1: /* $Id: imach.c,v 1.107 2006/01/19 16:20:37 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.107 2006/01/19 16:20:37 brouard
5: Test existence of gnuplot in imach path
6:
7: Revision 1.106 2006/01/19 13:24:36 brouard
8: Some cleaning and links added in html output
9:
10: Revision 1.105 2006/01/05 20:23:19 lievre
11: *** empty log message ***
12:
13: Revision 1.104 2005/09/30 16:11:43 lievre
14: (Module): sump fixed, loop imx fixed, and simplifications.
15: (Module): If the status is missing at the last wave but we know
16: that the person is alive, then we can code his/her status as -2
17: (instead of missing=-1 in earlier versions) and his/her
18: contributions to the likelihood is 1 - Prob of dying from last
19: health status (= 1-p13= p11+p12 in the easiest case of somebody in
20: the healthy state at last known wave). Version is 0.98
21:
22: Revision 1.103 2005/09/30 15:54:49 lievre
23: (Module): sump fixed, loop imx fixed, and simplifications.
24:
25: Revision 1.102 2004/09/15 17:31:30 brouard
26: Add the possibility to read data file including tab characters.
27:
28: Revision 1.101 2004/09/15 10:38:38 brouard
29: Fix on curr_time
30:
31: Revision 1.100 2004/07/12 18:29:06 brouard
32: Add version for Mac OS X. Just define UNIX in Makefile
33:
34: Revision 1.99 2004/06/05 08:57:40 brouard
35: *** empty log message ***
36:
37: Revision 1.98 2004/05/16 15:05:56 brouard
38: New version 0.97 . First attempt to estimate force of mortality
39: directly from the data i.e. without the need of knowing the health
40: state at each age, but using a Gompertz model: log u =a + b*age .
41: This is the basic analysis of mortality and should be done before any
42: other analysis, in order to test if the mortality estimated from the
43: cross-longitudinal survey is different from the mortality estimated
44: from other sources like vital statistic data.
45:
46: The same imach parameter file can be used but the option for mle should be -3.
47:
48: Agnès, who wrote this part of the code, tried to keep most of the
49: former routines in order to include the new code within the former code.
50:
51: The output is very simple: only an estimate of the intercept and of
52: the slope with 95% confident intervals.
53:
54: Current limitations:
55: A) Even if you enter covariates, i.e. with the
56: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
57: B) There is no computation of Life Expectancy nor Life Table.
58:
59: Revision 1.97 2004/02/20 13:25:42 lievre
60: Version 0.96d. Population forecasting command line is (temporarily)
61: suppressed.
62:
63: Revision 1.96 2003/07/15 15:38:55 brouard
64: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
65: rewritten within the same printf. Workaround: many printfs.
66:
67: Revision 1.95 2003/07/08 07:54:34 brouard
68: * imach.c (Repository):
69: (Repository): Using imachwizard code to output a more meaningful covariance
70: matrix (cov(a12,c31) instead of numbers.
71:
72: Revision 1.94 2003/06/27 13:00:02 brouard
73: Just cleaning
74:
75: Revision 1.93 2003/06/25 16:33:55 brouard
76: (Module): On windows (cygwin) function asctime_r doesn't
77: exist so I changed back to asctime which exists.
78: (Module): Version 0.96b
79:
80: Revision 1.92 2003/06/25 16:30:45 brouard
81: (Module): On windows (cygwin) function asctime_r doesn't
82: exist so I changed back to asctime which exists.
83:
84: Revision 1.91 2003/06/25 15:30:29 brouard
85: * imach.c (Repository): Duplicated warning errors corrected.
86: (Repository): Elapsed time after each iteration is now output. It
87: helps to forecast when convergence will be reached. Elapsed time
88: is stamped in powell. We created a new html file for the graphs
89: concerning matrix of covariance. It has extension -cov.htm.
90:
91: Revision 1.90 2003/06/24 12:34:15 brouard
92: (Module): Some bugs corrected for windows. Also, when
93: mle=-1 a template is output in file "or"mypar.txt with the design
94: of the covariance matrix to be input.
95:
96: Revision 1.89 2003/06/24 12:30:52 brouard
97: (Module): Some bugs corrected for windows. Also, when
98: mle=-1 a template is output in file "or"mypar.txt with the design
99: of the covariance matrix to be input.
100:
101: Revision 1.88 2003/06/23 17:54:56 brouard
102: * 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.
103:
104: Revision 1.87 2003/06/18 12:26:01 brouard
105: Version 0.96
106:
107: Revision 1.86 2003/06/17 20:04:08 brouard
108: (Module): Change position of html and gnuplot routines and added
109: routine fileappend.
110:
111: Revision 1.85 2003/06/17 13:12:43 brouard
112: * imach.c (Repository): Check when date of death was earlier that
113: current date of interview. It may happen when the death was just
114: prior to the death. In this case, dh was negative and likelihood
115: was wrong (infinity). We still send an "Error" but patch by
116: assuming that the date of death was just one stepm after the
117: interview.
118: (Repository): Because some people have very long ID (first column)
119: we changed int to long in num[] and we added a new lvector for
120: memory allocation. But we also truncated to 8 characters (left
121: truncation)
122: (Repository): No more line truncation errors.
123:
124: Revision 1.84 2003/06/13 21:44:43 brouard
125: * imach.c (Repository): Replace "freqsummary" at a correct
126: place. It differs from routine "prevalence" which may be called
127: many times. Probs is memory consuming and must be used with
128: parcimony.
129: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
130:
131: Revision 1.83 2003/06/10 13:39:11 lievre
132: *** empty log message ***
133:
134: Revision 1.82 2003/06/05 15:57:20 brouard
135: Add log in imach.c and fullversion number is now printed.
136:
137: */
138: /*
139: Interpolated Markov Chain
140:
141: Short summary of the programme:
142:
143: This program computes Healthy Life Expectancies from
144: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
145: first survey ("cross") where individuals from different ages are
146: interviewed on their health status or degree of disability (in the
147: case of a health survey which is our main interest) -2- at least a
148: second wave of interviews ("longitudinal") which measure each change
149: (if any) in individual health status. Health expectancies are
150: computed from the time spent in each health state according to a
151: model. More health states you consider, more time is necessary to reach the
152: Maximum Likelihood of the parameters involved in the model. The
153: simplest model is the multinomial logistic model where pij is the
154: probability to be observed in state j at the second wave
155: conditional to be observed in state i at the first wave. Therefore
156: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
157: 'age' is age and 'sex' is a covariate. If you want to have a more
158: complex model than "constant and age", you should modify the program
159: where the markup *Covariates have to be included here again* invites
160: you to do it. More covariates you add, slower the
161: convergence.
162:
163: The advantage of this computer programme, compared to a simple
164: multinomial logistic model, is clear when the delay between waves is not
165: identical for each individual. Also, if a individual missed an
166: intermediate interview, the information is lost, but taken into
167: account using an interpolation or extrapolation.
168:
169: hPijx is the probability to be observed in state i at age x+h
170: conditional to the observed state i at age x. The delay 'h' can be
171: split into an exact number (nh*stepm) of unobserved intermediate
172: states. This elementary transition (by month, quarter,
173: semester or year) is modelled as a multinomial logistic. The hPx
174: matrix is simply the matrix product of nh*stepm elementary matrices
175: and the contribution of each individual to the likelihood is simply
176: hPijx.
177:
178: Also this programme outputs the covariance matrix of the parameters but also
179: of the life expectancies. It also computes the stable prevalence.
180:
181: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
182: Institut national d'études démographiques, Paris.
183: This software have been partly granted by Euro-REVES, a concerted action
184: from the European Union.
185: It is copyrighted identically to a GNU software product, ie programme and
186: software can be distributed freely for non commercial use. Latest version
187: can be accessed at http://euroreves.ined.fr/imach .
188:
189: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
190: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
191:
192: **********************************************************************/
193: /*
194: main
195: read parameterfile
196: read datafile
197: concatwav
198: freqsummary
199: if (mle >= 1)
200: mlikeli
201: print results files
202: if mle==1
203: computes hessian
204: read end of parameter file: agemin, agemax, bage, fage, estepm
205: begin-prev-date,...
206: open gnuplot file
207: open html file
208: stable prevalence
209: for age prevalim()
210: h Pij x
211: variance of p varprob
212: forecasting if prevfcast==1 prevforecast call prevalence()
213: health expectancies
214: Variance-covariance of DFLE
215: prevalence()
216: movingaverage()
217: varevsij()
218: if popbased==1 varevsij(,popbased)
219: total life expectancies
220: Variance of stable prevalence
221: end
222: */
223:
224:
225:
226:
227: #include <math.h>
228: #include <stdio.h>
229: #include <stdlib.h>
230: #include <string.h>
231: #include <unistd.h>
232:
233: #include <sys/types.h>
234: #include <sys/stat.h>
235: #include <errno.h>
236: extern int errno;
237:
238: /* #include <sys/time.h> */
239: #include <time.h>
240: #include "timeval.h"
241:
242: /* #include <libintl.h> */
243: /* #define _(String) gettext (String) */
244:
245: #define MAXLINE 256
246: #define GNUPLOTPROGRAM "gnuplot"
247: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
248: #define FILENAMELENGTH 132
249: /*#define DEBUG*/
250: /*#define windows*/
251: #define GLOCK_ERROR_NOPATH -1 /* empty path */
252: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
253:
254: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
255: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
256:
257: #define NINTERVMAX 8
258: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
259: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
260: #define NCOVMAX 8 /* Maximum number of covariates */
261: #define MAXN 20000
262: #define YEARM 12. /* Number of months per year */
263: #define AGESUP 130
264: #define AGEBASE 40
265: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
266: #ifdef UNIX
267: #define DIRSEPARATOR '/'
268: #define CHARSEPARATOR "/"
269: #define ODIRSEPARATOR '\\'
270: #else
271: #define DIRSEPARATOR '\\'
272: #define CHARSEPARATOR "\\"
273: #define ODIRSEPARATOR '/'
274: #endif
275:
276: /* $Id: imach.c,v 1.107 2006/01/19 16:20:37 brouard Exp $ */
277: /* $State: Exp $ */
278:
279: char version[]="Imach version 0.98a, January 2006, INED-EUROREVES ";
280: char fullversion[]="$Revision: 1.107 $ $Date: 2006/01/19 16:20:37 $";
281: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
282: int nvar;
283: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
284: int npar=NPARMAX;
285: int nlstate=2; /* Number of live states */
286: int ndeath=1; /* Number of dead states */
287: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
288: int popbased=0;
289:
290: int *wav; /* Number of waves for this individuual 0 is possible */
291: int maxwav; /* Maxim number of waves */
292: int jmin, jmax; /* min, max spacing between 2 waves */
293: int gipmx, gsw; /* Global variables on the number of contributions
294: to the likelihood and the sum of weights (done by funcone)*/
295: int mle, weightopt;
296: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
297: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
298: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
299: * wave mi and wave mi+1 is not an exact multiple of stepm. */
300: double jmean; /* Mean space between 2 waves */
301: double **oldm, **newm, **savm; /* Working pointers to matrices */
302: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
303: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
304: FILE *ficlog, *ficrespow;
305: int globpr; /* Global variable for printing or not */
306: double fretone; /* Only one call to likelihood */
307: long ipmx; /* Number of contributions */
308: double sw; /* Sum of weights */
309: char filerespow[FILENAMELENGTH];
310: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
311: FILE *ficresilk;
312: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
313: FILE *ficresprobmorprev;
314: FILE *fichtm, *fichtmcov; /* Html File */
315: FILE *ficreseij;
316: char filerese[FILENAMELENGTH];
317: FILE *ficresvij;
318: char fileresv[FILENAMELENGTH];
319: FILE *ficresvpl;
320: char fileresvpl[FILENAMELENGTH];
321: char title[MAXLINE];
322: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
323: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
324: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
325: char command[FILENAMELENGTH];
326: int outcmd=0;
327:
328: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
329:
330: char filelog[FILENAMELENGTH]; /* Log file */
331: char filerest[FILENAMELENGTH];
332: char fileregp[FILENAMELENGTH];
333: char popfile[FILENAMELENGTH];
334:
335: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
336:
337: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
338: struct timezone tzp;
339: extern int gettimeofday();
340: struct tm tmg, tm, tmf, *gmtime(), *localtime();
341: long time_value;
342: extern long time();
343: char strcurr[80], strfor[80];
344:
345: #define NR_END 1
346: #define FREE_ARG char*
347: #define FTOL 1.0e-10
348:
349: #define NRANSI
350: #define ITMAX 200
351:
352: #define TOL 2.0e-4
353:
354: #define CGOLD 0.3819660
355: #define ZEPS 1.0e-10
356: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
357:
358: #define GOLD 1.618034
359: #define GLIMIT 100.0
360: #define TINY 1.0e-20
361:
362: static double maxarg1,maxarg2;
363: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
364: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
365:
366: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
367: #define rint(a) floor(a+0.5)
368:
369: static double sqrarg;
370: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
371: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
372: int agegomp= AGEGOMP;
373:
374: int imx;
375: int stepm=1;
376: /* Stepm, step in month: minimum step interpolation*/
377:
378: int estepm;
379: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
380:
381: int m,nb;
382: long *num;
383: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
384: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
385: double **pmmij, ***probs;
386: double *ageexmed,*agecens;
387: double dateintmean=0;
388:
389: double *weight;
390: int **s; /* Status */
391: double *agedc, **covar, idx;
392: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
393: double *lsurv, *lpop, *tpop;
394:
395: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
396: double ftolhess; /* Tolerance for computing hessian */
397:
398: /**************** split *************************/
399: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
400: {
401: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
402: the name of the file (name), its extension only (ext) and its first part of the name (finame)
403: */
404: char *ss; /* pointer */
405: int l1, l2; /* length counters */
406:
407: l1 = strlen(path ); /* length of path */
408: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
409: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
410: if ( ss == NULL ) { /* no directory, so determine current directory */
411: strcpy( name, path ); /* we got the fullname name because no directory */
412: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
413: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
414: /* get current working directory */
415: /* extern char* getcwd ( char *buf , int len);*/
416: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
417: return( GLOCK_ERROR_GETCWD );
418: }
419: /* got dirc from getcwd*/
420: printf(" DIRC = %s \n",dirc);
421: } else { /* strip direcotry from path */
422: ss++; /* after this, the filename */
423: l2 = strlen( ss ); /* length of filename */
424: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
425: strcpy( name, ss ); /* save file name */
426: strncpy( dirc, path, l1 - l2 ); /* now the directory */
427: dirc[l1-l2] = 0; /* add zero */
428: printf(" DIRC2 = %s \n",dirc);
429: }
430: /* We add a separator at the end of dirc if not exists */
431: l1 = strlen( dirc ); /* length of directory */
432: if( dirc[l1-1] != DIRSEPARATOR ){
433: dirc[l1] = DIRSEPARATOR;
434: dirc[l1+1] = 0;
435: printf(" DIRC3 = %s \n",dirc);
436: }
437: ss = strrchr( name, '.' ); /* find last / */
438: if (ss >0){
439: ss++;
440: strcpy(ext,ss); /* save extension */
441: l1= strlen( name);
442: l2= strlen(ss)+1;
443: strncpy( finame, name, l1-l2);
444: finame[l1-l2]= 0;
445: }
446:
447: return( 0 ); /* we're done */
448: }
449:
450:
451: /******************************************/
452:
453: void replace_back_to_slash(char *s, char*t)
454: {
455: int i;
456: int lg=0;
457: i=0;
458: lg=strlen(t);
459: for(i=0; i<= lg; i++) {
460: (s[i] = t[i]);
461: if (t[i]== '\\') s[i]='/';
462: }
463: }
464:
465: int nbocc(char *s, char occ)
466: {
467: int i,j=0;
468: int lg=20;
469: i=0;
470: lg=strlen(s);
471: for(i=0; i<= lg; i++) {
472: if (s[i] == occ ) j++;
473: }
474: return j;
475: }
476:
477: void cutv(char *u,char *v, char*t, char occ)
478: {
479: /* cuts string t into u and v where u ends before first occurence of char 'occ'
480: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
481: gives u="abcedf" and v="ghi2j" */
482: int i,lg,j,p=0;
483: i=0;
484: for(j=0; j<=strlen(t)-1; j++) {
485: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
486: }
487:
488: lg=strlen(t);
489: for(j=0; j<p; j++) {
490: (u[j] = t[j]);
491: }
492: u[p]='\0';
493:
494: for(j=0; j<= lg; j++) {
495: if (j>=(p+1))(v[j-p-1] = t[j]);
496: }
497: }
498:
499: /********************** nrerror ********************/
500:
501: void nrerror(char error_text[])
502: {
503: fprintf(stderr,"ERREUR ...\n");
504: fprintf(stderr,"%s\n",error_text);
505: exit(EXIT_FAILURE);
506: }
507: /*********************** vector *******************/
508: double *vector(int nl, int nh)
509: {
510: double *v;
511: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
512: if (!v) nrerror("allocation failure in vector");
513: return v-nl+NR_END;
514: }
515:
516: /************************ free vector ******************/
517: void free_vector(double*v, int nl, int nh)
518: {
519: free((FREE_ARG)(v+nl-NR_END));
520: }
521:
522: /************************ivector *******************************/
523: int *ivector(long nl,long nh)
524: {
525: int *v;
526: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
527: if (!v) nrerror("allocation failure in ivector");
528: return v-nl+NR_END;
529: }
530:
531: /******************free ivector **************************/
532: void free_ivector(int *v, long nl, long nh)
533: {
534: free((FREE_ARG)(v+nl-NR_END));
535: }
536:
537: /************************lvector *******************************/
538: long *lvector(long nl,long nh)
539: {
540: long *v;
541: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
542: if (!v) nrerror("allocation failure in ivector");
543: return v-nl+NR_END;
544: }
545:
546: /******************free lvector **************************/
547: void free_lvector(long *v, long nl, long nh)
548: {
549: free((FREE_ARG)(v+nl-NR_END));
550: }
551:
552: /******************* imatrix *******************************/
553: int **imatrix(long nrl, long nrh, long ncl, long nch)
554: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
555: {
556: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
557: int **m;
558:
559: /* allocate pointers to rows */
560: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
561: if (!m) nrerror("allocation failure 1 in matrix()");
562: m += NR_END;
563: m -= nrl;
564:
565:
566: /* allocate rows and set pointers to them */
567: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
568: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
569: m[nrl] += NR_END;
570: m[nrl] -= ncl;
571:
572: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
573:
574: /* return pointer to array of pointers to rows */
575: return m;
576: }
577:
578: /****************** free_imatrix *************************/
579: void free_imatrix(m,nrl,nrh,ncl,nch)
580: int **m;
581: long nch,ncl,nrh,nrl;
582: /* free an int matrix allocated by imatrix() */
583: {
584: free((FREE_ARG) (m[nrl]+ncl-NR_END));
585: free((FREE_ARG) (m+nrl-NR_END));
586: }
587:
588: /******************* matrix *******************************/
589: double **matrix(long nrl, long nrh, long ncl, long nch)
590: {
591: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
592: double **m;
593:
594: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
595: if (!m) nrerror("allocation failure 1 in matrix()");
596: m += NR_END;
597: m -= nrl;
598:
599: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
600: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
601: m[nrl] += NR_END;
602: m[nrl] -= ncl;
603:
604: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
605: return m;
606: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
607: */
608: }
609:
610: /*************************free matrix ************************/
611: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
612: {
613: free((FREE_ARG)(m[nrl]+ncl-NR_END));
614: free((FREE_ARG)(m+nrl-NR_END));
615: }
616:
617: /******************* ma3x *******************************/
