1: /* $Id: imach.c,v 1.86 2003/06/17 20:04:08 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.86 2003/06/17 20:04:08 brouard
5: (Module): Change position of html and gnuplot routines and added
6: routine fileappend.
7:
8: Revision 1.85 2003/06/17 13:12:43 brouard
9: * imach.c (Repository): Check when date of death was earlier that
10: current date of interview. It may happen when the death was just
11: prior to the death. In this case, dh was negative and likelihood
12: was wrong (infinity). We still send an "Error" but patch by
13: assuming that the date of death was just one stepm after the
14: interview.
15: (Repository): Because some people have very long ID (first column)
16: we changed int to long in num[] and we added a new lvector for
17: memory allocation. But we also truncated to 8 characters (left
18: truncation)
19: (Repository): No more line truncation errors.
20:
21: Revision 1.84 2003/06/13 21:44:43 brouard
22: * imach.c (Repository): Replace "freqsummary" at a correct
23: place. It differs from routine "prevalence" which may be called
24: many times. Probs is memory consuming and must be used with
25: parcimony.
26: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
27:
28: Revision 1.83 2003/06/10 13:39:11 lievre
29: *** empty log message ***
30:
31: Revision 1.82 2003/06/05 15:57:20 brouard
32: Add log in imach.c and fullversion number is now printed.
33:
34: */
35: /*
36: Interpolated Markov Chain
37:
38: Short summary of the programme:
39:
40: This program computes Healthy Life Expectancies from
41: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
42: first survey ("cross") where individuals from different ages are
43: interviewed on their health status or degree of disability (in the
44: case of a health survey which is our main interest) -2- at least a
45: second wave of interviews ("longitudinal") which measure each change
46: (if any) in individual health status. Health expectancies are
47: computed from the time spent in each health state according to a
48: model. More health states you consider, more time is necessary to reach the
49: Maximum Likelihood of the parameters involved in the model. The
50: simplest model is the multinomial logistic model where pij is the
51: probability to be observed in state j at the second wave
52: conditional to be observed in state i at the first wave. Therefore
53: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
54: 'age' is age and 'sex' is a covariate. If you want to have a more
55: complex model than "constant and age", you should modify the program
56: where the markup *Covariates have to be included here again* invites
57: you to do it. More covariates you add, slower the
58: convergence.
59:
60: The advantage of this computer programme, compared to a simple
61: multinomial logistic model, is clear when the delay between waves is not
62: identical for each individual. Also, if a individual missed an
63: intermediate interview, the information is lost, but taken into
64: account using an interpolation or extrapolation.
65:
66: hPijx is the probability to be observed in state i at age x+h
67: conditional to the observed state i at age x. The delay 'h' can be
68: split into an exact number (nh*stepm) of unobserved intermediate
69: states. This elementary transition (by month, quarter,
70: semester or year) is modelled as a multinomial logistic. The hPx
71: matrix is simply the matrix product of nh*stepm elementary matrices
72: and the contribution of each individual to the likelihood is simply
73: hPijx.
74:
75: Also this programme outputs the covariance matrix of the parameters but also
76: of the life expectancies. It also computes the stable prevalence.
77:
78: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
79: Institut national d'études démographiques, Paris.
80: This software have been partly granted by Euro-REVES, a concerted action
81: from the European Union.
82: It is copyrighted identically to a GNU software product, ie programme and
83: software can be distributed freely for non commercial use. Latest version
84: can be accessed at http://euroreves.ined.fr/imach .
85:
86: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
87: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
88:
89: **********************************************************************/
90: /*
91: main
92: read parameterfile
93: read datafile
94: concatwav
95: freqsummary
96: if (mle >= 1)
97: mlikeli
98: print results files
99: if mle==1
100: computes hessian
101: read end of parameter file: agemin, agemax, bage, fage, estepm
102: begin-prev-date,...
103: open gnuplot file
104: open html file
105: stable prevalence
106: for age prevalim()
107: h Pij x
108: variance of p varprob
109: forecasting if prevfcast==1 prevforecast call prevalence()
110: health expectancies
111: Variance-covariance of DFLE
112: prevalence()
113: movingaverage()
114: varevsij()
115: if popbased==1 varevsij(,popbased)
116: total life expectancies
117: Variance of stable prevalence
118: end
119: */
120:
121:
122:
123:
124: #include <math.h>
125: #include <stdio.h>
126: #include <stdlib.h>
127: #include <unistd.h>
128:
129: #include <sys/time.h>
130: #include <time.h>
131: #include "timeval.h"
132:
133: #define MAXLINE 256
134: #define GNUPLOTPROGRAM "gnuplot"
135: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
136: #define FILENAMELENGTH 132
137: /*#define DEBUG*/
138: /*#define windows*/
139: #define GLOCK_ERROR_NOPATH -1 /* empty path */
140: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
141:
142: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
143: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
144:
145: #define NINTERVMAX 8
146: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
147: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
148: #define NCOVMAX 8 /* Maximum number of covariates */
149: #define MAXN 20000
150: #define YEARM 12. /* Number of months per year */
