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