618: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
619: {
620: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
621: double ***m;
622:
623: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
624: if (!m) nrerror("allocation failure 1 in matrix()");
625: m += NR_END;
626: m -= nrl;
627:
628: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
629: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
630: m[nrl] += NR_END;
631: m[nrl] -= ncl;
632:
633: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
634:
635: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
636: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
637: m[nrl][ncl] += NR_END;
638: m[nrl][ncl] -= nll;
639: for (j=ncl+1; j<=nch; j++)
640: m[nrl][j]=m[nrl][j-1]+nlay;
641:
642: for (i=nrl+1; i<=nrh; i++) {
643: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
644: for (j=ncl+1; j<=nch; j++)
645: m[i][j]=m[i][j-1]+nlay;
646: }
647: return m;
648: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
649: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
650: */
651: }
652:
653: /*************************free ma3x ************************/
654: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
655: {
656: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
657: free((FREE_ARG)(m[nrl]+ncl-NR_END));
658: free((FREE_ARG)(m+nrl-NR_END));
659: }
660:
661: /*************** function subdirf ***********/
662: char *subdirf(char fileres[])
663: {
664: /* Caution optionfilefiname is hidden */
665: strcpy(tmpout,optionfilefiname);
666: strcat(tmpout,"/"); /* Add to the right */
667: strcat(tmpout,fileres);
668: return tmpout;
669: }
670:
671: /*************** function subdirf2 ***********/
672: char *subdirf2(char fileres[], char *preop)
673: {
674:
675: /* Caution optionfilefiname is hidden */
676: strcpy(tmpout,optionfilefiname);
677: strcat(tmpout,"/");
678: strcat(tmpout,preop);
679: strcat(tmpout,fileres);
680: return tmpout;
681: }
682:
683: /*************** function subdirf3 ***********/
684: char *subdirf3(char fileres[], char *preop, char *preop2)
685: {
686:
687: /* Caution optionfilefiname is hidden */
688: strcpy(tmpout,optionfilefiname);
689: strcat(tmpout,"/");
690: strcat(tmpout,preop);
691: strcat(tmpout,preop2);
692: strcat(tmpout,fileres);
693: return tmpout;
694: }
695:
696: /***************** f1dim *************************/
697: extern int ncom;
698: extern double *pcom,*xicom;
699: extern double (*nrfunc)(double []);
700:
701: double f1dim(double x)
702: {
703: int j;
704: double f;
705: double *xt;
706:
707: xt=vector(1,ncom);
708: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
709: f=(*nrfunc)(xt);
710: free_vector(xt,1,ncom);
711: return f;
712: }
713:
714: /*****************brent *************************/
715: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
716: {
717: int iter;
718: double a,b,d,etemp;
719: double fu,fv,fw,fx;
720: double ftemp;
721: double p,q,r,tol1,tol2,u,v,w,x,xm;
722: double e=0.0;
723:
724: a=(ax < cx ? ax : cx);
725: b=(ax > cx ? ax : cx);
726: x=w=v=bx;
727: fw=fv=fx=(*f)(x);
728: for (iter=1;iter<=ITMAX;iter++) {
729: xm=0.5*(a+b);
730: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
731: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
732: printf(".");fflush(stdout);
733: fprintf(ficlog,".");fflush(ficlog);
734: #ifdef DEBUG
735: 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);
736: 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);
737: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
738: #endif
739: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
740: *xmin=x;
741: return fx;
742: }
743: ftemp=fu;
744: if (fabs(e) > tol1) {
745: r=(x-w)*(fx-fv);
746: q=(x-v)*(fx-fw);
747: p=(x-v)*q-(x-w)*r;
748: q=2.0*(q-r);
749: if (q > 0.0) p = -p;
750: q=fabs(q);
751: etemp=e;
752: e=d;
753: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
754: d=CGOLD*(e=(x >= xm ? a-x : b-x));
755: else {
756: d=p/q;
757: u=x+d;
758: if (u-a < tol2 || b-u < tol2)
759: d=SIGN(tol1,xm-x);
760: }
761: } else {
762: d=CGOLD*(e=(x >= xm ? a-x : b-x));
763: }
764: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
765: fu=(*f)(u);
766: if (fu <= fx) {
767: if (u >= x) a=x; else b=x;
768: SHFT(v,w,x,u)
769: SHFT(fv,fw,fx,fu)
770: } else {
771: if (u < x) a=u; else b=u;
772: if (fu <= fw || w == x) {
773: v=w;
774: w=u;
775: fv=fw;
776: fw=fu;
777: } else if (fu <= fv || v == x || v == w) {
778: v=u;
779: fv=fu;
780: }
781: }
782: }
783: nrerror("Too many iterations in brent");
784: *xmin=x;
785: return fx;
786: }
787:
788: /****************** mnbrak ***********************/
789:
790: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
791: double (*func)(double))
792: {
793: double ulim,u,r,q, dum;
794: double fu;
795:
796: *fa=(*func)(*ax);
797: *fb=(*func)(*bx);
798: if (*fb > *fa) {
799: SHFT(dum,*ax,*bx,dum)
800: SHFT(dum,*fb,*fa,dum)
801: }
802: *cx=(*bx)+GOLD*(*bx-*ax);
803: *fc=(*func)(*cx);
804: while (*fb > *fc) {
805: r=(*bx-*ax)*(*fb-*fc);
806: q=(*bx-*cx)*(*fb-*fa);
807: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
808: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
809: ulim=(*bx)+GLIMIT*(*cx-*bx);
810: if ((*bx-u)*(u-*cx) > 0.0) {
811: fu=(*func)(u);
812: } else if ((*cx-u)*(u-ulim) > 0.0) {
813: fu=(*func)(u);
814: if (fu < *fc) {
815: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
816: SHFT(*fb,*fc,fu,(*func)(u))
817: }
818: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
819: u=ulim;
820: fu=(*func)(u);
821: } else {
822: u=(*cx)+GOLD*(*cx-*bx);
823: fu=(*func)(u);
824: }
825: SHFT(*ax,*bx,*cx,u)
826: SHFT(*fa,*fb,*fc,fu)
827: }
828: }
829:
830: /*************** linmin ************************/
831:
832: int ncom;
833: double *pcom,*xicom;
834: double (*nrfunc)(double []);
835:
836: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
837: {
838: double brent(double ax, double bx, double cx,
839: double (*f)(double), double tol, double *xmin);
840: double f1dim(double x);
841: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
842: double *fc, double (*func)(double));
843: int j;
844: double xx,xmin,bx,ax;
845: double fx,fb,fa;
846:
847: ncom=n;
848: pcom=vector(1,n);
849: xicom=vector(1,n);
850: nrfunc=func;
851: for (j=1;j<=n;j++) {
852: pcom[j]=p[j];
853: xicom[j]=xi[j];
854: }
855: ax=0.0;
856: xx=1.0;
857: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
858: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
859: #ifdef DEBUG
860: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
861: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
862: #endif
863: for (j=1;j<=n;j++) {
864: xi[j] *= xmin;
865: p[j] += xi[j];
866: }
867: free_vector(xicom,1,n);
868: free_vector(pcom,1,n);
869: }
870:
871: char *asc_diff_time(long time_sec, char ascdiff[])
872: {
873: long sec_left, days, hours, minutes;
874: days = (time_sec) / (60*60*24);
875: sec_left = (time_sec) % (60*60*24);
876: hours = (sec_left) / (60*60) ;
877: sec_left = (sec_left) %(60*60);
878: minutes = (sec_left) /60;
879: sec_left = (sec_left) % (60);
880: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
881: return ascdiff;
882: }
883:
884: /*************** powell ************************/
885: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
886: double (*func)(double []))
887: {
888: void linmin(double p[], double xi[], int n, double *fret,
889: double (*func)(double []));
890: int i,ibig,j;
891: double del,t,*pt,*ptt,*xit;
892: double fp,fptt;
893: double *xits;
894: int niterf, itmp;
895:
896: pt=vector(1,n);
897: ptt=vector(1,n);
898: xit=vector(1,n);
899: xits=vector(1,n);
900: *fret=(*func)(p);
901: for (j=1;j<=n;j++) pt[j]=p[j];
902: for (*iter=1;;++(*iter)) {
903: fp=(*fret);
904: ibig=0;
905: del=0.0;
906: last_time=curr_time;
907: (void) gettimeofday(&curr_time,&tzp);
908: 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);
909: /* 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);
910: fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
911: */
912: for (i=1;i<=n;i++) {
913: printf(" %d %.12f",i, p[i]);
914: fprintf(ficlog," %d %.12lf",i, p[i]);
915: fprintf(ficrespow," %.12lf", p[i]);
916: }
917: printf("\n");
918: fprintf(ficlog,"\n");
919: fprintf(ficrespow,"\n");fflush(ficrespow);
920: if(*iter <=3){
921: tm = *localtime(&curr_time.tv_sec);
922: strcpy(strcurr,asctime(&tm));
923: /* asctime_r(&tm,strcurr); */
924: forecast_time=curr_time;
925: itmp = strlen(strcurr);
926: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
927: strcurr[itmp-1]='\0';
928: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
929: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
930: for(niterf=10;niterf<=30;niterf+=10){
931: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
932: tmf = *localtime(&forecast_time.tv_sec);
933: /* asctime_r(&tmf,strfor); */
934: strcpy(strfor,asctime(&tmf));
935: itmp = strlen(strfor);
936: if(strfor[itmp-1]=='\n')
937: strfor[itmp-1]='\0';
938: 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);
939: 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);
940: }
941: }
942: for (i=1;i<=n;i++) {
943: for (j=1;j<=n;j++) xit[j]=xi[j][i];
944: fptt=(*fret);
945: #ifdef DEBUG
946: printf("fret=%lf \n",*fret);
947: fprintf(ficlog,"fret=%lf \n",*fret);
948: #endif
949: printf("%d",i);fflush(stdout);
950: fprintf(ficlog,"%d",i);fflush(ficlog);
951: linmin(p,xit,n,fret,func);
952: if (fabs(fptt-(*fret)) > del) {
953: del=fabs(fptt-(*fret));
954: ibig=i;
955: }
956: #ifdef DEBUG
957: printf("%d %.12e",i,(*fret));
958: fprintf(ficlog,"%d %.12e",i,(*fret));
959: for (j=1;j<=n;j++) {
960: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
961: printf(" x(%d)=%.12e",j,xit[j]);
962: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
963: }
964: for(j=1;j<=n;j++) {
965: printf(" p=%.12e",p[j]);
966: fprintf(ficlog," p=%.12e",p[j]);
967: }
968: printf("\n");
969: fprintf(ficlog,"\n");
970: #endif
971: }
972: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
973: #ifdef DEBUG
974: int k[2],l;
975: k[0]=1;
976: k[1]=-1;
977: printf("Max: %.12e",(*func)(p));
978: fprintf(ficlog,"Max: %.12e",(*func)(p));
979: for (j=1;j<=n;j++) {
980: printf(" %.12e",p[j]);
981: fprintf(ficlog," %.12e",p[j]);
982: }
983: printf("\n");
984: fprintf(ficlog,"\n");
985: for(l=0;l<=1;l++) {
986: for (j=1;j<=n;j++) {
987: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
988: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
989: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
990: }
991: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
992: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
993: }
994: #endif
995:
996:
997: free_vector(xit,1,n);
998: free_vector(xits,1,n);
999: free_vector(ptt,1,n);
1000: free_vector(pt,1,n);
1001: return;
1002: }
1003: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1004: for (j=1;j<=n;j++) {
1005: ptt[j]=2.0*p[j]-pt[j];
1006: xit[j]=p[j]-pt[j];
1007: pt[j]=p[j];
1008: }
1009: fptt=(*func)(ptt);
1010: if (fptt < fp) {
1011: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1012: if (t < 0.0) {
1013: linmin(p,xit,n,fret,func);
1014: for (j=1;j<=n;j++) {
1015: xi[j][ibig]=xi[j][n];
1016: xi[j][n]=xit[j];
1017: }
1018: #ifdef DEBUG
1019: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1020: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1021: for(j=1;j<=n;j++){
1022: printf(" %.12e",xit[j]);
1023: fprintf(ficlog," %.12e",xit[j]);
1024: }
1025: printf("\n");
1026: fprintf(ficlog,"\n");
1027: #endif
1028: }
1029: }
1030: }
1031: }
1032:
1033: /**** Prevalence limit (stable prevalence) ****************/
1034:
1035: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1036: {
1037: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1038: matrix by transitions matrix until convergence is reached */
1039:
1040: int i, ii,j,k;
1041: double min, max, maxmin, maxmax,sumnew=0.;
1042: double **matprod2();
1043: double **out, cov[NCOVMAX], **pmij();
1044: double **newm;
1045: double agefin, delaymax=50 ; /* Max number of years to converge */
1046:
1047: for (ii=1;ii<=nlstate+ndeath;ii++)
1048: for (j=1;j<=nlstate+ndeath;j++){
1049: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1050: }
1051:
1052: cov[1]=1.;
1053:
1054: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1055: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1056: newm=savm;
1057: /* Covariates have to be included here again */
1058: cov[2]=agefin;
1059:
1060: for (k=1; k<=cptcovn;k++) {
1061: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1062: /* 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]]);*/
1063: }
1064: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1065: for (k=1; k<=cptcovprod;k++)
1066: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1067:
1068: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1069: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1070: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1071: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1072:
1073: savm=oldm;
1074: oldm=newm;
1075: maxmax=0.;
1076: for(j=1;j<=nlstate;j++){
1077: min=1.;
1078: max=0.;
1079: for(i=1; i<=nlstate; i++) {
1080: sumnew=0;
1081: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1082: prlim[i][j]= newm[i][j]/(1-sumnew);
1083: max=FMAX(max,prlim[i][j]);
1084: min=FMIN(min,prlim[i][j]);
1085: }
1086: maxmin=max-min;
1087: maxmax=FMAX(maxmax,maxmin);
1088: }
1089: if(maxmax < ftolpl){
1090: return prlim;
1091: }
1092: }
1093: }
1094:
1095: /*************** transition probabilities ***************/
1096:
1097: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1098: {
1099: double s1, s2;
1100: /*double t34;*/
1101: int i,j,j1, nc, ii, jj;
1102:
1103: for(i=1; i<= nlstate; i++){
1104: for(j=1; j<i;j++){
1105: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1106: /*s2 += param[i][j][nc]*cov[nc];*/
1107: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1108: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1109: }
1110: ps[i][j]=s2;
1111: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1112: }
1113: for(j=i+1; j<=nlstate+ndeath;j++){
1114: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1115: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1116: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1117: }
1118: ps[i][j]=s2;
1119: }
1120: }
1121: /*ps[3][2]=1;*/
1122:
1123: for(i=1; i<= nlstate; i++){
1124: s1=0;
1125: for(j=1; j<i; j++)
1126: s1+=exp(ps[i][j]);
1127: for(j=i+1; j<=nlstate+ndeath; j++)
1128: s1+=exp(ps[i][j]);
1129: ps[i][i]=1./(s1+1.);
1130: for(j=1; j<i; j++)
1131: ps[i][j]= exp(ps[i][j])*ps[i][i];
1132: for(j=i+1; j<=nlstate+ndeath; j++)
1133: ps[i][j]= exp(ps[i][j])*ps[i][i];
1134: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1135: } /* end i */
1136:
1137: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1138: for(jj=1; jj<= nlstate+ndeath; jj++){
1139: ps[ii][jj]=0;
1140: ps[ii][ii]=1;
1141: }
1142: }
1143:
1144:
1145: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1146: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1147: /* printf("ddd %lf ",ps[ii][jj]); */
1148: /* } */
1149: /* printf("\n "); */
1150: /* } */
1151: /* printf("\n ");printf("%lf ",cov[2]); */
1152: /*
1153: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1154: goto end;*/
1155: return ps;
1156: }
1157:
1158: /**************** Product of 2 matrices ******************/
1159:
1160: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1161: {
1162: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1163: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1164: /* in, b, out are matrice of pointers which should have been initialized
1165: before: only the contents of out is modified. The function returns
1166: a pointer to pointers identical to out */
1167: long i, j, k;
1168: for(i=nrl; i<= nrh; i++)
1169: for(k=ncolol; k<=ncoloh; k++)
1170: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1171: out[i][k] +=in[i][j]*b[j][k];
1172:
1173: return out;
1174: }
1175:
1176:
1177: /************* Higher Matrix Product ***************/
1178:
1179: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1180: {
1181: /* Computes the transition matrix starting at age 'age' over
1182: 'nhstepm*hstepm*stepm' months (i.e. until
1183: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1184: nhstepm*hstepm matrices.
1185: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1186: (typically every 2 years instead of every month which is too big
1187: for the memory).
1188: Model is determined by parameters x and covariates have to be
1189: included manually here.
1190:
1191: */
1192:
1193: int i, j, d, h, k;
1194: double **out, cov[NCOVMAX];
1195: double **newm;
1196:
1197: /* Hstepm could be zero and should return the unit matrix */
1198: for (i=1;i<=nlstate+ndeath;i++)
1199: for (j=1;j<=nlstate+ndeath;j++){
1200: oldm[i][j]=(i==j ? 1.0 : 0.0);
1201: po[i][j][0]=(i==j ? 1.0 : 0.0);
1202: }
1203: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1204: for(h=1; h <=nhstepm; h++){
1205: for(d=1; d <=hstepm; d++){
1206: newm=savm;
1207: /* Covariates have to be included here again */
1208: cov[1]=1.;
1209: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1210: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1211: for (k=1; k<=cptcovage;k++)
1212: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1213: for (k=1; k<=cptcovprod;k++)
1214: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1215:
1216:
1217: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1218: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1219: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1220: pmij(pmmij,cov,ncovmodel,x,nlstate));
1221: savm=oldm;
1222: oldm=newm;
1223: }
1224: for(i=1; i<=nlstate+ndeath; i++)
1225: for(j=1;j<=nlstate+ndeath;j++) {
1226: po[i][j][h]=newm[i][j];
1227: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1228: */
1229: }
1230: } /* end h */
1231: return po;
1232: }
1233:
1234:
1235: /*************** log-likelihood *************/
1236: double func( double *x)
1237: {
1238: int i, ii, j, k, mi, d, kk;
1239: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1240: double **out;
1241: double sw; /* Sum of weights */
1242: double lli; /* Individual log likelihood */
1243: int s1, s2;
1244: double bbh, survp;
1245: long ipmx;
1246: /*extern weight */
1247: /* We are differentiating ll according to initial status */
1248: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1249: /*for(i=1;i<imx;i++)
1250: printf(" %d\n",s[4][i]);
1251: */
1252: cov[1]=1.;
1253:
1254: for(k=1; k<=nlstate; k++) ll[k]=0.;
1255:
1256: if(mle==1){
1257: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1258: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1259: for(mi=1; mi<= wav[i]-1; mi++){
1260: for (ii=1;ii<=nlstate+ndeath;ii++)
1261: for (j=1;j<=nlstate+ndeath;j++){
1262: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1263: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1264: }
1265: for(d=0; d<dh[mi][i]; d++){
1266: newm=savm;
1267: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1268: for (kk=1; kk<=cptcovage;kk++) {
1269: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1270: }
1271: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1272: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1273: savm=oldm;
1274: oldm=newm;
1275: } /* end mult */
1276:
1277: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1278: /* But now since version 0.9 we anticipate for bias at large stepm.
1279: * If stepm is larger than one month (smallest stepm) and if the exact delay
1280: * (in months) between two waves is not a multiple of stepm, we rounded to
1281: * the nearest (and in case of equal distance, to the lowest) interval but now
1282: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1283: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1284: * probability in order to take into account the bias as a fraction of the way
1285: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1286: * -stepm/2 to stepm/2 .
1287: * For stepm=1 the results are the same as for previous versions of Imach.
1288: * For stepm > 1 the results are less biased than in previous versions.
1289: */
1290: s1=s[mw[mi][i]][i];
1291: s2=s[mw[mi+1][i]][i];
1292: bbh=(double)bh[mi][i]/(double)stepm;
1293: /* bias bh is positive if real duration
1294: * is higher than the multiple of stepm and negative otherwise.
1295: */
1296: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1297: if( s2 > nlstate){
1298: /* i.e. if s2 is a death state and if the date of death is known
1299: then the contribution to the likelihood is the probability to
1300: die between last step unit time and current step unit time,
1301: which is also equal to probability to die before dh
1302: minus probability to die before dh-stepm .
1303: In version up to 0.92 likelihood was computed
1304: as if date of death was unknown. Death was treated as any other
1305: health state: the date of the interview describes the actual state
1306: and not the date of a change in health state. The former idea was
1307: to consider that at each interview the state was recorded
1308: (healthy, disable or death) and IMaCh was corrected; but when we
1309: introduced the exact date of death then we should have modified
1310: the contribution of an exact death to the likelihood. This new
1311: contribution is smaller and very dependent of the step unit
1312: stepm. It is no more the probability to die between last interview
1313: and month of death but the probability to survive from last
1314: interview up to one month before death multiplied by the
1315: probability to die within a month. Thanks to Chris
1316: Jackson for correcting this bug. Former versions increased
1317: mortality artificially. The bad side is that we add another loop
1318: which slows down the processing. The difference can be up to 10%
1319: lower mortality.