151: #define AGESUP 130
152: #define AGEBASE 40
153: #ifdef unix
154: #define DIRSEPARATOR '/'
155: #define ODIRSEPARATOR '\\'
156: #else
157: #define DIRSEPARATOR '\\'
158: #define ODIRSEPARATOR '/'
159: #endif
160:
161: /* $Id: imach.c,v 1.86 2003/06/17 20:04:08 brouard Exp $ */
162: /* $State: Exp $ */
163:
164: char version[]="Imach version 0.95a2, June 2003, INED-EUROREVES ";
165: char fullversion[]="$Revision: 1.86 $ $Date: 2003/06/17 20:04:08 $";
166: int erreur; /* Error number */
167: int nvar;
168: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
169: int npar=NPARMAX;
170: int nlstate=2; /* Number of live states */
171: int ndeath=1; /* Number of dead states */
172: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
173: int popbased=0;
174:
175: int *wav; /* Number of waves for this individuual 0 is possible */
176: int maxwav; /* Maxim number of waves */
177: int jmin, jmax; /* min, max spacing between 2 waves */
178: int mle, weightopt;
179: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
180: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
181: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
182: * wave mi and wave mi+1 is not an exact multiple of stepm. */
183: double jmean; /* Mean space between 2 waves */
184: double **oldm, **newm, **savm; /* Working pointers to matrices */
185: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
186: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
187: FILE *ficlog, *ficrespow;
188: int globpr; /* Global variable for printing or not */
189: double fretone; /* Only one call to likelihood */
190: long ipmx; /* Number of contributions */
191: double sw; /* Sum of weights */
192: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
193: FILE *ficresilk;
194: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
195: FILE *ficresprobmorprev;
196: FILE *fichtm; /* Html File */
197: FILE *ficreseij;
198: char filerese[FILENAMELENGTH];
199: FILE *ficresvij;
200: char fileresv[FILENAMELENGTH];
201: FILE *ficresvpl;
202: char fileresvpl[FILENAMELENGTH];
203: char title[MAXLINE];
204: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
205: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
206:
207: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
208: char filelog[FILENAMELENGTH]; /* Log file */
209: char filerest[FILENAMELENGTH];
210: char fileregp[FILENAMELENGTH];
211: char popfile[FILENAMELENGTH];
212:
213: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
214:
215: #define NR_END 1
216: #define FREE_ARG char*
217: #define FTOL 1.0e-10
218:
219: #define NRANSI
220: #define ITMAX 200
221:
222: #define TOL 2.0e-4
223:
224: #define CGOLD 0.3819660
225: #define ZEPS 1.0e-10
226: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
227:
228: #define GOLD 1.618034
229: #define GLIMIT 100.0
230: #define TINY 1.0e-20
231:
232: static double maxarg1,maxarg2;
233: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
234: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
235:
236: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
237: #define rint(a) floor(a+0.5)
238:
239: static double sqrarg;
240: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
241: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
242:
243: int imx;
244: int stepm;
245: /* Stepm, step in month: minimum step interpolation*/
246:
247: int estepm;
248: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
249:
250: int m,nb;
251: long *num;
252: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
253: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
254: double **pmmij, ***probs;
255: double dateintmean=0;
256:
257: double *weight;
258: int **s; /* Status */
259: double *agedc, **covar, idx;
260: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
261:
262: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
263: double ftolhess; /* Tolerance for computing hessian */
264:
265: /**************** split *************************/
266: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
267: {
268: char *ss; /* pointer */
269: int l1, l2; /* length counters */
270:
271: l1 = strlen(path ); /* length of path */
272: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
273: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
274: if ( ss == NULL ) { /* no directory, so use current */
275: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
276: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
277: /* get current working directory */
278: /* extern char* getcwd ( char *buf , int len);*/
279: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
280: return( GLOCK_ERROR_GETCWD );
281: }
282: strcpy( name, path ); /* we've got it */
283: } else { /* strip direcotry from path */
284: ss++; /* after this, the filename */
285: l2 = strlen( ss ); /* length of filename */
286: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
287: strcpy( name, ss ); /* save file name */
288: strncpy( dirc, path, l1 - l2 ); /* now the directory */
289: dirc[l1-l2] = 0; /* add zero */
290: }
291: l1 = strlen( dirc ); /* length of directory */
292: /*#ifdef windows
293: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
294: #else
295: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
296: #endif
297: */
298: ss = strrchr( name, '.' ); /* find last / */
299: ss++;
300: strcpy(ext,ss); /* save extension */
301: l1= strlen( name);
302: l2= strlen(ss)+1;
303: strncpy( finame, name, l1-l2);
304: finame[l1-l2]= 0;
305: return( 0 ); /* we're done */
306: }
307:
308:
309: /******************************************/
310:
311: void replace(char *s, char*t)
312: {
313: int i;
314: int lg=20;
315: i=0;
316: lg=strlen(t);
317: for(i=0; i<= lg; i++) {
318: (s[i] = t[i]);
319: if (t[i]== '\\') s[i]='/';
320: }
321: }
322:
323: int nbocc(char *s, char occ)
324: {
325: int i,j=0;
326: int lg=20;
327: i=0;
328: lg=strlen(s);
329: for(i=0; i<= lg; i++) {
330: if (s[i] == occ ) j++;
331: }
332: return j;
333: }
334:
335: void cutv(char *u,char *v, char*t, char occ)
336: {
337: /* cuts string t into u and v where u is ended by char occ excluding it
338: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
339: gives u="abcedf" and v="ghi2j" */
340: int i,lg,j,p=0;
341: i=0;
342: for(j=0; j<=strlen(t)-1; j++) {
343: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
344: }
345:
346: lg=strlen(t);
347: for(j=0; j<p; j++) {
348: (u[j] = t[j]);
349: }
350: u[p]='\0';
351:
352: for(j=0; j<= lg; j++) {
353: if (j>=(p+1))(v[j-p-1] = t[j]);
354: }
355: }
356:
357: /********************** nrerror ********************/
358:
359: void nrerror(char error_text[])
360: {
361: fprintf(stderr,"ERREUR ...\n");
362: fprintf(stderr,"%s\n",error_text);
363: exit(EXIT_FAILURE);
364: }
365: /*********************** vector *******************/
366: double *vector(int nl, int nh)
367: {
368: double *v;
369: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
370: if (!v) nrerror("allocation failure in vector");
371: return v-nl+NR_END;
372: }
373:
374: /************************ free vector ******************/
375: void free_vector(double*v, int nl, int nh)
376: {
377: free((FREE_ARG)(v+nl-NR_END));
378: }
379:
380: /************************ivector *******************************/
381: int *ivector(long nl,long nh)
382: {
383: int *v;
384: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
385: if (!v) nrerror("allocation failure in ivector");
386: return v-nl+NR_END;
387: }
388:
389: /******************free ivector **************************/
390: void free_ivector(int *v, long nl, long nh)
391: {
392: free((FREE_ARG)(v+nl-NR_END));
393: }
394:
395: /************************lvector *******************************/
396: long *lvector(long nl,long nh)
397: {
398: long *v;
399: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
400: if (!v) nrerror("allocation failure in ivector");
401: return v-nl+NR_END;
402: }
403:
404: /******************free lvector **************************/
405: void free_lvector(long *v, long nl, long nh)
406: {
407: free((FREE_ARG)(v+nl-NR_END));
408: }
409:
410: /******************* imatrix *******************************/
411: int **imatrix(long nrl, long nrh, long ncl, long nch)
412: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
413: {
414: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
415: int **m;
416:
417: /* allocate pointers to rows */
418: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
419: if (!m) nrerror("allocation failure 1 in matrix()");
420: m += NR_END;
421: m -= nrl;
422:
423:
424: /* allocate rows and set pointers to them */
425: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
426: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
427: m[nrl] += NR_END;
428: m[nrl] -= ncl;
429:
430: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
431:
432: /* return pointer to array of pointers to rows */
433: return m;
434: }
435:
436: /****************** free_imatrix *************************/
437: void free_imatrix(m,nrl,nrh,ncl,nch)
438: int **m;
439: long nch,ncl,nrh,nrl;
440: /* free an int matrix allocated by imatrix() */
441: {
442: free((FREE_ARG) (m[nrl]+ncl-NR_END));
443: free((FREE_ARG) (m+nrl-NR_END));
444: }
445:
446: /******************* matrix *******************************/
447: double **matrix(long nrl, long nrh, long ncl, long nch)
448: {
449: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
450: double **m;
451:
452: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
453: if (!m) nrerror("allocation failure 1 in matrix()");
454: m += NR_END;
455: m -= nrl;
456:
457: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
458: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
459: m[nrl] += NR_END;
460: m[nrl] -= ncl;
461:
462: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
463: return m;
464: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
465: */
466: }
467:
468: /*************************free matrix ************************/
469: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
470: {
471: free((FREE_ARG)(m[nrl]+ncl-NR_END));
472: free((FREE_ARG)(m+nrl-NR_END));
473: }
474:
475: /******************* ma3x *******************************/
476: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
477: {
478: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
479: double ***m;
480:
481: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
482: if (!m) nrerror("allocation failure 1 in matrix()");
483: m += NR_END;
484: m -= nrl;
485:
486: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
487: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
488: m[nrl] += NR_END;
489: m[nrl] -= ncl;
490:
491: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
492:
493: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
494: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
495: m[nrl][ncl] += NR_END;
496: m[nrl][ncl] -= nll;
497: for (j=ncl+1; j<=nch; j++)
498: m[nrl][j]=m[nrl][j-1]+nlay;
499:
500: for (i=nrl+1; i<=nrh; i++) {
501: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
502: for (j=ncl+1; j<=nch; j++)
503: m[i][j]=m[i][j-1]+nlay;
504: }
505: return m;
506: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
507: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
508: */
509: }
510:
511: /*************************free ma3x ************************/
512: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
513: {
514: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
515: free((FREE_ARG)(m[nrl]+ncl-NR_END));
516: free((FREE_ARG)(m+nrl-NR_END));
517: }
518:
519: /***************** f1dim *************************/
520: extern int ncom;
521: extern double *pcom,*xicom;
522: extern double (*nrfunc)(double []);
523:
524: double f1dim(double x)
525: {
526: int j;
527: double f;
528: double *xt;
529:
530: xt=vector(1,ncom);
531: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
532: f=(*nrfunc)(xt);
533: free_vector(xt,1,ncom);
534: return f;
535: }
536:
537: /*****************brent *************************/
