
535: /*********************** vector *******************/
536: double *vector(int nl, int nh)
537: {
538: double *v;
539: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
540: if (!v) nrerror("allocation failure in vector");
541: return v-nl+NR_END;
542: }
543:
544: /************************ free vector ******************/
545: void free_vector(double*v, int nl, int nh)
546: {
547: free((FREE_ARG)(v+nl-NR_END));
548: }
549:
550: /************************ivector *******************************/
551: int *ivector(long nl,long nh)
552: {
553: int *v;
554: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
555: if (!v) nrerror("allocation failure in ivector");
556: return v-nl+NR_END;
557: }
558:
559: /******************free ivector **************************/
560: void free_ivector(int *v, long nl, long nh)
561: {
562: free((FREE_ARG)(v+nl-NR_END));
563: }
564:
565: /************************lvector *******************************/
566: long *lvector(long nl,long nh)
567: {
568: long *v;
569: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
570: if (!v) nrerror("allocation failure in ivector");
571: return v-nl+NR_END;
572: }
573:
574: /******************free lvector **************************/
575: void free_lvector(long *v, long nl, long nh)
576: {
577: free((FREE_ARG)(v+nl-NR_END));
578: }
579:
580: /******************* imatrix *******************************/
581: int **imatrix(long nrl, long nrh, long ncl, long nch)
582: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
583: {
584: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
585: int **m;
586:
587: /* allocate pointers to rows */
588: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
589: if (!m) nrerror("allocation failure 1 in matrix()");
590: m += NR_END;
591: m -= nrl;
592:
593:
594: /* allocate rows and set pointers to them */
595: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
596: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
597: m[nrl] += NR_END;
598: m[nrl] -= ncl;
599:
600: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
601:
602: /* return pointer to array of pointers to rows */
603: return m;
604: }
605:
606: /****************** free_imatrix *************************/
607: void free_imatrix(m,nrl,nrh,ncl,nch)
608: int **m;
609: long nch,ncl,nrh,nrl;
610: /* free an int matrix allocated by imatrix() */
611: {
612: free((FREE_ARG) (m[nrl]+ncl-NR_END));
613: free((FREE_ARG) (m+nrl-NR_END));
614: }
615:
616: /******************* matrix *******************************/
617: double **matrix(long nrl, long nrh, long ncl, long nch)
618: {
619: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
620: double **m;
621:
622: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
623: if (!m) nrerror("allocation failure 1 in matrix()");
624: m += NR_END;
625: m -= nrl;
626:
627: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
628: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
629: m[nrl] += NR_END;
630: m[nrl] -= ncl;
631:
632: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
633: return m;
634: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
635: */
636: }
637:
638: /*************************free matrix ************************/
639: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
640: {
641: free((FREE_ARG)(m[nrl]+ncl-NR_END));
642: free((FREE_ARG)(m+nrl-NR_END));
643: }
644:
645: /******************* ma3x *******************************/
646: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
647: {
648: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
649: double ***m;
650:
651: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
652: if (!m) nrerror("allocation failure 1 in matrix()");
653: m += NR_END;
654: m -= nrl;
655:
656: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
657: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
658: m[nrl] += NR_END;
659: m[nrl] -= ncl;
660:
661: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
662:
663: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
664: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
665: m[nrl][ncl] += NR_END;
666: m[nrl][ncl] -= nll;
667: for (j=ncl+1; j<=nch; j++)
668: m[nrl][j]=m[nrl][j-1]+nlay;
669:
670: for (i=nrl+1; i<=nrh; i++) {
671: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
672: for (j=ncl+1; j<=nch; j++)
673: m[i][j]=m[i][j-1]+nlay;
674: }
675: return m;
676: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
677: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
678: */
679: }
680:
681: /*************************free ma3x ************************/
682: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
683: {
684: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
685: free((FREE_ARG)(m[nrl]+ncl-NR_END));
686: free((FREE_ARG)(m+nrl-NR_END));
687: }
688:
689: /*************** function subdirf ***********/
690: char *subdirf(char fileres[])
691: {
692: /* Caution optionfilefiname is hidden */
693: strcpy(tmpout,optionfilefiname);
694: strcat(tmpout,"/"); /* Add to the right */
695: strcat(tmpout,fileres);
696: return tmpout;
697: }
698:
699: /*************** function subdirf2 ***********/
700: char *subdirf2(char fileres[], char *preop)
701: {
702:
703: /* Caution optionfilefiname is hidden */
704: strcpy(tmpout,optionfilefiname);
705: strcat(tmpout,"/");
706: strcat(tmpout,preop);
707: strcat(tmpout,fileres);
708: return tmpout;
709: }
710:
711: /*************** function subdirf3 ***********/
712: char *subdirf3(char fileres[], char *preop, char *preop2)
713: {
714:
715: /* Caution optionfilefiname is hidden */
716: strcpy(tmpout,optionfilefiname);
717: strcat(tmpout,"/");
718: strcat(tmpout,preop);
719: strcat(tmpout,preop2);
720: strcat(tmpout,fileres);
721: return tmpout;
722: }
723:
724: /***************** f1dim *************************/
725: extern int ncom;
726: extern double *pcom,*xicom;
727: extern double (*nrfunc)(double []);
728:
729: double f1dim(double x)
730: {
731: int j;
732: double f;
733: double *xt;
734:
735: xt=vector(1,ncom);
736: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
737: f=(*nrfunc)(xt);
738: free_vector(xt,1,ncom);
739: return f;
740: }
741:
742: /*****************brent *************************/
743: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
744: {
745: int iter;
746: double a,b,d,etemp;
747: double fu,fv,fw,fx;
748: double ftemp;
749: double p,q,r,tol1,tol2,u,v,w,x,xm;
750: double e=0.0;
751:
752: a=(ax < cx ? ax : cx);
753: b=(ax > cx ? ax : cx);
754: x=w=v=bx;
755: fw=fv=fx=(*f)(x);
756: for (iter=1;iter<=ITMAX;iter++) {
757: xm=0.5*(a+b);
758: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
759: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
760: printf(".");fflush(stdout);
761: fprintf(ficlog,".");fflush(ficlog);
762: #ifdef DEBUG
763: 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);
764: 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);
765: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
766: #endif
767: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
768: *xmin=x;
769: return fx;
770: }
771: ftemp=fu;
772: if (fabs(e) > tol1) {
773: r=(x-w)*(fx-fv);
774: q=(x-v)*(fx-fw);
775: p=(x-v)*q-(x-w)*r;
776: q=2.0*(q-r);
777: if (q > 0.0) p = -p;
778: q=fabs(q);
779: etemp=e;
780: e=d;
781: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
782: d=CGOLD*(e=(x >= xm ? a-x : b-x));
783: else {
784: d=p/q;
785: u=x+d;
786: if (u-a < tol2 || b-u < tol2)
787: d=SIGN(tol1,xm-x);
788: }
789: } else {
790: d=CGOLD*(e=(x >= xm ? a-x : b-x));
791: }
792: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
793: fu=(*f)(u);
794: if (fu <= fx) {
795: if (u >= x) a=x; else b=x;
796: SHFT(v,w,x,u)
797: SHFT(fv,fw,fx,fu)
798: } else {
799: if (u < x) a=u; else b=u;
800: if (fu <= fw || w == x) {
801: v=w;
802: w=u;
803: fv=fw;
804: fw=fu;
805: } else if (fu <= fv || v == x || v == w) {
806: v=u;
807: fv=fu;
808: }
809: }
810: }
811: nrerror("Too many iterations in brent");
812: *xmin=x;
813: return fx;
814: }
815:
816: /****************** mnbrak ***********************/
817:
818: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
819: double (*func)(double))
820: {
821: double ulim,u,r,q, dum;
822: double fu;
823:
824: *fa=(*func)(*ax);
825: *fb=(*func)(*bx);
826: if (*fb > *fa) {
827: SHFT(dum,*ax,*bx,dum)
828: SHFT(dum,*fb,*fa,dum)
829: }
830: *cx=(*bx)+GOLD*(*bx-*ax);
831: *fc=(*func)(*cx);
832: while (*fb > *fc) {
833: r=(*bx-*ax)*(*fb-*fc);
834: q=(*bx-*cx)*(*fb-*fa);
835: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
836: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
837: ulim=(*bx)+GLIMIT*(*cx-*bx);
838: if ((*bx-u)*(u-*cx) > 0.0) {
839: fu=(*func)(u);
840: } else if ((*cx-u)*(u-ulim) > 0.0) {
841: fu=(*func)(u);
842: if (fu < *fc) {
843: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
844: SHFT(*fb,*fc,fu,(*func)(u))
845: }
846: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
847: u=ulim;
848: fu=(*func)(u);
849: } else {
850: u=(*cx)+GOLD*(*cx-*bx);
851: fu=(*func)(u);
852: }
853: SHFT(*ax,*bx,*cx,u)
854: SHFT(*fa,*fb,*fc,fu)
855: }
856: }
857:
858: /*************** linmin ************************/
859:
860: int ncom;
861: double *pcom,*xicom;
862: double (*nrfunc)(double []);
863:
864: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
865: {
866: double brent(double ax, double bx, double cx,
867: double (*f)(double), double tol, double *xmin);
868: double f1dim(double x);
869: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
870: double *fc, double (*func)(double));
871: int j;
872: double xx,xmin,bx,ax;
873: double fx,fb,fa;
874:
875: ncom=n;
876: pcom=vector(1,n);
877: xicom=vector(1,n);
878: nrfunc=func;
879: for (j=1;j<=n;j++) {
880: pcom[j]=p[j];
881: xicom[j]=xi[j];
882: }
883: ax=0.0;
884: xx=1.0;
885: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
886: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
887: #ifdef DEBUG
888: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
889: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
890: #endif
891: for (j=1;j<=n;j++) {
892: xi[j] *= xmin;
893: p[j] += xi[j];
894: }
895: free_vector(xicom,1,n);
896: free_vector(pcom,1,n);
897: }
898:
899: char *asc_diff_time(long time_sec, char ascdiff[])
900: {
901: long sec_left, days, hours, minutes;
902: days = (time_sec) / (60*60*24);
903: sec_left = (time_sec) % (60*60*24);
904: hours = (sec_left) / (60*60) ;
905: sec_left = (sec_left) %(60*60);
906: minutes = (sec_left) /60;
907: sec_left = (sec_left) % (60);
908: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
909: return ascdiff;
910: }
911:
912: /*************** powell ************************/
913: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
914: double (*func)(double []))
915: {
916: void linmin(double p[], double xi[], int n, double *fret,
917: double (*func)(double []));
918: int i,ibig,j;
919: double del,t,*pt,*ptt,*xit;
920: double fp,fptt;
921: double *xits;
922: int niterf, itmp;
923:
924: pt=vector(1,n);
925: ptt=vector(1,n);
926: xit=vector(1,n);
927: xits=vector(1,n);
928: *fret=(*func)(p);
929: for (j=1;j<=n;j++) pt[j]=p[j];
930: for (*iter=1;;++(*iter)) {
931: fp=(*fret);
932: ibig=0;
933: del=0.0;
934: last_time=curr_time;
935: (void) gettimeofday(&curr_time,&tzp);
936: 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);
937: /* 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);
938: fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
939: */
940: for (i=1;i<=n;i++) {
941: printf(" %d %.12f",i, p[i]);
942: fprintf(ficlog," %d %.12lf",i, p[i]);
943: fprintf(ficrespow," %.12lf", p[i]);
944: }
945: printf("\n");
946: fprintf(ficlog,"\n");
947: fprintf(ficrespow,"\n");fflush(ficrespow);
948: if(*iter <=3){
949: tm = *localtime(&curr_time.tv_sec);
950: strcpy(strcurr,asctime(&tm));
951: /* asctime_r(&tm,strcurr); */
952: forecast_time=curr_time;
953: itmp = strlen(strcurr);
954: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
955: strcurr[itmp-1]='\0';
956: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
957: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
958: for(niterf=10;niterf<=30;niterf+=10){
959: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
960: tmf = *localtime(&forecast_time.tv_sec);
961: /* asctime_r(&tmf,strfor); */
962: strcpy(strfor,asctime(&tmf));
963: itmp = strlen(strfor);
964: if(strfor[itmp-1]=='\n')
965: strfor[itmp-1]='\0';
966: 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);
967: 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);
968: }
969: }
970: for (i=1;i<=n;i++) {
971: for (j=1;j<=n;j++) xit[j]=xi[j][i];
972: fptt=(*fret);
973: #ifdef DEBUG
974: printf("fret=%lf \n",*fret);
975: fprintf(ficlog,"fret=%lf \n",*fret);
976: #endif
977: printf("%d",i);fflush(stdout);
978: fprintf(ficlog,"%d",i);fflush(ficlog);
979: linmin(p,xit,n,fret,func);
980: if (fabs(fptt-(*fret)) > del) {
981: del=fabs(fptt-(*fret));
982: ibig=i;
983: }
984: #ifdef DEBUG
985: printf("%d %.12e",i,(*fret));
986: fprintf(ficlog,"%d %.12e",i,(*fret));
987: for (j=1;j<=n;j++) {
988: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
989: printf(" x(%d)=%.12e",j,xit[j]);
990: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
991: }
992: for(j=1;j<=n;j++) {
993: printf(" p=%.12e",p[j]);
994: fprintf(ficlog," p=%.12e",p[j]);
995: }
996: printf("\n");
997: fprintf(ficlog,"\n");
998: #endif
999: }
1000: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1001: #ifdef DEBUG
1002: int k[2],l;
1003: k[0]=1;
1004: k[1]=-1;
1005: printf("Max: %.12e",(*func)(p));
1006: fprintf(ficlog,"Max: %.12e",(*func)(p));
1007: for (j=1;j<=n;j++) {
1008: printf(" %.12e",p[j]);
1009: fprintf(ficlog," %.12e",p[j]);
1010: }
1011: printf("\n");
1012: fprintf(ficlog,"\n");
1013: for(l=0;l<=1;l++) {
1014: for (j=1;j<=n;j++) {
1015: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1016: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1017: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1018: }
1019: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1020: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1021: }
1022: #endif
1023:
1024:
1025: free_vector(xit,1,n);
1026: free_vector(xits,1,n);
1027: free_vector(ptt,1,n);
1028: free_vector(pt,1,n);
1029: return;
1030: }
1031: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1032: for (j=1;j<=n;j++) {
1033: ptt[j]=2.0*p[j]-pt[j];
1034: xit[j]=p[j]-pt[j];
1035: pt[j]=p[j];
1036: }
1037: fptt=(*func)(ptt);
1038: if (fptt < fp) {
1039: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1040: if (t < 0.0) {
1041: linmin(p,xit,n,fret,func);
1042: for (j=1;j<=n;j++) {
1043: xi[j][ibig]=xi[j][n];
1044: xi[j][n]=xit[j];
1045: }
1046: #ifdef DEBUG
1047: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1048: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1049: for(j=1;j<=n;j++){
1050: printf(" %.12e",xit[j]);
1051: fprintf(ficlog," %.12e",xit[j]);
1052: }
1053: printf("\n");
1054: fprintf(ficlog,"\n");
1055: #endif
1056: }
1057: }
1058: }
1059: }
1060:
1061: /**** Prevalence limit (stable prevalence) ****************/
1062:
1063: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1064: {
1065: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1066: matrix by transitions matrix until convergence is reached */
1067:
1068: int i, ii,j,k;
1069: double min, max, maxmin, maxmax,sumnew=0.;
1070: double **matprod2();
1071: double **out, cov[NCOVMAX], **pmij();
1072: double **newm;
1073: double agefin, delaymax=50 ; /* Max number of years to converge */
1074:
1075: for (ii=1;ii<=nlstate+ndeath;ii++)
1076: for (j=1;j<=nlstate+ndeath;j++){
1077: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1078: }
1079:
1080: cov[1]=1.;
1081:
1082: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1083: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1084: newm=savm;
1085: /* Covariates have to be included here again */
1086: cov[2]=agefin;
1087:
1088: for (k=1; k<=cptcovn;k++) {
1089: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1090: /* 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]]);*/
1091: }
1092: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1093: for (k=1; k<=cptcovprod;k++)
1094: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1095:
1096: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1097: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1098: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1099: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1100:
1101: savm=oldm;
1102: oldm=newm;
1103: maxmax=0.;
1104: for(j=1;j<=nlstate;j++){
1105: min=1.;
1106: max=0.;
1107: for(i=1; i<=nlstate; i++) {
1108: sumnew=0;
1109: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1110: prlim[i][j]= newm[i][j]/(1-sumnew);
1111: max=FMAX(max,prlim[i][j]);
1112: min=FMIN(min,prlim[i][j]);
1113: }
1114: maxmin=max-min;
1115: maxmax=FMAX(maxmax,maxmin);
1116: }
1117: if(maxmax < ftolpl){
1118: return prlim;
1119: }
1120: }
1121: }
1122:
1123: /*************** transition probabilities ***************/
1124:
1125: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1126: {
1127: double s1, s2;
1128: /*double t34;*/
1129: int i,j,j1, nc, ii, jj;
1130:
1131: for(i=1; i<= nlstate; i++){
1132: for(j=1; j<i;j++){
1133: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1134: /*s2 += param[i][j][nc]*cov[nc];*/
1135: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1136: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1137: }
1138: ps[i][j]=s2;
1139: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1140: }
1141: for(j=i+1; j<=nlstate+ndeath;j++){
1142: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1143: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1144: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1145: }
1146: ps[i][j]=s2;
1147: }
1148: }
1149: /*ps[3][2]=1;*/
1150:
1151: for(i=1; i<= nlstate; i++){
1152: s1=0;
1153: for(j=1; j<i; j++)
1154: s1+=exp(ps[i][j]);
1155: for(j=i+1; j<=nlstate+ndeath; j++)
1156: s1+=exp(ps[i][j]);
1157: ps[i][i]=1./(s1+1.);
1158: for(j=1; j<i; j++)
1159: ps[i][j]= exp(ps[i][j])*ps[i][i];
1160: for(j=i+1; j<=nlstate+ndeath; j++)
1161: ps[i][j]= exp(ps[i][j])*ps[i][i];
1162: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1163: } /* end i */
1164:
1165: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1166: for(jj=1; jj<= nlstate+ndeath; jj++){
1167: ps[ii][jj]=0;
1168: ps[ii][ii]=1;
1169: }
1170: }
1171:
1172:
1173: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1174: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1175: /* printf("ddd %lf ",ps[ii][jj]); */
1176: /* } */
1177: /* printf("\n "); */
1178: /* } */
1179: /* printf("\n ");printf("%lf ",cov[2]); */
1180: /*
1181: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1182: goto end;*/
1183: return ps;
1184: }
1185:
1186: /**************** Product of 2 matrices ******************/
1187:
1188: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1189: {
1190: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1191: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1192: /* in, b, out are matrice of pointers which should have been initialized
1193: before: only the contents of out is modified. The function returns
1194: a pointer to pointers identical to out */
1195: long i, j, k;
1196: for(i=nrl; i<= nrh; i++)
1197: for(k=ncolol; k<=ncoloh; k++)
1198: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1199: out[i][k] +=in[i][j]*b[j][k];
1200:
1201: return out;
1202: }
1203:
1204:
1205: /************* Higher Matrix Product ***************/
1206:
1207: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1208: {
1209: /* Computes the transition matrix starting at age 'age' over
1210: 'nhstepm*hstepm*stepm' months (i.e. until
1211: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1212: nhstepm*hstepm matrices.