1320: */
1321: lli=log(out[s1][s2] - savm[s1][s2]);
1322:
1323:
1324: } else if (s2==-2) {
1325: for (j=1,survp=0. ; j<=nlstate; j++)
1326: survp += out[s1][j];
1327: lli= survp;
1328: }
1329:
1330: else if (s2==-4) {
1331: for (j=3,survp=0. ; j<=nlstate; j++)
1332: survp += out[s1][j];
1333: lli= survp;
1334: }
1335:
1336: else if (s2==-5) {
1337: for (j=1,survp=0. ; j<=2; j++)
1338: survp += out[s1][j];
1339: lli= survp;
1340: }
1341:
1342:
1343: else{
1344: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1345: /* 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 */
1346: }
1347: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1348: /*if(lli ==000.0)*/
1349: /*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); */
1350: ipmx +=1;
1351: sw += weight[i];
1352: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1353: } /* end of wave */
1354: } /* end of individual */
1355: } else if(mle==2){
1356: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1357: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1358: for(mi=1; mi<= wav[i]-1; mi++){
1359: for (ii=1;ii<=nlstate+ndeath;ii++)
1360: for (j=1;j<=nlstate+ndeath;j++){
1361: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1362: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1363: }
1364: for(d=0; d<=dh[mi][i]; d++){
1365: newm=savm;
1366: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1367: for (kk=1; kk<=cptcovage;kk++) {
1368: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1369: }
1370: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1371: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1372: savm=oldm;
1373: oldm=newm;
1374: } /* end mult */
1375:
1376: s1=s[mw[mi][i]][i];
1377: s2=s[mw[mi+1][i]][i];
1378: bbh=(double)bh[mi][i]/(double)stepm;
1379: 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 */
1380: ipmx +=1;
1381: sw += weight[i];
1382: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1383: } /* end of wave */
1384: } /* end of individual */
1385: } else if(mle==3){ /* exponential inter-extrapolation */
1386: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1387: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1388: for(mi=1; mi<= wav[i]-1; mi++){
1389: for (ii=1;ii<=nlstate+ndeath;ii++)
1390: for (j=1;j<=nlstate+ndeath;j++){
1391: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1392: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1393: }
1394: for(d=0; d<dh[mi][i]; d++){
1395: newm=savm;
1396: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1397: for (kk=1; kk<=cptcovage;kk++) {
1398: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1399: }
1400: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1401: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1402: savm=oldm;
1403: oldm=newm;
1404: } /* end mult */
1405:
1406: s1=s[mw[mi][i]][i];
1407: s2=s[mw[mi+1][i]][i];
1408: bbh=(double)bh[mi][i]/(double)stepm;
1409: 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 */
1410: ipmx +=1;
1411: sw += weight[i];
1412: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1413: } /* end of wave */
1414: } /* end of individual */
1415: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1416: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1417: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1418: for(mi=1; mi<= wav[i]-1; mi++){
1419: for (ii=1;ii<=nlstate+ndeath;ii++)
1420: for (j=1;j<=nlstate+ndeath;j++){
1421: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1422: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1423: }
1424: for(d=0; d<dh[mi][i]; d++){
1425: newm=savm;
1426: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1427: for (kk=1; kk<=cptcovage;kk++) {
1428: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1429: }
1430:
1431: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1432: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1433: savm=oldm;
1434: oldm=newm;
1435: } /* end mult */
1436:
1437: s1=s[mw[mi][i]][i];
1438: s2=s[mw[mi+1][i]][i];
1439: if( s2 > nlstate){
1440: lli=log(out[s1][s2] - savm[s1][s2]);
1441: }else{
1442: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1443: }
1444: ipmx +=1;
1445: sw += weight[i];
1446: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1447: /* 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]); */
1448: } /* end of wave */
1449: } /* end of individual */
1450: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1451: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1452: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1453: for(mi=1; mi<= wav[i]-1; mi++){
1454: for (ii=1;ii<=nlstate+ndeath;ii++)
1455: for (j=1;j<=nlstate+ndeath;j++){
1456: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1457: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1458: }
1459: for(d=0; d<dh[mi][i]; d++){
1460: newm=savm;
1461: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1462: for (kk=1; kk<=cptcovage;kk++) {
1463: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1464: }
1465:
1466: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1467: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1468: savm=oldm;
1469: oldm=newm;
1470: } /* end mult */
1471:
1472: s1=s[mw[mi][i]][i];
1473: s2=s[mw[mi+1][i]][i];
1474: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1475: ipmx +=1;
1476: sw += weight[i];
1477: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1478: /*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]);*/
1479: } /* end of wave */
1480: } /* end of individual */
1481: } /* End of if */
1482: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1483: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1484: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1485: return -l;
1486: }
1487:
1488: /*************** log-likelihood *************/
1489: double funcone( double *x)
1490: {
1491: /* Same as likeli but slower because of a lot of printf and if */
1492: int i, ii, j, k, mi, d, kk;
1493: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1494: double **out;
1495: double lli; /* Individual log likelihood */
1496: double llt;
1497: int s1, s2;
1498: double bbh, survp;
1499: /*extern weight */
1500: /* We are differentiating ll according to initial status */
1501: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1502: /*for(i=1;i<imx;i++)
1503: printf(" %d\n",s[4][i]);
1504: */
1505: cov[1]=1.;
1506:
1507: for(k=1; k<=nlstate; k++) ll[k]=0.;
1508:
1509: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1510: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1511: for(mi=1; mi<= wav[i]-1; mi++){
1512: for (ii=1;ii<=nlstate+ndeath;ii++)
1513: for (j=1;j<=nlstate+ndeath;j++){
1514: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1515: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1516: }
1517: for(d=0; d<dh[mi][i]; d++){
1518: newm=savm;
1519: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1520: for (kk=1; kk<=cptcovage;kk++) {
1521: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1522: }
1523: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1524: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1525: savm=oldm;
1526: oldm=newm;
1527: } /* end mult */
1528:
1529: s1=s[mw[mi][i]][i];
1530: s2=s[mw[mi+1][i]][i];
1531: bbh=(double)bh[mi][i]/(double)stepm;
1532: /* bias is positive if real duration
1533: * is higher than the multiple of stepm and negative otherwise.
1534: */
1535: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1536: lli=log(out[s1][s2] - savm[s1][s2]);
1537: } else if (mle==1){
1538: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1539: } else if(mle==2){
1540: 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 */
1541: } else if(mle==3){ /* exponential inter-extrapolation */
1542: 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 */
1543: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1544: lli=log(out[s1][s2]); /* Original formula */
1545: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1546: lli=log(out[s1][s2]); /* Original formula */
1547: } /* End of if */
1548: ipmx +=1;
1549: sw += weight[i];
1550: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1551: /* 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]); */
1552: if(globpr){
1553: fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
1554: %10.6f %10.6f %10.6f ", \
1555: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1556: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1557: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1558: llt +=ll[k]*gipmx/gsw;
1559: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1560: }
1561: fprintf(ficresilk," %10.6f\n", -llt);
1562: }
1563: } /* end of wave */
1564: } /* end of individual */
1565: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1566: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1567: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1568: if(globpr==0){ /* First time we count the contributions and weights */
1569: gipmx=ipmx;
1570: gsw=sw;
1571: }
1572: return -l;
1573: }
1574:
1575:
1576: /*************** function likelione ***********/
1577: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1578: {
1579: /* This routine should help understanding what is done with
1580: the selection of individuals/waves and
1581: to check the exact contribution to the likelihood.
1582: Plotting could be done.
1583: */
1584: int k;
1585:
1586: if(*globpri !=0){ /* Just counts and sums, no printings */
1587: strcpy(fileresilk,"ilk");
1588: strcat(fileresilk,fileres);
1589: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1590: printf("Problem with resultfile: %s\n", fileresilk);
1591: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1592: }
1593: 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");
1594: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1595: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1596: for(k=1; k<=nlstate; k++)
1597: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1598: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1599: }
1600:
1601: *fretone=(*funcone)(p);
1602: if(*globpri !=0){
1603: fclose(ficresilk);
1604: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1605: fflush(fichtm);
1606: }
1607: return;
1608: }
1609:
1610:
1611: /*********** Maximum Likelihood Estimation ***************/
1612:
1613: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1614: {
1615: int i,j, iter;
1616: double **xi;
1617: double fret;
1618: double fretone; /* Only one call to likelihood */
1619: /* char filerespow[FILENAMELENGTH];*/
1620: xi=matrix(1,npar,1,npar);
1621: for (i=1;i<=npar;i++)
1622: for (j=1;j<=npar;j++)
1623: xi[i][j]=(i==j ? 1.0 : 0.0);
1624: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1625: strcpy(filerespow,"pow");
1626: strcat(filerespow,fileres);
1627: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1628: printf("Problem with resultfile: %s\n", filerespow);
1629: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1630: }
1631: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1632: for (i=1;i<=nlstate;i++)
1633: for(j=1;j<=nlstate+ndeath;j++)
1634: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1635: fprintf(ficrespow,"\n");
1636:
1637: powell(p,xi,npar,ftol,&iter,&fret,func);
1638:
1639: fclose(ficrespow);
1640: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1641: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1642: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1643:
1644: }
1645:
1646: /**** Computes Hessian and covariance matrix ***/
1647: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1648: {
1649: double **a,**y,*x,pd;
1650: double **hess;
1651: int i, j,jk;
1652: int *indx;
1653:
1654: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1655: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1656: void lubksb(double **a, int npar, int *indx, double b[]) ;
1657: void ludcmp(double **a, int npar, int *indx, double *d) ;
1658: double gompertz(double p[]);
1659: hess=matrix(1,npar,1,npar);
1660:
1661: printf("\nCalculation of the hessian matrix. Wait...\n");
1662: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1663: for (i=1;i<=npar;i++){
1664: printf("%d",i);fflush(stdout);
1665: fprintf(ficlog,"%d",i);fflush(ficlog);
1666:
1667: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1668:
1669: /* printf(" %f ",p[i]);
1670: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1671: }
1672:
1673: for (i=1;i<=npar;i++) {
1674: for (j=1;j<=npar;j++) {
1675: if (j>i) {
1676: printf(".%d%d",i,j);fflush(stdout);
1677: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1678: hess[i][j]=hessij(p,delti,i,j,func,npar);
1679:
1680: hess[j][i]=hess[i][j];
1681: /*printf(" %lf ",hess[i][j]);*/
1682: }
1683: }
1684: }
1685: printf("\n");
1686: fprintf(ficlog,"\n");
1687:
1688: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1689: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1690:
1691: a=matrix(1,npar,1,npar);
1692: y=matrix(1,npar,1,npar);
1693: x=vector(1,npar);
1694: indx=ivector(1,npar);
1695: for (i=1;i<=npar;i++)
1696: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1697: ludcmp(a,npar,indx,&pd);
1698:
1699: for (j=1;j<=npar;j++) {
1700: for (i=1;i<=npar;i++) x[i]=0;
1701: x[j]=1;
1702: lubksb(a,npar,indx,x);
1703: for (i=1;i<=npar;i++){
1704: matcov[i][j]=x[i];
1705: }
1706: }
1707:
1708: printf("\n#Hessian matrix#\n");
1709: fprintf(ficlog,"\n#Hessian matrix#\n");
1710: for (i=1;i<=npar;i++) {
1711: for (j=1;j<=npar;j++) {
1712: printf("%.3e ",hess[i][j]);
1713: fprintf(ficlog,"%.3e ",hess[i][j]);
1714: }
1715: printf("\n");
1716: fprintf(ficlog,"\n");
1717: }
1718:
1719: /* Recompute Inverse */
1720: for (i=1;i<=npar;i++)
1721: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1722: ludcmp(a,npar,indx,&pd);
1723:
1724: /* printf("\n#Hessian matrix recomputed#\n");
1725:
1726: for (j=1;j<=npar;j++) {
1727: for (i=1;i<=npar;i++) x[i]=0;
1728: x[j]=1;
1729: lubksb(a,npar,indx,x);
1730: for (i=1;i<=npar;i++){
1731: y[i][j]=x[i];
1732: printf("%.3e ",y[i][j]);
1733: fprintf(ficlog,"%.3e ",y[i][j]);
1734: }
1735: printf("\n");
1736: fprintf(ficlog,"\n");
1737: }
1738: */
1739:
1740: free_matrix(a,1,npar,1,npar);
1741: free_matrix(y,1,npar,1,npar);
1742: free_vector(x,1,npar);
1743: free_ivector(indx,1,npar);
1744: free_matrix(hess,1,npar,1,npar);
1745:
1746:
1747: }
1748:
1749: /*************** hessian matrix ****************/
1750: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1751: {
1752: int i;
1753: int l=1, lmax=20;
1754: double k1,k2;
1755: double p2[NPARMAX+1];
1756: double res;
1757: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1758: double fx;
1759: int k=0,kmax=10;
1760: double l1;
1761:
1762: fx=func(x);
1763: for (i=1;i<=npar;i++) p2[i]=x[i];
1764: for(l=0 ; l <=lmax; l++){
1765: l1=pow(10,l);
1766: delts=delt;
1767: for(k=1 ; k <kmax; k=k+1){
1768: delt = delta*(l1*k);
1769: p2[theta]=x[theta] +delt;
1770: k1=func(p2)-fx;
1771: p2[theta]=x[theta]-delt;
1772: k2=func(p2)-fx;
1773: /*res= (k1-2.0*fx+k2)/delt/delt; */
1774: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1775:
1776: #ifdef DEBUG
1777: 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);
1778: 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);
1779: #endif
1780: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1781: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1782: k=kmax;
1783: }
1784: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1785: k=kmax; l=lmax*10.;
1786: }
1787: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1788: delts=delt;
1789: }
1790: }
1791: }
1792: delti[theta]=delts;
1793: return res;
1794:
1795: }
1796:
1797: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1798: {
1799: int i;
1800: int l=1, l1, lmax=20;
1801: double k1,k2,k3,k4,res,fx;
1802: double p2[NPARMAX+1];
1803: int k;
1804:
1805: fx=func(x);
1806: for (k=1; k<=2; k++) {
1807: for (i=1;i<=npar;i++) p2[i]=x[i];
1808: p2[thetai]=x[thetai]+delti[thetai]/k;
1809: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1810: k1=func(p2)-fx;
1811:
1812: p2[thetai]=x[thetai]+delti[thetai]/k;
1813: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1814: k2=func(p2)-fx;
1815:
1816: p2[thetai]=x[thetai]-delti[thetai]/k;
1817: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1818: k3=func(p2)-fx;
1819:
1820: p2[thetai]=x[thetai]-delti[thetai]/k;
1821: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1822: k4=func(p2)-fx;
1823: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1824: #ifdef DEBUG
1825: 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);
1826: 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);
1827: #endif
1828: }
1829: return res;
1830: }
1831:
1832: /************** Inverse of matrix **************/
1833: void ludcmp(double **a, int n, int *indx, double *d)
1834: {
1835: int i,imax,j,k;
1836: double big,dum,sum,temp;
1837: double *vv;
1838:
1839: vv=vector(1,n);
1840: *d=1.0;
1841: for (i=1;i<=n;i++) {
1842: big=0.0;
1843: for (j=1;j<=n;j++)
1844: if ((temp=fabs(a[i][j])) > big) big=temp;
1845: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1846: vv[i]=1.0/big;
1847: }
1848: for (j=1;j<=n;j++) {
1849: for (i=1;i<j;i++) {
1850: sum=a[i][j];
1851: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1852: a[i][j]=sum;
1853: }
1854: big=0.0;
1855: for (i=j;i<=n;i++) {
1856: sum=a[i][j];
1857: for (k=1;k<j;k++)
1858: sum -= a[i][k]*a[k][j];
1859: a[i][j]=sum;
1860: if ( (dum=vv[i]*fabs(sum)) >= big) {
1861: big=dum;
1862: imax=i;
1863: }
1864: }
1865: if (j != imax) {
1866: for (k=1;k<=n;k++) {
1867: dum=a[imax][k];
1868: a[imax][k]=a[j][k];
1869: a[j][k]=dum;
1870: }
1871: *d = -(*d);
1872: vv[imax]=vv[j];
1873: }
1874: indx[j]=imax;
1875: if (a[j][j] == 0.0) a[j][j]=TINY;
1876: if (j != n) {
1877: dum=1.0/(a[j][j]);
1878: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1879: }
1880: }
1881: free_vector(vv,1,n); /* Doesn't work */
1882: ;
1883: }
1884:
1885: void lubksb(double **a, int n, int *indx, double b[])
1886: {
1887: int i,ii=0,ip,j;
1888: double sum;
1889:
1890: for (i=1;i<=n;i++) {
1891: ip=indx[i];
1892: sum=b[ip];
1893: b[ip]=b[i];
1894: if (ii)
1895: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1896: else if (sum) ii=i;
1897: b[i]=sum;
1898: }
1899: for (i=n;i>=1;i--) {
1900: sum=b[i];
1901: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1902: b[i]=sum/a[i][i];
1903: }
1904: }
1905:
1906: /************ Frequencies ********************/
1907: 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[])
1908: { /* Some frequencies */
1909:
1910: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1911: int first;
1912: double ***freq; /* Frequencies */
1913: double *pp, **prop;
1914: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1915: FILE *ficresp;
1916: char fileresp[FILENAMELENGTH];
1917:
1918: pp=vector(1,nlstate);
1919: prop=matrix(1,nlstate,iagemin,iagemax+3);
1920: strcpy(fileresp,"p");
1921: strcat(fileresp,fileres);
1922: if((ficresp=fopen(fileresp,"w"))==NULL) {
1923: printf("Problem with prevalence resultfile: %s\n", fileresp);
1924: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1925: exit(0);
1926: }
1927: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
1928: j1=0;
1929:
1930: j=cptcoveff;
1931: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1932:
1933: first=1;
1934:
1935: for(k1=1; k1<=j;k1++){
1936: for(i1=1; i1<=ncodemax[k1];i1++){
1937: j1++;
1938: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1939: scanf("%d", i);*/
1940: for (i=-5; i<=nlstate+ndeath; i++)
1941: for (jk=-5; jk<=nlstate+ndeath; jk++)
1942: for(m=iagemin; m <= iagemax+3; m++)
1943: freq[i][jk][m]=0;
1944:
1945: for (i=1; i<=nlstate; i++)
1946: for(m=iagemin; m <= iagemax+3; m++)
1947: prop[i][m]=0;
1948:
1949: dateintsum=0;
1950: k2cpt=0;
1951: for (i=1; i<=imx; i++) {
1952: bool=1;
1953: if (cptcovn>0) {
1954: for (z1=1; z1<=cptcoveff; z1++)
1955: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1956: bool=0;
1957: }
1958: if (bool==1){
1959: for(m=firstpass; m<=lastpass; m++){
1960: k2=anint[m][i]+(mint[m][i]/12.);
1961: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1962: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1963: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1964: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1965: if (m<lastpass) {
1966: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1967: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1968: }
1969:
1970: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1971: dateintsum=dateintsum+k2;
1972: k2cpt++;
1973: }
1974: /*}*/
1975: }
1976: }
1977: }
1978:
1979: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1980: fprintf(ficresp, "#Local time at start: %s", strstart);
1981: if (cptcovn>0) {
1982: fprintf(ficresp, "\n#********** Variable ");
1983: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1984: fprintf(ficresp, "**********\n#");
1985: }
1986: for(i=1; i<=nlstate;i++)
1987: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1988: fprintf(ficresp, "\n");
1989:
1990: for(i=iagemin; i <= iagemax+3; i++){
1991: if(i==iagemax+3){
1992: fprintf(ficlog,"Total");
1993: }else{
1994: if(first==1){
1995: first=0;
1996: printf("See log file for details...\n");
1997: }
1998: fprintf(ficlog,"Age %d", i);
1999: }
2000: for(jk=1; jk <=nlstate ; jk++){
2001: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2002: pp[jk] += freq[jk][m][i];
2003: }
2004: for(jk=1; jk <=nlstate ; jk++){
2005: for(m=-1, pos=0; m <=0 ; m++)
2006: pos += freq[jk][m][i];
2007: if(pp[jk]>=1.e-10){
2008: if(first==1){
2009: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2010: }
2011: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2012: }else{
2013: if(first==1)
2014: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2015: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2016: }
2017: }
2018:
2019: for(jk=1; jk <=nlstate ; jk++){
2020: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2021: pp[jk] += freq[jk][m][i];
2022: }
2023: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2024: pos += pp[jk];
2025: posprop += prop[jk][i];
2026: }
2027: for(jk=1; jk <=nlstate ; jk++){
2028: if(pos>=1.e-5){
2029: if(first==1)
2030: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2031: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2032: }else{
2033: if(first==1)
2034: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2035: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2036: }
2037: if( i <= iagemax){
2038: if(pos>=1.e-5){
2039: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2040: /*probs[i][jk][j1]= pp[jk]/pos;*/
2041: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2042: }
2043: else
2044: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2045: }
2046: }
2047:
2048: for(jk=-1; jk <=nlstate+ndeath; jk++)
2049: for(m=-1; m <=nlstate+ndeath; m++)
2050: if(freq[jk][m][i] !=0 ) {
2051: if(first==1)
2052: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2053: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2054: }
2055: if(i <= iagemax)
2056: fprintf(ficresp,"\n");
2057: if(first==1)
2058: printf("Others in log...\n");
2059: fprintf(ficlog,"\n");
2060: }
2061: }
2062: }
2063: dateintmean=dateintsum/k2cpt;
2064:
2065: fclose(ficresp);
2066: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2067: free_vector(pp,1,nlstate);
2068: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2069: /* End of Freq */
2070: }
2071:
2072: /************ Prevalence ********************/
2073: 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)
2074: {
2075: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2076: in each health status at the date of interview (if between dateprev1 and dateprev2).