538: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
539: {
540: int iter;
541: double a,b,d,etemp;
542: double fu,fv,fw,fx;
543: double ftemp;
544: double p,q,r,tol1,tol2,u,v,w,x,xm;
545: double e=0.0;
546:
547: a=(ax < cx ? ax : cx);
548: b=(ax > cx ? ax : cx);
549: x=w=v=bx;
550: fw=fv=fx=(*f)(x);
551: for (iter=1;iter<=ITMAX;iter++) {
552: xm=0.5*(a+b);
553: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
554: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
555: printf(".");fflush(stdout);
556: fprintf(ficlog,".");fflush(ficlog);
557: #ifdef DEBUG
558: 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);
559: 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);
560: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
561: #endif
562: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
563: *xmin=x;
564: return fx;
565: }
566: ftemp=fu;
567: if (fabs(e) > tol1) {
568: r=(x-w)*(fx-fv);
569: q=(x-v)*(fx-fw);
570: p=(x-v)*q-(x-w)*r;
571: q=2.0*(q-r);
572: if (q > 0.0) p = -p;
573: q=fabs(q);
574: etemp=e;
575: e=d;
576: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
577: d=CGOLD*(e=(x >= xm ? a-x : b-x));
578: else {
579: d=p/q;
580: u=x+d;
581: if (u-a < tol2 || b-u < tol2)
582: d=SIGN(tol1,xm-x);
583: }
584: } else {
585: d=CGOLD*(e=(x >= xm ? a-x : b-x));
586: }
587: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
588: fu=(*f)(u);
589: if (fu <= fx) {
590: if (u >= x) a=x; else b=x;
591: SHFT(v,w,x,u)
592: SHFT(fv,fw,fx,fu)
593: } else {
594: if (u < x) a=u; else b=u;
595: if (fu <= fw || w == x) {
596: v=w;
597: w=u;
598: fv=fw;
599: fw=fu;
600: } else if (fu <= fv || v == x || v == w) {
601: v=u;
602: fv=fu;
603: }
604: }
605: }
606: nrerror("Too many iterations in brent");
607: *xmin=x;
608: return fx;
609: }
610:
611: /****************** mnbrak ***********************/
612:
613: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
614: double (*func)(double))
615: {
616: double ulim,u,r,q, dum;
617: double fu;
618:
619: *fa=(*func)(*ax);
620: *fb=(*func)(*bx);
621: if (*fb > *fa) {
622: SHFT(dum,*ax,*bx,dum)
623: SHFT(dum,*fb,*fa,dum)
624: }
625: *cx=(*bx)+GOLD*(*bx-*ax);
626: *fc=(*func)(*cx);
627: while (*fb > *fc) {
628: r=(*bx-*ax)*(*fb-*fc);
629: q=(*bx-*cx)*(*fb-*fa);
630: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
631: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
632: ulim=(*bx)+GLIMIT*(*cx-*bx);
633: if ((*bx-u)*(u-*cx) > 0.0) {
634: fu=(*func)(u);
635: } else if ((*cx-u)*(u-ulim) > 0.0) {
636: fu=(*func)(u);
637: if (fu < *fc) {
638: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
639: SHFT(*fb,*fc,fu,(*func)(u))
640: }
641: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
642: u=ulim;
643: fu=(*func)(u);
644: } else {
645: u=(*cx)+GOLD*(*cx-*bx);
646: fu=(*func)(u);
647: }
648: SHFT(*ax,*bx,*cx,u)
649: SHFT(*fa,*fb,*fc,fu)
650: }
651: }
652:
653: /*************** linmin ************************/
654:
655: int ncom;
656: double *pcom,*xicom;
657: double (*nrfunc)(double []);
658:
659: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
660: {
661: double brent(double ax, double bx, double cx,
662: double (*f)(double), double tol, double *xmin);
663: double f1dim(double x);
664: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
665: double *fc, double (*func)(double));
666: int j;
667: double xx,xmin,bx,ax;
668: double fx,fb,fa;
669:
670: ncom=n;
671: pcom=vector(1,n);
672: xicom=vector(1,n);
673: nrfunc=func;
674: for (j=1;j<=n;j++) {
675: pcom[j]=p[j];
676: xicom[j]=xi[j];
677: }
678: ax=0.0;
679: xx=1.0;
680: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
681: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
682: #ifdef DEBUG
683: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
684: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
685: #endif
686: for (j=1;j<=n;j++) {
687: xi[j] *= xmin;
688: p[j] += xi[j];
689: }
690: free_vector(xicom,1,n);
691: free_vector(pcom,1,n);
692: }
693:
694: /*************** powell ************************/
695: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
696: double (*func)(double []))
697: {
698: void linmin(double p[], double xi[], int n, double *fret,
699: double (*func)(double []));
700: int i,ibig,j;
701: double del,t,*pt,*ptt,*xit;
702: double fp,fptt;
703: double *xits;
704: pt=vector(1,n);
705: ptt=vector(1,n);
706: xit=vector(1,n);
707: xits=vector(1,n);
708: *fret=(*func)(p);
709: for (j=1;j<=n;j++) pt[j]=p[j];
710: for (*iter=1;;++(*iter)) {
711: fp=(*fret);
712: ibig=0;
713: del=0.0;
714: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
715: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
716: fprintf(ficrespow,"%d %.12f",*iter,*fret);
717: for (i=1;i<=n;i++) {
718: printf(" %d %.12f",i, p[i]);
719: fprintf(ficlog," %d %.12lf",i, p[i]);
720: fprintf(ficrespow," %.12lf", p[i]);
721: }
722: printf("\n");
723: fprintf(ficlog,"\n");
724: fprintf(ficrespow,"\n");
725: for (i=1;i<=n;i++) {
726: for (j=1;j<=n;j++) xit[j]=xi[j][i];
727: fptt=(*fret);
728: #ifdef DEBUG
729: printf("fret=%lf \n",*fret);
730: fprintf(ficlog,"fret=%lf \n",*fret);
731: #endif
732: printf("%d",i);fflush(stdout);
733: fprintf(ficlog,"%d",i);fflush(ficlog);
734: linmin(p,xit,n,fret,func);
735: if (fabs(fptt-(*fret)) > del) {
736: del=fabs(fptt-(*fret));
737: ibig=i;
738: }
739: #ifdef DEBUG
740: printf("%d %.12e",i,(*fret));
741: fprintf(ficlog,"%d %.12e",i,(*fret));
742: for (j=1;j<=n;j++) {
743: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
744: printf(" x(%d)=%.12e",j,xit[j]);
745: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
746: }
747: for(j=1;j<=n;j++) {
748: printf(" p=%.12e",p[j]);
749: fprintf(ficlog," p=%.12e",p[j]);
750: }
751: printf("\n");
752: fprintf(ficlog,"\n");
753: #endif
754: }
755: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
756: #ifdef DEBUG
757: int k[2],l;
758: k[0]=1;
759: k[1]=-1;
760: printf("Max: %.12e",(*func)(p));
761: fprintf(ficlog,"Max: %.12e",(*func)(p));