1213: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1214: (typically every 2 years instead of every month which is too big
1215: for the memory).
1216: Model is determined by parameters x and covariates have to be
1217: included manually here.
1218:
1219: */
1220:
1221: int i, j, d, h, k;
1222: double **out, cov[NCOVMAX];
1223: double **newm;
1224:
1225: /* Hstepm could be zero and should return the unit matrix */
1226: for (i=1;i<=nlstate+ndeath;i++)
1227: for (j=1;j<=nlstate+ndeath;j++){
1228: oldm[i][j]=(i==j ? 1.0 : 0.0);
1229: po[i][j][0]=(i==j ? 1.0 : 0.0);
1230: }
1231: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1232: for(h=1; h <=nhstepm; h++){
1233: for(d=1; d <=hstepm; d++){
1234: newm=savm;
1235: /* Covariates have to be included here again */
1236: cov[1]=1.;
1237: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1238: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1239: for (k=1; k<=cptcovage;k++)
1240: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1241: for (k=1; k<=cptcovprod;k++)
1242: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1243:
1244:
1245: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1246: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1247: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1248: pmij(pmmij,cov,ncovmodel,x,nlstate));
1249: savm=oldm;
1250: oldm=newm;
1251: }
1252: for(i=1; i<=nlstate+ndeath; i++)
1253: for(j=1;j<=nlstate+ndeath;j++) {
1254: po[i][j][h]=newm[i][j];
1255: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1256: */
1257: }
1258: } /* end h */
1259: return po;
1260: }
1261:
1262:
1263: /*************** log-likelihood *************/
1264: double func( double *x)
1265: {
1266: int i, ii, j, k, mi, d, kk;
1267: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1268: double **out;
1269: double sw; /* Sum of weights */
1270: double lli; /* Individual log likelihood */
1271: int s1, s2;
1272: double bbh, survp;
1273: long ipmx;
1274: /*extern weight */
1275: /* We are differentiating ll according to initial status */
1276: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1277: /*for(i=1;i<imx;i++)
1278: printf(" %d\n",s[4][i]);
1279: */
1280: cov[1]=1.;
1281:
1282: for(k=1; k<=nlstate; k++) ll[k]=0.;
1283:
1284: if(mle==1){
1285: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1286: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1287: for(mi=1; mi<= wav[i]-1; mi++){
1288: for (ii=1;ii<=nlstate+ndeath;ii++)
1289: for (j=1;j<=nlstate+ndeath;j++){
1290: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1291: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1292: }
1293: for(d=0; d<dh[mi][i]; d++){
1294: newm=savm;
1295: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1296: for (kk=1; kk<=cptcovage;kk++) {
1297: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1298: }
1299: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1300: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1301: savm=oldm;
1302: oldm=newm;
1303: } /* end mult */
1304:
1305: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1306: /* But now since version 0.9 we anticipate for bias at large stepm.
1307: * If stepm is larger than one month (smallest stepm) and if the exact delay
1308: * (in months) between two waves is not a multiple of stepm, we rounded to
1309: * the nearest (and in case of equal distance, to the lowest) interval but now
1310: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1311: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1312: * probability in order to take into account the bias as a fraction of the way
1313: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1314: * -stepm/2 to stepm/2 .
1315: * For stepm=1 the results are the same as for previous versions of Imach.
1316: * For stepm > 1 the results are less biased than in previous versions.
1317: */
1318: s1=s[mw[mi][i]][i];
1319: s2=s[mw[mi+1][i]][i];
1320: bbh=(double)bh[mi][i]/(double)stepm;
1321: /* bias bh is positive if real duration
1322: * is higher than the multiple of stepm and negative otherwise.
1323: */
1324: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1325: if( s2 > nlstate){
1326: /* i.e. if s2 is a death state and if the date of death is known
1327: then the contribution to the likelihood is the probability to
1328: die between last step unit time and current step unit time,
1329: which is also equal to probability to die before dh
1330: minus probability to die before dh-stepm .
1331: In version up to 0.92 likelihood was computed
1332: as if date of death was unknown. Death was treated as any other
1333: health state: the date of the interview describes the actual state
1334: and not the date of a change in health state. The former idea was
1335: to consider that at each interview the state was recorded
1336: (healthy, disable or death) and IMaCh was corrected; but when we
1337: introduced the exact date of death then we should have modified
1338: the contribution of an exact death to the likelihood. This new
1339: contribution is smaller and very dependent of the step unit
1340: stepm. It is no more the probability to die between last interview
1341: and month of death but the probability to survive from last
1342: interview up to one month before death multiplied by the
1343: probability to die within a month. Thanks to Chris
1344: Jackson for correcting this bug. Former versions increased
1345: mortality artificially. The bad side is that we add another loop
1346: which slows down the processing. The difference can be up to 10%
1347: lower mortality.
1348: */
1349: lli=log(out[s1][s2] - savm[s1][s2]);
1350:
1351:
1352: } else if (s2==-2) {
1353: for (j=1,survp=0. ; j<=nlstate; j++)
1354: survp += out[s1][j];
1355: lli= survp;
1356: }
1357:
1358: else if (s2==-4) {
1359: for (j=3,survp=0. ; j<=nlstate; j++)
1360: survp += out[s1][j];
1361: lli= survp;
1362: }
1363:
1364: else if (s2==-5) {
1365: for (j=1,survp=0. ; j<=2; j++)
1366: survp += out[s1][j];
1367: lli= survp;
1368: }
1369:
1370:
1371: else{
1372: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1373: /* 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 */
1374: }
1375: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1376: /*if(lli ==000.0)*/
1377: /*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); */
1378: ipmx +=1;
1379: sw += weight[i];
1380: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1381: } /* end of wave */
1382: } /* end of individual */
1383: } else if(mle==2){
1384: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1385: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1386: for(mi=1; mi<= wav[i]-1; mi++){
1387: for (ii=1;ii<=nlstate+ndeath;ii++)
1388: for (j=1;j<=nlstate+ndeath;j++){
1389: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1390: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1391: }
1392: for(d=0; d<=dh[mi][i]; d++){
1393: newm=savm;
1394: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1395: for (kk=1; kk<=cptcovage;kk++) {
1396: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1397: }
1398: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1399: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1400: savm=oldm;
1401: oldm=newm;
1402: } /* end mult */
1403:
1404: s1=s[mw[mi][i]][i];
1405: s2=s[mw[mi+1][i]][i];
1406: bbh=(double)bh[mi][i]/(double)stepm;
1407: 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 */
1408: ipmx +=1;
1409: sw += weight[i];
1410: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1411: } /* end of wave */
1412: } /* end of individual */
1413: } else if(mle==3){ /* exponential inter-extrapolation */
1414: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1415: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1416: for(mi=1; mi<= wav[i]-1; mi++){
1417: for (ii=1;ii<=nlstate+ndeath;ii++)
1418: for (j=1;j<=nlstate+ndeath;j++){
1419: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1420: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1421: }
1422: for(d=0; d<dh[mi][i]; d++){
1423: newm=savm;
1424: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1425: for (kk=1; kk<=cptcovage;kk++) {
1426: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1427: }
1428: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1429: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1430: savm=oldm;
1431: oldm=newm;
1432: } /* end mult */
1433:
1434: s1=s[mw[mi][i]][i];
1435: s2=s[mw[mi+1][i]][i];
1436: bbh=(double)bh[mi][i]/(double)stepm;
1437: 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 */
1438: ipmx +=1;
1439: sw += weight[i];
1440: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1441: } /* end of wave */
1442: } /* end of individual */
1443: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1444: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1445: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1446: for(mi=1; mi<= wav[i]-1; mi++){
1447: for (ii=1;ii<=nlstate+ndeath;ii++)
1448: for (j=1;j<=nlstate+ndeath;j++){
1449: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1450: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1451: }
1452: for(d=0; d<dh[mi][i]; d++){
1453: newm=savm;
1454: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1455: for (kk=1; kk<=cptcovage;kk++) {
1456: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1457: }
1458:
1459: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1460: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1461: savm=oldm;
1462: oldm=newm;
1463: } /* end mult */
1464:
1465: s1=s[mw[mi][i]][i];
1466: s2=s[mw[mi+1][i]][i];
1467: if( s2 > nlstate){
1468: lli=log(out[s1][s2] - savm[s1][s2]);
1469: }else{
1470: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1471: }
1472: ipmx +=1;
1473: sw += weight[i];
1474: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1475: /* 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]); */
1476: } /* end of wave */
1477: } /* end of individual */
1478: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1479: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1480: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1481: for(mi=1; mi<= wav[i]-1; mi++){
1482: for (ii=1;ii<=nlstate+ndeath;ii++)
1483: for (j=1;j<=nlstate+ndeath;j++){
1484: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1485: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1486: }
1487: for(d=0; d<dh[mi][i]; d++){
1488: newm=savm;
1489: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1490: for (kk=1; kk<=cptcovage;kk++) {
1491: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1492: }
1493:
1494: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1495: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1496: savm=oldm;
1497: oldm=newm;
1498: } /* end mult */
1499:
1500: s1=s[mw[mi][i]][i];
1501: s2=s[mw[mi+1][i]][i];
1502: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1503: ipmx +=1;
1504: sw += weight[i];
1505: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1506: /*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]);*/
1507: } /* end of wave */
1508: } /* end of individual */
1509: } /* End of if */
1510: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1511: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1512: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1513: return -l;
1514: }
1515:
1516: /*************** log-likelihood *************/
1517: double funcone( double *x)
1518: {
1519: /* Same as likeli but slower because of a lot of printf and if */
1520: int i, ii, j, k, mi, d, kk;
1521: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1522: double **out;
1523: double lli; /* Individual log likelihood */
1524: double llt;
1525: int s1, s2;
1526: double bbh, survp;
1527: /*extern weight */
1528: /* We are differentiating ll according to initial status */
1529: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1530: /*for(i=1;i<imx;i++)
1531: printf(" %d\n",s[4][i]);
1532: */
1533: cov[1]=1.;
1534:
1535: for(k=1; k<=nlstate; k++) ll[k]=0.;
1536:
1537: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1538: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1539: for(mi=1; mi<= wav[i]-1; mi++){
1540: for (ii=1;ii<=nlstate+ndeath;ii++)
1541: for (j=1;j<=nlstate+ndeath;j++){
1542: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1543: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1544: }
1545: for(d=0; d<dh[mi][i]; d++){
1546: newm=savm;
1547: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1548: for (kk=1; kk<=cptcovage;kk++) {
1549: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1550: }
1551: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1552: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1553: savm=oldm;
1554: oldm=newm;
1555: } /* end mult */
1556:
1557: s1=s[mw[mi][i]][i];
1558: s2=s[mw[mi+1][i]][i];
1559: bbh=(double)bh[mi][i]/(double)stepm;
1560: /* bias is positive if real duration
1561: * is higher than the multiple of stepm and negative otherwise.
1562: */
1563: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1564: lli=log(out[s1][s2] - savm[s1][s2]);
1565: } else if (mle==1){
1566: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1567: } else if(mle==2){
1568: 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 */
1569: } else if(mle==3){ /* exponential inter-extrapolation */
1570: 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 */
1571: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1572: lli=log(out[s1][s2]); /* Original formula */
1573: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1574: lli=log(out[s1][s2]); /* Original formula */
1575: } /* End of if */
1576: ipmx +=1;
1577: sw += weight[i];
1578: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1579: /* 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]); */
1580: if(globpr){
1581: fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
1582: %10.6f %10.6f %10.6f ", \
1583: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1584: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1585: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1586: llt +=ll[k]*gipmx/gsw;
1587: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1588: }
1589: fprintf(ficresilk," %10.6f\n", -llt);
1590: }
1591: } /* end of wave */
1592: } /* end of individual */
1593: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1594: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1595: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1596: if(globpr==0){ /* First time we count the contributions and weights */
1597: gipmx=ipmx;
1598: gsw=sw;
1599: }
1600: return -l;
1601: }
1602:
1603:
1604: /*************** function likelione ***********/
1605: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1606: {
1607: /* This routine should help understanding what is done with
1608: the selection of individuals/waves and
1609: to check the exact contribution to the likelihood.
1610: Plotting could be done.
1611: */
1612: int k;
1613:
1614: if(*globpri !=0){ /* Just counts and sums, no printings */
1615: strcpy(fileresilk,"ilk");
1616: strcat(fileresilk,fileres);
1617: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1618: printf("Problem with resultfile: %s\n", fileresilk);
1619: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1620: }
1621: 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");
1622: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1623: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1624: for(k=1; k<=nlstate; k++)
1625: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1626: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1627: }
1628:
1629: *fretone=(*funcone)(p);
1630: if(*globpri !=0){
1631: fclose(ficresilk);
1632: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1633: fflush(fichtm);
1634: }
1635: return;
1636: }
1637:
1638:
1639: /*********** Maximum Likelihood Estimation ***************/
1640:
1641: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1642: {
1643: int i,j, iter;
1644: double **xi;
1645: double fret;
1646: double fretone; /* Only one call to likelihood */
1647: /* char filerespow[FILENAMELENGTH];*/
1648: xi=matrix(1,npar,1,npar);
1649: for (i=1;i<=npar;i++)
1650: for (j=1;j<=npar;j++)
1651: xi[i][j]=(i==j ? 1.0 : 0.0);
1652: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1653: strcpy(filerespow,"pow");
1654: strcat(filerespow,fileres);
1655: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1656: printf("Problem with resultfile: %s\n", filerespow);
1657: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1658: }
1659: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1660: for (i=1;i<=nlstate;i++)
1661: for(j=1;j<=nlstate+ndeath;j++)
1662: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1663: fprintf(ficrespow,"\n");
1664:
1665: powell(p,xi,npar,ftol,&iter,&fret,func);
1666:
1667: fclose(ficrespow);
1668: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1669: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1670: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1671:
1672: }
1673:
1674: /**** Computes Hessian and covariance matrix ***/
1675: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1676: {
1677: double **a,**y,*x,pd;
1678: double **hess;
1679: int i, j,jk;
1680: int *indx;
1681:
1682: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1683: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1684: void lubksb(double **a, int npar, int *indx, double b[]) ;
1685: void ludcmp(double **a, int npar, int *indx, double *d) ;
1686: double gompertz(double p[]);
1687: hess=matrix(1,npar,1,npar);
1688:
1689: printf("\nCalculation of the hessian matrix. Wait...\n");
1690: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1691: for (i=1;i<=npar;i++){
1692: printf("%d",i);fflush(stdout);
1693: fprintf(ficlog,"%d",i);fflush(ficlog);
1694:
1695: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1696:
1697: /* printf(" %f ",p[i]);
1698: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1699: }
1700:
1701: for (i=1;i<=npar;i++) {
1702: for (j=1;j<=npar;j++) {
1703: if (j>i) {
1704: printf(".%d%d",i,j);fflush(stdout);
1705: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1706: hess[i][j]=hessij(p,delti,i,j,func,npar);
1707:
1708: hess[j][i]=hess[i][j];
1709: /*printf(" %lf ",hess[i][j]);*/
1710: }
1711: }
1712: }
1713: printf("\n");
1714: fprintf(ficlog,"\n");
1715:
1716: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1717: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1718:
1719: a=matrix(1,npar,1,npar);
1720: y=matrix(1,npar,1,npar);
1721: x=vector(1,npar);
1722: indx=ivector(1,npar);
1723: for (i=1;i<=npar;i++)
1724: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1725: ludcmp(a,npar,indx,&pd);
1726:
1727: for (j=1;j<=npar;j++) {
1728: for (i=1;i<=npar;i++) x[i]=0;
1729: x[j]=1;
1730: lubksb(a,npar,indx,x);
1731: for (i=1;i<=npar;i++){
1732: matcov[i][j]=x[i];
1733: }
1734: }
1735:
1736: printf("\n#Hessian matrix#\n");
1737: fprintf(ficlog,"\n#Hessian matrix#\n");
1738: for (i=1;i<=npar;i++) {
1739: for (j=1;j<=npar;j++) {
1740: printf("%.3e ",hess[i][j]);
1741: fprintf(ficlog,"%.3e ",hess[i][j]);
1742: }
1743: printf("\n");
1744: fprintf(ficlog,"\n");
1745: }
1746:
1747: /* Recompute Inverse */
1748: for (i=1;i<=npar;i++)
1749: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1750: ludcmp(a,npar,indx,&pd);
1751:
1752: /* printf("\n#Hessian matrix recomputed#\n");
1753:
1754: for (j=1;j<=npar;j++) {
1755: for (i=1;i<=npar;i++) x[i]=0;
1756: x[j]=1;
1757: lubksb(a,npar,indx,x);
1758: for (i=1;i<=npar;i++){
1759: y[i][j]=x[i];
1760: printf("%.3e ",y[i][j]);
1761: fprintf(ficlog,"%.3e ",y[i][j]);
1762: }
1763: printf("\n");
1764: fprintf(ficlog,"\n");
1765: }
1766: */
1767:
1768: free_matrix(a,1,npar,1,npar);
1769: free_matrix(y,1,npar,1,npar);
1770: free_vector(x,1,npar);
1771: free_ivector(indx,1,npar);
1772: free_matrix(hess,1,npar,1,npar);