2077: We still use firstpass and lastpass as another selection.
2078: */
2079:
2080: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
2081: double ***freq; /* Frequencies */
2082: double *pp, **prop;
2083: double pos,posprop;
2084: double y2; /* in fractional years */
2085: int iagemin, iagemax;
2086:
2087: iagemin= (int) agemin;
2088: iagemax= (int) agemax;
2089: /*pp=vector(1,nlstate);*/
2090: prop=matrix(1,nlstate,iagemin,iagemax+3);
2091: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2092: j1=0;
2093:
2094: j=cptcoveff;
2095: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2096:
2097: for(k1=1; k1<=j;k1++){
2098: for(i1=1; i1<=ncodemax[k1];i1++){
2099: j1++;
2100:
2101: for (i=1; i<=nlstate; i++)
2102: for(m=iagemin; m <= iagemax+3; m++)
2103: prop[i][m]=0.0;
2104:
2105: for (i=1; i<=imx; i++) { /* Each individual */
2106: bool=1;
2107: if (cptcovn>0) {
2108: for (z1=1; z1<=cptcoveff; z1++)
2109: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2110: bool=0;
2111: }
2112: if (bool==1) {
2113: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2114: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2115: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2116: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2117: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2118: 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);
2119: if (s[m][i]>0 && s[m][i]<=nlstate) {
2120: /*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]]);*/
2121: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2122: prop[s[m][i]][iagemax+3] += weight[i];
2123: }
2124: }
2125: } /* end selection of waves */
2126: }
2127: }
2128: for(i=iagemin; i <= iagemax+3; i++){
2129:
2130: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2131: posprop += prop[jk][i];
2132: }
2133:
2134: for(jk=1; jk <=nlstate ; jk++){
2135: if( i <= iagemax){
2136: if(posprop>=1.e-5){
2137: probs[i][jk][j1]= prop[jk][i]/posprop;
2138: }
2139: }
2140: }/* end jk */
2141: }/* end i */
2142: } /* end i1 */
2143: } /* end k1 */
2144:
2145: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2146: /*free_vector(pp,1,nlstate);*/
2147: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2148: } /* End of prevalence */
2149:
2150: /************* Waves Concatenation ***************/
2151:
2152: 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)
2153: {
2154: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2155: Death is a valid wave (if date is known).
2156: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2157: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2158: and mw[mi+1][i]. dh depends on stepm.
2159: */
2160:
2161: int i, mi, m;
2162: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2163: double sum=0., jmean=0.;*/
2164: int first;
2165: int j, k=0,jk, ju, jl;
2166: double sum=0.;
2167: first=0;
2168: jmin=1e+5;
2169: jmax=-1;
2170: jmean=0.;
2171: for(i=1; i<=imx; i++){
2172: mi=0;
2173: m=firstpass;
2174: while(s[m][i] <= nlstate){
2175: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2176: mw[++mi][i]=m;
2177: if(m >=lastpass)
2178: break;
2179: else
2180: m++;
2181: }/* end while */
2182: if (s[m][i] > nlstate){
2183: mi++; /* Death is another wave */
2184: /* if(mi==0) never been interviewed correctly before death */
2185: /* Only death is a correct wave */
2186: mw[mi][i]=m;
2187: }
2188:
2189: wav[i]=mi;
2190: if(mi==0){
2191: nbwarn++;
2192: if(first==0){
2193: printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2194: first=1;
2195: }
2196: if(first==1){
2197: fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
2198: }
2199: } /* end mi==0 */
2200: } /* End individuals */
2201:
2202: for(i=1; i<=imx; i++){
2203: for(mi=1; mi<wav[i];mi++){
2204: if (stepm <=0)
2205: dh[mi][i]=1;
2206: else{
2207: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2208: if (agedc[i] < 2*AGESUP) {
2209: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2210: if(j==0) j=1; /* Survives at least one month after exam */
2211: else if(j<0){
2212: nberr++;
2213: 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]);
2214: j=1; /* Temporary Dangerous patch */
2215: 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);
2216: 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]);
2217: 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);
2218: }
2219: k=k+1;
2220: if (j >= jmax) jmax=j;
2221: if (j <= jmin) jmin=j;
2222: sum=sum+j;
2223: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2224: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2225: }
2226: }
2227: else{
2228: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2229: /* 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]); */
2230:
2231: k=k+1;
2232: if (j >= jmax) jmax=j;
2233: else if (j <= jmin)jmin=j;
2234: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2235: /*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]);*/
2236: if(j<0){
2237: nberr++;
2238: 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]);
2239: 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]);
2240: }
2241: sum=sum+j;
2242: }
2243: jk= j/stepm;
2244: jl= j -jk*stepm;
2245: ju= j -(jk+1)*stepm;
2246: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2247: if(jl==0){
2248: dh[mi][i]=jk;
2249: bh[mi][i]=0;
2250: }else{ /* We want a negative bias in order to only have interpolation ie
2251: * at the price of an extra matrix product in likelihood */
2252: dh[mi][i]=jk+1;
2253: bh[mi][i]=ju;
2254: }
2255: }else{
2256: if(jl <= -ju){
2257: dh[mi][i]=jk;
2258: bh[mi][i]=jl; /* bias is positive if real duration
2259: * is higher than the multiple of stepm and negative otherwise.
2260: */
2261: }
2262: else{
2263: dh[mi][i]=jk+1;
2264: bh[mi][i]=ju;
2265: }
2266: if(dh[mi][i]==0){
2267: dh[mi][i]=1; /* At least one step */
2268: bh[mi][i]=ju; /* At least one step */
2269: /* 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);*/
2270: }
2271: } /* end if mle */
2272: }
2273: } /* end wave */
2274: }
2275: jmean=sum/k;
2276: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2277: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2278: }
2279:
2280: /*********** Tricode ****************************/
2281: void tricode(int *Tvar, int **nbcode, int imx)
2282: {
2283:
2284: int Ndum[20],ij=1, k, j, i, maxncov=19;
2285: int cptcode=0;
2286: cptcoveff=0;
2287:
2288: for (k=0; k<maxncov; k++) Ndum[k]=0;
2289: for (k=1; k<=7; k++) ncodemax[k]=0;
2290:
2291: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
2292: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2293: modality*/
2294: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2295: Ndum[ij]++; /*store the modality */
2296: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2297: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2298: Tvar[j]. If V=sex and male is 0 and
2299: female is 1, then cptcode=1.*/
2300: }
2301:
2302: for (i=0; i<=cptcode; i++) {
2303: 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 */
2304: }
2305:
2306: ij=1;
2307: for (i=1; i<=ncodemax[j]; i++) {
2308: for (k=0; k<= maxncov; k++) {
2309: if (Ndum[k] != 0) {
2310: nbcode[Tvar[j]][ij]=k;
2311: /* 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; */
2312:
2313: ij++;
2314: }
2315: if (ij > ncodemax[j]) break;
2316: }
2317: }
2318: }
2319:
2320: for (k=0; k< maxncov; k++) Ndum[k]=0;
2321:
2322: for (i=1; i<=ncovmodel-2; i++) {
2323: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2324: ij=Tvar[i];
2325: Ndum[ij]++;
2326: }
2327:
2328: ij=1;
2329: for (i=1; i<= maxncov; i++) {
2330: if((Ndum[i]!=0) && (i<=ncovcol)){
2331: Tvaraff[ij]=i; /*For printing */
2332: ij++;
2333: }
2334: }
2335:
2336: cptcoveff=ij-1; /*Number of simple covariates*/
2337: }
2338:
2339: /*********** Health Expectancies ****************/
2340:
2341: 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[] )
2342:
2343: {
2344: /* Health expectancies */
2345: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
2346: double age, agelim, hf;
2347: double ***p3mat,***varhe;
2348: double **dnewm,**doldm;
2349: double *xp;
2350: double **gp, **gm;
2351: double ***gradg, ***trgradg;
2352: int theta;
2353:
2354: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2355: xp=vector(1,npar);
2356: dnewm=matrix(1,nlstate*nlstate,1,npar);
2357: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2358:
2359: fprintf(ficreseij,"# Local time at start: %s", strstart);
2360: fprintf(ficreseij,"# Health expectancies\n");
2361: fprintf(ficreseij,"# Age");
2362: for(i=1; i<=nlstate;i++)
2363: for(j=1; j<=nlstate;j++)
2364: fprintf(ficreseij," %1d-%1d (SE)",i,j);
2365: fprintf(ficreseij,"\n");
2366:
2367: if(estepm < stepm){
2368: printf ("Problem %d lower than %d\n",estepm, stepm);
2369: }
2370: else hstepm=estepm;
2371: /* We compute the life expectancy from trapezoids spaced every estepm months
2372: * This is mainly to measure the difference between two models: for example
2373: * if stepm=24 months pijx are given only every 2 years and by summing them
2374: * we are calculating an estimate of the Life Expectancy assuming a linear
2375: * progression in between and thus overestimating or underestimating according
2376: * to the curvature of the survival function. If, for the same date, we
2377: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2378: * to compare the new estimate of Life expectancy with the same linear
2379: * hypothesis. A more precise result, taking into account a more precise
2380: * curvature will be obtained if estepm is as small as stepm. */
2381:
2382: /* For example we decided to compute the life expectancy with the smallest unit */
2383: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2384: nhstepm is the number of hstepm from age to agelim
2385: nstepm is the number of stepm from age to agelin.
2386: Look at hpijx to understand the reason of that which relies in memory size
2387: and note for a fixed period like estepm months */
2388: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2389: survival function given by stepm (the optimization length). Unfortunately it
2390: means that if the survival funtion is printed only each two years of age and if
2391: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2392: results. So we changed our mind and took the option of the best precision.
2393: */
2394: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2395:
2396: agelim=AGESUP;
2397: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2398: /* nhstepm age range expressed in number of stepm */
2399: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2400: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2401: /* if (stepm >= YEARM) hstepm=1;*/
2402: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2403: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2404: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2405: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2406: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2407:
2408: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2409: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2410: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
2411:
2412:
2413: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2414:
2415: /* Computing Variances of health expectancies */
2416:
2417: for(theta=1; theta <=npar; theta++){
2418: for(i=1; i<=npar; i++){
2419: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2420: }
2421: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2422:
2423: cptj=0;
2424: for(j=1; j<= nlstate; j++){
2425: for(i=1; i<=nlstate; i++){
2426: cptj=cptj+1;
2427: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2428: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2429: }
2430: }
2431: }
2432:
2433:
2434: for(i=1; i<=npar; i++)
2435: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2436: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2437:
2438: cptj=0;
2439: for(j=1; j<= nlstate; j++){
2440: for(i=1;i<=nlstate;i++){
2441: cptj=cptj+1;
2442: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
2443:
2444: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2445: }
2446: }
2447: }
2448: for(j=1; j<= nlstate*nlstate; j++)
2449: for(h=0; h<=nhstepm-1; h++){
2450: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2451: }
2452: }
2453:
2454: /* End theta */
2455:
2456: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2457:
2458: for(h=0; h<=nhstepm-1; h++)
2459: for(j=1; j<=nlstate*nlstate;j++)
2460: for(theta=1; theta <=npar; theta++)
2461: trgradg[h][j][theta]=gradg[h][theta][j];
2462:
2463:
2464: for(i=1;i<=nlstate*nlstate;i++)
2465: for(j=1;j<=nlstate*nlstate;j++)
2466: varhe[i][j][(int)age] =0.;
2467:
2468: printf("%d|",(int)age);fflush(stdout);
2469: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2470: for(h=0;h<=nhstepm-1;h++){
2471: for(k=0;k<=nhstepm-1;k++){
2472: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2473: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2474: for(i=1;i<=nlstate*nlstate;i++)
2475: for(j=1;j<=nlstate*nlstate;j++)
2476: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2477: }
2478: }
2479: /* Computing expectancies */
2480: for(i=1; i<=nlstate;i++)
2481: for(j=1; j<=nlstate;j++)
2482: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2483: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2484:
2485: /* 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]);*/
2486:
2487: }
2488:
2489: fprintf(ficreseij,"%3.0f",age );
2490: cptj=0;
2491: for(i=1; i<=nlstate;i++)
2492: for(j=1; j<=nlstate;j++){
2493: cptj++;
2494: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2495: }
2496: fprintf(ficreseij,"\n");
2497:
2498: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2499: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2500: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2501: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2502: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2503: }
2504: printf("\n");
2505: fprintf(ficlog,"\n");
2506:
2507: free_vector(xp,1,npar);
2508: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2509: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2510: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2511: }
2512:
2513: /************ Variance ******************/
2514: 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[])
2515: {
2516: /* Variance of health expectancies */
2517: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2518: /* double **newm;*/
2519: double **dnewm,**doldm;
2520: double **dnewmp,**doldmp;
2521: int i, j, nhstepm, hstepm, h, nstepm ;
2522: int k, cptcode;
2523: double *xp;
2524: double **gp, **gm; /* for var eij */
2525: double ***gradg, ***trgradg; /*for var eij */
2526: double **gradgp, **trgradgp; /* for var p point j */
2527: double *gpp, *gmp; /* for var p point j */
2528: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2529: double ***p3mat;
2530: double age,agelim, hf;
2531: double ***mobaverage;
2532: int theta;
2533: char digit[4];
2534: char digitp[25];
2535:
2536: char fileresprobmorprev[FILENAMELENGTH];
2537:
2538: if(popbased==1){
2539: if(mobilav!=0)
2540: strcpy(digitp,"-populbased-mobilav-");
2541: else strcpy(digitp,"-populbased-nomobil-");
2542: }
2543: else
2544: strcpy(digitp,"-stablbased-");
2545:
2546: if (mobilav!=0) {
2547: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2548: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2549: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2550: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2551: }
2552: }
2553:
2554: strcpy(fileresprobmorprev,"prmorprev");
2555: sprintf(digit,"%-d",ij);
2556: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2557: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2558: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2559: strcat(fileresprobmorprev,fileres);
2560: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2561: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2562: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2563: }
2564: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2565:
2566: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2567: fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
2568: 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);
2569: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2570: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2571: fprintf(ficresprobmorprev," p.%-d SE",j);
2572: for(i=1; i<=nlstate;i++)
2573: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2574: }
2575: fprintf(ficresprobmorprev,"\n");
2576: fprintf(ficgp,"\n# Routine varevsij");
2577: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
2578: 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");
2579: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2580: /* } */
2581: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2582: fprintf(ficresvij, "#Local time at start: %s", strstart);
2583: 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");
2584: fprintf(ficresvij,"# Age");
2585: for(i=1; i<=nlstate;i++)
2586: for(j=1; j<=nlstate;j++)
2587: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2588: fprintf(ficresvij,"\n");
2589:
2590: xp=vector(1,npar);
2591: dnewm=matrix(1,nlstate,1,npar);
2592: doldm=matrix(1,nlstate,1,nlstate);
2593: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2594: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2595:
2596: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2597: gpp=vector(nlstate+1,nlstate+ndeath);
2598: gmp=vector(nlstate+1,nlstate+ndeath);
2599: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2600:
2601: if(estepm < stepm){
2602: printf ("Problem %d lower than %d\n",estepm, stepm);
2603: }
2604: else hstepm=estepm;
2605: /* For example we decided to compute the life expectancy with the smallest unit */
2606: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2607: nhstepm is the number of hstepm from age to agelim
2608: nstepm is the number of stepm from age to agelin.
2609: Look at hpijx to understand the reason of that which relies in memory size
2610: and note for a fixed period like k years */
2611: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2612: survival function given by stepm (the optimization length). Unfortunately it
2613: means that if the survival funtion is printed every two years of age and if
2614: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2615: results. So we changed our mind and took the option of the best precision.
2616: */
2617: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2618: agelim = AGESUP;
2619: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2620: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2621: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2622: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2623: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2624: gp=matrix(0,nhstepm,1,nlstate);
2625: gm=matrix(0,nhstepm,1,nlstate);
2626:
2627:
2628: for(theta=1; theta <=npar; theta++){
2629: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2630: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2631: }
2632: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2633: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2634:
2635: if (popbased==1) {
2636: if(mobilav ==0){
2637: for(i=1; i<=nlstate;i++)
2638: prlim[i][i]=probs[(int)age][i][ij];
2639: }else{ /* mobilav */
2640: for(i=1; i<=nlstate;i++)
2641: prlim[i][i]=mobaverage[(int)age][i][ij];
2642: }
2643: }
2644:
2645: for(j=1; j<= nlstate; j++){
2646: for(h=0; h<=nhstepm; h++){
2647: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2648: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2649: }
2650: }
2651: /* This for computing probability of death (h=1 means
2652: computed over hstepm matrices product = hstepm*stepm months)
2653: as a weighted average of prlim.
2654: */
2655: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2656: for(i=1,gpp[j]=0.; i<= nlstate; i++)
2657: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2658: }
2659: /* end probability of death */
2660:
2661: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
2662: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2663: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2664: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2665:
2666: if (popbased==1) {
2667: if(mobilav ==0){
2668: for(i=1; i<=nlstate;i++)
2669: prlim[i][i]=probs[(int)age][i][ij];
2670: }else{ /* mobilav */
2671: for(i=1; i<=nlstate;i++)
2672: prlim[i][i]=mobaverage[(int)age][i][ij];
2673: }
2674: }
2675:
2676: for(j=1; j<= nlstate; j++){
2677: for(h=0; h<=nhstepm; h++){
2678: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2679: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2680: }
2681: }
2682: /* This for computing probability of death (h=1 means
2683: computed over hstepm matrices product = hstepm*stepm months)
2684: as a weighted average of prlim.
2685: */
2686: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2687: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2688: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2689: }
2690: /* end probability of death */
2691:
2692: for(j=1; j<= nlstate; j++) /* vareij */
2693: for(h=0; h<=nhstepm; h++){
2694: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2695: }
2696:
2697: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2698: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2699: }
2700:
2701: } /* End theta */
2702:
2703: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2704:
2705: for(h=0; h<=nhstepm; h++) /* veij */
2706: for(j=1; j<=nlstate;j++)
2707: for(theta=1; theta <=npar; theta++)
2708: trgradg[h][j][theta]=gradg[h][theta][j];
2709:
2710: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
2711: for(theta=1; theta <=npar; theta++)
2712: trgradgp[j][theta]=gradgp[theta][j];
2713:
2714:
2715: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2716: for(i=1;i<=nlstate;i++)
2717: for(j=1;j<=nlstate;j++)
2718: vareij[i][j][(int)age] =0.;
2719:
2720: for(h=0;h<=nhstepm;h++){
2721: for(k=0;k<=nhstepm;k++){
2722: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2723: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2724: for(i=1;i<=nlstate;i++)
2725: for(j=1;j<=nlstate;j++)
2726: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2727: }
2728: }
2729:
2730: /* pptj */
2731: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2732: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
2733: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2734: for(i=nlstate+1;i<=nlstate+ndeath;i++)
2735: varppt[j][i]=doldmp[j][i];
2736: /* end ppptj */
2737: /* x centered again */
2738: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2739: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2740:
2741: if (popbased==1) {
2742: if(mobilav ==0){
2743: for(i=1; i<=nlstate;i++)
2744: prlim[i][i]=probs[(int)age][i][ij];
2745: }else{ /* mobilav */
2746: for(i=1; i<=nlstate;i++)
2747: prlim[i][i]=mobaverage[(int)age][i][ij];
2748: }
2749: }
2750:
2751: /* This for computing probability of death (h=1 means
2752: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2753: as a weighted average of prlim.