762: for (j=1;j<=n;j++) {
763: printf(" %.12e",p[j]);
764: fprintf(ficlog," %.12e",p[j]);
765: }
766: printf("\n");
767: fprintf(ficlog,"\n");
768: for(l=0;l<=1;l++) {
769: for (j=1;j<=n;j++) {
770: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
771: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
772: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
773: }
774: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
775: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
776: }
777: #endif
778:
779:
780: free_vector(xit,1,n);
781: free_vector(xits,1,n);
782: free_vector(ptt,1,n);
783: free_vector(pt,1,n);
784: return;
785: }
786: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
787: for (j=1;j<=n;j++) {
788: ptt[j]=2.0*p[j]-pt[j];
789: xit[j]=p[j]-pt[j];
790: pt[j]=p[j];
791: }
792: fptt=(*func)(ptt);
793: if (fptt < fp) {
794: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
795: if (t < 0.0) {
796: linmin(p,xit,n,fret,func);
797: for (j=1;j<=n;j++) {
798: xi[j][ibig]=xi[j][n];
799: xi[j][n]=xit[j];
800: }
801: #ifdef DEBUG
802: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
803: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
804: for(j=1;j<=n;j++){
805: printf(" %.12e",xit[j]);
806: fprintf(ficlog," %.12e",xit[j]);
807: }
808: printf("\n");
809: fprintf(ficlog,"\n");
810: #endif
811: }
812: }
813: }
814: }
815:
816: /**** Prevalence limit (stable prevalence) ****************/
817:
818: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
819: {
820: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
821: matrix by transitions matrix until convergence is reached */
822:
823: int i, ii,j,k;
824: double min, max, maxmin, maxmax,sumnew=0.;
825: double **matprod2();
826: double **out, cov[NCOVMAX], **pmij();
827: double **newm;
828: double agefin, delaymax=50 ; /* Max number of years to converge */
829:
830: for (ii=1;ii<=nlstate+ndeath;ii++)
831: for (j=1;j<=nlstate+ndeath;j++){
832: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
833: }
834:
835: cov[1]=1.;
836:
837: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
838: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
839: newm=savm;
840: /* Covariates have to be included here again */
841: cov[2]=agefin;
842:
843: for (k=1; k<=cptcovn;k++) {
844: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
845: /* 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]]);*/
846: }
847: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
848: for (k=1; k<=cptcovprod;k++)
849: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
850:
851: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
852: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
853: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
854: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
855:
856: savm=oldm;
857: oldm=newm;
858: maxmax=0.;
859: for(j=1;j<=nlstate;j++){
860: min=1.;
861: max=0.;
862: for(i=1; i<=nlstate; i++) {
863: sumnew=0;
864: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
865: prlim[i][j]= newm[i][j]/(1-sumnew);
866: max=FMAX(max,prlim[i][j]);
867: min=FMIN(min,prlim[i][j]);
868: }
869: maxmin=max-min;
870: maxmax=FMAX(maxmax,maxmin);
871: }
872: if(maxmax < ftolpl){
873: return prlim;
874: }
875: }
876: }
877:
878: /*************** transition probabilities ***************/
879:
880: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
881: {
882: double s1, s2;
883: /*double t34;*/
884: int i,j,j1, nc, ii, jj;
885:
886: for(i=1; i<= nlstate; i++){
887: for(j=1; j<i;j++){
888: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
889: /*s2 += param[i][j][nc]*cov[nc];*/
890: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
891: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
892: }
893: ps[i][j]=s2;
894: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
895: }
896: for(j=i+1; j<=nlstate+ndeath;j++){
897: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
898: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
899: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
900: }
901: ps[i][j]=s2;
902: }
903: }
904: /*ps[3][2]=1;*/
905:
906: for(i=1; i<= nlstate; i++){
907: s1=0;
908: for(j=1; j<i; j++)
909: s1+=exp(ps[i][j]);
910: for(j=i+1; j<=nlstate+ndeath; j++)
911: s1+=exp(ps[i][j]);
912: ps[i][i]=1./(s1+1.);
913: for(j=1; j<i; j++)
914: ps[i][j]= exp(ps[i][j])*ps[i][i];
915: for(j=i+1; j<=nlstate+ndeath; j++)
916: ps[i][j]= exp(ps[i][j])*ps[i][i];
917: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
918: } /* end i */
919:
920: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
921: for(jj=1; jj<= nlstate+ndeath; jj++){
922: ps[ii][jj]=0;
923: ps[ii][ii]=1;
924: }
925: }
926:
927:
928: /* for(ii=1; ii<= nlstate+ndeath; ii++){
929: for(jj=1; jj<= nlstate+ndeath; jj++){
930: printf("%lf ",ps[ii][jj]);
931: }
932: printf("\n ");
933: }
934: printf("\n ");printf("%lf ",cov[2]);*/
935: /*
936: for(i=1; i<= npar; i++) printf("%f ",x[i]);
937: goto end;*/
938: return ps;
939: }
940:
941: /**************** Product of 2 matrices ******************/
942:
943: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
944: {
945: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
946: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
947: /* in, b, out are matrice of pointers which should have been initialized
948: before: only the contents of out is modified. The function returns
949: a pointer to pointers identical to out */
950: long i, j, k;
951: for(i=nrl; i<= nrh; i++)
952: for(k=ncolol; k<=ncoloh; k++)
953: for(j=ncl,out[i][k]=0.; j<=nch; j++)
954: out[i][k] +=in[i][j]*b[j][k];
955:
956: return out;
957: }
958:
959:
960: /************* Higher Matrix Product ***************/
961:
962: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
963: {
964: /* Computes the transition matrix starting at age 'age' over
965: 'nhstepm*hstepm*stepm' months (i.e. until
966: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
967: nhstepm*hstepm matrices.