1773:
1774:
1775: }
1776:
1777: /*************** hessian matrix ****************/
1778: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1779: {
1780: int i;
1781: int l=1, lmax=20;
1782: double k1,k2;
1783: double p2[NPARMAX+1];
1784: double res;
1785: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1786: double fx;
1787: int k=0,kmax=10;
1788: double l1;
1789:
1790: fx=func(x);
1791: for (i=1;i<=npar;i++) p2[i]=x[i];
1792: for(l=0 ; l <=lmax; l++){
1793: l1=pow(10,l);
1794: delts=delt;
1795: for(k=1 ; k <kmax; k=k+1){
1796: delt = delta*(l1*k);
1797: p2[theta]=x[theta] +delt;
1798: k1=func(p2)-fx;
1799: p2[theta]=x[theta]-delt;
1800: k2=func(p2)-fx;
1801: /*res= (k1-2.0*fx+k2)/delt/delt; */
1802: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1803:
1804: #ifdef DEBUG
1805: 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);
1806: 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);
1807: #endif
1808: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1809: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1810: k=kmax;
1811: }
1812: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1813: k=kmax; l=lmax*10.;
1814: }
1815: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1816: delts=delt;
1817: }
1818: }
1819: }
1820: delti[theta]=delts;
1821: return res;
1822:
1823: }
1824:
1825: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1826: {
1827: int i;
1828: int l=1, l1, lmax=20;
1829: double k1,k2,k3,k4,res,fx;
1830: double p2[NPARMAX+1];
1831: int k;
1832:
1833: fx=func(x);
1834: for (k=1; k<=2; k++) {
1835: for (i=1;i<=npar;i++) p2[i]=x[i];
1836: p2[thetai]=x[thetai]+delti[thetai]/k;
1837: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1838: k1=func(p2)-fx;
1839:
1840: p2[thetai]=x[thetai]+delti[thetai]/k;
1841: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1842: k2=func(p2)-fx;
1843:
1844: p2[thetai]=x[thetai]-delti[thetai]/k;
1845: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1846: k3=func(p2)-fx;
1847:
1848: p2[thetai]=x[thetai]-delti[thetai]/k;
1849: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1850: k4=func(p2)-fx;
1851: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1852: #ifdef DEBUG
1853: 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);
1854: 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);
1855: #endif
1856: }
1857: return res;
1858: }
1859:
1860: /************** Inverse of matrix **************/
1861: void ludcmp(double **a, int n, int *indx, double *d)
1862: {
1863: int i,imax,j,k;
1864: double big,dum,sum,temp;
1865: double *vv;
1866:
1867: vv=vector(1,n);
1868: *d=1.0;
1869: for (i=1;i<=n;i++) {
1870: big=0.0;
1871: for (j=1;j<=n;j++)
1872: if ((temp=fabs(a[i][j])) > big) big=temp;
1873: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1874: vv[i]=1.0/big;
1875: }
1876: for (j=1;j<=n;j++) {
1877: for (i=1;i<j;i++) {
1878: sum=a[i][j];
1879: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1880: a[i][j]=sum;
1881: }
1882: big=0.0;
1883: for (i=j;i<=n;i++) {
1884: sum=a[i][j];
1885: for (k=1;k<j;k++)
1886: sum -= a[i][k]*a[k][j];
1887: a[i][j]=sum;
1888: if ( (dum=vv[i]*fabs(sum)) >= big) {
1889: big=dum;
1890: imax=i;
1891: }
1892: }
1893: if (j != imax) {
1894: for (k=1;k<=n;k++) {
1895: dum=a[imax][k];
1896: a[imax][k]=a[j][k];
1897: a[j][k]=dum;
1898: }
1899: *d = -(*d);
1900: vv[imax]=vv[j];
1901: }
1902: indx[j]=imax;
1903: if (a[j][j] == 0.0) a[j][j]=TINY;
1904: if (j != n) {
1905: dum=1.0/(a[j][j]);
1906: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1907: }
1908: }
1909: free_vector(vv,1,n); /* Doesn't work */
1910: ;
1911: }
1912:
1913: void lubksb(double **a, int n, int *indx, double b[])
1914: {
1915: int i,ii=0,ip,j;
1916: double sum;
1917:
1918: for (i=1;i<=n;i++) {
1919: ip=indx[i];
1920: sum=b[ip];
1921: b[ip]=b[i];
1922: if (ii)
1923: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1924: else if (sum) ii=i;
1925: b[i]=sum;
1926: }
1927: for (i=n;i>=1;i--) {
1928: sum=b[i];
1929: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1930: b[i]=sum/a[i][i];
1931: }
1932: }
1933:
1934: /************ Frequencies ********************/
1935: 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[])
1936: { /* Some frequencies */
1937:
1938: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1939: int first;
1940: double ***freq; /* Frequencies */
1941: double *pp, **prop;
1942: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1943: FILE *ficresp;
1944: char fileresp[FILENAMELENGTH];
1945:
1946: pp=vector(1,nlstate);
1947: prop=matrix(1,nlstate,iagemin,iagemax+3);
1948: strcpy(fileresp,"p");
1949: strcat(fileresp,fileres);
1950: if((ficresp=fopen(fileresp,"w"))==NULL) {
1951: printf("Problem with prevalence resultfile: %s\n", fileresp);
1952: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1953: exit(0);
1954: }
1955: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
1956: j1=0;
1957:
1958: j=cptcoveff;
1959: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1960:
1961: first=1;
1962:
1963: for(k1=1; k1<=j;k1++){
1964: for(i1=1; i1<=ncodemax[k1];i1++){
1965: j1++;
1966: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1967: scanf("%d", i);*/
1968: for (i=-5; i<=nlstate+ndeath; i++)
1969: for (jk=-5; jk<=nlstate+ndeath; jk++)
1970: for(m=iagemin; m <= iagemax+3; m++)
1971: freq[i][jk][m]=0;
1972:
1973: for (i=1; i<=nlstate; i++)
1974: for(m=iagemin; m <= iagemax+3; m++)
1975: prop[i][m]=0;
1976:
1977: dateintsum=0;
1978: k2cpt=0;
1979: for (i=1; i<=imx; i++) {
1980: bool=1;
1981: if (cptcovn>0) {
1982: for (z1=1; z1<=cptcoveff; z1++)
1983: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1984: bool=0;
1985: }
1986: if (bool==1){
1987: for(m=firstpass; m<=lastpass; m++){
1988: k2=anint[m][i]+(mint[m][i]/12.);
1989: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1990: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1991: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1992: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1993: if (m<lastpass) {
1994: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1995: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1996: }
1997:
1998: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1999: dateintsum=dateintsum+k2;
2000: k2cpt++;
2001: }
2002: /*}*/
2003: }
2004: }
2005: }
2006:
2007: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2008: fprintf(ficresp, "#Local time at start: %s", strstart);
2009: if (cptcovn>0) {
2010: fprintf(ficresp, "\n#********** Variable ");
2011: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2012: fprintf(ficresp, "**********\n#");
2013: }
2014: for(i=1; i<=nlstate;i++)
2015: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2016: fprintf(ficresp, "\n");
2017:
2018: for(i=iagemin; i <= iagemax+3; i++){
2019: if(i==iagemax+3){
2020: fprintf(ficlog,"Total");
2021: }else{
2022: if(first==1){
2023: first=0;
2024: printf("See log file for details...\n");
2025: }
2026: fprintf(ficlog,"Age %d", i);
2027: }
2028: for(jk=1; jk <=nlstate ; jk++){
2029: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2030: pp[jk] += freq[jk][m][i];
2031: }
2032: for(jk=1; jk <=nlstate ; jk++){
2033: for(m=-1, pos=0; m <=0 ; m++)
2034: pos += freq[jk][m][i];
2035: if(pp[jk]>=1.e-10){
2036: if(first==1){
2037: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2038: }
2039: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2040: }else{
2041: if(first==1)
2042: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2043: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2044: }
2045: }
2046:
2047: for(jk=1; jk <=nlstate ; jk++){
2048: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2049: pp[jk] += freq[jk][m][i];
2050: }
2051: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2052: pos += pp[jk];
2053: posprop += prop[jk][i];
2054: }
2055: for(jk=1; jk <=nlstate ; jk++){
2056: if(pos>=1.e-5){
2057: if(first==1)
2058: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2059: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2060: }else{
2061: if(first==1)
2062: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2063: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2064: }
2065: if( i <= iagemax){
2066: if(pos>=1.e-5){
2067: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2068: /*probs[i][jk][j1]= pp[jk]/pos;*/
2069: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2070: }
2071: else
2072: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2073: }
2074: }
2075:
2076: for(jk=-1; jk <=nlstate+ndeath; jk++)
2077: for(m=-1; m <=nlstate+ndeath; m++)
2078: if(freq[jk][m][i] !=0 ) {
2079: if(first==1)
2080: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2081: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2082: }
2083: if(i <= iagemax)
2084: fprintf(ficresp,"\n");
2085: if(first==1)
2086: printf("Others in log...\n");
2087: fprintf(ficlog,"\n");
2088: }
2089: }
2090: }
2091: dateintmean=dateintsum/k2cpt;
2092:
2093: fclose(ficresp);
2094: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2095: free_vector(pp,1,nlstate);
2096: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2097: /* End of Freq */
2098: }
2099:
2100: /************ Prevalence ********************/
2101: 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)
2102: {
2103: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2104: in each health status at the date of interview (if between dateprev1 and dateprev2).
2105: We still use firstpass and lastpass as another selection.
2106: */
2107:
2108: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
2109: double ***freq; /* Frequencies */
2110: double *pp, **prop;
2111: double pos,posprop;
2112: double y2; /* in fractional years */
2113: int iagemin, iagemax;
2114:
2115: iagemin= (int) agemin;
2116: iagemax= (int) agemax;
2117: /*pp=vector(1,nlstate);*/
2118: prop=matrix(1,nlstate,iagemin,iagemax+3);
2119: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2120: j1=0;
2121:
2122: j=cptcoveff;
2123: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2124:
2125: for(k1=1; k1<=j;k1++){
2126: for(i1=1; i1<=ncodemax[k1];i1++){
2127: j1++;
2128:
2129: for (i=1; i<=nlstate; i++)
2130: for(m=iagemin; m <= iagemax+3; m++)
2131: prop[i][m]=0.0;
2132:
2133: for (i=1; i<=imx; i++) { /* Each individual */
2134: bool=1;
2135: if (cptcovn>0) {
2136: for (z1=1; z1<=cptcoveff; z1++)
2137: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2138: bool=0;
2139: }
2140: if (bool==1) {
2141: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2142: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2143: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2144: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2145: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2146: 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);
2147: if (s[m][i]>0 && s[m][i]<=nlstate) {
2148: /*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]]);*/
2149: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2150: prop[s[m][i]][iagemax+3] += weight[i];
2151: }
2152: }
2153: } /* end selection of waves */
2154: }
2155: }
2156: for(i=iagemin; i <= iagemax+3; i++){
2157:
2158: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2159: posprop += prop[jk][i];
2160: }
2161:
2162: for(jk=1; jk <=nlstate ; jk++){
2163: if( i <= iagemax){
2164: if(posprop>=1.e-5){
2165: probs[i][jk][j1]= prop[jk][i]/posprop;
2166: }
2167: }
2168: }/* end jk */
2169: }/* end i */
2170: } /* end i1 */
2171: } /* end k1 */
2172:
2173: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2174: /*free_vector(pp,1,nlstate);*/
2175: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2176: } /* End of prevalence */
2177:
2178: /************* Waves Concatenation ***************/
2179:
2180: 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)
2181: {
2182: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2183: Death is a valid wave (if date is known).
2184: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2185: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2186: and mw[mi+1][i]. dh depends on stepm.
2187: */
2188:
2189: int i, mi, m;
2190: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2191: double sum=0., jmean=0.;*/
2192: int first;
2193: int j, k=0,jk, ju, jl;
2194: double sum=0.;
2195: first=0;
2196: jmin=1e+5;
2197: jmax=-1;
2198: jmean=0.;
2199: for(i=1; i<=imx; i++){
2200: mi=0;
2201: m=firstpass;
2202: while(s[m][i] <= nlstate){
2203: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2204: mw[++mi][i]=m;
2205: if(m >=lastpass)
2206: break;
2207: else
2208: m++;
2209: }/* end while */
2210: if (s[m][i] > nlstate){
2211: mi++; /* Death is another wave */
2212: /* if(mi==0) never been interviewed correctly before death */
2213: /* Only death is a correct wave */
2214: mw[mi][i]=m;
2215: }
2216:
2217: wav[i]=mi;
2218: if(mi==0){
2219: nbwarn++;
2220: if(first==0){
2221: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2222: first=1;
2223: }
2224: if(first==1){
2225: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2226: }
2227: } /* end mi==0 */
2228: } /* End individuals */
2229:
2230: for(i=1; i<=imx; i++){
2231: for(mi=1; mi<wav[i];mi++){
2232: if (stepm <=0)
2233: dh[mi][i]=1;
2234: else{
2235: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2236: if (agedc[i] < 2*AGESUP) {
2237: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2238: if(j==0) j=1; /* Survives at least one month after exam */
2239: else if(j<0){
2240: nberr++;
2241: 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]);
2242: j=1; /* Temporary Dangerous patch */
2243: 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);
2244: 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]);
2245: 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);
2246: }
2247: k=k+1;
2248: if (j >= jmax){
2249: jmax=j;
2250: ijmax=i;
2251: }
2252: if (j <= jmin){
2253: jmin=j;
2254: ijmin=i;
2255: }
2256: sum=sum+j;
2257: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2258: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2259: }
2260: }
2261: else{
2262: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2263: /* 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]); */
2264:
2265: k=k+1;
2266: if (j >= jmax) {
2267: jmax=j;
2268: ijmax=i;
2269: }
2270: else if (j <= jmin){
2271: jmin=j;
2272: ijmin=i;
2273: }
2274: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2275: /*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]);*/
2276: if(j<0){
2277: nberr++;
2278: 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]);
2279: 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]);
2280: }
2281: sum=sum+j;
2282: }
2283: jk= j/stepm;
2284: jl= j -jk*stepm;
2285: ju= j -(jk+1)*stepm;
2286: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2287: if(jl==0){
2288: dh[mi][i]=jk;
2289: bh[mi][i]=0;
2290: }else{ /* We want a negative bias in order to only have interpolation ie
2291: * at the price of an extra matrix product in likelihood */
2292: dh[mi][i]=jk+1;
2293: bh[mi][i]=ju;
2294: }
2295: }else{
2296: if(jl <= -ju){
2297: dh[mi][i]=jk;
2298: bh[mi][i]=jl; /* bias is positive if real duration
2299: * is higher than the multiple of stepm and negative otherwise.
2300: */
2301: }
2302: else{
2303: dh[mi][i]=jk+1;
2304: bh[mi][i]=ju;
2305: }
2306: if(dh[mi][i]==0){
2307: dh[mi][i]=1; /* At least one step */
2308: bh[mi][i]=ju; /* At least one step */
2309: /* 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);*/
2310: }
2311: } /* end if mle */
2312: }
2313: } /* end wave */
2314: }
2315: jmean=sum/k;
2316: 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);
2317: 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);
2318: }
2319:
2320: /*********** Tricode ****************************/
2321: void tricode(int *Tvar, int **nbcode, int imx)
2322: {
2323:
2324: int Ndum[20],ij=1, k, j, i, maxncov=19;
2325: int cptcode=0;
2326: cptcoveff=0;
2327:
2328: for (k=0; k<maxncov; k++) Ndum[k]=0;
2329: for (k=1; k<=7; k++) ncodemax[k]=0;
2330:
2331: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
2332: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2333: modality*/
2334: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2335: Ndum[ij]++; /*store the modality */
2336: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2337: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2338: Tvar[j]. If V=sex and male is 0 and
2339: female is 1, then cptcode=1.*/
2340: }
2341:
2342: for (i=0; i<=cptcode; i++) {
2343: 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 */
2344: }
2345:
2346: ij=1;
2347: for (i=1; i<=ncodemax[j]; i++) {
2348: for (k=0; k<= maxncov; k++) {
2349: if (Ndum[k] != 0) {
2350: nbcode[Tvar[j]][ij]=k;
2351: /* 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; */
2352:
2353: ij++;
2354: }
2355: if (ij > ncodemax[j]) break;
2356: }
2357: }
2358: }
2359:
2360: for (k=0; k< maxncov; k++) Ndum[k]=0;
2361:
2362: for (i=1; i<=ncovmodel-2; i++) {
2363: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2364: ij=Tvar[i];
2365: Ndum[ij]++;
2366: }
2367:
2368: ij=1;
2369: for (i=1; i<= maxncov; i++) {
2370: if((Ndum[i]!=0) && (i<=ncovcol)){
2371: Tvaraff[ij]=i; /*For printing */
2372: ij++;
2373: }
2374: }
2375:
2376: cptcoveff=ij-1; /*Number of simple covariates*/
2377: }
2378:
2379: /*********** Health Expectancies ****************/
2380:
2381: void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov,char strstart[] )
2382:
2383: {
2384: /* Health expectancies */
2385: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
2386: double age, agelim, hf;
2387: double ***p3mat,***varhe;
2388: double **dnewm,**doldm;
2389: double *xp;
2390: double **gp, **gm;
2391: double ***gradg, ***trgradg;
2392: int theta;
2393:
2394: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2395: xp=vector(1,npar);
2396: dnewm=matrix(1,nlstate*nlstate,1,npar);
2397: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2398:
2399: fprintf(ficreseij,"# Local time at start: %s", strstart);
2400: fprintf(ficreseij,"# Health expectancies\n");
2401: fprintf(ficreseij,"# Age");
2402: for(i=1; i<=nlstate;i++)
2403: for(j=1; j<=nlstate;j++)
2404: fprintf(ficreseij," %1d-%1d (SE)",i,j);
2405: fprintf(ficreseij,"\n");
2406:
2407: if(estepm < stepm){
2408: printf ("Problem %d lower than %d\n",estepm, stepm);
2409: }
2410: else hstepm=estepm;
2411: /* We compute the life expectancy from trapezoids spaced every estepm months
2412: * This is mainly to measure the difference between two models: for example
2413: * if stepm=24 months pijx are given only every 2 years and by summing them
2414: * we are calculating an estimate of the Life Expectancy assuming a linear
2415: * progression in between and thus overestimating or underestimating according
2416: * to the curvature of the survival function. If, for the same date, we
2417: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2418: * to compare the new estimate of Life expectancy with the same linear
2419: * hypothesis. A more precise result, taking into account a more precise
2420: * curvature will be obtained if estepm is as small as stepm. */
2421:
2422: /* For example we decided to compute the life expectancy with the smallest unit */
2423: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2424: nhstepm is the number of hstepm from age to agelim
2425: nstepm is the number of stepm from age to agelin.
2426: Look at hpijx to understand the reason of that which relies in memory size
2427: and note for a fixed period like estepm months */
2428: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2429: survival function given by stepm (the optimization length). Unfortunately it
2430: means that if the survival funtion is printed only each two years of age and if
2431: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2432: results. So we changed our mind and took the option of the best precision.