2754: */
2755: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2756: for(i=1,gmp[j]=0.;i<= nlstate; i++)
2757: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2758: }
2759: /* end probability of death */
2760:
2761: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2762: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2763: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2764: for(i=1; i<=nlstate;i++){
2765: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2766: }
2767: }
2768: fprintf(ficresprobmorprev,"\n");
2769:
2770: fprintf(ficresvij,"%.0f ",age );
2771: for(i=1; i<=nlstate;i++)
2772: for(j=1; j<=nlstate;j++){
2773: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2774: }
2775: fprintf(ficresvij,"\n");
2776: free_matrix(gp,0,nhstepm,1,nlstate);
2777: free_matrix(gm,0,nhstepm,1,nlstate);
2778: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2779: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2780: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2781: } /* End age */
2782: free_vector(gpp,nlstate+1,nlstate+ndeath);
2783: free_vector(gmp,nlstate+1,nlstate+ndeath);
2784: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2785: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2786: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2787: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2788: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
2789: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2790: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2791: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
2792: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
2793: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
2794: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
2795: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
2796: 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);
2797: /* 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);
2798: */
2799: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
2800: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
2801:
2802: free_vector(xp,1,npar);
2803: free_matrix(doldm,1,nlstate,1,nlstate);
2804: free_matrix(dnewm,1,nlstate,1,npar);
2805: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2806: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2807: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2808: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2809: fclose(ficresprobmorprev);
2810: fflush(ficgp);
2811: fflush(fichtm);
2812: } /* end varevsij */
2813:
2814: /************ Variance of prevlim ******************/
2815: 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[])
2816: {
2817: /* Variance of prevalence limit */
2818: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
2819: double **newm;
2820: double **dnewm,**doldm;
2821: int i, j, nhstepm, hstepm;
2822: int k, cptcode;
2823: double *xp;
2824: double *gp, *gm;
2825: double **gradg, **trgradg;
2826: double age,agelim;
2827: int theta;
2828: fprintf(ficresvpl, "#Local time at start: %s", strstart);
2829: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
2830: fprintf(ficresvpl,"# Age");
2831: for(i=1; i<=nlstate;i++)
2832: fprintf(ficresvpl," %1d-%1d",i,i);
2833: fprintf(ficresvpl,"\n");
2834:
2835: xp=vector(1,npar);
2836: dnewm=matrix(1,nlstate,1,npar);
2837: doldm=matrix(1,nlstate,1,nlstate);
2838:
2839: hstepm=1*YEARM; /* Every year of age */
2840: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2841: agelim = AGESUP;
2842: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2843: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2844: if (stepm >= YEARM) hstepm=1;
2845: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2846: gradg=matrix(1,npar,1,nlstate);
2847: gp=vector(1,nlstate);
2848: gm=vector(1,nlstate);
2849:
2850: for(theta=1; theta <=npar; theta++){
2851: for(i=1; i<=npar; i++){ /* Computes gradient */
2852: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2853: }
2854: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2855: for(i=1;i<=nlstate;i++)
2856: gp[i] = prlim[i][i];
2857:
2858: for(i=1; i<=npar; i++) /* Computes gradient */
2859: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2860: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2861: for(i=1;i<=nlstate;i++)
2862: gm[i] = prlim[i][i];
2863:
2864: for(i=1;i<=nlstate;i++)
2865: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2866: } /* End theta */
2867:
2868: trgradg =matrix(1,nlstate,1,npar);
2869:
2870: for(j=1; j<=nlstate;j++)
2871: for(theta=1; theta <=npar; theta++)
2872: trgradg[j][theta]=gradg[theta][j];
2873:
2874: for(i=1;i<=nlstate;i++)
2875: varpl[i][(int)age] =0.;
2876: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2877: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2878: for(i=1;i<=nlstate;i++)
2879: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2880:
2881: fprintf(ficresvpl,"%.0f ",age );
2882: for(i=1; i<=nlstate;i++)
2883: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2884: fprintf(ficresvpl,"\n");
2885: free_vector(gp,1,nlstate);
2886: free_vector(gm,1,nlstate);
2887: free_matrix(gradg,1,npar,1,nlstate);
2888: free_matrix(trgradg,1,nlstate,1,npar);
2889: } /* End age */
2890:
2891: free_vector(xp,1,npar);
2892: free_matrix(doldm,1,nlstate,1,npar);
2893: free_matrix(dnewm,1,nlstate,1,nlstate);
2894:
2895: }
2896:
2897: /************ Variance of one-step probabilities ******************/
2898: 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[])
2899: {
2900: int i, j=0, i1, k1, l1, t, tj;
2901: int k2, l2, j1, z1;
2902: int k=0,l, cptcode;
2903: int first=1, first1;
2904: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2905: double **dnewm,**doldm;
2906: double *xp;
2907: double *gp, *gm;
2908: double **gradg, **trgradg;
2909: double **mu;
2910: double age,agelim, cov[NCOVMAX];
2911: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2912: int theta;
2913: char fileresprob[FILENAMELENGTH];
2914: char fileresprobcov[FILENAMELENGTH];
2915: char fileresprobcor[FILENAMELENGTH];
2916:
2917: double ***varpij;
2918:
2919: strcpy(fileresprob,"prob");
2920: strcat(fileresprob,fileres);
2921: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2922: printf("Problem with resultfile: %s\n", fileresprob);
2923: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2924: }
2925: strcpy(fileresprobcov,"probcov");
2926: strcat(fileresprobcov,fileres);
2927: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2928: printf("Problem with resultfile: %s\n", fileresprobcov);
2929: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2930: }
2931: strcpy(fileresprobcor,"probcor");
2932: strcat(fileresprobcor,fileres);
2933: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2934: printf("Problem with resultfile: %s\n", fileresprobcor);
2935: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2936: }
2937: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2938: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2939: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2940: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2941: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2942: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2943: fprintf(ficresprob, "#Local time at start: %s", strstart);
2944: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2945: fprintf(ficresprob,"# Age");
2946: fprintf(ficresprobcov, "#Local time at start: %s", strstart);
2947: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2948: fprintf(ficresprobcov,"# Age");
2949: fprintf(ficresprobcor, "#Local time at start: %s", strstart);
2950: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2951: fprintf(ficresprobcov,"# Age");
2952:
2953:
2954: for(i=1; i<=nlstate;i++)
2955: for(j=1; j<=(nlstate+ndeath);j++){
2956: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2957: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2958: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2959: }
2960: /* fprintf(ficresprob,"\n");
2961: fprintf(ficresprobcov,"\n");
2962: fprintf(ficresprobcor,"\n");
2963: */
2964: xp=vector(1,npar);
2965: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2966: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2967: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2968: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2969: first=1;
2970: fprintf(ficgp,"\n# Routine varprob");
2971: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2972: fprintf(fichtm,"\n");
2973:
2974: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
2975: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
2976: file %s<br>\n",optionfilehtmcov);
2977: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
2978: and drawn. It helps understanding how is the covariance between two incidences.\
2979: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
2980: 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. \
2981: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
2982: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
2983: standard deviations wide on each axis. <br>\
2984: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
2985: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
2986: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
2987:
2988: cov[1]=1;
2989: tj=cptcoveff;
2990: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2991: j1=0;
2992: for(t=1; t<=tj;t++){
2993: for(i1=1; i1<=ncodemax[t];i1++){
2994: j1++;
2995: if (cptcovn>0) {
2996: fprintf(ficresprob, "\n#********** Variable ");
2997: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2998: fprintf(ficresprob, "**********\n#\n");
2999: fprintf(ficresprobcov, "\n#********** Variable ");
3000: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3001: fprintf(ficresprobcov, "**********\n#\n");
3002:
3003: fprintf(ficgp, "\n#********** Variable ");
3004: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3005: fprintf(ficgp, "**********\n#\n");
3006:
3007:
3008: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3009: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3010: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3011:
3012: fprintf(ficresprobcor, "\n#********** Variable ");
3013: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3014: fprintf(ficresprobcor, "**********\n#");
3015: }
3016:
3017: for (age=bage; age<=fage; age ++){
3018: cov[2]=age;
3019: for (k=1; k<=cptcovn;k++) {
3020: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3021: }
3022: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3023: for (k=1; k<=cptcovprod;k++)
3024: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3025:
3026: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3027: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3028: gp=vector(1,(nlstate)*(nlstate+ndeath));
3029: gm=vector(1,(nlstate)*(nlstate+ndeath));
3030:
3031: for(theta=1; theta <=npar; theta++){
3032: for(i=1; i<=npar; i++)
3033: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3034:
3035: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3036:
3037: k=0;
3038: for(i=1; i<= (nlstate); i++){
3039: for(j=1; j<=(nlstate+ndeath);j++){
3040: k=k+1;
3041: gp[k]=pmmij[i][j];
3042: }
3043: }
3044:
3045: for(i=1; i<=npar; i++)
3046: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3047:
3048: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3049: k=0;
3050: for(i=1; i<=(nlstate); i++){
3051: for(j=1; j<=(nlstate+ndeath);j++){
3052: k=k+1;
3053: gm[k]=pmmij[i][j];
3054: }
3055: }
3056:
3057: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3058: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3059: }
3060:
3061: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3062: for(theta=1; theta <=npar; theta++)
3063: trgradg[j][theta]=gradg[theta][j];
3064:
3065: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3066: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3067: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3068: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3069: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3070: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3071:
3072: pmij(pmmij,cov,ncovmodel,x,nlstate);
3073:
3074: k=0;
3075: for(i=1; i<=(nlstate); i++){
3076: for(j=1; j<=(nlstate+ndeath);j++){
3077: k=k+1;
3078: mu[k][(int) age]=pmmij[i][j];
3079: }
3080: }
3081: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3082: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3083: varpij[i][j][(int)age] = doldm[i][j];
3084:
3085: /*printf("\n%d ",(int)age);
3086: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3087: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3088: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3089: }*/
3090:
3091: fprintf(ficresprob,"\n%d ",(int)age);
3092: fprintf(ficresprobcov,"\n%d ",(int)age);
3093: fprintf(ficresprobcor,"\n%d ",(int)age);
3094:
3095: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3096: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3097: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3098: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3099: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3100: }
3101: i=0;
3102: for (k=1; k<=(nlstate);k++){
3103: for (l=1; l<=(nlstate+ndeath);l++){
3104: i=i++;
3105: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3106: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3107: for (j=1; j<=i;j++){
3108: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3109: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3110: }
3111: }
3112: }/* end of loop for state */
3113: } /* end of loop for age */
3114:
3115: /* Confidence intervalle of pij */
3116: /*
3117: fprintf(ficgp,"\nset noparametric;unset label");
3118: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3119: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3120: 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);
3121: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3122: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3123: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3124: */
3125:
3126: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3127: first1=1;
3128: for (k2=1; k2<=(nlstate);k2++){
3129: for (l2=1; l2<=(nlstate+ndeath);l2++){
3130: if(l2==k2) continue;
3131: j=(k2-1)*(nlstate+ndeath)+l2;
3132: for (k1=1; k1<=(nlstate);k1++){
3133: for (l1=1; l1<=(nlstate+ndeath);l1++){
3134: if(l1==k1) continue;
3135: i=(k1-1)*(nlstate+ndeath)+l1;
3136: if(i<=j) continue;
3137: for (age=bage; age<=fage; age ++){
3138: if ((int)age %5==0){
3139: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3140: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3141: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3142: mu1=mu[i][(int) age]/stepm*YEARM ;
3143: mu2=mu[j][(int) age]/stepm*YEARM;
3144: c12=cv12/sqrt(v1*v2);
3145: /* Computing eigen value of matrix of covariance */
3146: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3147: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3148: /* Eigen vectors */
3149: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3150: /*v21=sqrt(1.-v11*v11); *//* error */
3151: v21=(lc1-v1)/cv12*v11;
3152: v12=-v21;
3153: v22=v11;
3154: tnalp=v21/v11;
3155: if(first1==1){
3156: first1=0;
3157: 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);
3158: }
3159: 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);
3160: /*printf(fignu*/
3161: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3162: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3163: if(first==1){
3164: first=0;
3165: fprintf(ficgp,"\nset parametric;unset label");
3166: 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);
3167: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3168: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3169: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3170: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3171: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3172: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3173: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3174: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3175: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3176: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3177: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3178: 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",\
3179: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3180: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3181: }else{
3182: first=0;
3183: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3184: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3185: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3186: 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",\
3187: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3188: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3189: }/* if first */
3190: } /* age mod 5 */
3191: } /* end loop age */
3192: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3193: first=1;
3194: } /*l12 */
3195: } /* k12 */
3196: } /*l1 */
3197: }/* k1 */
3198: } /* loop covariates */
3199: }
3200: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3201: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3202: free_vector(xp,1,npar);
3203: fclose(ficresprob);
3204: fclose(ficresprobcov);
3205: fclose(ficresprobcor);
3206: fflush(ficgp);
3207: fflush(fichtmcov);
3208: }
3209:
3210:
3211: /******************* Printing html file ***********/
3212: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3213: int lastpass, int stepm, int weightopt, char model[],\
3214: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3215: int popforecast, int estepm ,\
3216: double jprev1, double mprev1,double anprev1, \
3217: double jprev2, double mprev2,double anprev2){
3218: int jj1, k1, i1, cpt;
3219:
3220: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3221: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3222: </ul>");
3223: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3224: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3225: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3226: fprintf(fichtm,"\
3227: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3228: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3229: fprintf(fichtm,"\
3230: - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3231: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3232: fprintf(fichtm,"\
3233: - Life expectancies by age and initial health status (estepm=%2d months): \
3234: <a href=\"%s\">%s</a> <br>\n</li>",
3235: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3236:
3237: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3238:
3239: m=cptcoveff;
3240: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3241:
3242: jj1=0;
3243: for(k1=1; k1<=m;k1++){
3244: for(i1=1; i1<=ncodemax[k1];i1++){
3245: jj1++;
3246: if (cptcovn > 0) {
3247: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3248: for (cpt=1; cpt<=cptcoveff;cpt++)
3249: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3250: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3251: }
3252: /* Pij */
3253: 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> \
3254: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3255: /* Quasi-incidences */
3256: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3257: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
3258: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3259: /* Stable prevalence in each health state */
3260: for(cpt=1; cpt<nlstate;cpt++){
3261: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
3262: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3263: }
3264: for(cpt=1; cpt<=nlstate;cpt++) {
3265: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
3266: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3267: }
3268: } /* end i1 */
3269: }/* End k1 */
3270: fprintf(fichtm,"</ul>");
3271:
3272:
3273: fprintf(fichtm,"\
3274: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3275: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3276:
3277: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3278: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3279: fprintf(fichtm,"\
3280: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3281: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3282:
3283: fprintf(fichtm,"\
3284: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3285: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3286: fprintf(fichtm,"\
3287: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
3288: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3289: fprintf(fichtm,"\
3290: - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
3291: subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3292: fprintf(fichtm,"\
3293: - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
3294: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3295:
3296: /* if(popforecast==1) fprintf(fichtm,"\n */
3297: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3298: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3299: /* <br>",fileres,fileres,fileres,fileres); */
3300: /* else */
3301: /* 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); */
3302: fflush(fichtm);
3303: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3304:
3305: m=cptcoveff;
3306: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3307:
3308: jj1=0;
3309: for(k1=1; k1<=m;k1++){
3310: for(i1=1; i1<=ncodemax[k1];i1++){
3311: jj1++;
3312: if (cptcovn > 0) {
3313: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3314: for (cpt=1; cpt<=cptcoveff;cpt++)
3315: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3316: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3317: }
3318: for(cpt=1; cpt<=nlstate;cpt++) {
3319: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3320: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
3321: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3322: }
3323: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3324: health expectancies in states (1) and (2): %s%d.png<br>\
3325: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3326: } /* end i1 */
3327: }/* End k1 */
3328: fprintf(fichtm,"</ul>");
3329: fflush(fichtm);
3330: }
3331:
3332: /******************* Gnuplot file **************/
3333: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3334:
3335: char dirfileres[132],optfileres[132];
3336: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3337: int ng;
3338: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3339: /* printf("Problem with file %s",optionfilegnuplot); */
3340: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3341: /* } */
3342:
3343: /*#ifdef windows */
3344: fprintf(ficgp,"cd \"%s\" \n",pathc);
3345: /*#endif */
3346: m=pow(2,cptcoveff);
3347:
3348: strcpy(dirfileres,optionfilefiname);
3349: strcpy(optfileres,"vpl");
3350: /* 1eme*/
3351: for (cpt=1; cpt<= nlstate ; cpt ++) {
3352: for (k1=1; k1<= m ; k1 ++) {
3353: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3354: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3355: fprintf(ficgp,"set xlabel \"Age\" \n\
3356: set ylabel \"Probability\" \n\
3357: set ter png small\n\
3358: set size 0.65,0.65\n\
3359: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3360:
3361: for (i=1; i<= nlstate ; i ++) {
3362: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3363: else fprintf(ficgp," \%%*lf (\%%*lf)");
3364: }
3365: 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);
3366: for (i=1; i<= nlstate ; i ++) {
3367: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3368: else fprintf(ficgp," \%%*lf (\%%*lf)");
3369: }
3370: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3371: for (i=1; i<= nlstate ; i ++) {
3372: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3373: else fprintf(ficgp," \%%*lf (\%%*lf)");
3374: }
3375: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
3376: }
3377: }
3378: /*2 eme*/
3379:
3380: for (k1=1; k1<= m ; k1 ++) {
3381: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
3382: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3383:
3384: for (i=1; i<= nlstate+1 ; i ++) {
3385: k=2*i;
3386: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3387: for (j=1; j<= nlstate+1 ; j ++) {
3388: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3389: else fprintf(ficgp," \%%*lf (\%%*lf)");
3390: }
3391: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3392: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3393: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3394: for (j=1; j<= nlstate+1 ; j ++) {
3395: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3396: else fprintf(ficgp," \%%*lf (\%%*lf)");
3397: }
3398: fprintf(ficgp,"\" t\"\" w l 0,");
3399: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3400: for (j=1; j<= nlstate+1 ; j ++) {
3401: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3402: else fprintf(ficgp," \%%*lf (\%%*lf)");
3403: }
3404: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3405: else fprintf(ficgp,"\" t\"\" w l 0,");
3406: }
3407: }
3408:
3409: /*3eme*/
3410:
3411: for (k1=1; k1<= m ; k1 ++) {
3412: for (cpt=1; cpt<= nlstate ; cpt ++) {
3413: k=2+nlstate*(2*cpt-2);
3414: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3415: fprintf(ficgp,"set ter png small\n\
3416: set size 0.65,0.65\n\
3417: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
3418: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3419: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3420: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3421: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3422: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3423: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3424:
3425: */
3426: for (i=1; i< nlstate ; i ++) {
3427: 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);
3428:
3429: }
3430: }
3431: }
3432:
3433: /* CV preval stable (period) */
3434: for (k1=1; k1<= m ; k1 ++) {
3435: for (cpt=1; cpt<=nlstate ; cpt ++) {
3436: k=3;
3437: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3438: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3439: set ter png small\nset size 0.65,0.65\n\
3440: unset log y\n\
3441: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
3442:
3443: for (i=1; i< nlstate ; i ++)
3444: fprintf(ficgp,"+$%d",k+i+1);
3445: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3446:
3447: l=3+(nlstate+ndeath)*cpt;
3448: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
3449: for (i=1; i< nlstate ; i ++) {
3450: l=3+(nlstate+ndeath)*cpt;
3451: fprintf(ficgp,"+$%d",l+i+1);
3452: }
3453: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3454: }
3455: }
3456:
3457: /* proba elementaires */
3458: for(i=1,jk=1; i <=nlstate; i++){
3459: for(k=1; k <=(nlstate+ndeath); k++){
3460: if (k != i) {
3461: for(j=1; j <=ncovmodel; j++){
3462: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3463: jk++;
3464: fprintf(ficgp,"\n");
3465: }
3466: }
3467: }
3468: }
3469:
3470: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3471: for(jk=1; jk <=m; jk++) {
3472: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
3473: if (ng==2)
3474: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3475: else
3476: fprintf(ficgp,"\nset title \"Probability\"\n");
3477: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3478: i=1;
3479: for(k2=1; k2<=nlstate; k2++) {
3480: k3=i;
3481: for(k=1; k<=(nlstate+ndeath); k++) {
3482: if (k != k2){
3483: if(ng==2)
3484: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3485: else
3486: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3487: ij=1;
3488: for(j=3; j <=ncovmodel; j++) {
3489: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3490: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3491: ij++;
3492: }
3493: else
3494: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3495: }
3496: fprintf(ficgp,")/(1");
3497:
3498: for(k1=1; k1 <=nlstate; k1++){
3499: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3500: ij=1;
3501: for(j=3; j <=ncovmodel; j++){
3502: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3503: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3504: ij++;
3505: }
3506: else
3507: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3508: }
3509: fprintf(ficgp,")");
3510: }
3511: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3512: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3513: i=i+ncovmodel;
3514: }
3515: } /* end k */
3516: } /* end k2 */
3517: } /* end jk */
3518: } /* end ng */
3519: fflush(ficgp);
3520: } /* end gnuplot */
3521:
3522:
3523: /*************** Moving average **************/
3524: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3525:
3526: int i, cpt, cptcod;
3527: int modcovmax =1;
3528: int mobilavrange, mob;
3529: double age;
3530:
3531: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3532: a covariate has 2 modalities */
3533: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3534:
3535: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3536: if(mobilav==1) mobilavrange=5; /* default */
3537: else mobilavrange=mobilav;
3538: for (age=bage; age<=fage; age++)
3539: for (i=1; i<=nlstate;i++)
3540: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3541: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3542: /* We keep the original values on the extreme ages bage, fage and for
3543: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3544: we use a 5 terms etc. until the borders are no more concerned.