968: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
969: (typically every 2 years instead of every month which is too big
970: for the memory).
971: Model is determined by parameters x and covariates have to be
972: included manually here.
973:
974: */
975:
976: int i, j, d, h, k;
977: double **out, cov[NCOVMAX];
978: double **newm;
979:
980: /* Hstepm could be zero and should return the unit matrix */
981: for (i=1;i<=nlstate+ndeath;i++)
982: for (j=1;j<=nlstate+ndeath;j++){
983: oldm[i][j]=(i==j ? 1.0 : 0.0);
984: po[i][j][0]=(i==j ? 1.0 : 0.0);
985: }
986: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
987: for(h=1; h <=nhstepm; h++){
988: for(d=1; d <=hstepm; d++){
989: newm=savm;
990: /* Covariates have to be included here again */
991: cov[1]=1.;
992: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
993: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
994: for (k=1; k<=cptcovage;k++)
995: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
996: for (k=1; k<=cptcovprod;k++)
997: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
998:
999:
1000: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1001: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1002: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1003: pmij(pmmij,cov,ncovmodel,x,nlstate));
1004: savm=oldm;
1005: oldm=newm;
1006: }
1007: for(i=1; i<=nlstate+ndeath; i++)
1008: for(j=1;j<=nlstate+ndeath;j++) {
1009: po[i][j][h]=newm[i][j];
1010: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1011: */
1012: }
1013: } /* end h */
1014: return po;
1015: }
1016:
1017:
1018: /*************** log-likelihood *************/
1019: double func( double *x)
1020: {
1021: int i, ii, j, k, mi, d, kk;
1022: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1023: double **out;
1024: double sw; /* Sum of weights */
1025: double lli; /* Individual log likelihood */
1026: int s1, s2;
1027: double bbh, survp;
1028: long ipmx;
1029: /*extern weight */
1030: /* We are differentiating ll according to initial status */
1031: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1032: /*for(i=1;i<imx;i++)
1033: printf(" %d\n",s[4][i]);
1034: */
1035: cov[1]=1.;
1036:
1037: for(k=1; k<=nlstate; k++) ll[k]=0.;
1038:
1039: if(mle==1){
1040: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1041: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1042: for(mi=1; mi<= wav[i]-1; mi++){
1043: for (ii=1;ii<=nlstate+ndeath;ii++)
1044: for (j=1;j<=nlstate+ndeath;j++){
1045: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1046: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1047: }
1048: for(d=0; d<dh[mi][i]; d++){
1049: newm=savm;
1050: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1051: for (kk=1; kk<=cptcovage;kk++) {
1052: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1053: }
1054: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1055: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1056: savm=oldm;
1057: oldm=newm;
1058: } /* end mult */
1059:
1060: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1061: /* But now since version 0.9 we anticipate for bias and large stepm.
1062: * If stepm is larger than one month (smallest stepm) and if the exact delay
1063: * (in months) between two waves is not a multiple of stepm, we rounded to
1064: * the nearest (and in case of equal distance, to the lowest) interval but now
1065: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1066: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1067: * probability in order to take into account the bias as a fraction of the way
1068: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1069: * -stepm/2 to stepm/2 .
1070: * For stepm=1 the results are the same as for previous versions of Imach.
1071: * For stepm > 1 the results are less biased than in previous versions.
1072: */
1073: s1=s[mw[mi][i]][i];
1074: s2=s[mw[mi+1][i]][i];
1075: bbh=(double)bh[mi][i]/(double)stepm;
1076: /* bias is positive if real duration
1077: * is higher than the multiple of stepm and negative otherwise.
1078: */
1079: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1080: if( s2 > nlstate){
1081: /* i.e. if s2 is a death state and if the date of death is known then the contribution
1082: to the likelihood is the probability to die between last step unit time and current
1083: step unit time, which is also the differences between probability to die before dh
1084: and probability to die before dh-stepm .