2433: */
2434: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2435:
2436: agelim=AGESUP;
2437: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2438: /* nhstepm age range expressed in number of stepm */
2439: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2440: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2441: /* if (stepm >= YEARM) hstepm=1;*/
2442: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2443: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2444: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2445: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2446: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2447:
2448: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2449: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2450: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
2451:
2452:
2453: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2454:
2455: /* Computing Variances of health expectancies */
2456:
2457: for(theta=1; theta <=npar; theta++){
2458: for(i=1; i<=npar; i++){
2459: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2460: }
2461: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2462:
2463: cptj=0;
2464: for(j=1; j<= nlstate; j++){
2465: for(i=1; i<=nlstate; i++){
2466: cptj=cptj+1;
2467: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2468: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2469: }
2470: }
2471: }
2472:
2473:
2474: for(i=1; i<=npar; i++)
2475: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2476: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2477:
2478: cptj=0;
2479: for(j=1; j<= nlstate; j++){
2480: for(i=1;i<=nlstate;i++){
2481: cptj=cptj+1;
2482: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
2483:
2484: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2485: }
2486: }
2487: }
2488: for(j=1; j<= nlstate*nlstate; j++)
2489: for(h=0; h<=nhstepm-1; h++){
2490: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2491: }
2492: }
2493:
2494: /* End theta */
2495:
2496: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2497:
2498: for(h=0; h<=nhstepm-1; h++)
2499: for(j=1; j<=nlstate*nlstate;j++)
2500: for(theta=1; theta <=npar; theta++)
2501: trgradg[h][j][theta]=gradg[h][theta][j];
2502:
2503:
2504: for(i=1;i<=nlstate*nlstate;i++)
2505: for(j=1;j<=nlstate*nlstate;j++)
2506: varhe[i][j][(int)age] =0.;
2507:
2508: printf("%d|",(int)age);fflush(stdout);
2509: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2510: for(h=0;h<=nhstepm-1;h++){
2511: for(k=0;k<=nhstepm-1;k++){
2512: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2513: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2514: for(i=1;i<=nlstate*nlstate;i++)
2515: for(j=1;j<=nlstate*nlstate;j++)
2516: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2517: }
2518: }
2519: /* Computing expectancies */
2520: for(i=1; i<=nlstate;i++)
2521: for(j=1; j<=nlstate;j++)
2522: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2523: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2524:
2525: /* 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]);*/
2526:
2527: }
2528:
2529: fprintf(ficreseij,"%3.0f",age );
2530: cptj=0;
2531: for(i=1; i<=nlstate;i++)
2532: for(j=1; j<=nlstate;j++){
2533: cptj++;
2534: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2535: }
2536: fprintf(ficreseij,"\n");
2537:
2538: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2539: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2540: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2541: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2542: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2543: }
2544: printf("\n");
2545: fprintf(ficlog,"\n");
2546:
2547: free_vector(xp,1,npar);
2548: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2549: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2550: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2551: }
2552:
2553: /************ Variance ******************/
2554: 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[])
2555: {
2556: /* Variance of health expectancies */
2557: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2558: /* double **newm;*/
2559: double **dnewm,**doldm;
2560: double **dnewmp,**doldmp;
2561: int i, j, nhstepm, hstepm, h, nstepm ;
2562: int k, cptcode;
2563: double *xp;
2564: double **gp, **gm; /* for var eij */
2565: double ***gradg, ***trgradg; /*for var eij */
2566: double **gradgp, **trgradgp; /* for var p point j */
2567: double *gpp, *gmp; /* for var p point j */
2568: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2569: double ***p3mat;
2570: double age,agelim, hf;
2571: double ***mobaverage;
2572: int theta;
2573: char digit[4];
2574: char digitp[25];
2575:
2576: char fileresprobmorprev[FILENAMELENGTH];
2577:
2578: if(popbased==1){
2579: if(mobilav!=0)
2580: strcpy(digitp,"-populbased-mobilav-");
2581: else strcpy(digitp,"-populbased-nomobil-");
2582: }
2583: else
2584: strcpy(digitp,"-stablbased-");
2585:
2586: if (mobilav!=0) {
2587: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2588: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2589: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2590: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2591: }
2592: }
2593:
2594: strcpy(fileresprobmorprev,"prmorprev");
2595: sprintf(digit,"%-d",ij);
2596: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2597: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2598: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2599: strcat(fileresprobmorprev,fileres);
2600: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2601: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2602: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2603: }
2604: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2605:
2606: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2607: fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
2608: 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);
2609: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2610: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2611: fprintf(ficresprobmorprev," p.%-d SE",j);
2612: for(i=1; i<=nlstate;i++)
2613: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2614: }
2615: fprintf(ficresprobmorprev,"\n");
2616: fprintf(ficgp,"\n# Routine varevsij");
2617: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
2618: 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");
2619: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2620: /* } */
2621: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2622: fprintf(ficresvij, "#Local time at start: %s", strstart);
2623: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are the stable prevalence in health states i\n");
2624: fprintf(ficresvij,"# Age");
2625: for(i=1; i<=nlstate;i++)
2626: for(j=1; j<=nlstate;j++)
2627: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2628: fprintf(ficresvij,"\n");
2629:
2630: xp=vector(1,npar);
2631: dnewm=matrix(1,nlstate,1,npar);
2632: doldm=matrix(1,nlstate,1,nlstate);
2633: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2634: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2635:
2636: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2637: gpp=vector(nlstate+1,nlstate+ndeath);
2638: gmp=vector(nlstate+1,nlstate+ndeath);
2639: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2640:
2641: if(estepm < stepm){
2642: printf ("Problem %d lower than %d\n",estepm, stepm);
2643: }
2644: else hstepm=estepm;
2645: /* For example we decided to compute the life expectancy with the smallest unit */
2646: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2647: nhstepm is the number of hstepm from age to agelim
2648: nstepm is the number of stepm from age to agelin.
2649: Look at hpijx to understand the reason of that which relies in memory size
2650: and note for a fixed period like k years */
2651: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2652: survival function given by stepm (the optimization length). Unfortunately it
2653: means that if the survival funtion is printed every two years of age and if
2654: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2655: results. So we changed our mind and took the option of the best precision.
2656: */
2657: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2658: agelim = AGESUP;
2659: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2660: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2661: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2662: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2663: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2664: gp=matrix(0,nhstepm,1,nlstate);
2665: gm=matrix(0,nhstepm,1,nlstate);
2666:
2667:
2668: for(theta=1; theta <=npar; theta++){
2669: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2670: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2671: }
2672: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2673: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2674:
2675: if (popbased==1) {
2676: if(mobilav ==0){
2677: for(i=1; i<=nlstate;i++)
2678: prlim[i][i]=probs[(int)age][i][ij];
2679: }else{ /* mobilav */
2680: for(i=1; i<=nlstate;i++)
2681: prlim[i][i]=mobaverage[(int)age][i][ij];
2682: }
2683: }
2684:
2685: for(j=1; j<= nlstate; j++){
2686: for(h=0; h<=nhstepm; h++){
2687: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2688: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2689: }
2690: }
2691: /* This for computing probability of death (h=1 means
2692: computed over hstepm matrices product = hstepm*stepm months)
2693: as a weighted average of prlim.
2694: */
2695: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2696: for(i=1,gpp[j]=0.; i<= nlstate; i++)
2697: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2698: }
2699: /* end probability of death */
2700:
2701: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
2702: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2703: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2704: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2705:
2706: if (popbased==1) {
2707: if(mobilav ==0){
2708: for(i=1; i<=nlstate;i++)
2709: prlim[i][i]=probs[(int)age][i][ij];
2710: }else{ /* mobilav */
2711: for(i=1; i<=nlstate;i++)
2712: prlim[i][i]=mobaverage[(int)age][i][ij];
2713: }
2714: }
2715:
2716: for(j=1; j<= nlstate; j++){
2717: for(h=0; h<=nhstepm; h++){
2718: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2719: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2720: }
2721: }
2722: /* This for computing probability of death (h=1 means
2723: computed over hstepm matrices product = hstepm*stepm months)
2724: as a weighted average of prlim.
2725: */
2726: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2727: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2728: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2729: }
2730: /* end probability of death */
2731:
2732: for(j=1; j<= nlstate; j++) /* vareij */
2733: for(h=0; h<=nhstepm; h++){
2734: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2735: }
2736:
2737: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2738: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2739: }
2740:
2741: } /* End theta */
2742:
2743: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2744:
2745: for(h=0; h<=nhstepm; h++) /* veij */
2746: for(j=1; j<=nlstate;j++)
2747: for(theta=1; theta <=npar; theta++)
2748: trgradg[h][j][theta]=gradg[h][theta][j];
2749:
2750: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
2751: for(theta=1; theta <=npar; theta++)
2752: trgradgp[j][theta]=gradgp[theta][j];
2753:
2754:
2755: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2756: for(i=1;i<=nlstate;i++)
2757: for(j=1;j<=nlstate;j++)
2758: vareij[i][j][(int)age] =0.;
2759:
2760: for(h=0;h<=nhstepm;h++){
2761: for(k=0;k<=nhstepm;k++){
2762: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2763: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2764: for(i=1;i<=nlstate;i++)
2765: for(j=1;j<=nlstate;j++)
2766: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2767: }
2768: }
2769:
2770: /* pptj */
2771: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2772: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
2773: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2774: for(i=nlstate+1;i<=nlstate+ndeath;i++)
2775: varppt[j][i]=doldmp[j][i];
2776: /* end ppptj */
2777: /* x centered again */
2778: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2779: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2780:
2781: if (popbased==1) {
2782: if(mobilav ==0){
2783: for(i=1; i<=nlstate;i++)
2784: prlim[i][i]=probs[(int)age][i][ij];
2785: }else{ /* mobilav */
2786: for(i=1; i<=nlstate;i++)
2787: prlim[i][i]=mobaverage[(int)age][i][ij];
2788: }
2789: }
2790:
2791: /* This for computing probability of death (h=1 means
2792: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2793: as a weighted average of prlim.
2794: */
2795: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2796: for(i=1,gmp[j]=0.;i<= nlstate; i++)
2797: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2798: }
2799: /* end probability of death */
2800:
2801: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2802: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2803: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2804: for(i=1; i<=nlstate;i++){
2805: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2806: }
2807: }
2808: fprintf(ficresprobmorprev,"\n");
2809:
2810: fprintf(ficresvij,"%.0f ",age );
2811: for(i=1; i<=nlstate;i++)
2812: for(j=1; j<=nlstate;j++){
2813: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2814: }
2815: fprintf(ficresvij,"\n");
2816: free_matrix(gp,0,nhstepm,1,nlstate);
2817: free_matrix(gm,0,nhstepm,1,nlstate);
2818: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2819: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2820: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2821: } /* End age */
2822: free_vector(gpp,nlstate+1,nlstate+ndeath);
2823: free_vector(gmp,nlstate+1,nlstate+ndeath);
2824: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2825: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2826: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2827: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2828: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
2829: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2830: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2831: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
2832: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
2833: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
2834: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
2835: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
2836: 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);
2837: /* 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);
2838: */
2839: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
2840: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
2841:
2842: free_vector(xp,1,npar);
2843: free_matrix(doldm,1,nlstate,1,nlstate);
2844: free_matrix(dnewm,1,nlstate,1,npar);
2845: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2846: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2847: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2848: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2849: fclose(ficresprobmorprev);
2850: fflush(ficgp);
2851: fflush(fichtm);
2852: } /* end varevsij */
2853:
2854: /************ Variance of prevlim ******************/
2855: 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[])
2856: {
2857: /* Variance of prevalence limit */
2858: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
2859: double **newm;
2860: double **dnewm,**doldm;
2861: int i, j, nhstepm, hstepm;
2862: int k, cptcode;
2863: double *xp;
2864: double *gp, *gm;
2865: double **gradg, **trgradg;
2866: double age,agelim;
2867: int theta;
2868: fprintf(ficresvpl, "#Local time at start: %s", strstart);
2869: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
2870: fprintf(ficresvpl,"# Age");
2871: for(i=1; i<=nlstate;i++)
2872: fprintf(ficresvpl," %1d-%1d",i,i);
2873: fprintf(ficresvpl,"\n");
2874:
2875: xp=vector(1,npar);
2876: dnewm=matrix(1,nlstate,1,npar);
2877: doldm=matrix(1,nlstate,1,nlstate);
2878:
2879: hstepm=1*YEARM; /* Every year of age */
2880: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2881: agelim = AGESUP;
2882: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2883: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2884: if (stepm >= YEARM) hstepm=1;
2885: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2886: gradg=matrix(1,npar,1,nlstate);
2887: gp=vector(1,nlstate);
2888: gm=vector(1,nlstate);
2889:
2890: for(theta=1; theta <=npar; theta++){
2891: for(i=1; i<=npar; i++){ /* Computes gradient */
2892: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2893: }
2894: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2895: for(i=1;i<=nlstate;i++)
2896: gp[i] = prlim[i][i];
2897:
2898: for(i=1; i<=npar; i++) /* Computes gradient */
2899: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2900: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2901: for(i=1;i<=nlstate;i++)
2902: gm[i] = prlim[i][i];
2903:
2904: for(i=1;i<=nlstate;i++)
2905: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2906: } /* End theta */
2907:
2908: trgradg =matrix(1,nlstate,1,npar);
2909:
2910: for(j=1; j<=nlstate;j++)
2911: for(theta=1; theta <=npar; theta++)
2912: trgradg[j][theta]=gradg[theta][j];
2913:
2914: for(i=1;i<=nlstate;i++)
2915: varpl[i][(int)age] =0.;
2916: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2917: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2918: for(i=1;i<=nlstate;i++)
2919: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2920:
2921: fprintf(ficresvpl,"%.0f ",age );
2922: for(i=1; i<=nlstate;i++)
2923: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2924: fprintf(ficresvpl,"\n");
2925: free_vector(gp,1,nlstate);
2926: free_vector(gm,1,nlstate);
2927: free_matrix(gradg,1,npar,1,nlstate);
2928: free_matrix(trgradg,1,nlstate,1,npar);
2929: } /* End age */
2930:
2931: free_vector(xp,1,npar);
2932: free_matrix(doldm,1,nlstate,1,npar);
2933: free_matrix(dnewm,1,nlstate,1,nlstate);
2934:
2935: }
2936:
2937: /************ Variance of one-step probabilities ******************/
2938: 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[])
2939: {
2940: int i, j=0, i1, k1, l1, t, tj;
2941: int k2, l2, j1, z1;
2942: int k=0,l, cptcode;
2943: int first=1, first1;
2944: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2945: double **dnewm,**doldm;
2946: double *xp;
2947: double *gp, *gm;
2948: double **gradg, **trgradg;
2949: double **mu;
2950: double age,agelim, cov[NCOVMAX];
2951: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2952: int theta;
2953: char fileresprob[FILENAMELENGTH];
2954: char fileresprobcov[FILENAMELENGTH];
2955: char fileresprobcor[FILENAMELENGTH];
2956:
2957: double ***varpij;
2958:
2959: strcpy(fileresprob,"prob");
2960: strcat(fileresprob,fileres);
2961: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2962: printf("Problem with resultfile: %s\n", fileresprob);
2963: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2964: }
2965: strcpy(fileresprobcov,"probcov");
2966: strcat(fileresprobcov,fileres);
2967: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2968: printf("Problem with resultfile: %s\n", fileresprobcov);
2969: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2970: }
2971: strcpy(fileresprobcor,"probcor");
2972: strcat(fileresprobcor,fileres);
2973: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2974: printf("Problem with resultfile: %s\n", fileresprobcor);
2975: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2976: }
2977: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2978: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2979: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2980: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2981: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2982: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2983: fprintf(ficresprob, "#Local time at start: %s", strstart);
2984: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2985: fprintf(ficresprob,"# Age");
2986: fprintf(ficresprobcov, "#Local time at start: %s", strstart);
2987: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2988: fprintf(ficresprobcov,"# Age");
2989: fprintf(ficresprobcor, "#Local time at start: %s", strstart);
2990: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2991: fprintf(ficresprobcov,"# Age");
2992:
2993:
2994: for(i=1; i<=nlstate;i++)
2995: for(j=1; j<=(nlstate+ndeath);j++){
2996: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2997: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2998: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2999: }
3000: /* fprintf(ficresprob,"\n");
3001: fprintf(ficresprobcov,"\n");
3002: fprintf(ficresprobcor,"\n");
3003: */
3004: xp=vector(1,npar);
3005: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3006: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3007: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3008: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3009: first=1;
3010: fprintf(ficgp,"\n# Routine varprob");
3011: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3012: fprintf(fichtm,"\n");
3013:
3014: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3015: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3016: file %s<br>\n",optionfilehtmcov);
3017: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3018: and drawn. It helps understanding how is the covariance between two incidences.\
3019: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3020: 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. \
3021: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3022: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3023: standard deviations wide on each axis. <br>\
3024: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3025: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3026: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3027:
3028: cov[1]=1;
3029: tj=cptcoveff;
3030: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3031: j1=0;
3032: for(t=1; t<=tj;t++){
3033: for(i1=1; i1<=ncodemax[t];i1++){
3034: j1++;