3545: */
3546: for (mob=3;mob <=mobilavrange;mob=mob+2){
3547: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3548: for (i=1; i<=nlstate;i++){
3549: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3550: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3551: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3552: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3553: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3554: }
3555: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3556: }
3557: }
3558: }/* end age */
3559: }/* end mob */
3560: }else return -1;
3561: return 0;
3562: }/* End movingaverage */
3563:
3564:
3565: /************** Forecasting ******************/
3566: 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){
3567: /* proj1, year, month, day of starting projection
3568: agemin, agemax range of age
3569: dateprev1 dateprev2 range of dates during which prevalence is computed
3570: anproj2 year of en of projection (same day and month as proj1).
3571: */
3572: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
3573: int *popage;
3574: double agec; /* generic age */
3575: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3576: double *popeffectif,*popcount;
3577: double ***p3mat;
3578: double ***mobaverage;
3579: char fileresf[FILENAMELENGTH];
3580:
3581: agelim=AGESUP;
3582: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3583:
3584: strcpy(fileresf,"f");
3585: strcat(fileresf,fileres);
3586: if((ficresf=fopen(fileresf,"w"))==NULL) {
3587: printf("Problem with forecast resultfile: %s\n", fileresf);
3588: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3589: }
3590: printf("Computing forecasting: result on file '%s' \n", fileresf);
3591: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3592:
3593: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3594:
3595: if (mobilav!=0) {
3596: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3597: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3598: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3599: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3600: }
3601: }
3602:
3603: stepsize=(int) (stepm+YEARM-1)/YEARM;
3604: if (stepm<=12) stepsize=1;
3605: if(estepm < stepm){
3606: printf ("Problem %d lower than %d\n",estepm, stepm);
3607: }
3608: else hstepm=estepm;
3609:
3610: hstepm=hstepm/stepm;
3611: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3612: fractional in yp1 */
3613: anprojmean=yp;
3614: yp2=modf((yp1*12),&yp);
3615: mprojmean=yp;
3616: yp1=modf((yp2*30.5),&yp);
3617: jprojmean=yp;
3618: if(jprojmean==0) jprojmean=1;
3619: if(mprojmean==0) jprojmean=1;
3620:
3621: i1=cptcoveff;
3622: if (cptcovn < 1){i1=1;}
3623:
3624: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
3625:
3626: fprintf(ficresf,"#****** Routine prevforecast **\n");
3627:
3628: /* if (h==(int)(YEARM*yearp)){ */
3629: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
3630: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3631: k=k+1;
3632: fprintf(ficresf,"\n#******");
3633: for(j=1;j<=cptcoveff;j++) {
3634: 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]]);
3635: }
3636: fprintf(ficresf,"******\n");
3637: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3638: for(j=1; j<=nlstate+ndeath;j++){
3639: for(i=1; i<=nlstate;i++)
3640: fprintf(ficresf," p%d%d",i,j);
3641: fprintf(ficresf," p.%d",j);
3642: }
3643: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
3644: fprintf(ficresf,"\n");
3645: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
3646:
3647: for (agec=fage; agec>=(ageminpar-1); agec--){
3648: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
3649: nhstepm = nhstepm/hstepm;
3650: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3651: oldm=oldms;savm=savms;
3652: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
3653:
3654: for (h=0; h<=nhstepm; h++){
3655: if (h*hstepm/YEARM*stepm ==yearp) {
3656: fprintf(ficresf,"\n");
3657: for(j=1;j<=cptcoveff;j++)
3658: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3659: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
3660: }
3661: for(j=1; j<=nlstate+ndeath;j++) {
3662: ppij=0.;
3663: for(i=1; i<=nlstate;i++) {
3664: if (mobilav==1)
3665: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
3666: else {
3667: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
3668: }
3669: if (h*hstepm/YEARM*stepm== yearp) {
3670: fprintf(ficresf," %.3f", p3mat[i][j][h]);
3671: }
3672: } /* end i */
3673: if (h*hstepm/YEARM*stepm==yearp) {
3674: fprintf(ficresf," %.3f", ppij);
3675: }
3676: }/* end j */
3677: } /* end h */
3678: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3679: } /* end agec */
3680: } /* end yearp */
3681: } /* end cptcod */
3682: } /* end cptcov */
3683:
3684: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3685:
3686: fclose(ficresf);
3687: }
3688:
3689: /************** Forecasting *****not tested NB*************/
3690: 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){
3691:
3692: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3693: int *popage;
3694: double calagedatem, agelim, kk1, kk2;
3695: double *popeffectif,*popcount;
3696: double ***p3mat,***tabpop,***tabpopprev;
3697: double ***mobaverage;
3698: char filerespop[FILENAMELENGTH];
3699:
3700: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3701: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3702: agelim=AGESUP;
3703: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
3704:
3705: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3706:
3707:
3708: strcpy(filerespop,"pop");
3709: strcat(filerespop,fileres);
3710: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3711: printf("Problem with forecast resultfile: %s\n", filerespop);
3712: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3713: }
3714: printf("Computing forecasting: result on file '%s' \n", filerespop);
3715: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3716:
3717: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3718:
3719: if (mobilav!=0) {
3720: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3721: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3722: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3723: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3724: }
3725: }
3726:
3727: stepsize=(int) (stepm+YEARM-1)/YEARM;
3728: if (stepm<=12) stepsize=1;
3729:
3730: agelim=AGESUP;
3731:
3732: hstepm=1;
3733: hstepm=hstepm/stepm;
3734:
3735: if (popforecast==1) {
3736: if((ficpop=fopen(popfile,"r"))==NULL) {
3737: printf("Problem with population file : %s\n",popfile);exit(0);
3738: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3739: }
3740: popage=ivector(0,AGESUP);
3741: popeffectif=vector(0,AGESUP);
3742: popcount=vector(0,AGESUP);
3743:
3744: i=1;
3745: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3746:
3747: imx=i;
3748: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3749: }
3750:
3751: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
3752: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3753: k=k+1;
3754: fprintf(ficrespop,"\n#******");
3755: for(j=1;j<=cptcoveff;j++) {
3756: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3757: }
3758: fprintf(ficrespop,"******\n");
3759: fprintf(ficrespop,"# Age");
3760: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3761: if (popforecast==1) fprintf(ficrespop," [Population]");
3762:
3763: for (cpt=0; cpt<=0;cpt++) {
3764: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3765:
3766: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3767: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3768: nhstepm = nhstepm/hstepm;
3769:
3770: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3771: oldm=oldms;savm=savms;
3772: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3773:
3774: for (h=0; h<=nhstepm; h++){
3775: if (h==(int) (calagedatem+YEARM*cpt)) {
3776: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3777: }
3778: for(j=1; j<=nlstate+ndeath;j++) {
3779: kk1=0.;kk2=0;
3780: for(i=1; i<=nlstate;i++) {
3781: if (mobilav==1)
3782: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3783: else {
3784: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3785: }
3786: }
3787: if (h==(int)(calagedatem+12*cpt)){
3788: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3789: /*fprintf(ficrespop," %.3f", kk1);
3790: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3791: }
3792: }
3793: for(i=1; i<=nlstate;i++){
3794: kk1=0.;
3795: for(j=1; j<=nlstate;j++){
3796: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3797: }
3798: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
3799: }
3800:
3801: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
3802: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3803: }
3804: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3805: }
3806: }
3807:
3808: /******/
3809:
3810: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3811: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3812: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3813: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3814: nhstepm = nhstepm/hstepm;
3815:
3816: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3817: oldm=oldms;savm=savms;
3818: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3819: for (h=0; h<=nhstepm; h++){
3820: if (h==(int) (calagedatem+YEARM*cpt)) {
3821: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3822: }
3823: for(j=1; j<=nlstate+ndeath;j++) {
3824: kk1=0.;kk2=0;
3825: for(i=1; i<=nlstate;i++) {
3826: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3827: }
3828: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
3829: }
3830: }
3831: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3832: }
3833: }
3834: }
3835: }
3836:
3837: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3838:
3839: if (popforecast==1) {
3840: free_ivector(popage,0,AGESUP);
3841: free_vector(popeffectif,0,AGESUP);
3842: free_vector(popcount,0,AGESUP);
3843: }
3844: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3845: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3846: fclose(ficrespop);
3847: } /* End of popforecast */
3848:
3849: int fileappend(FILE *fichier, char *optionfich)
3850: {
3851: if((fichier=fopen(optionfich,"a"))==NULL) {
3852: printf("Problem with file: %s\n", optionfich);
3853: fprintf(ficlog,"Problem with file: %s\n", optionfich);
3854: return (0);
3855: }
3856: fflush(fichier);
3857: return (1);
3858: }
3859:
3860:
3861: /**************** function prwizard **********************/
3862: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
3863: {
3864:
3865: /* Wizard to print covariance matrix template */
3866:
3867: char ca[32], cb[32], cc[32];
3868: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
3869: int numlinepar;
3870:
3871: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3872: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3873: for(i=1; i <=nlstate; i++){
3874: jj=0;
3875: for(j=1; j <=nlstate+ndeath; j++){
3876: if(j==i) continue;
3877: jj++;
3878: /*ca[0]= k+'a'-1;ca[1]='\0';*/
3879: printf("%1d%1d",i,j);
3880: fprintf(ficparo,"%1d%1d",i,j);
3881: for(k=1; k<=ncovmodel;k++){
3882: /* printf(" %lf",param[i][j][k]); */
3883: /* fprintf(ficparo," %lf",param[i][j][k]); */
3884: printf(" 0.");
3885: fprintf(ficparo," 0.");
3886: }
3887: printf("\n");
3888: fprintf(ficparo,"\n");
3889: }
3890: }
3891: printf("# Scales (for hessian or gradient estimation)\n");
3892: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
3893: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
3894: for(i=1; i <=nlstate; i++){
3895: jj=0;
3896: for(j=1; j <=nlstate+ndeath; j++){
3897: if(j==i) continue;
3898: jj++;
3899: fprintf(ficparo,"%1d%1d",i,j);
3900: printf("%1d%1d",i,j);
3901: fflush(stdout);
3902: for(k=1; k<=ncovmodel;k++){
3903: /* printf(" %le",delti3[i][j][k]); */
3904: /* fprintf(ficparo," %le",delti3[i][j][k]); */
3905: printf(" 0.");
3906: fprintf(ficparo," 0.");
3907: }
3908: numlinepar++;
3909: printf("\n");
3910: fprintf(ficparo,"\n");
3911: }
3912: }
3913: printf("# Covariance matrix\n");
3914: /* # 121 Var(a12)\n\ */
3915: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3916: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
3917: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
3918: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
3919: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
3920: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
3921: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3922: fflush(stdout);
3923: fprintf(ficparo,"# Covariance matrix\n");
3924: /* # 121 Var(a12)\n\ */
3925: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3926: /* # ...\n\ */
3927: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3928:
3929: for(itimes=1;itimes<=2;itimes++){
3930: jj=0;
3931: for(i=1; i <=nlstate; i++){
3932: for(j=1; j <=nlstate+ndeath; j++){
3933: if(j==i) continue;
3934: for(k=1; k<=ncovmodel;k++){
3935: jj++;
3936: ca[0]= k+'a'-1;ca[1]='\0';
3937: if(itimes==1){
3938: printf("#%1d%1d%d",i,j,k);
3939: fprintf(ficparo,"#%1d%1d%d",i,j,k);
3940: }else{
3941: printf("%1d%1d%d",i,j,k);
3942: fprintf(ficparo,"%1d%1d%d",i,j,k);
3943: /* printf(" %.5le",matcov[i][j]); */
3944: }
3945: ll=0;
3946: for(li=1;li <=nlstate; li++){
3947: for(lj=1;lj <=nlstate+ndeath; lj++){
3948: if(lj==li) continue;
3949: for(lk=1;lk<=ncovmodel;lk++){
3950: ll++;
3951: if(ll<=jj){
3952: cb[0]= lk +'a'-1;cb[1]='\0';
3953: if(ll<jj){
3954: if(itimes==1){
3955: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3956: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3957: }else{
3958: printf(" 0.");
3959: fprintf(ficparo," 0.");
3960: }
3961: }else{
3962: if(itimes==1){
3963: printf(" Var(%s%1d%1d)",ca,i,j);
3964: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
3965: }else{
3966: printf(" 0.");
3967: fprintf(ficparo," 0.");
3968: }
3969: }
3970: }
3971: } /* end lk */
3972: } /* end lj */
3973: } /* end li */
3974: printf("\n");
3975: fprintf(ficparo,"\n");
3976: numlinepar++;
3977: } /* end k*/
3978: } /*end j */
3979: } /* end i */
3980: } /* end itimes */
3981:
3982: } /* end of prwizard */
3983: /******************* Gompertz Likelihood ******************************/
3984: double gompertz(double x[])
3985: {
3986: double A,B,L=0.0,sump=0.,num=0.;
3987: int i,n=0; /* n is the size of the sample */
3988: for (i=0;i<=imx-1 ; i++) {
3989: sump=sump+weight[i];
3990: /* sump=sump+1;*/
3991: num=num+1;
3992: }
3993:
3994:
3995: /* for (i=0; i<=imx; i++)
3996: 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]);*/
3997:
3998: for (i=1;i<=imx ; i++)
3999: {
4000: if (cens[i]==1 & wav[i]>1)
4001: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4002:
4003: if (cens[i]==0 & wav[i]>1)
4004: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4005: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4006:
4007: if (wav[i]>1 & agecens[i]>15) {
4008: L=L+A*weight[i];
4009: /* 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]);*/
4010: }
4011: }
4012:
4013: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4014:
4015: return -2*L*num/sump;
4016: }
4017:
4018: /******************* Printing html file ***********/
4019: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4020: int lastpass, int stepm, int weightopt, char model[],\
4021: int imx, double p[],double **matcov,double agemortsup){
4022: int i,k;
4023:
4024: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4025: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4026: for (i=1;i<=2;i++)
4027: 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]));
4028: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4029: fprintf(fichtm,"</ul>");
4030:
4031: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4032:
4033: 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>");
4034:
4035: for (k=agegomp;k<(agemortsup-2);k++)
4036: 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]);
4037:
4038:
4039: fflush(fichtm);
4040: }
4041:
4042: /******************* Gnuplot file **************/
4043: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4044:
4045: char dirfileres[132],optfileres[132];
4046: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4047: int ng;
4048:
4049:
4050: /*#ifdef windows */
4051: fprintf(ficgp,"cd \"%s\" \n",pathc);
4052: /*#endif */
4053:
4054:
4055: strcpy(dirfileres,optionfilefiname);
4056: strcpy(optfileres,"vpl");
4057: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4058: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4059: fprintf(ficgp, "set ter png small\n set log y\n");
4060: fprintf(ficgp, "set size 0.65,0.65\n");
4061: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4062:
4063: }
4064:
4065:
4066:
4067:
4068: /***********************************************/
4069: /**************** Main Program *****************/
4070: /***********************************************/
4071:
4072: int main(int argc, char *argv[])
4073: {
4074: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
4075: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
4076: int jj, ll, li, lj, lk, imk;
4077: int numlinepar=0; /* Current linenumber of parameter file */
4078: int itimes;
4079: int NDIM=2;
4080:
4081: char ca[32], cb[32], cc[32];
4082: /* FILE *fichtm; *//* Html File */
4083: /* FILE *ficgp;*/ /*Gnuplot File */
4084: struct stat info;
4085: double agedeb, agefin,hf;
4086: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
4087:
4088: double fret;
4089: double **xi,tmp,delta;
4090:
4091: double dum; /* Dummy variable */
4092: double ***p3mat;
4093: double ***mobaverage;
4094: int *indx;
4095: char line[MAXLINE], linepar[MAXLINE];
4096: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
4097: char pathr[MAXLINE], pathimach[MAXLINE];
4098: int firstobs=1, lastobs=10;
4099: int sdeb, sfin; /* Status at beginning and end */
4100: int c, h , cpt,l;
4101: int ju,jl, mi;
4102: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
4103: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
4104: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
4105: int mobilav=0,popforecast=0;
4106: int hstepm, nhstepm;
4107: int agemortsup;
4108: float sumlpop=0.;
4109: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
4110: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
4111:
4112: double bage, fage, age, agelim, agebase;
4113: double ftolpl=FTOL;
4114: double **prlim;
4115: double *severity;
4116: double ***param; /* Matrix of parameters */
4117: double *p;
4118: double **matcov; /* Matrix of covariance */
4119: double ***delti3; /* Scale */
4120: double *delti; /* Scale */
4121: double ***eij, ***vareij;
4122: double **varpl; /* Variances of prevalence limits by age */
4123: double *epj, vepp;
4124: double kk1, kk2;
4125: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
4126: double **ximort;
4127: char *alph[]={"a","a","b","c","d","e"}, str[4];
4128: int *dcwave;
4129:
4130: char z[1]="c", occ;
4131:
4132: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
4133: char strstart[80], *strt, strtend[80];
4134: char *stratrunc;
4135: int lstra;
4136:
4137: long total_usecs;
4138:
4139: /* setlocale (LC_ALL, ""); */
4140: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4141: /* textdomain (PACKAGE); */
4142: /* setlocale (LC_CTYPE, ""); */
4143: /* setlocale (LC_MESSAGES, ""); */
4144:
4145: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4146: (void) gettimeofday(&start_time,&tzp);
4147: curr_time=start_time;
4148: tm = *localtime(&start_time.tv_sec);
4149: tmg = *gmtime(&start_time.tv_sec);
4150: strcpy(strstart,asctime(&tm));
4151:
4152: /* printf("Localtime (at start)=%s",strstart); */
4153: /* tp.tv_sec = tp.tv_sec +86400; */
4154: /* tm = *localtime(&start_time.tv_sec); */
4155: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4156: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4157: /* tmg.tm_hour=tmg.tm_hour + 1; */
4158: /* tp.tv_sec = mktime(&tmg); */
4159: /* strt=asctime(&tmg); */
4160: /* printf("Time(after) =%s",strstart); */
4161: /* (void) time (&time_value);
4162: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4163: * tm = *localtime(&time_value);
4164: * strstart=asctime(&tm);
4165: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
4166: */
4167:
4168: nberr=0; /* Number of errors and warnings */
4169: nbwarn=0;
4170: getcwd(pathcd, size);
4171:
4172: printf("\n%s\n%s",version,fullversion);
4173: if(argc <=1){
4174: printf("\nEnter the parameter file name: ");
4175: scanf("%s",pathtot);
4176: }
4177: else{
4178: strcpy(pathtot,argv[1]);
4179: }
4180: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
4181: /*cygwin_split_path(pathtot,path,optionfile);
4182: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
4183: /* cutv(path,optionfile,pathtot,'\\');*/
4184:
4185: /* Split argv[0], imach program to get pathimach */
4186: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
4187: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4188: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4189: /* strcpy(pathimach,argv[0]); */
4190: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
4191: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
4192: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
4193: chdir(path);
4194: strcpy(command,"mkdir ");
4195: strcat(command,optionfilefiname);
4196: if((outcmd=system(command)) != 0){
4197: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
4198: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
4199: /* fclose(ficlog); */
4200: /* exit(1); */
4201: }
4202: /* if((imk=mkdir(optionfilefiname))<0){ */
4203: /* perror("mkdir"); */
4204: /* } */
4205:
4206: /*-------- arguments in the command line --------*/
4207:
4208: /* Log file */
4209: strcat(filelog, optionfilefiname);
4210: strcat(filelog,".log"); /* */
4211: if((ficlog=fopen(filelog,"w"))==NULL) {
4212: printf("Problem with logfile %s\n",filelog);
4213: goto end;
4214: }
4215: fprintf(ficlog,"Log filename:%s\n",filelog);
4216: fprintf(ficlog,"\n%s\n%s",version,fullversion);
4217: fprintf(ficlog,"\nEnter the parameter file name: \n");
4218: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
4219: path=%s \n\
4220: optionfile=%s\n\
4221: optionfilext=%s\n\
4222: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
4223:
4224: printf("Local time (at start):%s",strstart);