1085: In version up to 0.92 likelihood was computed
1086: as if date of death was unknown. Death was treated as any other
1087: health state: the date of the interview describes the actual state
1088: and not the date of a change in health state. The former idea was
1089: to consider that at each interview the state was recorded
1090: (healthy, disable or death) and IMaCh was corrected; but when we
1091: introduced the exact date of death then we should have modified
1092: the contribution of an exact death to the likelihood. This new
1093: contribution is smaller and very dependent of the step unit
1094: stepm. It is no more the probability to die between last interview
1095: and month of death but the probability to survive from last
1096: interview up to one month before death multiplied by the
1097: probability to die within a month. Thanks to Chris
1098: Jackson for correcting this bug. Former versions increased
1099: mortality artificially. The bad side is that we add another loop
1100: which slows down the processing. The difference can be up to 10%
1101: lower mortality.
1102: */
1103: lli=log(out[s1][s2] - savm[s1][s2]);
1104: }else{
1105: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1106: /* 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 */
1107: }
1108: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1109: /*if(lli ==000.0)*/
1110: /*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); */
1111: ipmx +=1;
1112: sw += weight[i];
1113: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1114: } /* end of wave */
1115: } /* end of individual */
1116: } else if(mle==2){
1117: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1118: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1119: for(mi=1; mi<= wav[i]-1; mi++){
1120: for (ii=1;ii<=nlstate+ndeath;ii++)
1121: for (j=1;j<=nlstate+ndeath;j++){
1122: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1123: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1124: }
1125: for(d=0; d<=dh[mi][i]; d++){
1126: newm=savm;
1127: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1128: for (kk=1; kk<=cptcovage;kk++) {
1129: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1130: }
1131: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1132: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1133: savm=oldm;
1134: oldm=newm;
1135: } /* end mult */
1136:
1137: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1138: /* But now since version 0.9 we anticipate for bias and large stepm.
1139: * If stepm is larger than one month (smallest stepm) and if the exact delay
1140: * (in months) between two waves is not a multiple of stepm, we rounded to
1141: * the nearest (and in case of equal distance, to the lowest) interval but now
1142: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1143: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1144: * probability in order to take into account the bias as a fraction of the way
1145: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1146: * -stepm/2 to stepm/2 .
1147: * For stepm=1 the results are the same as for previous versions of Imach.
1148: * For stepm > 1 the results are less biased than in previous versions.
1149: */
1150: s1=s[mw[mi][i]][i];
1151: s2=s[mw[mi+1][i]][i];
1152: bbh=(double)bh[mi][i]/(double)stepm;
1153: /* bias is positive if real duration
1154: * is higher than the multiple of stepm and negative otherwise.
1155: */
1156: 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 */
1157: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1158: /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
1159: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1160: /*if(lli ==000.0)*/
1161: /*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); */
1162: ipmx +=1;
1163: sw += weight[i];
1164: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1165: } /* end of wave */
1166: } /* end of individual */
1167: } else if(mle==3){ /* exponential inter-extrapolation */
1168: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1169: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1170: for(mi=1; mi<= wav[i]-1; mi++){
1171: for (ii=1;ii<=nlstate+ndeath;ii++)
1172: for (j=1;j<=nlstate+ndeath;j++){
1173: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1174: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1175: }
1176: for(d=0; d<dh[mi][i]; d++){
1177: newm=savm;
1178: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1179: for (kk=1; kk<=cptcovage;kk++) {
1180: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1181: }
1182: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1183: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1184: savm=oldm;
1185: oldm=newm;
1186: } /* end mult */
1187:
1188: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1189: /* But now since version 0.9 we anticipate for bias and large stepm.
1190: * If stepm is larger than one month (smallest stepm) and if the exact delay
1191: * (in months) between two waves is not a multiple of stepm, we rounded to
1192: * the nearest (and in case of equal distance, to the lowest) interval but now
1193: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1194: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1195: * probability in order to take into account the bias as a fraction of the way
1196: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1197: * -stepm/2 to stepm/2 .
1198: * For stepm=1 the results are the same as for previous versions of Imach.
1199: * For stepm > 1 the results are less biased than in previous versions.
1200: */
1201: s1=s[mw[mi][i]][i];
1202: s2=s[mw[mi+1][i]][i];
1203: bbh=(double)bh[mi][i]/(double)stepm;
1204: /* bias is positive if real duration
1205: * is higher than the multiple of stepm and negative otherwise.