3035: if (cptcovn>0) {
3036: fprintf(ficresprob, "\n#********** Variable ");
3037: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3038: fprintf(ficresprob, "**********\n#\n");
3039: fprintf(ficresprobcov, "\n#********** Variable ");
3040: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3041: fprintf(ficresprobcov, "**********\n#\n");
3042:
3043: fprintf(ficgp, "\n#********** Variable ");
3044: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3045: fprintf(ficgp, "**********\n#\n");
3046:
3047:
3048: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3049: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3050: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3051:
3052: fprintf(ficresprobcor, "\n#********** Variable ");
3053: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3054: fprintf(ficresprobcor, "**********\n#");
3055: }
3056:
3057: for (age=bage; age<=fage; age ++){
3058: cov[2]=age;
3059: for (k=1; k<=cptcovn;k++) {
3060: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3061: }
3062: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3063: for (k=1; k<=cptcovprod;k++)
3064: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3065:
3066: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3067: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3068: gp=vector(1,(nlstate)*(nlstate+ndeath));
3069: gm=vector(1,(nlstate)*(nlstate+ndeath));
3070:
3071: for(theta=1; theta <=npar; theta++){
3072: for(i=1; i<=npar; i++)
3073: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3074:
3075: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3076:
3077: k=0;
3078: for(i=1; i<= (nlstate); i++){
3079: for(j=1; j<=(nlstate+ndeath);j++){
3080: k=k+1;
3081: gp[k]=pmmij[i][j];
3082: }
3083: }
3084:
3085: for(i=1; i<=npar; i++)
3086: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3087:
3088: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3089: k=0;
3090: for(i=1; i<=(nlstate); i++){
3091: for(j=1; j<=(nlstate+ndeath);j++){
3092: k=k+1;
3093: gm[k]=pmmij[i][j];
3094: }
3095: }
3096:
3097: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3098: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3099: }
3100:
3101: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3102: for(theta=1; theta <=npar; theta++)
3103: trgradg[j][theta]=gradg[theta][j];
3104:
3105: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3106: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3107: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3108: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3109: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3110: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3111:
3112: pmij(pmmij,cov,ncovmodel,x,nlstate);
3113:
3114: k=0;
3115: for(i=1; i<=(nlstate); i++){
3116: for(j=1; j<=(nlstate+ndeath);j++){
3117: k=k+1;
3118: mu[k][(int) age]=pmmij[i][j];
3119: }
3120: }
3121: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3122: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3123: varpij[i][j][(int)age] = doldm[i][j];
3124:
3125: /*printf("\n%d ",(int)age);
3126: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3127: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3128: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3129: }*/
3130:
3131: fprintf(ficresprob,"\n%d ",(int)age);
3132: fprintf(ficresprobcov,"\n%d ",(int)age);
3133: fprintf(ficresprobcor,"\n%d ",(int)age);
3134:
3135: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3136: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3137: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3138: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3139: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3140: }
3141: i=0;
3142: for (k=1; k<=(nlstate);k++){
3143: for (l=1; l<=(nlstate+ndeath);l++){
3144: i=i++;
3145: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3146: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3147: for (j=1; j<=i;j++){
3148: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3149: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3150: }
3151: }
3152: }/* end of loop for state */
3153: } /* end of loop for age */
3154:
3155: /* Confidence intervalle of pij */
3156: /*
3157: fprintf(ficgp,"\nset noparametric;unset label");
3158: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3159: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3160: 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);
3161: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3162: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3163: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3164: */
3165:
3166: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3167: first1=1;
3168: for (k2=1; k2<=(nlstate);k2++){
3169: for (l2=1; l2<=(nlstate+ndeath);l2++){
3170: if(l2==k2) continue;
3171: j=(k2-1)*(nlstate+ndeath)+l2;
3172: for (k1=1; k1<=(nlstate);k1++){
3173: for (l1=1; l1<=(nlstate+ndeath);l1++){
3174: if(l1==k1) continue;
3175: i=(k1-1)*(nlstate+ndeath)+l1;
3176: if(i<=j) continue;
3177: for (age=bage; age<=fage; age ++){
3178: if ((int)age %5==0){
3179: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3180: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3181: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3182: mu1=mu[i][(int) age]/stepm*YEARM ;
3183: mu2=mu[j][(int) age]/stepm*YEARM;
3184: c12=cv12/sqrt(v1*v2);
3185: /* Computing eigen value of matrix of covariance */
3186: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3187: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3188: /* Eigen vectors */
3189: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3190: /*v21=sqrt(1.-v11*v11); *//* error */
3191: v21=(lc1-v1)/cv12*v11;
3192: v12=-v21;
3193: v22=v11;
3194: tnalp=v21/v11;
3195: if(first1==1){
3196: first1=0;
3197: 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);
3198: }
3199: 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);
3200: /*printf(fignu*/
3201: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3202: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3203: if(first==1){
3204: first=0;
3205: fprintf(ficgp,"\nset parametric;unset label");
3206: 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);
3207: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3208: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3209: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3210: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3211: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3212: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3213: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3214: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3215: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3216: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3217: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3218: 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",\
3219: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3220: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3221: }else{
3222: first=0;
3223: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3224: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3225: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3226: 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",\
3227: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3228: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3229: }/* if first */
3230: } /* age mod 5 */
3231: } /* end loop age */
3232: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3233: first=1;
3234: } /*l12 */
3235: } /* k12 */
3236: } /*l1 */
3237: }/* k1 */
3238: } /* loop covariates */
3239: }
3240: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3241: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3242: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3243: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
3244: free_vector(xp,1,npar);
3245: fclose(ficresprob);
3246: fclose(ficresprobcov);
3247: fclose(ficresprobcor);
3248: fflush(ficgp);
3249: fflush(fichtmcov);
3250: }
3251:
3252:
3253: /******************* Printing html file ***********/
3254: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3255: int lastpass, int stepm, int weightopt, char model[],\
3256: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3257: int popforecast, int estepm ,\
3258: double jprev1, double mprev1,double anprev1, \
3259: double jprev2, double mprev2,double anprev2){
3260: int jj1, k1, i1, cpt;
3261:
3262: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3263: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3264: </ul>");
3265: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3266: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3267: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3268: fprintf(fichtm,"\
3269: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3270: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3271: fprintf(fichtm,"\
3272: - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3273: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3274: fprintf(fichtm,"\
3275: - Life expectancies by age and initial health status (estepm=%2d months): \
3276: <a href=\"%s\">%s</a> <br>\n</li>",
3277: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3278:
3279: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3280:
3281: m=cptcoveff;
3282: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3283:
3284: jj1=0;
3285: for(k1=1; k1<=m;k1++){
3286: for(i1=1; i1<=ncodemax[k1];i1++){
3287: jj1++;
3288: if (cptcovn > 0) {
3289: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3290: for (cpt=1; cpt<=cptcoveff;cpt++)
3291: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3292: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3293: }
3294: /* Pij */
3295: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
3296: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3297: /* Quasi-incidences */
3298: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3299: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
3300: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3301: /* Stable prevalence in each health state */
3302: for(cpt=1; cpt<nlstate;cpt++){
3303: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
3304: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3305: }
3306: for(cpt=1; cpt<=nlstate;cpt++) {
3307: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
3308: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3309: }
3310: } /* end i1 */
3311: }/* End k1 */
3312: fprintf(fichtm,"</ul>");
3313:
3314:
3315: fprintf(fichtm,"\
3316: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3317: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3318:
3319: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3320: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3321: fprintf(fichtm,"\
3322: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3323: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3324:
3325: fprintf(fichtm,"\
3326: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3327: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3328: fprintf(fichtm,"\
3329: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
3330: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3331: fprintf(fichtm,"\
3332: - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
3333: subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3334: fprintf(fichtm,"\
3335: - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
3336: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3337:
3338: /* if(popforecast==1) fprintf(fichtm,"\n */
3339: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3340: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3341: /* <br>",fileres,fileres,fileres,fileres); */
3342: /* else */
3343: /* 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); */
3344: fflush(fichtm);
3345: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3346:
3347: m=cptcoveff;
3348: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3349:
3350: jj1=0;
3351: for(k1=1; k1<=m;k1++){
3352: for(i1=1; i1<=ncodemax[k1];i1++){
3353: jj1++;
3354: if (cptcovn > 0) {
3355: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3356: for (cpt=1; cpt<=cptcoveff;cpt++)
3357: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3358: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3359: }
3360: for(cpt=1; cpt<=nlstate;cpt++) {
3361: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3362: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
3363: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3364: }
3365: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3366: health expectancies in states (1) and (2): %s%d.png<br>\
3367: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3368: } /* end i1 */
3369: }/* End k1 */
3370: fprintf(fichtm,"</ul>");
3371: fflush(fichtm);
3372: }
3373:
3374: /******************* Gnuplot file **************/
3375: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3376:
3377: char dirfileres[132],optfileres[132];
3378: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3379: int ng;
3380: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3381: /* printf("Problem with file %s",optionfilegnuplot); */
3382: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3383: /* } */
3384:
3385: /*#ifdef windows */
3386: fprintf(ficgp,"cd \"%s\" \n",pathc);
3387: /*#endif */
3388: m=pow(2,cptcoveff);
3389:
3390: strcpy(dirfileres,optionfilefiname);
3391: strcpy(optfileres,"vpl");
3392: /* 1eme*/
3393: for (cpt=1; cpt<= nlstate ; cpt ++) {
3394: for (k1=1; k1<= m ; k1 ++) {
3395: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3396: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3397: fprintf(ficgp,"set xlabel \"Age\" \n\
3398: set ylabel \"Probability\" \n\
3399: set ter png small\n\
3400: set size 0.65,0.65\n\
3401: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3402:
3403: for (i=1; i<= nlstate ; i ++) {
3404: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3405: else fprintf(ficgp," \%%*lf (\%%*lf)");
3406: }
3407: fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3408: for (i=1; i<= nlstate ; i ++) {
3409: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3410: else fprintf(ficgp," \%%*lf (\%%*lf)");
3411: }
3412: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3413: for (i=1; i<= nlstate ; i ++) {
3414: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3415: else fprintf(ficgp," \%%*lf (\%%*lf)");
3416: }
3417: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
3418: }
3419: }
3420: /*2 eme*/
3421:
3422: for (k1=1; k1<= m ; k1 ++) {
3423: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
3424: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3425:
3426: for (i=1; i<= nlstate+1 ; i ++) {
3427: k=2*i;
3428: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3429: for (j=1; j<= nlstate+1 ; j ++) {
3430: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3431: else fprintf(ficgp," \%%*lf (\%%*lf)");
3432: }
3433: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3434: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3435: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3436: for (j=1; j<= nlstate+1 ; j ++) {
3437: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3438: else fprintf(ficgp," \%%*lf (\%%*lf)");
3439: }
3440: fprintf(ficgp,"\" t\"\" w l 0,");
3441: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3442: for (j=1; j<= nlstate+1 ; j ++) {
3443: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3444: else fprintf(ficgp," \%%*lf (\%%*lf)");
3445: }
3446: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3447: else fprintf(ficgp,"\" t\"\" w l 0,");
3448: }
3449: }
3450:
3451: /*3eme*/
3452:
3453: for (k1=1; k1<= m ; k1 ++) {
3454: for (cpt=1; cpt<= nlstate ; cpt ++) {
3455: k=2+nlstate*(2*cpt-2);
3456: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3457: fprintf(ficgp,"set ter png small\n\
3458: set size 0.65,0.65\n\
3459: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
3460: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3461: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3462: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3463: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3464: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3465: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3466:
3467: */
3468: for (i=1; i< nlstate ; i ++) {
3469: 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);
3470:
3471: }
3472: }
3473: }
3474:
3475: /* CV preval stable (period) */
3476: for (k1=1; k1<= m ; k1 ++) {
3477: for (cpt=1; cpt<=nlstate ; cpt ++) {
3478: k=3;
3479: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3480: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3481: set ter png small\nset size 0.65,0.65\n\
3482: unset log y\n\
3483: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
3484:
3485: for (i=1; i< nlstate ; i ++)
3486: fprintf(ficgp,"+$%d",k+i+1);
3487: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3488:
3489: l=3+(nlstate+ndeath)*cpt;
3490: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
3491: for (i=1; i< nlstate ; i ++) {
3492: l=3+(nlstate+ndeath)*cpt;
3493: fprintf(ficgp,"+$%d",l+i+1);
3494: }
3495: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3496: }
3497: }
3498:
3499: /* proba elementaires */
3500: for(i=1,jk=1; i <=nlstate; i++){
3501: for(k=1; k <=(nlstate+ndeath); k++){
3502: if (k != i) {
3503: for(j=1; j <=ncovmodel; j++){
3504: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3505: jk++;
3506: fprintf(ficgp,"\n");
3507: }
3508: }
3509: }
3510: }
3511:
3512: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3513: for(jk=1; jk <=m; jk++) {
3514: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
3515: if (ng==2)
3516: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3517: else
3518: fprintf(ficgp,"\nset title \"Probability\"\n");
3519: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3520: i=1;
3521: for(k2=1; k2<=nlstate; k2++) {
3522: k3=i;
3523: for(k=1; k<=(nlstate+ndeath); k++) {
3524: if (k != k2){
3525: if(ng==2)
3526: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3527: else
3528: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3529: ij=1;
3530: for(j=3; j <=ncovmodel; j++) {
3531: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3532: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3533: ij++;
3534: }
3535: else
3536: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3537: }
3538: fprintf(ficgp,")/(1");
3539:
3540: for(k1=1; k1 <=nlstate; k1++){
3541: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3542: ij=1;
3543: for(j=3; j <=ncovmodel; j++){
3544: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3545: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3546: ij++;
3547: }
3548: else
3549: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3550: }
3551: fprintf(ficgp,")");
3552: }
3553: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3554: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3555: i=i+ncovmodel;
3556: }
3557: } /* end k */
3558: } /* end k2 */
3559: } /* end jk */
3560: } /* end ng */
3561: fflush(ficgp);
3562: } /* end gnuplot */
3563:
3564:
3565: /*************** Moving average **************/
3566: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3567:
3568: int i, cpt, cptcod;
3569: int modcovmax =1;
3570: int mobilavrange, mob;
3571: double age;
3572:
3573: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3574: a covariate has 2 modalities */
3575: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3576:
3577: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3578: if(mobilav==1) mobilavrange=5; /* default */
3579: else mobilavrange=mobilav;
3580: for (age=bage; age<=fage; age++)
3581: for (i=1; i<=nlstate;i++)
3582: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3583: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3584: /* We keep the original values on the extreme ages bage, fage and for
3585: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3586: we use a 5 terms etc. until the borders are no more concerned.
3587: */
3588: for (mob=3;mob <=mobilavrange;mob=mob+2){
3589: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3590: for (i=1; i<=nlstate;i++){
3591: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3592: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3593: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3594: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3595: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3596: }
3597: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3598: }
3599: }
3600: }/* end age */
3601: }/* end mob */
3602: }else return -1;
3603: return 0;
3604: }/* End movingaverage */
3605:
3606:
3607: /************** Forecasting ******************/
3608: 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){
3609: /* proj1, year, month, day of starting projection
3610: agemin, agemax range of age
3611: dateprev1 dateprev2 range of dates during which prevalence is computed
3612: anproj2 year of en of projection (same day and month as proj1).
3613: */
3614: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
3615: int *popage;
3616: double agec; /* generic age */
3617: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3618: double *popeffectif,*popcount;
3619: double ***p3mat;
3620: double ***mobaverage;
3621: char fileresf[FILENAMELENGTH];
3622:
3623: agelim=AGESUP;
3624: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3625:
3626: strcpy(fileresf,"f");
3627: strcat(fileresf,fileres);
3628: if((ficresf=fopen(fileresf,"w"))==NULL) {
3629: printf("Problem with forecast resultfile: %s\n", fileresf);
3630: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3631: }
3632: printf("Computing forecasting: result on file '%s' \n", fileresf);
3633: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3634:
3635: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3636:
3637: if (mobilav!=0) {
3638: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3639: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3640: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3641: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3642: }
3643: }
3644:
3645: stepsize=(int) (stepm+YEARM-1)/YEARM;
3646: if (stepm<=12) stepsize=1;
3647: if(estepm < stepm){
3648: printf ("Problem %d lower than %d\n",estepm, stepm);