4225: fprintf(ficlog,"Local time (at start): %s",strstart);
4226: fflush(ficlog);
4227: /* (void) gettimeofday(&curr_time,&tzp); */
4228: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
4229:
4230: /* */
4231: strcpy(fileres,"r");
4232: strcat(fileres, optionfilefiname);
4233: strcat(fileres,".txt"); /* Other files have txt extension */
4234:
4235: /*---------arguments file --------*/
4236:
4237: if((ficpar=fopen(optionfile,"r"))==NULL) {
4238: printf("Problem with optionfile %s\n",optionfile);
4239: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
4240: fflush(ficlog);
4241: goto end;
4242: }
4243:
4244:
4245:
4246: strcpy(filereso,"o");
4247: strcat(filereso,fileres);
4248: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
4249: printf("Problem with Output resultfile: %s\n", filereso);
4250: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
4251: fflush(ficlog);
4252: goto end;
4253: }
4254:
4255: /* Reads comments: lines beginning with '#' */
4256: numlinepar=0;
4257: while((c=getc(ficpar))=='#' && c!= EOF){
4258: ungetc(c,ficpar);
4259: fgets(line, MAXLINE, ficpar);
4260: numlinepar++;
4261: puts(line);
4262: fputs(line,ficparo);
4263: fputs(line,ficlog);
4264: }
4265: ungetc(c,ficpar);
4266:
4267: 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);
4268: numlinepar++;
4269: 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);
4270: 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);
4271: 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);
4272: fflush(ficlog);
4273: while((c=getc(ficpar))=='#' && c!= EOF){
4274: ungetc(c,ficpar);
4275: fgets(line, MAXLINE, ficpar);
4276: numlinepar++;
4277: puts(line);
4278: fputs(line,ficparo);
4279: fputs(line,ficlog);
4280: }
4281: ungetc(c,ficpar);
4282:
4283:
4284: covar=matrix(0,NCOVMAX,1,n);
4285: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
4286: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4287:
4288: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
4289: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
4290: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4291:
4292: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4293: delti=delti3[1][1];
4294: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
4295: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4296: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4297: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4298: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4299: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4300: fclose (ficparo);
4301: fclose (ficlog);
4302: exit(0);
4303: }
4304: else if(mle==-3) {
4305: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4306: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4307: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4308: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4309: matcov=matrix(1,npar,1,npar);
4310: }
4311: else{
4312: /* Read guess parameters */
4313: /* Reads comments: lines beginning with '#' */
4314: while((c=getc(ficpar))=='#' && c!= EOF){
4315: ungetc(c,ficpar);
4316: fgets(line, MAXLINE, ficpar);
4317: numlinepar++;
4318: puts(line);
4319: fputs(line,ficparo);
4320: fputs(line,ficlog);
4321: }
4322: ungetc(c,ficpar);
4323:
4324: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4325: for(i=1; i <=nlstate; i++){
4326: j=0;
4327: for(jj=1; jj <=nlstate+ndeath; jj++){
4328: if(jj==i) continue;
4329: j++;
4330: fscanf(ficpar,"%1d%1d",&i1,&j1);
4331: if ((i1 != i) && (j1 != j)){
4332: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4333: exit(1);
4334: }
4335: fprintf(ficparo,"%1d%1d",i1,j1);
4336: if(mle==1)
4337: printf("%1d%1d",i,j);
4338: fprintf(ficlog,"%1d%1d",i,j);
4339: for(k=1; k<=ncovmodel;k++){
4340: fscanf(ficpar," %lf",¶m[i][j][k]);
4341: if(mle==1){
4342: printf(" %lf",param[i][j][k]);
4343: fprintf(ficlog," %lf",param[i][j][k]);
4344: }
4345: else
4346: fprintf(ficlog," %lf",param[i][j][k]);
4347: fprintf(ficparo," %lf",param[i][j][k]);
4348: }
4349: fscanf(ficpar,"\n");
4350: numlinepar++;
4351: if(mle==1)
4352: printf("\n");
4353: fprintf(ficlog,"\n");
4354: fprintf(ficparo,"\n");
4355: }
4356: }
4357: fflush(ficlog);
4358:
4359:
4360: p=param[1][1];
4361:
4362: /* Reads comments: lines beginning with '#' */
4363: while((c=getc(ficpar))=='#' && c!= EOF){
4364: ungetc(c,ficpar);
4365: fgets(line, MAXLINE, ficpar);
4366: numlinepar++;
4367: puts(line);
4368: fputs(line,ficparo);
4369: fputs(line,ficlog);
4370: }
4371: ungetc(c,ficpar);
4372:
4373: for(i=1; i <=nlstate; i++){
4374: for(j=1; j <=nlstate+ndeath-1; j++){
4375: fscanf(ficpar,"%1d%1d",&i1,&j1);
4376: if ((i1-i)*(j1-j)!=0){
4377: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4378: exit(1);
4379: }
4380: printf("%1d%1d",i,j);
4381: fprintf(ficparo,"%1d%1d",i1,j1);
4382: fprintf(ficlog,"%1d%1d",i1,j1);
4383: for(k=1; k<=ncovmodel;k++){
4384: fscanf(ficpar,"%le",&delti3[i][j][k]);
4385: printf(" %le",delti3[i][j][k]);
4386: fprintf(ficparo," %le",delti3[i][j][k]);
4387: fprintf(ficlog," %le",delti3[i][j][k]);
4388: }
4389: fscanf(ficpar,"\n");
4390: numlinepar++;
4391: printf("\n");
4392: fprintf(ficparo,"\n");
4393: fprintf(ficlog,"\n");
4394: }
4395: }
4396: fflush(ficlog);
4397:
4398: delti=delti3[1][1];
4399:
4400:
4401: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
4402:
4403: /* Reads comments: lines beginning with '#' */
4404: while((c=getc(ficpar))=='#' && c!= EOF){
4405: ungetc(c,ficpar);
4406: fgets(line, MAXLINE, ficpar);
4407: numlinepar++;
4408: puts(line);
4409: fputs(line,ficparo);
4410: fputs(line,ficlog);
4411: }
4412: ungetc(c,ficpar);
4413:
4414: matcov=matrix(1,npar,1,npar);
4415: for(i=1; i <=npar; i++){
4416: fscanf(ficpar,"%s",&str);
4417: if(mle==1)
4418: printf("%s",str);
4419: fprintf(ficlog,"%s",str);
4420: fprintf(ficparo,"%s",str);
4421: for(j=1; j <=i; j++){
4422: fscanf(ficpar," %le",&matcov[i][j]);
4423: if(mle==1){
4424: printf(" %.5le",matcov[i][j]);
4425: }
4426: fprintf(ficlog," %.5le",matcov[i][j]);
4427: fprintf(ficparo," %.5le",matcov[i][j]);
4428: }
4429: fscanf(ficpar,"\n");
4430: numlinepar++;
4431: if(mle==1)
4432: printf("\n");
4433: fprintf(ficlog,"\n");
4434: fprintf(ficparo,"\n");
4435: }
4436: for(i=1; i <=npar; i++)
4437: for(j=i+1;j<=npar;j++)
4438: matcov[i][j]=matcov[j][i];
4439:
4440: if(mle==1)
4441: printf("\n");
4442: fprintf(ficlog,"\n");
4443:
4444: fflush(ficlog);
4445:
4446: /*-------- Rewriting parameter file ----------*/
4447: strcpy(rfileres,"r"); /* "Rparameterfile */
4448: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4449: strcat(rfileres,"."); /* */
4450: strcat(rfileres,optionfilext); /* Other files have txt extension */
4451: if((ficres =fopen(rfileres,"w"))==NULL) {
4452: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4453: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4454: }
4455: fprintf(ficres,"#%s\n",version);
4456: } /* End of mle != -3 */
4457:
4458: /*-------- data file ----------*/
4459: if((fic=fopen(datafile,"r"))==NULL) {
4460: printf("Problem with datafile: %s\n", datafile);goto end;
4461: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
4462: }
4463:
4464: n= lastobs;
4465: severity = vector(1,maxwav);
4466: outcome=imatrix(1,maxwav+1,1,n);
4467: num=lvector(1,n);
4468: moisnais=vector(1,n);
4469: annais=vector(1,n);
4470: moisdc=vector(1,n);
4471: andc=vector(1,n);
4472: agedc=vector(1,n);
4473: cod=ivector(1,n);
4474: weight=vector(1,n);
4475: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4476: mint=matrix(1,maxwav,1,n);
4477: anint=matrix(1,maxwav,1,n);
4478: s=imatrix(1,maxwav+1,1,n);
4479: tab=ivector(1,NCOVMAX);
4480: ncodemax=ivector(1,8);
4481:
4482: i=1;
4483: while (fgets(line, MAXLINE, fic) != NULL) {
4484: if ((i >= firstobs) && (i <=lastobs)) {
4485: for(j=0; line[j] != '\n';j++){ /* Untabifies line */
4486: if(line[j] == '\t')
4487: line[j] = ' ';
4488: }
4489: for (j=maxwav;j>=1;j--){
4490: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
4491: strcpy(line,stra);
4492: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4493: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4494: }
4495:
4496: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
4497: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
4498:
4499: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
4500: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
4501:
4502: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
4503: for (j=ncovcol;j>=1;j--){
4504: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4505: }
4506: lstra=strlen(stra);
4507: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4508: stratrunc = &(stra[lstra-9]);
4509: num[i]=atol(stratrunc);
4510: }
4511: else
4512: num[i]=atol(stra);
4513:
4514: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4515: 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;}*/
4516:
4517: i=i+1;
4518: }
4519: }
4520: /* printf("ii=%d", ij);
4521: scanf("%d",i);*/
4522: imx=i-1; /* Number of individuals */
4523:
4524: /* for (i=1; i<=imx; i++){
4525: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4526: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4527: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4528: }*/
4529: /* for (i=1; i<=imx; i++){
4530: if (s[4][i]==9) s[4][i]=-1;
4531: 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]));}*/
4532:
4533: /* for (i=1; i<=imx; i++) */
4534:
4535: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4536: else weight[i]=1;*/
4537:
4538: /* Calculation of the number of parameters from char model */
4539: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4540: Tprod=ivector(1,15);
4541: Tvaraff=ivector(1,15);
4542: Tvard=imatrix(1,15,1,2);
4543: Tage=ivector(1,15);
4544:
4545: if (strlen(model) >1){ /* If there is at least 1 covariate */
4546: j=0, j1=0, k1=1, k2=1;
4547: j=nbocc(model,'+'); /* j=Number of '+' */
4548: j1=nbocc(model,'*'); /* j1=Number of '*' */
4549: cptcovn=j+1;
4550: cptcovprod=j1; /*Number of products */
4551:
4552: strcpy(modelsav,model);
4553: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4554: printf("Error. Non available option model=%s ",model);
4555: fprintf(ficlog,"Error. Non available option model=%s ",model);
4556: goto end;
4557: }
4558:
4559: /* This loop fills the array Tvar from the string 'model'.*/
4560:
4561: for(i=(j+1); i>=1;i--){
4562: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
4563: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
4564: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4565: /*scanf("%d",i);*/
4566: if (strchr(strb,'*')) { /* Model includes a product */
4567: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4568: if (strcmp(strc,"age")==0) { /* Vn*age */
4569: cptcovprod--;
4570: cutv(strb,stre,strd,'V');
4571: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4572: cptcovage++;
4573: Tage[cptcovage]=i;
4574: /*printf("stre=%s ", stre);*/
4575: }
4576: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4577: cptcovprod--;
4578: cutv(strb,stre,strc,'V');
4579: Tvar[i]=atoi(stre);
4580: cptcovage++;
4581: Tage[cptcovage]=i;
4582: }
4583: else { /* Age is not in the model */
4584: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4585: Tvar[i]=ncovcol+k1;
4586: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4587: Tprod[k1]=i;
4588: Tvard[k1][1]=atoi(strc); /* m*/
4589: Tvard[k1][2]=atoi(stre); /* n */
4590: Tvar[cptcovn+k2]=Tvard[k1][1];
4591: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4592: for (k=1; k<=lastobs;k++)
4593: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4594: k1++;
4595: k2=k2+2;
4596: }
4597: }
4598: else { /* no more sum */
4599: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4600: /* scanf("%d",i);*/
4601: cutv(strd,strc,strb,'V');
4602: Tvar[i]=atoi(strc);
4603: }
4604: strcpy(modelsav,stra);
4605: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4606: scanf("%d",i);*/
4607: } /* end of loop + */
4608: } /* end model */
4609:
4610: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4611: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4612:
4613: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4614: printf("cptcovprod=%d ", cptcovprod);
4615: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
4616:
4617: scanf("%d ",i);
4618: fclose(fic);*/
4619:
4620: /* if(mle==1){*/
4621: if (weightopt != 1) { /* Maximisation without weights*/
4622: for(i=1;i<=n;i++) weight[i]=1.0;
4623: }
4624: /*-calculation of age at interview from date of interview and age at death -*/
4625: agev=matrix(1,maxwav,1,imx);
4626:
4627: for (i=1; i<=imx; i++) {
4628: for(m=2; (m<= maxwav); m++) {
4629: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
4630: anint[m][i]=9999;
4631: s[m][i]=-1;
4632: }
4633: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
4634: nberr++;
4635: 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);
4636: 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);
4637: s[m][i]=-1;
4638: }
4639: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
4640: nberr++;
4641: 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]);
4642: 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]);
4643: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
4644: }
4645: }
4646: }
4647:
4648: for (i=1; i<=imx; i++) {
4649: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
4650: for(m=firstpass; (m<= lastpass); m++){
4651: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
4652: if (s[m][i] >= nlstate+1) {
4653: if(agedc[i]>0)
4654: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
4655: agev[m][i]=agedc[i];
4656: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4657: else {
4658: if ((int)andc[i]!=9999){
4659: nbwarn++;
4660: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4661: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
4662: agev[m][i]=-1;
4663: }
4664: }
4665: }
4666: else if(s[m][i] !=9){ /* Standard case, age in fractional
4667: years but with the precision of a
4668: month */
4669: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
4670: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
4671: agev[m][i]=1;
4672: else if(agev[m][i] <agemin){
4673: agemin=agev[m][i];
4674: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
4675: }
4676: else if(agev[m][i] >agemax){
4677: agemax=agev[m][i];
4678: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
4679: }
4680: /*agev[m][i]=anint[m][i]-annais[i];*/
4681: /* agev[m][i] = age[i]+2*m;*/
4682: }
4683: else { /* =9 */
4684: agev[m][i]=1;
4685: s[m][i]=-1;
4686: }
4687: }
4688: else /*= 0 Unknown */
4689: agev[m][i]=1;
4690: }
4691:
4692: }
4693: for (i=1; i<=imx; i++) {
4694: for(m=firstpass; (m<=lastpass); m++){
4695: if (s[m][i] > (nlstate+ndeath)) {
4696: nberr++;
4697: 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);
4698: 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);
4699: goto end;
4700: }
4701: }
4702: }
4703:
4704: /*for (i=1; i<=imx; i++){
4705: for (m=firstpass; (m<lastpass); m++){
4706: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
4707: }
4708:
4709: }*/
4710:
4711:
4712: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4713: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4714:
4715: agegomp=(int)agemin;
4716: free_vector(severity,1,maxwav);
4717: free_imatrix(outcome,1,maxwav+1,1,n);
4718: free_vector(moisnais,1,n);
4719: free_vector(annais,1,n);
4720: /* free_matrix(mint,1,maxwav,1,n);
4721: free_matrix(anint,1,maxwav,1,n);*/
4722: free_vector(moisdc,1,n);
4723: free_vector(andc,1,n);
4724:
4725:
4726: wav=ivector(1,imx);
4727: dh=imatrix(1,lastpass-firstpass+1,1,imx);
4728: bh=imatrix(1,lastpass-firstpass+1,1,imx);
4729: mw=imatrix(1,lastpass-firstpass+1,1,imx);
4730:
4731: /* Concatenates waves */
4732: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
4733:
4734: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
4735:
4736: Tcode=ivector(1,100);
4737: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
4738: ncodemax[1]=1;
4739: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
4740:
4741: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
4742: the estimations*/
4743: h=0;
4744: m=pow(2,cptcoveff);
4745:
4746: for(k=1;k<=cptcoveff; k++){
4747: for(i=1; i <=(m/pow(2,k));i++){
4748: for(j=1; j <= ncodemax[k]; j++){
4749: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
4750: h++;
4751: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
4752: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
4753: }
4754: }
4755: }
4756: }
4757: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
4758: codtab[1][2]=1;codtab[2][2]=2; */
4759: /* for(i=1; i <=m ;i++){
4760: for(k=1; k <=cptcovn; k++){
4761: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
4762: }
4763: printf("\n");
4764: }
4765: scanf("%d",i);*/
4766:
4767: /*------------ gnuplot -------------*/
4768: strcpy(optionfilegnuplot,optionfilefiname);
4769: if(mle==-3)
4770: strcat(optionfilegnuplot,"-mort");
4771: strcat(optionfilegnuplot,".gp");
4772:
4773: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4774: printf("Problem with file %s",optionfilegnuplot);
4775: }
4776: else{
4777: fprintf(ficgp,"\n# %s\n", version);
4778: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4779: fprintf(ficgp,"set missing 'NaNq'\n");
4780: }
4781: /* fclose(ficgp);*/
4782: /*--------- index.htm --------*/
4783:
4784: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
4785: if(mle==-3)
4786: strcat(optionfilehtm,"-mort");
4787: strcat(optionfilehtm,".htm");
4788: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4789: printf("Problem with %s \n",optionfilehtm), exit(0);
4790: }
4791:
4792: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
4793: strcat(optionfilehtmcov,"-cov.htm");
4794: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
4795: printf("Problem with %s \n",optionfilehtmcov), exit(0);
4796: }
4797: else{
4798: fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
4799: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4800: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
4801: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4802: }
4803:
4804: fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
4805: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4806: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
4807: \n\
4808: <hr size=\"2\" color=\"#EC5E5E\">\
4809: <ul><li><h4>Parameter files</h4>\n\
4810: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
4811: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
4812: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
4813: - Date and time at start: %s</ul>\n",\
4814: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
4815: fileres,fileres,\
4816: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
4817: fflush(fichtm);
4818:
4819: strcpy(pathr,path);
4820: strcat(pathr,optionfilefiname);
4821: chdir(optionfilefiname); /* Move to directory named optionfile */
4822:
4823: /* Calculates basic frequencies. Computes observed prevalence at single age
4824: and prints on file fileres'p'. */
4825: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
4826:
4827: fprintf(fichtm,"\n");
4828: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
4829: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
4830: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
4831: imx,agemin,agemax,jmin,jmax,jmean);
4832: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4833: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4834: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4835: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4836: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
4837:
4838:
4839: /* For Powell, parameters are in a vector p[] starting at p[1]
4840: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
4841: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
4842:
4843: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
4844: if (mle==-3){
4845: ximort=matrix(1,NDIM,1,NDIM);
4846: cens=ivector(1,n);
4847: ageexmed=vector(1,n);
4848: agecens=vector(1,n);
4849: dcwave=ivector(1,n);
4850:
4851: for (i=1; i<=imx; i++){
4852: dcwave[i]=-1;
4853: for (j=1; j<=lastpass; j++)
4854: if (s[j][i]>nlstate) {
4855: dcwave[i]=j;
4856: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
4857: break;
4858: }
4859: }
4860:
4861: for (i=1; i<=imx; i++) {
4862: if (wav[i]>0){
4863: ageexmed[i]=agev[mw[1][i]][i];
4864: j=wav[i];agecens[i]=1.;
4865: if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
4866: cens[i]=1;
4867:
4868: if (ageexmed[i]<1) cens[i]=-1;
4869: if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
4870: }
4871: else cens[i]=-1;
4872: }
4873:
4874: for (i=1;i<=NDIM;i++) {
4875: for (j=1;j<=NDIM;j++)
4876: ximort[i][j]=(i == j ? 1.0 : 0.0);
4877: }
4878:
4879: p[1]=0.1; p[2]=0.1;
4880: /*printf("%lf %lf", p[1], p[2]);*/
4881:
4882:
4883: printf("Powell\n"); fprintf(ficlog,"Powell\n");
4884: strcpy(filerespow,"pow-mort");
4885: strcat(filerespow,fileres);
4886: if((ficrespow=fopen(filerespow,"w"))==NULL) {
4887: printf("Problem with resultfile: %s\n", filerespow);
4888: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
4889: }
4890: fprintf(ficrespow,"# Powell\n# iter -2*LL");
4891: /* for (i=1;i<=nlstate;i++)
4892: for(j=1;j<=nlstate+ndeath;j++)
4893: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
4894: */
4895: fprintf(ficrespow,"\n");
4896:
4897: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
4898: fclose(ficrespow);
4899:
4900: hesscov(matcov, p, NDIM,delti, 1e-4, gompertz);
4901:
4902: for(i=1; i <=NDIM; i++)
4903: for(j=i+1;j<=NDIM;j++)
4904: matcov[i][j]=matcov[j][i];
4905:
4906: printf("\nCovariance matrix\n ");
4907: for(i=1; i <=NDIM; i++) {
4908: for(j=1;j<=NDIM;j++){
4909: printf("%f ",matcov[i][j]);
4910: }
4911: printf("\n ");
4912: }
4913:
4914: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
4915: for (i=1;i<=NDIM;i++)
4916: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
4917:
4918: lsurv=vector(1,AGESUP);
4919: lpop=vector(1,AGESUP);
4920: tpop=vector(1,AGESUP);
4921: lsurv[agegomp]=100000;
4922:
4923: for (k=agegomp;k<=AGESUP;k++) {
4924: agemortsup=k;
4925: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
4926: }
4927:
4928: for (k=agegomp;k<agemortsup;k++)
4929: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