3649: }
3650: else hstepm=estepm;
3651:
3652: hstepm=hstepm/stepm;
3653: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3654: fractional in yp1 */
3655: anprojmean=yp;
3656: yp2=modf((yp1*12),&yp);
3657: mprojmean=yp;
3658: yp1=modf((yp2*30.5),&yp);
3659: jprojmean=yp;
3660: if(jprojmean==0) jprojmean=1;
3661: if(mprojmean==0) jprojmean=1;
3662:
3663: i1=cptcoveff;
3664: if (cptcovn < 1){i1=1;}
3665:
3666: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
3667:
3668: fprintf(ficresf,"#****** Routine prevforecast **\n");
3669:
3670: /* if (h==(int)(YEARM*yearp)){ */
3671: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
3672: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3673: k=k+1;
3674: fprintf(ficresf,"\n#******");
3675: for(j=1;j<=cptcoveff;j++) {
3676: 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]]);
3677: }
3678: fprintf(ficresf,"******\n");
3679: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3680: for(j=1; j<=nlstate+ndeath;j++){
3681: for(i=1; i<=nlstate;i++)
3682: fprintf(ficresf," p%d%d",i,j);
3683: fprintf(ficresf," p.%d",j);
3684: }
3685: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
3686: fprintf(ficresf,"\n");
3687: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
3688:
3689: for (agec=fage; agec>=(ageminpar-1); agec--){
3690: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
3691: nhstepm = nhstepm/hstepm;
3692: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3693: oldm=oldms;savm=savms;
3694: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
3695:
3696: for (h=0; h<=nhstepm; h++){
3697: if (h*hstepm/YEARM*stepm ==yearp) {
3698: fprintf(ficresf,"\n");
3699: for(j=1;j<=cptcoveff;j++)
3700: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3701: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
3702: }
3703: for(j=1; j<=nlstate+ndeath;j++) {
3704: ppij=0.;
3705: for(i=1; i<=nlstate;i++) {
3706: if (mobilav==1)
3707: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
3708: else {
3709: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
3710: }
3711: if (h*hstepm/YEARM*stepm== yearp) {
3712: fprintf(ficresf," %.3f", p3mat[i][j][h]);
3713: }
3714: } /* end i */
3715: if (h*hstepm/YEARM*stepm==yearp) {
3716: fprintf(ficresf," %.3f", ppij);
3717: }
3718: }/* end j */
3719: } /* end h */
3720: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3721: } /* end agec */
3722: } /* end yearp */
3723: } /* end cptcod */
3724: } /* end cptcov */
3725:
3726: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3727:
3728: fclose(ficresf);
3729: }
3730:
3731: /************** Forecasting *****not tested NB*************/
3732: 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){
3733:
3734: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3735: int *popage;
3736: double calagedatem, agelim, kk1, kk2;
3737: double *popeffectif,*popcount;
3738: double ***p3mat,***tabpop,***tabpopprev;
3739: double ***mobaverage;
3740: char filerespop[FILENAMELENGTH];
3741:
3742: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3743: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3744: agelim=AGESUP;
3745: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
3746:
3747: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3748:
3749:
3750: strcpy(filerespop,"pop");
3751: strcat(filerespop,fileres);
3752: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3753: printf("Problem with forecast resultfile: %s\n", filerespop);
3754: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3755: }
3756: printf("Computing forecasting: result on file '%s' \n", filerespop);
3757: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3758:
3759: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3760:
3761: if (mobilav!=0) {
3762: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3763: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3764: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3765: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3766: }
3767: }
3768:
3769: stepsize=(int) (stepm+YEARM-1)/YEARM;
3770: if (stepm<=12) stepsize=1;
3771:
3772: agelim=AGESUP;
3773:
3774: hstepm=1;
3775: hstepm=hstepm/stepm;
3776:
3777: if (popforecast==1) {
3778: if((ficpop=fopen(popfile,"r"))==NULL) {
3779: printf("Problem with population file : %s\n",popfile);exit(0);
3780: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3781: }
3782: popage=ivector(0,AGESUP);
3783: popeffectif=vector(0,AGESUP);
3784: popcount=vector(0,AGESUP);
3785:
3786: i=1;
3787: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3788:
3789: imx=i;
3790: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3791: }
3792:
3793: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
3794: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3795: k=k+1;
3796: fprintf(ficrespop,"\n#******");
3797: for(j=1;j<=cptcoveff;j++) {
3798: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3799: }
3800: fprintf(ficrespop,"******\n");
3801: fprintf(ficrespop,"# Age");
3802: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3803: if (popforecast==1) fprintf(ficrespop," [Population]");
3804:
3805: for (cpt=0; cpt<=0;cpt++) {
3806: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3807:
3808: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3809: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3810: nhstepm = nhstepm/hstepm;
3811:
3812: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3813: oldm=oldms;savm=savms;
3814: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3815:
3816: for (h=0; h<=nhstepm; h++){
3817: if (h==(int) (calagedatem+YEARM*cpt)) {
3818: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3819: }
3820: for(j=1; j<=nlstate+ndeath;j++) {
3821: kk1=0.;kk2=0;
3822: for(i=1; i<=nlstate;i++) {
3823: if (mobilav==1)
3824: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3825: else {
3826: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3827: }
3828: }
3829: if (h==(int)(calagedatem+12*cpt)){
3830: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3831: /*fprintf(ficrespop," %.3f", kk1);
3832: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3833: }
3834: }
3835: for(i=1; i<=nlstate;i++){
3836: kk1=0.;
3837: for(j=1; j<=nlstate;j++){
3838: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3839: }
3840: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
3841: }
3842:
3843: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
3844: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3845: }
3846: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3847: }
3848: }
3849:
3850: /******/
3851:
3852: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3853: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3854: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3855: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3856: nhstepm = nhstepm/hstepm;
3857:
3858: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3859: oldm=oldms;savm=savms;
3860: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3861: for (h=0; h<=nhstepm; h++){
3862: if (h==(int) (calagedatem+YEARM*cpt)) {
3863: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3864: }
3865: for(j=1; j<=nlstate+ndeath;j++) {
3866: kk1=0.;kk2=0;
3867: for(i=1; i<=nlstate;i++) {
3868: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3869: }
3870: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
3871: }
3872: }
3873: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3874: }
3875: }
3876: }
3877: }
3878:
3879: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3880:
3881: if (popforecast==1) {
3882: free_ivector(popage,0,AGESUP);
3883: free_vector(popeffectif,0,AGESUP);
3884: free_vector(popcount,0,AGESUP);
3885: }
3886: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3887: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3888: fclose(ficrespop);
3889: } /* End of popforecast */
3890:
3891: int fileappend(FILE *fichier, char *optionfich)
3892: {
3893: if((fichier=fopen(optionfich,"a"))==NULL) {
3894: printf("Problem with file: %s\n", optionfich);
3895: fprintf(ficlog,"Problem with file: %s\n", optionfich);
3896: return (0);
3897: }
3898: fflush(fichier);
3899: return (1);
3900: }
3901:
3902:
3903: /**************** function prwizard **********************/
3904: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
3905: {
3906:
3907: /* Wizard to print covariance matrix template */
3908:
3909: char ca[32], cb[32], cc[32];
3910: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
3911: int numlinepar;
3912:
3913: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3914: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3915: for(i=1; i <=nlstate; i++){
3916: jj=0;
3917: for(j=1; j <=nlstate+ndeath; j++){
3918: if(j==i) continue;
3919: jj++;
3920: /*ca[0]= k+'a'-1;ca[1]='\0';*/
3921: printf("%1d%1d",i,j);
3922: fprintf(ficparo,"%1d%1d",i,j);
3923: for(k=1; k<=ncovmodel;k++){
3924: /* printf(" %lf",param[i][j][k]); */
3925: /* fprintf(ficparo," %lf",param[i][j][k]); */
3926: printf(" 0.");
3927: fprintf(ficparo," 0.");
3928: }
3929: printf("\n");
3930: fprintf(ficparo,"\n");
3931: }
3932: }
3933: printf("# Scales (for hessian or gradient estimation)\n");
3934: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
3935: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
3936: for(i=1; i <=nlstate; i++){
3937: jj=0;
3938: for(j=1; j <=nlstate+ndeath; j++){
3939: if(j==i) continue;
3940: jj++;
3941: fprintf(ficparo,"%1d%1d",i,j);
3942: printf("%1d%1d",i,j);
3943: fflush(stdout);
3944: for(k=1; k<=ncovmodel;k++){
3945: /* printf(" %le",delti3[i][j][k]); */
3946: /* fprintf(ficparo," %le",delti3[i][j][k]); */
3947: printf(" 0.");
3948: fprintf(ficparo," 0.");
3949: }
3950: numlinepar++;
3951: printf("\n");
3952: fprintf(ficparo,"\n");
3953: }
3954: }
3955: printf("# Covariance matrix\n");
3956: /* # 121 Var(a12)\n\ */
3957: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3958: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
3959: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
3960: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
3961: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
3962: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
3963: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3964: fflush(stdout);
3965: fprintf(ficparo,"# Covariance matrix\n");
3966: /* # 121 Var(a12)\n\ */
3967: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3968: /* # ...\n\ */
3969: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3970:
3971: for(itimes=1;itimes<=2;itimes++){
3972: jj=0;
3973: for(i=1; i <=nlstate; i++){
3974: for(j=1; j <=nlstate+ndeath; j++){
3975: if(j==i) continue;
3976: for(k=1; k<=ncovmodel;k++){
3977: jj++;
3978: ca[0]= k+'a'-1;ca[1]='\0';
3979: if(itimes==1){
3980: printf("#%1d%1d%d",i,j,k);
3981: fprintf(ficparo,"#%1d%1d%d",i,j,k);
3982: }else{
3983: printf("%1d%1d%d",i,j,k);
3984: fprintf(ficparo,"%1d%1d%d",i,j,k);
3985: /* printf(" %.5le",matcov[i][j]); */
3986: }
3987: ll=0;
3988: for(li=1;li <=nlstate; li++){
3989: for(lj=1;lj <=nlstate+ndeath; lj++){
3990: if(lj==li) continue;
3991: for(lk=1;lk<=ncovmodel;lk++){
3992: ll++;
3993: if(ll<=jj){
3994: cb[0]= lk +'a'-1;cb[1]='\0';
3995: if(ll<jj){
3996: if(itimes==1){
3997: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3998: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3999: }else{
4000: printf(" 0.");
4001: fprintf(ficparo," 0.");
4002: }
4003: }else{
4004: if(itimes==1){
4005: printf(" Var(%s%1d%1d)",ca,i,j);
4006: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4007: }else{
4008: printf(" 0.");
4009: fprintf(ficparo," 0.");
4010: }
4011: }
4012: }
4013: } /* end lk */
4014: } /* end lj */
4015: } /* end li */
4016: printf("\n");
4017: fprintf(ficparo,"\n");
4018: numlinepar++;
4019: } /* end k*/
4020: } /*end j */
4021: } /* end i */
4022: } /* end itimes */
4023:
4024: } /* end of prwizard */
4025: /******************* Gompertz Likelihood ******************************/
4026: double gompertz(double x[])
4027: {
4028: double A,B,L=0.0,sump=0.,num=0.;
4029: int i,n=0; /* n is the size of the sample */
4030:
4031: for (i=0;i<=imx-1 ; i++) {
4032: sump=sump+weight[i];
4033: /* sump=sump+1;*/
4034: num=num+1;
4035: }
4036:
4037:
4038: /* for (i=0; i<=imx; i++)
4039: 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]);*/
4040:
4041: for (i=1;i<=imx ; i++)
4042: {
4043: if (cens[i] == 1 && wav[i]>1)
4044: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4045:
4046: if (cens[i] == 0 && wav[i]>1)
4047: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4048: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4049:
4050: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4051: if (wav[i] > 1 ) { /* ??? */
4052: L=L+A*weight[i];
4053: /* 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]);*/
4054: }
4055: }
4056:
4057: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4058:
4059: return -2*L*num/sump;
4060: }
4061:
4062: /******************* Printing html file ***********/
4063: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4064: int lastpass, int stepm, int weightopt, char model[],\
4065: int imx, double p[],double **matcov,double agemortsup){
4066: int i,k;
4067:
4068: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4069: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4070: for (i=1;i<=2;i++)
4071: 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]));
4072: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4073: fprintf(fichtm,"</ul>");
4074:
4075: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4076:
4077: 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>");
4078:
4079: for (k=agegomp;k<(agemortsup-2);k++)
4080: 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]);
4081:
4082:
4083: fflush(fichtm);
4084: }
4085:
4086: /******************* Gnuplot file **************/
4087: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4088:
4089: char dirfileres[132],optfileres[132];
4090: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4091: int ng;
4092:
4093:
4094: /*#ifdef windows */
4095: fprintf(ficgp,"cd \"%s\" \n",pathc);
4096: /*#endif */
4097:
4098:
4099: strcpy(dirfileres,optionfilefiname);
4100: strcpy(optfileres,"vpl");
4101: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4102: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4103: fprintf(ficgp, "set ter png small\n set log y\n");
4104: fprintf(ficgp, "set size 0.65,0.65\n");
4105: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4106:
4107: }
4108:
4109:
4110:
4111:
4112: /***********************************************/
4113: /**************** Main Program *****************/
4114: /***********************************************/
4115:
4116: int main(int argc, char *argv[])
4117: {
4118: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
4119: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
4120: int linei, month, year,iout;
4121: int jj, ll, li, lj, lk, imk;
4122: int numlinepar=0; /* Current linenumber of parameter file */
4123: int itimes;
4124: int NDIM=2;
4125:
4126: char ca[32], cb[32], cc[32];
4127: char dummy[]=" ";
4128: /* FILE *fichtm; *//* Html File */
4129: /* FILE *ficgp;*/ /*Gnuplot File */
4130: struct stat info;
4131: double agedeb, agefin,hf;
4132: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
4133:
4134: double fret;
4135: double **xi,tmp,delta;
4136:
4137: double dum; /* Dummy variable */
4138: double ***p3mat;
4139: double ***mobaverage;
4140: int *indx;
4141: char line[MAXLINE], linepar[MAXLINE];
4142: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
4143: char pathr[MAXLINE], pathimach[MAXLINE];
4144: int firstobs=1, lastobs=10;
4145: int sdeb, sfin; /* Status at beginning and end */
4146: int c, h , cpt,l;
4147: int ju,jl, mi;
4148: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
4149: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
4150: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
4151: int mobilav=0,popforecast=0;
4152: int hstepm, nhstepm;
4153: int agemortsup;
4154: float sumlpop=0.;
4155: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
4156: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
4157:
4158: double bage, fage, age, agelim, agebase;
4159: double ftolpl=FTOL;
4160: double **prlim;
4161: double *severity;
4162: double ***param; /* Matrix of parameters */
4163: double *p;
4164: double **matcov; /* Matrix of covariance */
4165: double ***delti3; /* Scale */
4166: double *delti; /* Scale */
4167: double ***eij, ***vareij;
4168: double **varpl; /* Variances of prevalence limits by age */
4169: double *epj, vepp;
4170: double kk1, kk2;
4171: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
4172: double **ximort;
4173: char *alph[]={"a","a","b","c","d","e"}, str[4];
4174: int *dcwave;
4175:
4176: char z[1]="c", occ;
4177:
4178: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
4179: char strstart[80], *strt, strtend[80];
4180: char *stratrunc;
4181: int lstra;
4182:
4183: long total_usecs;
4184:
4185: /* setlocale (LC_ALL, ""); */
4186: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4187: /* textdomain (PACKAGE); */
4188: /* setlocale (LC_CTYPE, ""); */
4189: /* setlocale (LC_MESSAGES, ""); */
4190:
4191: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4192: (void) gettimeofday(&start_time,&tzp);
4193: curr_time=start_time;
4194: tm = *localtime(&start_time.tv_sec);
4195: tmg = *gmtime(&start_time.tv_sec);
4196: strcpy(strstart,asctime(&tm));
4197:
4198: /* printf("Localtime (at start)=%s",strstart); */
4199: /* tp.tv_sec = tp.tv_sec +86400; */
4200: /* tm = *localtime(&start_time.tv_sec); */
4201: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4202: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4203: /* tmg.tm_hour=tmg.tm_hour + 1; */
4204: /* tp.tv_sec = mktime(&tmg); */
4205: /* strt=asctime(&tmg); */
4206: /* printf("Time(after) =%s",strstart); */
4207: /* (void) time (&time_value);
4208: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4209: * tm = *localtime(&time_value);
4210: * strstart=asctime(&tm);
4211: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
4212: */
4213:
4214: nberr=0; /* Number of errors and warnings */
4215: nbwarn=0;
4216: getcwd(pathcd, size);
4217:
4218: printf("\n%s\n%s",version,fullversion);
4219: if(argc <=1){
4220: printf("\nEnter the parameter file name: ");
4221: scanf("%s",pathtot);
4222: }
4223: else{
4224: strcpy(pathtot,argv[1]);
4225: }
4226: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
4227: /*cygwin_split_path(pathtot,path,optionfile);
4228: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
4229: /* cutv(path,optionfile,pathtot,'\\');*/
4230:
4231: /* Split argv[0], imach program to get pathimach */
4232: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
4233: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4234: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4235: /* strcpy(pathimach,argv[0]); */
4236: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
4237: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
4238: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
4239: chdir(path);
4240: strcpy(command,"mkdir ");
4241: strcat(command,optionfilefiname);
4242: if((outcmd=system(command)) != 0){
4243: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
4244: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
4245: /* fclose(ficlog); */
4246: /* exit(1); */
4247: }
4248: /* if((imk=mkdir(optionfilefiname))<0){ */
4249: /* perror("mkdir"); */
4250: /* } */
4251:
4252: /*-------- arguments in the command line --------*/
4253:
4254: /* Log file */
4255: strcat(filelog, optionfilefiname);
4256: strcat(filelog,".log"); /* */
4257: if((ficlog=fopen(filelog,"w"))==NULL) {
4258: printf("Problem with logfile %s\n",filelog);
4259: goto end;
4260: }
4261: fprintf(ficlog,"Log filename:%s\n",filelog);
4262: fprintf(ficlog,"\n%s\n%s",version,fullversion);
4263: fprintf(ficlog,"\nEnter the parameter file name: \n");
4264: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
4265: path=%s \n\
4266: optionfile=%s\n\
4267: optionfilext=%s\n\
4268: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
4269:
4270: printf("Local time (at start):%s",strstart);
4271: fprintf(ficlog,"Local time (at start): %s",strstart);
4272: fflush(ficlog);
4273: /* (void) gettimeofday(&curr_time,&tzp); */
4274: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
4275:
4276: /* */
4277: strcpy(fileres,"r");
4278: strcat(fileres, optionfilefiname);
4279: strcat(fileres,".txt"); /* Other files have txt extension */
4280:
4281: /*---------arguments file --------*/
4282:
4283: if((ficpar=fopen(optionfile,"r"))==NULL) {
4284: printf("Problem with optionfile %s\n",optionfile);
4285: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
4286: fflush(ficlog);
4287: goto end;
4288: }
4289:
4290:
4291:
4292: strcpy(filereso,"o");
4293: strcat(filereso,fileres);
4294: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
4295: printf("Problem with Output resultfile: %s\n", filereso);
4296: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
4297: fflush(ficlog);
4298: goto end;
4299: }
4300:
4301: /* Reads comments: lines beginning with '#' */
4302: numlinepar=0;
4303: while((c=getc(ficpar))=='#' && c!= EOF){
4304: ungetc(c,ficpar);
4305: fgets(line, MAXLINE, ficpar);
4306: numlinepar++;
4307: puts(line);
4308: fputs(line,ficparo);
4309: fputs(line,ficlog);
4310: }
4311: ungetc(c,ficpar);
4312:
4313: 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);
4314: numlinepar++;
4315: 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);
4316: 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);
4317: 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);
4318: fflush(ficlog);
4319: while((c=getc(ficpar))=='#' && c!= EOF){
4320: ungetc(c,ficpar);
4321: fgets(line, MAXLINE, ficpar);
4322: numlinepar++;
4323: puts(line);
4324: fputs(line,ficparo);
4325: fputs(line,ficlog);
4326: }
4327: ungetc(c,ficpar);
4328:
4329:
4330: covar=matrix(0,NCOVMAX,1,n);
4331: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
4332: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4333:
4334: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
4335: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
4336: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4337:
4338: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4339: delti=delti3[1][1];
4340: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