4930:
4931: for (k=agegomp;k<agemortsup;k++){
4932: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
4933: sumlpop=sumlpop+lpop[k];
4934: }
4935:
4936: tpop[agegomp]=sumlpop;
4937: for (k=agegomp;k<(agemortsup-3);k++){
4938: /* tpop[k+1]=2;*/
4939: tpop[k+1]=tpop[k]-lpop[k];
4940: }
4941:
4942:
4943: printf("\nAge lx qx dx Lx Tx e(x)\n");
4944: for (k=agegomp;k<(agemortsup-2);k++)
4945: 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]);
4946:
4947:
4948: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
4949: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
4950:
4951: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
4952: stepm, weightopt,\
4953: model,imx,p,matcov,agemortsup);
4954:
4955: free_vector(lsurv,1,AGESUP);
4956: free_vector(lpop,1,AGESUP);
4957: free_vector(tpop,1,AGESUP);
4958: } /* Endof if mle==-3 */
4959:
4960: else{ /* For mle >=1 */
4961:
4962: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4963: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4964: for (k=1; k<=npar;k++)
4965: printf(" %d %8.5f",k,p[k]);
4966: printf("\n");
4967: globpr=1; /* to print the contributions */
4968: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4969: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4970: for (k=1; k<=npar;k++)
4971: printf(" %d %8.5f",k,p[k]);
4972: printf("\n");
4973: if(mle>=1){ /* Could be 1 or 2 */
4974: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
4975: }
4976:
4977: /*--------- results files --------------*/
4978: 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);
4979:
4980:
4981: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4982: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4983: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4984: for(i=1,jk=1; i <=nlstate; i++){
4985: for(k=1; k <=(nlstate+ndeath); k++){
4986: if (k != i) {
4987: printf("%d%d ",i,k);
4988: fprintf(ficlog,"%d%d ",i,k);
4989: fprintf(ficres,"%1d%1d ",i,k);
4990: for(j=1; j <=ncovmodel; j++){
4991: printf("%f ",p[jk]);
4992: fprintf(ficlog,"%f ",p[jk]);
4993: fprintf(ficres,"%f ",p[jk]);
4994: jk++;
4995: }
4996: printf("\n");
4997: fprintf(ficlog,"\n");
4998: fprintf(ficres,"\n");
4999: }
5000: }
5001: }
5002: if(mle!=0){
5003: /* Computing hessian and covariance matrix */
5004: ftolhess=ftol; /* Usually correct */
5005: hesscov(matcov, p, npar, delti, ftolhess, func);
5006: }
5007: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
5008: printf("# Scales (for hessian or gradient estimation)\n");
5009: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
5010: for(i=1,jk=1; i <=nlstate; i++){
5011: for(j=1; j <=nlstate+ndeath; j++){
5012: if (j!=i) {
5013: fprintf(ficres,"%1d%1d",i,j);
5014: printf("%1d%1d",i,j);
5015: fprintf(ficlog,"%1d%1d",i,j);
5016: for(k=1; k<=ncovmodel;k++){
5017: printf(" %.5e",delti[jk]);
5018: fprintf(ficlog," %.5e",delti[jk]);
5019: fprintf(ficres," %.5e",delti[jk]);
5020: jk++;
5021: }
5022: printf("\n");
5023: fprintf(ficlog,"\n");
5024: fprintf(ficres,"\n");
5025: }
5026: }
5027: }
5028:
5029: 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");
5030: if(mle>=1)
5031: 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");
5032: 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");
5033: /* # 121 Var(a12)\n\ */
5034: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5035: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5036: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5037: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5038: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5039: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5040: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5041:
5042:
5043: /* Just to have a covariance matrix which will be more understandable
5044: even is we still don't want to manage dictionary of variables
5045: */
5046: for(itimes=1;itimes<=2;itimes++){
5047: jj=0;
5048: for(i=1; i <=nlstate; i++){
5049: for(j=1; j <=nlstate+ndeath; j++){
5050: if(j==i) continue;
5051: for(k=1; k<=ncovmodel;k++){
5052: jj++;
5053: ca[0]= k+'a'-1;ca[1]='\0';
5054: if(itimes==1){
5055: if(mle>=1)
5056: printf("#%1d%1d%d",i,j,k);
5057: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5058: fprintf(ficres,"#%1d%1d%d",i,j,k);
5059: }else{
5060: if(mle>=1)
5061: printf("%1d%1d%d",i,j,k);
5062: fprintf(ficlog,"%1d%1d%d",i,j,k);
5063: fprintf(ficres,"%1d%1d%d",i,j,k);
5064: }
5065: ll=0;
5066: for(li=1;li <=nlstate; li++){
5067: for(lj=1;lj <=nlstate+ndeath; lj++){
5068: if(lj==li) continue;
5069: for(lk=1;lk<=ncovmodel;lk++){
5070: ll++;
5071: if(ll<=jj){
5072: cb[0]= lk +'a'-1;cb[1]='\0';
5073: if(ll<jj){
5074: if(itimes==1){
5075: if(mle>=1)
5076: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5077: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5078: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5079: }else{
5080: if(mle>=1)
5081: printf(" %.5e",matcov[jj][ll]);
5082: fprintf(ficlog," %.5e",matcov[jj][ll]);
5083: fprintf(ficres," %.5e",matcov[jj][ll]);
5084: }
5085: }else{
5086: if(itimes==1){
5087: if(mle>=1)
5088: printf(" Var(%s%1d%1d)",ca,i,j);
5089: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5090: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5091: }else{
5092: if(mle>=1)
5093: printf(" %.5e",matcov[jj][ll]);
5094: fprintf(ficlog," %.5e",matcov[jj][ll]);
5095: fprintf(ficres," %.5e",matcov[jj][ll]);
5096: }
5097: }
5098: }
5099: } /* end lk */
5100: } /* end lj */
5101: } /* end li */
5102: if(mle>=1)
5103: printf("\n");
5104: fprintf(ficlog,"\n");
5105: fprintf(ficres,"\n");
5106: numlinepar++;
5107: } /* end k*/
5108: } /*end j */
5109: } /* end i */
5110: } /* end itimes */
5111:
5112: fflush(ficlog);
5113: fflush(ficres);
5114:
5115: while((c=getc(ficpar))=='#' && c!= EOF){
5116: ungetc(c,ficpar);
5117: fgets(line, MAXLINE, ficpar);
5118: puts(line);
5119: fputs(line,ficparo);
5120: }
5121: ungetc(c,ficpar);
5122:
5123: estepm=0;
5124: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5125: if (estepm==0 || estepm < stepm) estepm=stepm;
5126: if (fage <= 2) {
5127: bage = ageminpar;
5128: fage = agemaxpar;
5129: }
5130:
5131: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5132: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5133: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5134:
5135: while((c=getc(ficpar))=='#' && c!= EOF){
5136: ungetc(c,ficpar);
5137: fgets(line, MAXLINE, ficpar);
5138: puts(line);
5139: fputs(line,ficparo);
5140: }
5141: ungetc(c,ficpar);
5142:
5143: 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);
5144: 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);
5145: 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);
5146: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5147: 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);
5148:
5149: while((c=getc(ficpar))=='#' && c!= EOF){
5150: ungetc(c,ficpar);
5151: fgets(line, MAXLINE, ficpar);
5152: puts(line);
5153: fputs(line,ficparo);
5154: }
5155: ungetc(c,ficpar);
5156:
5157:
5158: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5159: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5160:
5161: fscanf(ficpar,"pop_based=%d\n",&popbased);
5162: fprintf(ficparo,"pop_based=%d\n",popbased);
5163: fprintf(ficres,"pop_based=%d\n",popbased);
5164:
5165: while((c=getc(ficpar))=='#' && c!= EOF){
5166: ungetc(c,ficpar);
5167: fgets(line, MAXLINE, ficpar);
5168: puts(line);
5169: fputs(line,ficparo);
5170: }
5171: ungetc(c,ficpar);
5172:
5173: 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);
5174: 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);
5175: 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);
5176: 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);
5177: 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);
5178: /* day and month of proj2 are not used but only year anproj2.*/
5179:
5180:
5181:
5182: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5183: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5184:
5185: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
5186: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5187:
5188: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5189: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5190: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5191:
5192: /*------------ free_vector -------------*/
5193: /* chdir(path); */
5194:
5195: free_ivector(wav,1,imx);
5196: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5197: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5198: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5199: free_lvector(num,1,n);
5200: free_vector(agedc,1,n);
5201: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5202: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5203: fclose(ficparo);
5204: fclose(ficres);
5205:
5206:
5207: /*--------------- Prevalence limit (stable prevalence) --------------*/
5208:
5209: strcpy(filerespl,"pl");
5210: strcat(filerespl,fileres);
5211: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5212: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
5213: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
5214: }
5215: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
5216: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
5217: fprintf(ficrespl, "#Local time at start: %s", strstart);
5218: fprintf(ficrespl,"#Stable prevalence \n");
5219: fprintf(ficrespl,"#Age ");
5220: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5221: fprintf(ficrespl,"\n");
5222:
5223: prlim=matrix(1,nlstate,1,nlstate);
5224:
5225: agebase=ageminpar;
5226: agelim=agemaxpar;
5227: ftolpl=1.e-10;
5228: i1=cptcoveff;
5229: if (cptcovn < 1){i1=1;}
5230:
5231: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5232: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5233: k=k+1;
5234: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
5235: fprintf(ficrespl,"\n#******");
5236: printf("\n#******");
5237: fprintf(ficlog,"\n#******");
5238: for(j=1;j<=cptcoveff;j++) {
5239: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5240: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5241: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5242: }
5243: fprintf(ficrespl,"******\n");
5244: printf("******\n");
5245: fprintf(ficlog,"******\n");
5246:
5247: for (age=agebase; age<=agelim; age++){
5248: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5249: fprintf(ficrespl,"%.0f ",age );
5250: for(j=1;j<=cptcoveff;j++)
5251: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5252: for(i=1; i<=nlstate;i++)
5253: fprintf(ficrespl," %.5f", prlim[i][i]);
5254: fprintf(ficrespl,"\n");
5255: }
5256: }
5257: }
5258: fclose(ficrespl);
5259:
5260: /*------------- h Pij x at various ages ------------*/
5261:
5262: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5263: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5264: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
5265: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
5266: }
5267: printf("Computing pij: result on file '%s' \n", filerespij);
5268: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
5269:
5270: stepsize=(int) (stepm+YEARM-1)/YEARM;
5271: /*if (stepm<=24) stepsize=2;*/
5272:
5273: agelim=AGESUP;
5274: hstepm=stepsize*YEARM; /* Every year of age */
5275: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
5276:
5277: /* hstepm=1; aff par mois*/
5278: fprintf(ficrespij, "#Local time at start: %s", strstart);
5279: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5280: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5281: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5282: k=k+1;
5283: fprintf(ficrespij,"\n#****** ");
5284: for(j=1;j<=cptcoveff;j++)
5285: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5286: fprintf(ficrespij,"******\n");
5287:
5288: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5289: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5290: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5291:
5292: /* nhstepm=nhstepm*YEARM; aff par mois*/
5293:
5294: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5295: oldm=oldms;savm=savms;
5296: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5297: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
5298: for(i=1; i<=nlstate;i++)
5299: for(j=1; j<=nlstate+ndeath;j++)
5300: fprintf(ficrespij," %1d-%1d",i,j);
5301: fprintf(ficrespij,"\n");
5302: for (h=0; h<=nhstepm; h++){
5303: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
5304: for(i=1; i<=nlstate;i++)
5305: for(j=1; j<=nlstate+ndeath;j++)
5306: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
5307: fprintf(ficrespij,"\n");
5308: }
5309: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5310: fprintf(ficrespij,"\n");
5311: }
5312: }
5313: }
5314:
5315: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
5316:
5317: fclose(ficrespij);
5318:
5319: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5320: for(i=1;i<=AGESUP;i++)
5321: for(j=1;j<=NCOVMAX;j++)
5322: for(k=1;k<=NCOVMAX;k++)
5323: probs[i][j][k]=0.;
5324:
5325: /*---------- Forecasting ------------------*/
5326: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
5327: if(prevfcast==1){
5328: /* if(stepm ==1){*/
5329: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
5330: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
5331: /* } */
5332: /* else{ */
5333: /* erreur=108; */
5334: /* 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); */
5335: /* 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); */
5336: /* } */
5337: }
5338:
5339:
5340: /*---------- Health expectancies and variances ------------*/
5341:
5342: strcpy(filerest,"t");
5343: strcat(filerest,fileres);
5344: if((ficrest=fopen(filerest,"w"))==NULL) {
5345: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
5346: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
5347: }
5348: printf("Computing Total LEs with variances: file '%s' \n", filerest);
5349: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
5350:
5351:
5352: strcpy(filerese,"e");
5353: strcat(filerese,fileres);
5354: if((ficreseij=fopen(filerese,"w"))==NULL) {
5355: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5356: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5357: }
5358: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
5359: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
5360:
5361: strcpy(fileresv,"v");
5362: strcat(fileresv,fileres);
5363: if((ficresvij=fopen(fileresv,"w"))==NULL) {
5364: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
5365: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
5366: }
5367: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5368: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5369:
5370: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
5371: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5372: /* 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",\
5373: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
5374: */
5375:
5376: if (mobilav!=0) {
5377: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5378: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
5379: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5380: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5381: }
5382: }
5383:
5384: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5385: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5386: k=k+1;
5387: fprintf(ficrest,"\n#****** ");
5388: for(j=1;j<=cptcoveff;j++)
5389: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5390: fprintf(ficrest,"******\n");
5391:
5392: fprintf(ficreseij,"\n#****** ");
5393: for(j=1;j<=cptcoveff;j++)
5394: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5395: fprintf(ficreseij,"******\n");
5396:
5397: fprintf(ficresvij,"\n#****** ");
5398: for(j=1;j<=cptcoveff;j++)
5399: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5400: fprintf(ficresvij,"******\n");
5401:
5402: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5403: oldm=oldms;savm=savms;
5404: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
5405:
5406: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5407: oldm=oldms;savm=savms;
5408: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
5409: if(popbased==1){
5410: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
5411: }
5412:
5413: fprintf(ficrest, "#Local time at start: %s", strstart);
5414: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
5415: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5416: fprintf(ficrest,"\n");
5417:
5418: epj=vector(1,nlstate+1);
5419: for(age=bage; age <=fage ;age++){
5420: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5421: if (popbased==1) {
5422: if(mobilav ==0){
5423: for(i=1; i<=nlstate;i++)
5424: prlim[i][i]=probs[(int)age][i][k];
5425: }else{ /* mobilav */
5426: for(i=1; i<=nlstate;i++)
5427: prlim[i][i]=mobaverage[(int)age][i][k];
5428: }
5429: }
5430:
5431: fprintf(ficrest," %4.0f",age);
5432: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5433: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5434: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5435: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5436: }
5437: epj[nlstate+1] +=epj[j];
5438: }
5439:
5440: for(i=1, vepp=0.;i <=nlstate;i++)
5441: for(j=1;j <=nlstate;j++)
5442: vepp += vareij[i][j][(int)age];
5443: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5444: for(j=1;j <=nlstate;j++){
5445: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5446: }
5447: fprintf(ficrest,"\n");
5448: }
5449: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5450: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5451: free_vector(epj,1,nlstate+1);
5452: }
5453: }
5454: free_vector(weight,1,n);
5455: free_imatrix(Tvard,1,15,1,2);
5456: free_imatrix(s,1,maxwav+1,1,n);
5457: free_matrix(anint,1,maxwav,1,n);
5458: free_matrix(mint,1,maxwav,1,n);
5459: free_ivector(cod,1,n);
5460: free_ivector(tab,1,NCOVMAX);
5461: fclose(ficreseij);
5462: fclose(ficresvij);
5463: fclose(ficrest);
5464: fclose(ficpar);
5465:
5466: /*------- Variance of stable prevalence------*/
5467:
5468: strcpy(fileresvpl,"vpl");
5469: strcat(fileresvpl,fileres);
5470: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
5471: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
5472: exit(0);
5473: }
5474: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
5475:
5476: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5477: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5478: k=k+1;
5479: fprintf(ficresvpl,"\n#****** ");
5480: for(j=1;j<=cptcoveff;j++)
5481: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5482: fprintf(ficresvpl,"******\n");
5483:
5484: varpl=matrix(1,nlstate,(int) bage, (int) fage);
5485: oldm=oldms;savm=savms;
5486: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
5487: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
5488: }
5489: }
5490:
5491: fclose(ficresvpl);
5492:
5493: /*---------- End : free ----------------*/
5494: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5495: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5496:
5497: } /* mle==-3 arrives here for freeing */
5498: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
5499: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
5500: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
5501: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
5502:
5503: free_matrix(covar,0,NCOVMAX,1,n);
5504: free_matrix(matcov,1,npar,1,npar);
5505: /*free_vector(delti,1,npar);*/
5506: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5507: free_matrix(agev,1,maxwav,1,imx);
5508: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5509:
5510: free_ivector(ncodemax,1,8);
5511: free_ivector(Tvar,1,15);
5512: free_ivector(Tprod,1,15);
5513: free_ivector(Tvaraff,1,15);
5514: free_ivector(Tage,1,15);
5515: free_ivector(Tcode,1,100);
5516:
5517:
5518: fflush(fichtm);
5519: fflush(ficgp);
5520:
5521:
5522: if((nberr >0) || (nbwarn>0)){
5523: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
5524: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
5525: }else{
5526: printf("End of Imach\n");
5527: fprintf(ficlog,"End of Imach\n");
5528: }
5529: printf("See log file on %s\n",filelog);
5530: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
5531: (void) gettimeofday(&end_time,&tzp);
5532: tm = *localtime(&end_time.tv_sec);
5533: tmg = *gmtime(&end_time.tv_sec);
5534: strcpy(strtend,asctime(&tm));
5535: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
5536: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
5537: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5538:
5539: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5540: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5541: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5542: /* printf("Total time was %d uSec.\n", total_usecs);*/
5543: /* if(fileappend(fichtm,optionfilehtm)){ */
5544: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
5545: fclose(fichtm);
5546: fclose(fichtmcov);
5547: fclose(ficgp);
5548: fclose(ficlog);
5549: /*------ End -----------*/
5550:
5551: chdir(path);
5552: #ifndef UNIX
5553: strcpy(plotcmd,"\"");
5554: #endif
5555: strcat(plotcmd,pathimach);
5556: /*strcat(plotcmd,CHARSEPARATOR);*/
5557: strcat(plotcmd,GNUPLOTPROGRAM);
5558: #ifndef UNIX
5559: strcat(plotcmd,"\"");
5560: #endif
5561: if(stat(plotcmd,&info)){
5562: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
5563: }
5564: strcat(plotcmd," ");
5565: strcat(plotcmd,optionfilegnuplot);
5566: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
5567:
5568: if((outcmd=system(plotcmd)) != 0){
5569: printf(" Problem with gnuplot\n");
5570: }
5571: printf(" Wait...");
5572: while (z[0] != 'q') {
5573: /* chdir(path); */
5574: printf("\nType e to edit output files, g to graph again and q for exiting: ");
5575: scanf("%s",z);
5576: /* if (z[0] == 'c') system("./imach"); */
5577: if (z[0] == 'e') {
5578: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
5579: system(optionfilehtm);
5580: }
5581: else if (z[0] == 'g') system(plotcmd);
5582: else if (z[0] == 'q') exit(0);
5583: }
5584: end:
5585: while (z[0] != 'q') {
5586: printf("\nType q for exiting: ");
5587: scanf("%s",z);
5588: }
5589: }
5590:
5591:
5592:
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