4341: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4342: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4343: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4344: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4345: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4346: fclose (ficparo);
4347: fclose (ficlog);
4348: exit(0);
4349: }
4350: else if(mle==-3) {
4351: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4352: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4353: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4354: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4355: matcov=matrix(1,npar,1,npar);
4356: }
4357: else{
4358: /* Read guess parameters */
4359: /* Reads comments: lines beginning with '#' */
4360: while((c=getc(ficpar))=='#' && c!= EOF){
4361: ungetc(c,ficpar);
4362: fgets(line, MAXLINE, ficpar);
4363: numlinepar++;
4364: puts(line);
4365: fputs(line,ficparo);
4366: fputs(line,ficlog);
4367: }
4368: ungetc(c,ficpar);
4369:
4370: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4371: for(i=1; i <=nlstate; i++){
4372: j=0;
4373: for(jj=1; jj <=nlstate+ndeath; jj++){
4374: if(jj==i) continue;
4375: j++;
4376: fscanf(ficpar,"%1d%1d",&i1,&j1);
4377: if ((i1 != i) && (j1 != j)){
4378: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4379: exit(1);
4380: }
4381: fprintf(ficparo,"%1d%1d",i1,j1);
4382: if(mle==1)
4383: printf("%1d%1d",i,j);
4384: fprintf(ficlog,"%1d%1d",i,j);
4385: for(k=1; k<=ncovmodel;k++){
4386: fscanf(ficpar," %lf",¶m[i][j][k]);
4387: if(mle==1){
4388: printf(" %lf",param[i][j][k]);
4389: fprintf(ficlog," %lf",param[i][j][k]);
4390: }
4391: else
4392: fprintf(ficlog," %lf",param[i][j][k]);
4393: fprintf(ficparo," %lf",param[i][j][k]);
4394: }
4395: fscanf(ficpar,"\n");
4396: numlinepar++;
4397: if(mle==1)
4398: printf("\n");
4399: fprintf(ficlog,"\n");
4400: fprintf(ficparo,"\n");
4401: }
4402: }
4403: fflush(ficlog);
4404:
4405: p=param[1][1];
4406:
4407: /* Reads comments: lines beginning with '#' */
4408: while((c=getc(ficpar))=='#' && c!= EOF){
4409: ungetc(c,ficpar);
4410: fgets(line, MAXLINE, ficpar);
4411: numlinepar++;
4412: puts(line);
4413: fputs(line,ficparo);
4414: fputs(line,ficlog);
4415: }
4416: ungetc(c,ficpar);
4417:
4418: for(i=1; i <=nlstate; i++){
4419: for(j=1; j <=nlstate+ndeath-1; j++){
4420: fscanf(ficpar,"%1d%1d",&i1,&j1);
4421: if ((i1-i)*(j1-j)!=0){
4422: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4423: exit(1);
4424: }
4425: printf("%1d%1d",i,j);
4426: fprintf(ficparo,"%1d%1d",i1,j1);
4427: fprintf(ficlog,"%1d%1d",i1,j1);
4428: for(k=1; k<=ncovmodel;k++){
4429: fscanf(ficpar,"%le",&delti3[i][j][k]);
4430: printf(" %le",delti3[i][j][k]);
4431: fprintf(ficparo," %le",delti3[i][j][k]);
4432: fprintf(ficlog," %le",delti3[i][j][k]);
4433: }
4434: fscanf(ficpar,"\n");
4435: numlinepar++;
4436: printf("\n");
4437: fprintf(ficparo,"\n");
4438: fprintf(ficlog,"\n");
4439: }
4440: }
4441: fflush(ficlog);
4442:
4443: delti=delti3[1][1];
4444:
4445:
4446: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
4447:
4448: /* Reads comments: lines beginning with '#' */
4449: while((c=getc(ficpar))=='#' && c!= EOF){
4450: ungetc(c,ficpar);
4451: fgets(line, MAXLINE, ficpar);
4452: numlinepar++;
4453: puts(line);
4454: fputs(line,ficparo);
4455: fputs(line,ficlog);
4456: }
4457: ungetc(c,ficpar);
4458:
4459: matcov=matrix(1,npar,1,npar);
4460: for(i=1; i <=npar; i++){
4461: fscanf(ficpar,"%s",&str);
4462: if(mle==1)
4463: printf("%s",str);
4464: fprintf(ficlog,"%s",str);
4465: fprintf(ficparo,"%s",str);
4466: for(j=1; j <=i; j++){
4467: fscanf(ficpar," %le",&matcov[i][j]);
4468: if(mle==1){
4469: printf(" %.5le",matcov[i][j]);
4470: }
4471: fprintf(ficlog," %.5le",matcov[i][j]);
4472: fprintf(ficparo," %.5le",matcov[i][j]);
4473: }
4474: fscanf(ficpar,"\n");
4475: numlinepar++;
4476: if(mle==1)
4477: printf("\n");
4478: fprintf(ficlog,"\n");
4479: fprintf(ficparo,"\n");
4480: }
4481: for(i=1; i <=npar; i++)
4482: for(j=i+1;j<=npar;j++)
4483: matcov[i][j]=matcov[j][i];
4484:
4485: if(mle==1)
4486: printf("\n");
4487: fprintf(ficlog,"\n");
4488:
4489: fflush(ficlog);
4490:
4491: /*-------- Rewriting parameter file ----------*/
4492: strcpy(rfileres,"r"); /* "Rparameterfile */
4493: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4494: strcat(rfileres,"."); /* */
4495: strcat(rfileres,optionfilext); /* Other files have txt extension */
4496: if((ficres =fopen(rfileres,"w"))==NULL) {
4497: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4498: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4499: }
4500: fprintf(ficres,"#%s\n",version);
4501: } /* End of mle != -3 */
4502:
4503: /*-------- data file ----------*/
4504: if((fic=fopen(datafile,"r"))==NULL) {
4505: printf("Problem with datafile: %s\n", datafile);goto end;
4506: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
4507: }
4508:
4509: n= lastobs;
4510: severity = vector(1,maxwav);
4511: outcome=imatrix(1,maxwav+1,1,n);
4512: num=lvector(1,n);
4513: moisnais=vector(1,n);
4514: annais=vector(1,n);
4515: moisdc=vector(1,n);
4516: andc=vector(1,n);
4517: agedc=vector(1,n);
4518: cod=ivector(1,n);
4519: weight=vector(1,n);
4520: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4521: mint=matrix(1,maxwav,1,n);
4522: anint=matrix(1,maxwav,1,n);
4523: s=imatrix(1,maxwav+1,1,n);
4524: tab=ivector(1,NCOVMAX);
4525: ncodemax=ivector(1,8);
4526:
4527: i=1;
4528: linei=0;
4529: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4530: linei=linei+1;
4531: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4532: if(line[j] == '\t')
4533: line[j] = ' ';
4534: }
4535: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4536: ;
4537: };
4538: line[j+1]=0; /* Trims blanks at end of line */
4539: if(line[0]=='#'){
4540: fprintf(ficlog,"Comment line\n%s\n",line);
4541: printf("Comment line\n%s\n",line);
4542: continue;
4543: }
4544:
4545: for (j=maxwav;j>=1;j--){
4546: cutv(stra, strb,line,' ');
4547: errno=0;
4548: lval=strtol(strb,&endptr,10);
4549: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4550: if( strb[0]=='\0' || (*endptr != '\0')){
4551: 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);
4552: exit(1);
4553: }
4554: s[j][i]=lval;
4555:
4556: strcpy(line,stra);
4557: cutv(stra, strb,line,' ');
4558: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4559: }
4560: else if(iout=sscanf(strb,"%s.") != 0){
4561: month=99;
4562: year=9999;
4563: }else{
4564: 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);
4565: exit(1);
4566: }
4567: anint[j][i]= (double) year;
4568: mint[j][i]= (double)month;
4569: strcpy(line,stra);
4570: } /* ENd Waves */
4571:
4572: cutv(stra, strb,line,' ');
4573: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4574: }
4575: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4576: month=99;
4577: year=9999;
4578: }else{
4579: 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);
4580: exit(1);
4581: }
4582: andc[i]=(double) year;
4583: moisdc[i]=(double) month;
4584: strcpy(line,stra);
4585:
4586: cutv(stra, strb,line,' ');
4587: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4588: }
4589: else if(iout=sscanf(strb,"%s.") != 0){
4590: month=99;
4591: year=9999;
4592: }else{
4593: 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);
4594: exit(1);
4595: }
4596: annais[i]=(double)(year);
4597: moisnais[i]=(double)(month);
4598: strcpy(line,stra);
4599:
4600: cutv(stra, strb,line,' ');
4601: errno=0;
4602: lval=strtol(strb,&endptr,10);
4603: if( strb[0]=='\0' || (*endptr != '\0')){
4604: printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight. Exiting.\n",lval, i,line,linei);
4605: exit(1);
4606: }
4607: weight[i]=(double)(lval);
4608: strcpy(line,stra);
4609:
4610: for (j=ncovcol;j>=1;j--){
4611: cutv(stra, strb,line,' ');
4612: errno=0;
4613: lval=strtol(strb,&endptr,10);
4614: if( strb[0]=='\0' || (*endptr != '\0')){
4615: 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);
4616: exit(1);
4617: }
4618: if(lval <-1 || lval >1){
4619: printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self). Exiting.\n",lval,linei, i,line,j);
4620: exit(1);
4621: }
4622: covar[j][i]=(double)(lval);
4623: strcpy(line,stra);
4624: }
4625: lstra=strlen(stra);
4626:
4627: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4628: stratrunc = &(stra[lstra-9]);
4629: num[i]=atol(stratrunc);
4630: }
4631: else
4632: num[i]=atol(stra);
4633: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4634: 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;}*/
4635:
4636: i=i+1;
4637: } /* End loop reading data */
4638: fclose(fic);
4639: /* printf("ii=%d", ij);
4640: scanf("%d",i);*/
4641: imx=i-1; /* Number of individuals */
4642:
4643: /* for (i=1; i<=imx; i++){
4644: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4645: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4646: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4647: }*/
4648: /* for (i=1; i<=imx; i++){
4649: if (s[4][i]==9) s[4][i]=-1;
4650: 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]));}*/
4651:
4652: /* for (i=1; i<=imx; i++) */
4653:
4654: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4655: else weight[i]=1;*/
4656:
4657: /* Calculation of the number of parameters from char model */
4658: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4659: Tprod=ivector(1,15);
4660: Tvaraff=ivector(1,15);
4661: Tvard=imatrix(1,15,1,2);
4662: Tage=ivector(1,15);
4663:
4664: if (strlen(model) >1){ /* If there is at least 1 covariate */
4665: j=0, j1=0, k1=1, k2=1;
4666: j=nbocc(model,'+'); /* j=Number of '+' */
4667: j1=nbocc(model,'*'); /* j1=Number of '*' */
4668: cptcovn=j+1;
4669: cptcovprod=j1; /*Number of products */
4670:
4671: strcpy(modelsav,model);
4672: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4673: printf("Error. Non available option model=%s ",model);
4674: fprintf(ficlog,"Error. Non available option model=%s ",model);
4675: goto end;
4676: }
4677:
4678: /* This loop fills the array Tvar from the string 'model'.*/
4679:
4680: for(i=(j+1); i>=1;i--){
4681: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
4682: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
4683: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4684: /*scanf("%d",i);*/
4685: if (strchr(strb,'*')) { /* Model includes a product */
4686: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4687: if (strcmp(strc,"age")==0) { /* Vn*age */
4688: cptcovprod--;
4689: cutv(strb,stre,strd,'V');
4690: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4691: cptcovage++;
4692: Tage[cptcovage]=i;
4693: /*printf("stre=%s ", stre);*/
4694: }
4695: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4696: cptcovprod--;
4697: cutv(strb,stre,strc,'V');
4698: Tvar[i]=atoi(stre);
4699: cptcovage++;
4700: Tage[cptcovage]=i;
4701: }
4702: else { /* Age is not in the model */
4703: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4704: Tvar[i]=ncovcol+k1;
4705: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4706: Tprod[k1]=i;
4707: Tvard[k1][1]=atoi(strc); /* m*/
4708: Tvard[k1][2]=atoi(stre); /* n */
4709: Tvar[cptcovn+k2]=Tvard[k1][1];
4710: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4711: for (k=1; k<=lastobs;k++)
4712: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4713: k1++;
4714: k2=k2+2;
4715: }
4716: }
4717: else { /* no more sum */
4718: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4719: /* scanf("%d",i);*/
4720: cutv(strd,strc,strb,'V');
4721: Tvar[i]=atoi(strc);
4722: }
4723: strcpy(modelsav,stra);
4724: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4725: scanf("%d",i);*/
4726: } /* end of loop + */
4727: } /* end model */
4728:
4729: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4730: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4731:
4732: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4733: printf("cptcovprod=%d ", cptcovprod);
4734: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
4735:
4736: scanf("%d ",i);*/
4737:
4738: /* if(mle==1){*/
4739: if (weightopt != 1) { /* Maximisation without weights*/
4740: for(i=1;i<=n;i++) weight[i]=1.0;
4741: }
4742: /*-calculation of age at interview from date of interview and age at death -*/
4743: agev=matrix(1,maxwav,1,imx);
4744:
4745: for (i=1; i<=imx; i++) {
4746: for(m=2; (m<= maxwav); m++) {
4747: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
4748: anint[m][i]=9999;
4749: s[m][i]=-1;
4750: }
4751: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
4752: nberr++;
4753: 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);
4754: 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);
4755: s[m][i]=-1;
4756: }
4757: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
4758: nberr++;
4759: 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]);
4760: 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]);
4761: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
4762: }
4763: }
4764: }
4765:
4766: for (i=1; i<=imx; i++) {
4767: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
4768: for(m=firstpass; (m<= lastpass); m++){
4769: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
4770: if (s[m][i] >= nlstate+1) {
4771: if(agedc[i]>0)
4772: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
4773: agev[m][i]=agedc[i];
4774: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4775: else {
4776: if ((int)andc[i]!=9999){
4777: nbwarn++;
4778: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4779: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
4780: agev[m][i]=-1;
4781: }
4782: }
4783: }
4784: else if(s[m][i] !=9){ /* Standard case, age in fractional
4785: years but with the precision of a month */
4786: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
4787: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
4788: agev[m][i]=1;
4789: else if(agev[m][i] <agemin){
4790: agemin=agev[m][i];
4791: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
4792: }
4793: else if(agev[m][i] >agemax){
4794: agemax=agev[m][i];
4795: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
4796: }
4797: /*agev[m][i]=anint[m][i]-annais[i];*/
4798: /* agev[m][i] = age[i]+2*m;*/
4799: }
4800: else { /* =9 */
4801: agev[m][i]=1;
4802: s[m][i]=-1;
4803: }
4804: }
4805: else /*= 0 Unknown */
4806: agev[m][i]=1;
4807: }
4808:
4809: }
4810: for (i=1; i<=imx; i++) {
4811: for(m=firstpass; (m<=lastpass); m++){
4812: if (s[m][i] > (nlstate+ndeath)) {
4813: nberr++;
4814: 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);
4815: 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);
4816: goto end;
4817: }
4818: }
4819: }
4820:
4821: /*for (i=1; i<=imx; i++){
4822: for (m=firstpass; (m<lastpass); m++){
4823: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
4824: }
4825:
4826: }*/
4827:
4828:
4829: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4830: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4831:
4832: agegomp=(int)agemin;
4833: free_vector(severity,1,maxwav);
4834: free_imatrix(outcome,1,maxwav+1,1,n);
4835: free_vector(moisnais,1,n);
4836: free_vector(annais,1,n);
4837: /* free_matrix(mint,1,maxwav,1,n);
4838: free_matrix(anint,1,maxwav,1,n);*/
4839: free_vector(moisdc,1,n);
4840: free_vector(andc,1,n);
4841:
4842:
4843: wav=ivector(1,imx);
4844: dh=imatrix(1,lastpass-firstpass+1,1,imx);
4845: bh=imatrix(1,lastpass-firstpass+1,1,imx);
4846: mw=imatrix(1,lastpass-firstpass+1,1,imx);
4847:
4848: /* Concatenates waves */
4849: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
4850:
4851: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
4852:
4853: Tcode=ivector(1,100);
4854: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
4855: ncodemax[1]=1;
4856: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
4857:
4858: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
4859: the estimations*/
4860: h=0;
4861: m=pow(2,cptcoveff);
4862:
4863: for(k=1;k<=cptcoveff; k++){
4864: for(i=1; i <=(m/pow(2,k));i++){
4865: for(j=1; j <= ncodemax[k]; j++){
4866: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
4867: h++;
4868: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
4869: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
4870: }
4871: }
4872: }
4873: }
4874: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
4875: codtab[1][2]=1;codtab[2][2]=2; */
4876: /* for(i=1; i <=m ;i++){
4877: for(k=1; k <=cptcovn; k++){
4878: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
4879: }
4880: printf("\n");
4881: }
4882: scanf("%d",i);*/
4883:
4884: /*------------ gnuplot -------------*/
4885: strcpy(optionfilegnuplot,optionfilefiname);
4886: if(mle==-3)
4887: strcat(optionfilegnuplot,"-mort");
4888: strcat(optionfilegnuplot,".gp");
4889:
4890: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4891: printf("Problem with file %s",optionfilegnuplot);
4892: }
4893: else{
4894: fprintf(ficgp,"\n# %s\n", version);
4895: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4896: fprintf(ficgp,"set missing 'NaNq'\n");
4897: }
4898: /* fclose(ficgp);*/
4899: /*--------- index.htm --------*/
4900:
4901: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
4902: if(mle==-3)
4903: strcat(optionfilehtm,"-mort");
4904: strcat(optionfilehtm,".htm");
4905: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4906: printf("Problem with %s \n",optionfilehtm), exit(0);
4907: }
4908:
4909: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
4910: strcat(optionfilehtmcov,"-cov.htm");
4911: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
4912: printf("Problem with %s \n",optionfilehtmcov), exit(0);
4913: }
4914: else{
4915: fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
4916: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4917: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
4918: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4919: }
4920:
4921: fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
4922: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4923: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
4924: \n\
4925: <hr size=\"2\" color=\"#EC5E5E\">\
4926: <ul><li><h4>Parameter files</h4>\n\
4927: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
4928: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
4929: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
4930: - Date and time at start: %s</ul>\n",\
4931: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
4932: fileres,fileres,\
4933: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
4934: fflush(fichtm);
4935:
4936: strcpy(pathr,path);
4937: strcat(pathr,optionfilefiname);
4938: chdir(optionfilefiname); /* Move to directory named optionfile */
4939:
4940: /* Calculates basic frequencies. Computes observed prevalence at single age
4941: and prints on file fileres'p'. */
4942: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
4943:
4944: fprintf(fichtm,"\n");
4945: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
4946: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
4947: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
4948: imx,agemin,agemax,jmin,jmax,jmean);
4949: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4950: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4951: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4952: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4953: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
4954:
4955:
4956: /* For Powell, parameters are in a vector p[] starting at p[1]
4957: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
4958: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
4959:
4960: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
4961:
4962: if (mle==-3){
4963: ximort=matrix(1,NDIM,1,NDIM);
4964: cens=ivector(1,n);
4965: ageexmed=vector(1,n);
4966: agecens=vector(1,n);
4967: dcwave=ivector(1,n);
4968:
4969: for (i=1; i<=imx; i++){
4970: dcwave[i]=-1;
4971: for (m=firstpass; m<=lastpass; m++)
4972: if (s[m][i]>nlstate) {
4973: dcwave[i]=m;
4974: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
4975: break;
4976: }
4977: }
4978:
4979: for (i=1; i<=imx; i++) {
4980: if (wav[i]>0){
4981: ageexmed[i]=agev[mw[1][i]][i];
4982: j=wav[i];
4983: agecens[i]=1.;
4984:
4985: if (ageexmed[i]> 1 && wav[i] > 0){
4986: agecens[i]=agev[mw[j][i]][i];
4987: cens[i]= 1;
4988: }else if (ageexmed[i]< 1)
4989: cens[i]= -1;
4990: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
4991: cens[i]=0 ;
4992: }
4993: else cens[i]=-1;
4994: }
4995:
4996: for (i=1;i<=NDIM;i++) {
4997: for (j=1;j<=NDIM;j++)
4998: ximort[i][j]=(i == j ? 1.0 : 0.0);
4999: }
5000:
5001: p[1]=0.0268; p[NDIM]=0.083;
5002: /*printf("%lf %lf", p[1], p[2]);*/
5003:
5004:
5005: printf("Powell\n"); fprintf(ficlog,"Powell\n");
5006: strcpy(filerespow,"pow-mort");
5007: strcat(filerespow,fileres);
5008: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5009: printf("Problem with resultfile: %s\n", filerespow);
5010: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5011: }
5012: fprintf(ficrespow,"# Powell\n# iter -2*LL");
5013: /* for (i=1;i<=nlstate;i++)
5014: for(j=1;j<=nlstate+ndeath;j++)
5015: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5016: */
5017: fprintf(ficrespow,"\n");
5018:
5019: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
5020: fclose(ficrespow);
5021:
5022: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
5023:
5024: for(i=1; i <=NDIM; i++)
5025: for(j=i+1;j<=NDIM;j++)
5026: matcov[i][j]=matcov[j][i];
5027:
5028: printf("\nCovariance matrix\n ");
5029: for(i=1; i <=NDIM; i++) {
5030: for(j=1;j<=NDIM;j++){
5031: printf("%f ",matcov[i][j]);
5032: }
5033: printf("\n ");
5034: }
5035:
5036: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
5037: for (i=1;i<=NDIM;i++)
5038: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
5039:
5040: lsurv=vector(1,AGESUP);
5041: lpop=vector(1,AGESUP);
5042: tpop=vector(1,AGESUP);
5043: lsurv[agegomp]=100000;
5044:
5045: for (k=agegomp;k<=AGESUP;k++) {
5046: agemortsup=k;
5047: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
5048: }
5049:
5050: for (k=agegomp;k<agemortsup;k++)
5051: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
5052:
5053: for (k=agegomp;k<agemortsup;k++){
5054: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
5055: sumlpop=sumlpop+lpop[k];
5056: }
5057:
5058: tpop[agegomp]=sumlpop;
5059: for (k=agegomp;k<(agemortsup-3);k++){
5060: /* tpop[k+1]=2;*/
5061: tpop[k+1]=tpop[k]-lpop[k];
5062: }
5063:
5064:
5065: printf("\nAge lx qx dx Lx Tx e(x)\n");
5066: for (k=agegomp;k<(agemortsup-2);k++)
5067: 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]);
5068:
5069:
5070: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
5071: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5072:
5073: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
5074: stepm, weightopt,\
5075: model,imx,p,matcov,agemortsup);
5076:
5077: free_vector(lsurv,1,AGESUP);
5078: free_vector(lpop,1,AGESUP);
5079: free_vector(tpop,1,AGESUP);
5080: } /* Endof if mle==-3 */
5081:
5082: else{ /* For mle >=1 */
5083:
5084: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5085: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5086: for (k=1; k<=npar;k++)
5087: printf(" %d %8.5f",k,p[k]);
5088: printf("\n");
5089: globpr=1; /* to print the contributions */
5090: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5091: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5092: for (k=1; k<=npar;k++)
5093: printf(" %d %8.5f",k,p[k]);
5094: printf("\n");
5095: if(mle>=1){ /* Could be 1 or 2 */
5096: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
5097: }
5098:
5099: /*--------- results files --------------*/
5100: 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);
5101:
5102:
5103: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5104: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5105: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5106: for(i=1,jk=1; i <=nlstate; i++){
5107: for(k=1; k <=(nlstate+ndeath); k++){
5108: if (k != i) {
5109: printf("%d%d ",i,k);
5110: fprintf(ficlog,"%d%d ",i,k);
5111: fprintf(ficres,"%1d%1d ",i,k);
5112: for(j=1; j <=ncovmodel; j++){
5113: printf("%f ",p[jk]);
5114: fprintf(ficlog,"%f ",p[jk]);
5115: fprintf(ficres,"%f ",p[jk]);
5116: jk++;
5117: }
5118: printf("\n");
5119: fprintf(ficlog,"\n");
5120: fprintf(ficres,"\n");
5121: }
5122: }
5123: }
5124: if(mle!=0){
5125: /* Computing hessian and covariance matrix */
5126: ftolhess=ftol; /* Usually correct */
5127: hesscov(matcov, p, npar, delti, ftolhess, func);
5128: }
5129: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
5130: printf("# Scales (for hessian or gradient estimation)\n");
5131: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
5132: for(i=1,jk=1; i <=nlstate; i++){
5133: for(j=1; j <=nlstate+ndeath; j++){
5134: if (j!=i) {
5135: fprintf(ficres,"%1d%1d",i,j);
5136: printf("%1d%1d",i,j);
5137: fprintf(ficlog,"%1d%1d",i,j);
5138: for(k=1; k<=ncovmodel;k++){
5139: printf(" %.5e",delti[jk]);
5140: fprintf(ficlog," %.5e",delti[jk]);
5141: fprintf(ficres," %.5e",delti[jk]);
5142: jk++;
5143: }
5144: printf("\n");
5145: fprintf(ficlog,"\n");
5146: fprintf(ficres,"\n");
5147: }
5148: }
5149: }
5150:
5151: 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");
5152: if(mle>=1)
5153: 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");
5154: 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");
5155: /* # 121 Var(a12)\n\ */
5156: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5157: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5158: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5159: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5160: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5161: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5162: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5163:
5164:
5165: /* Just to have a covariance matrix which will be more understandable
5166: even is we still don't want to manage dictionary of variables
5167: */
5168: for(itimes=1;itimes<=2;itimes++){
5169: jj=0;
5170: for(i=1; i <=nlstate; i++){
5171: for(j=1; j <=nlstate+ndeath; j++){
5172: if(j==i) continue;
5173: for(k=1; k<=ncovmodel;k++){
5174: jj++;
5175: ca[0]= k+'a'-1;ca[1]='\0';
5176: if(itimes==1){
5177: if(mle>=1)
5178: printf("#%1d%1d%d",i,j,k);
5179: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5180: fprintf(ficres,"#%1d%1d%d",i,j,k);
5181: }else{
5182: if(mle>=1)
5183: printf("%1d%1d%d",i,j,k);
5184: fprintf(ficlog,"%1d%1d%d",i,j,k);
5185: fprintf(ficres,"%1d%1d%d",i,j,k);
5186: }
5187: ll=0;
5188: for(li=1;li <=nlstate; li++){
5189: for(lj=1;lj <=nlstate+ndeath; lj++){
5190: if(lj==li) continue;
5191: for(lk=1;lk<=ncovmodel;lk++){
5192: ll++;
5193: if(ll<=jj){
5194: cb[0]= lk +'a'-1;cb[1]='\0';
5195: if(ll<jj){
5196: if(itimes==1){
5197: if(mle>=1)
5198: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5199: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5200: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5201: }else{
5202: if(mle>=1)
5203: printf(" %.5e",matcov[jj][ll]);
5204: fprintf(ficlog," %.5e",matcov[jj][ll]);
5205: fprintf(ficres," %.5e",matcov[jj][ll]);
5206: }
5207: }else{
5208: if(itimes==1){
5209: if(mle>=1)
5210: printf(" Var(%s%1d%1d)",ca,i,j);
5211: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5212: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5213: }else{
5214: if(mle>=1)
5215: printf(" %.5e",matcov[jj][ll]);
5216: fprintf(ficlog," %.5e",matcov[jj][ll]);
5217: fprintf(ficres," %.5e",matcov[jj][ll]);
5218: }
5219: }
5220: }
5221: } /* end lk */
5222: } /* end lj */
5223: } /* end li */
5224: if(mle>=1)
5225: printf("\n");
5226: fprintf(ficlog,"\n");
5227: fprintf(ficres,"\n");
5228: numlinepar++;
5229: } /* end k*/
5230: } /*end j */
5231: } /* end i */
5232: } /* end itimes */
5233:
5234: fflush(ficlog);
5235: fflush(ficres);
5236:
5237: while((c=getc(ficpar))=='#' && c!= EOF){
5238: ungetc(c,ficpar);
5239: fgets(line, MAXLINE, ficpar);
5240: puts(line);
5241: fputs(line,ficparo);
5242: }
5243: ungetc(c,ficpar);
5244:
5245: estepm=0;
5246: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5247: if (estepm==0 || estepm < stepm) estepm=stepm;
5248: if (fage <= 2) {
5249: bage = ageminpar;
5250: fage = agemaxpar;
5251: }
5252:
5253: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5254: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5255: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5256:
5257: while((c=getc(ficpar))=='#' && c!= EOF){
5258: ungetc(c,ficpar);
5259: fgets(line, MAXLINE, ficpar);
5260: puts(line);
5261: fputs(line,ficparo);
5262: }
5263: ungetc(c,ficpar);
5264:
5265: 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);
5266: 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);
5267: 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);
5268: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5269: 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);
5270:
5271: while((c=getc(ficpar))=='#' && c!= EOF){
5272: ungetc(c,ficpar);
5273: fgets(line, MAXLINE, ficpar);
5274: puts(line);
5275: fputs(line,ficparo);
5276: }
5277: ungetc(c,ficpar);
5278:
5279:
5280: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5281: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5282:
5283: fscanf(ficpar,"pop_based=%d\n",&popbased);
5284: fprintf(ficparo,"pop_based=%d\n",popbased);
5285: fprintf(ficres,"pop_based=%d\n",popbased);
5286:
5287: while((c=getc(ficpar))=='#' && c!= EOF){
5288: ungetc(c,ficpar);
5289: fgets(line, MAXLINE, ficpar);
5290: puts(line);
5291: fputs(line,ficparo);
5292: }
5293: ungetc(c,ficpar);
5294:
5295: 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);
5296: 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);
5297: 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);
5298: 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);
5299: 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);
5300: /* day and month of proj2 are not used but only year anproj2.*/
5301:
5302:
5303:
5304: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5305: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5306:
5307: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
5308: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5309:
5310: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5311: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5312: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5313:
5314: /*------------ free_vector -------------*/
5315: /* chdir(path); */
5316:
5317: free_ivector(wav,1,imx);
5318: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5319: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5320: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5321: free_lvector(num,1,n);
5322: free_vector(agedc,1,n);
5323: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5324: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5325: fclose(ficparo);
5326: fclose(ficres);
5327:
5328:
5329: /*--------------- Prevalence limit (stable prevalence) --------------*/
5330:
5331: strcpy(filerespl,"pl");
5332: strcat(filerespl,fileres);
5333: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5334: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
5335: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
5336: }
5337: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
5338: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
5339: fprintf(ficrespl, "#Local time at start: %s", strstart);
5340: fprintf(ficrespl,"#Stable prevalence \n");
5341: fprintf(ficrespl,"#Age ");
5342: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5343: fprintf(ficrespl,"\n");
5344:
5345: prlim=matrix(1,nlstate,1,nlstate);
5346:
5347: agebase=ageminpar;
5348: agelim=agemaxpar;
5349: ftolpl=1.e-10;
5350: i1=cptcoveff;
5351: if (cptcovn < 1){i1=1;}
5352:
5353: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5354: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5355: k=k+1;
5356: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
5357: fprintf(ficrespl,"\n#******");
5358: printf("\n#******");
5359: fprintf(ficlog,"\n#******");
5360: for(j=1;j<=cptcoveff;j++) {
5361: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5362: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5363: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5364: }
5365: fprintf(ficrespl,"******\n");
5366: printf("******\n");
5367: fprintf(ficlog,"******\n");
5368:
5369: for (age=agebase; age<=agelim; age++){
5370: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5371: fprintf(ficrespl,"%.0f ",age );
5372: for(j=1;j<=cptcoveff;j++)
5373: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5374: for(i=1; i<=nlstate;i++)
5375: fprintf(ficrespl," %.5f", prlim[i][i]);
5376: fprintf(ficrespl,"\n");
5377: }
5378: }
5379: }
5380: fclose(ficrespl);
5381:
5382: /*------------- h Pij x at various ages ------------*/
5383:
5384: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5385: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5386: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
5387: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
5388: }
5389: printf("Computing pij: result on file '%s' \n", filerespij);
5390: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
5391:
5392: stepsize=(int) (stepm+YEARM-1)/YEARM;
5393: /*if (stepm<=24) stepsize=2;*/
5394:
5395: agelim=AGESUP;
5396: hstepm=stepsize*YEARM; /* Every year of age */
5397: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
5398:
5399: /* hstepm=1; aff par mois*/
5400: fprintf(ficrespij, "#Local time at start: %s", strstart);
5401: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5402: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5403: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5404: k=k+1;
5405: fprintf(ficrespij,"\n#****** ");
5406: for(j=1;j<=cptcoveff;j++)
5407: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5408: fprintf(ficrespij,"******\n");
5409:
5410: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5411: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5412: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5413:
5414: /* nhstepm=nhstepm*YEARM; aff par mois*/
5415:
5416: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5417: oldm=oldms;savm=savms;
5418: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5419: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
5420: for(i=1; i<=nlstate;i++)
5421: for(j=1; j<=nlstate+ndeath;j++)
5422: fprintf(ficrespij," %1d-%1d",i,j);
5423: fprintf(ficrespij,"\n");
5424: for (h=0; h<=nhstepm; h++){
5425: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
5426: for(i=1; i<=nlstate;i++)
5427: for(j=1; j<=nlstate+ndeath;j++)
5428: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
5429: fprintf(ficrespij,"\n");
5430: }
5431: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5432: fprintf(ficrespij,"\n");
5433: }
5434: }
5435: }
5436:
5437: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
5438:
5439: fclose(ficrespij);
5440:
5441: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5442: for(i=1;i<=AGESUP;i++)
5443: for(j=1;j<=NCOVMAX;j++)
5444: for(k=1;k<=NCOVMAX;k++)
5445: probs[i][j][k]=0.;
5446:
5447: /*---------- Forecasting ------------------*/
5448: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
5449: if(prevfcast==1){
5450: /* if(stepm ==1){*/
5451: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
5452: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
5453: /* } */
5454: /* else{ */
5455: /* erreur=108; */
5456: /* 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); */
5457: /* 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); */
5458: /* } */
5459: }
5460:
5461:
5462: /*---------- Health expectancies and variances ------------*/
5463:
5464: strcpy(filerest,"t");
5465: strcat(filerest,fileres);
5466: if((ficrest=fopen(filerest,"w"))==NULL) {
5467: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
5468: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
5469: }
5470: printf("Computing Total LEs with variances: file '%s' \n", filerest);
5471: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
5472:
5473:
5474: strcpy(filerese,"e");
5475: strcat(filerese,fileres);
5476: if((ficreseij=fopen(filerese,"w"))==NULL) {
5477: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5478: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5479: }
5480: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
5481: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
5482:
5483: strcpy(fileresv,"v");
5484: strcat(fileresv,fileres);
5485: if((ficresvij=fopen(fileresv,"w"))==NULL) {
5486: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
5487: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
5488: }
5489: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5490: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5491:
5492: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
5493: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5494: /* 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",\
5495: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
5496: */
5497:
5498: if (mobilav!=0) {
5499: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5500: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
5501: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5502: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5503: }
5504: }
5505:
5506: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5507: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5508: k=k+1;
5509: fprintf(ficrest,"\n#****** ");
5510: for(j=1;j<=cptcoveff;j++)
5511: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5512: fprintf(ficrest,"******\n");
5513:
5514: fprintf(ficreseij,"\n#****** ");
5515: for(j=1;j<=cptcoveff;j++)
5516: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5517: fprintf(ficreseij,"******\n");
5518:
5519: fprintf(ficresvij,"\n#****** ");
5520: for(j=1;j<=cptcoveff;j++)
5521: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5522: fprintf(ficresvij,"******\n");
5523:
5524: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5525: oldm=oldms;savm=savms;
5526: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
5527:
5528: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5529: oldm=oldms;savm=savms;
5530: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
5531: if(popbased==1){
5532: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
5533: }
5534:
5535: fprintf(ficrest, "#Local time at start: %s", strstart);
5536: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
5537: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5538: fprintf(ficrest,"\n");
5539:
5540: epj=vector(1,nlstate+1);
5541: for(age=bage; age <=fage ;age++){
5542: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5543: if (popbased==1) {
5544: if(mobilav ==0){
5545: for(i=1; i<=nlstate;i++)
5546: prlim[i][i]=probs[(int)age][i][k];
5547: }else{ /* mobilav */
5548: for(i=1; i<=nlstate;i++)
5549: prlim[i][i]=mobaverage[(int)age][i][k];
5550: }
5551: }
5552:
5553: fprintf(ficrest," %4.0f",age);
5554: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5555: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5556: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5557: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5558: }
5559: epj[nlstate+1] +=epj[j];
5560: }
5561:
5562: for(i=1, vepp=0.;i <=nlstate;i++)
5563: for(j=1;j <=nlstate;j++)
5564: vepp += vareij[i][j][(int)age];
5565: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5566: for(j=1;j <=nlstate;j++){
5567: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5568: }
5569: fprintf(ficrest,"\n");
5570: }
5571: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5572: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5573: free_vector(epj,1,nlstate+1);
5574: }
5575: }
5576: free_vector(weight,1,n);
5577: free_imatrix(Tvard,1,15,1,2);
5578: free_imatrix(s,1,maxwav+1,1,n);
5579: free_matrix(anint,1,maxwav,1,n);
5580: free_matrix(mint,1,maxwav,1,n);
5581: free_ivector(cod,1,n);
5582: free_ivector(tab,1,NCOVMAX);
5583: fclose(ficreseij);
5584: fclose(ficresvij);
5585: fclose(ficrest);
5586: fclose(ficpar);
5587:
5588: /*------- Variance of stable prevalence------*/
5589:
5590: strcpy(fileresvpl,"vpl");
5591: strcat(fileresvpl,fileres);
5592: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
5593: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
5594: exit(0);
5595: }
5596: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
5597:
5598: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5599: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5600: k=k+1;
5601: fprintf(ficresvpl,"\n#****** ");
5602: for(j=1;j<=cptcoveff;j++)
5603: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5604: fprintf(ficresvpl,"******\n");
5605:
5606: varpl=matrix(1,nlstate,(int) bage, (int) fage);
5607: oldm=oldms;savm=savms;
5608: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
5609: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
5610: }
5611: }
5612:
5613: fclose(ficresvpl);
5614:
5615: /*---------- End : free ----------------*/
5616: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5617: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5618:
5619: } /* mle==-3 arrives here for freeing */
5620: free_matrix(prlim,1,nlstate,1,nlstate);
5621: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
5622: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
5623: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
5624: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
5625: free_matrix(covar,0,NCOVMAX,1,n);
5626: free_matrix(matcov,1,npar,1,npar);
5627: /*free_vector(delti,1,npar);*/
5628: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5629: free_matrix(agev,1,maxwav,1,imx);
5630: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5631:
5632: free_ivector(ncodemax,1,8);
5633: free_ivector(Tvar,1,15);
5634: free_ivector(Tprod,1,15);
5635: free_ivector(Tvaraff,1,15);
5636: free_ivector(Tage,1,15);
5637: free_ivector(Tcode,1,100);
5638:
5639: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
5640: free_imatrix(codtab,1,100,1,10);
5641: fflush(fichtm);
5642: fflush(ficgp);
5643:
5644:
5645: if((nberr >0) || (nbwarn>0)){
5646: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
5647: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
5648: }else{
5649: printf("End of Imach\n");
5650: fprintf(ficlog,"End of Imach\n");
5651: }
5652: printf("See log file on %s\n",filelog);
5653: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
5654: (void) gettimeofday(&end_time,&tzp);
5655: tm = *localtime(&end_time.tv_sec);
5656: tmg = *gmtime(&end_time.tv_sec);
5657: strcpy(strtend,asctime(&tm));
5658: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
5659: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
5660: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5661:
5662: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5663: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5664: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5665: /* printf("Total time was %d uSec.\n", total_usecs);*/
5666: /* if(fileappend(fichtm,optionfilehtm)){ */
5667: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
5668: fclose(fichtm);
5669: fclose(fichtmcov);
5670: fclose(ficgp);
5671: fclose(ficlog);
5672: /*------ End -----------*/
5673:
5674: chdir(path);
5675: /*strcat(plotcmd,CHARSEPARATOR);*/
5676: sprintf(plotcmd,"gnuplot");
5677: #ifndef UNIX
5678: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
5679: #endif
5680: if(!stat(plotcmd,&info)){
5681: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
5682: if(!stat(getenv("GNUPLOTBIN"),&info)){
5683: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
5684: }else
5685: strcpy(pplotcmd,plotcmd);
5686: #ifdef UNIX
5687: strcpy(plotcmd,GNUPLOTPROGRAM);
5688: if(!stat(plotcmd,&info)){
5689: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
5690: }else
5691: strcpy(pplotcmd,plotcmd);
5692: #endif
5693: }else
5694: strcpy(pplotcmd,plotcmd);
5695:
5696: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
5697: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
5698:
5699: if((outcmd=system(plotcmd)) != 0){
5700: printf("\n Problem with gnuplot\n");
5701: }
5702: printf(" Wait...");
5703: while (z[0] != 'q') {
5704: /* chdir(path); */
5705: printf("\nType e to edit output files, g to graph again and q for exiting: ");
5706: scanf("%s",z);
5707: /* if (z[0] == 'c') system("./imach"); */
5708: if (z[0] == 'e') {
5709: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
5710: system(optionfilehtm);
5711: }
5712: else if (z[0] == 'g') system(plotcmd);
5713: else if (z[0] == 'q') exit(0);
5714: }
5715: end:
5716: while (z[0] != 'q') {
5717: printf("\nType q for exiting: ");
5718: scanf("%s",z);
5719: }
5720: }
5721:
5722:
5723:
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