1206: */
1207: /* 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 */
1208: 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 */
1209: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1210: /*if(lli ==000.0)*/
1211: /*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); */
1212: ipmx +=1;
1213: sw += weight[i];
1214: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1215: } /* end of wave */
1216: } /* end of individual */
1217: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1218: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1219: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1220: for(mi=1; mi<= wav[i]-1; mi++){
1221: for (ii=1;ii<=nlstate+ndeath;ii++)
1222: for (j=1;j<=nlstate+ndeath;j++){
1223: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1224: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1225: }
1226: for(d=0; d<dh[mi][i]; d++){
1227: newm=savm;
1228: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1229: for (kk=1; kk<=cptcovage;kk++) {
1230: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1231: }
1232:
1233: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1234: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1235: savm=oldm;
1236: oldm=newm;
1237: } /* end mult */
1238:
1239: s1=s[mw[mi][i]][i];
1240: s2=s[mw[mi+1][i]][i];
1241: if( s2 > nlstate){
1242: lli=log(out[s1][s2] - savm[s1][s2]);
1243: }else{
1244: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1245: }
1246: ipmx +=1;
1247: sw += weight[i];
1248: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1249: /* 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]); */
1250: } /* end of wave */
1251: } /* end of individual */
1252: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1253: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1254: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1255: for(mi=1; mi<= wav[i]-1; mi++){
1256: for (ii=1;ii<=nlstate+ndeath;ii++)
1257: for (j=1;j<=nlstate+ndeath;j++){
1258: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1259: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1260: }
1261: for(d=0; d<dh[mi][i]; d++){
1262: newm=savm;
1263: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1264: for (kk=1; kk<=cptcovage;kk++) {
1265: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1266: }
1267:
1268: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1269: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1270: savm=oldm;
1271: oldm=newm;
1272: } /* end mult */
1273:
1274: s1=s[mw[mi][i]][i];
1275: s2=s[mw[mi+1][i]][i];
1276: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1277: ipmx +=1;
1278: sw += weight[i];
1279: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1280: /*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]);*/
1281: } /* end of wave */
1282: } /* end of individual */
1283: } /* End of if */
1284: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1285: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1286: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1287: return -l;
1288: }
1289:
1290: /*************** log-likelihood *************/
1291: double funcone( double *x)
1292: {
1293: int i, ii, j, k, mi, d, kk;
1294: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1295: double **out;
1296: double lli; /* Individual log likelihood */
1297: int s1, s2;
1298: double bbh, survp;
1299: /*extern weight */
1300: /* We are differentiating ll according to initial status */
1301: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1302: /*for(i=1;i<imx;i++)
1303: printf(" %d\n",s[4][i]);
1304: */
1305: cov[1]=1.;
1306:
1307: for(k=1; k<=nlstate; k++) ll[k]=0.;
1308:
1309: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1310: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1311: for(mi=1; mi<= wav[i]-1; mi++){
1312: for (ii=1;ii<=nlstate+ndeath;ii++)
1313: for (j=1;j<=nlstate+ndeath;j++){
1314: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1315: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1316: }
1317: for(d=0; d<dh[mi][i]; d++){
1318: newm=savm;
1319: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1320: for (kk=1; kk<=cptcovage;kk++) {
1321: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1322: }
1323: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1324: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1325: savm=oldm;
1326: oldm=newm;
1327: } /* end mult */
1328:
1329: s1=s[mw[mi][i]][i];
1330: s2=s[mw[mi+1][i]][i];
1331: bbh=(double)bh[mi][i]/(double)stepm;
1332: /* bias is positive if real duration
1333: * is higher than the multiple of stepm and negative otherwise.
1334: */
1335: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1336: lli=log(out[s1][s2] - savm[s1][s2]);
1337: } else if (mle==1){
1338: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1339: } else if(mle==2){
1340: 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 */
1341: } else if(mle==3){ /* exponential inter-extrapolation */
1342: 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 */
1343: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1344: lli=log(out[s1][s2]); /* Original formula */
1345: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1346: lli=log(out[s1][s2]); /* Original formula */
1347: } /* End of if */
1348: ipmx +=1;
1349: sw += weight[i];
1350: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1351: /* 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]); */
1352: if(globpr){
1353: fprintf(ficresilk,"%ld %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
1354: %10.6f %10.6f %10.6f ", \
1355: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1356: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1357: for(k=1,l=0.; k<=nlstate; k++)
1358: fprintf(ficresilk," %10.6f",ll[k]);
1359: fprintf(ficresilk,"\n");
1360: }
1361: } /* end of wave */
1362: } /* end of individual */
1363: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1364: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1365: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1366: return -l;
1367: }
1368:
1369:
1370: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpr, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1371: {
1372: /* This routine should help understanding what is done with the selection of individuals/waves and
1373: to check the exact contribution to the likelihood.
1374: Plotting could be done.
1375: */
1376: int k;
1377: if(globpr !=0){ /* Just counts and sums no printings */
1378: strcpy(fileresilk,"ilk");
1379: strcat(fileresilk,fileres);
1380: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1381: printf("Problem with resultfile: %s\n", fileresilk);
1382: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1383: }
1384: fprintf(ficresilk, "#individual(line's record) s1 s2 wave# effective_wave# number_of_product_matrix pij weight 2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state\n");
1385: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight out sav ");
1386: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1387: for(k=1; k<=nlstate; k++)
1388: fprintf(ficresilk," ll[%d]",k);
1389: fprintf(ficresilk,"\n");
1390: }
1391:
1392: *fretone=(*funcone)(p);
1393: if(globpr !=0){
1394: fclose(ficresilk);
1395: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
1396: printf("Problem with html file: %s\n", optionfilehtm);
1397: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
1398: exit(0);
1399: }
1400: else{
1401: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",fileresilk);
1402: fclose(fichtm);
1403: }
1404: }
1405: return;
1406: }
1407:
1408: /*********** Maximum Likelihood Estimation ***************/
1409:
1410: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1411: {
1412: int i,j, iter;
1413: double **xi;
1414: double fret;
1415: double fretone; /* Only one call to likelihood */
1416: char filerespow[FILENAMELENGTH];
1417: xi=matrix(1,npar,1,npar);
1418: for (i=1;i<=npar;i++)
1419: for (j=1;j<=npar;j++)
1420: xi[i][j]=(i==j ? 1.0 : 0.0);
1421: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1422: strcpy(filerespow,"pow");
1423: strcat(filerespow,fileres);
1424: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1425: printf("Problem with resultfile: %s\n", filerespow);
1426: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1427: }
1428: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1429: for (i=1;i<=nlstate;i++)
1430: for(j=1;j<=nlstate+ndeath;j++)
1431: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1432: fprintf(ficrespow,"\n");
1433:
1434: powell(p,xi,npar,ftol,&iter,&fret,func);
1435:
1436: fclose(ficrespow);
1437: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1438: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1439: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1440:
1441: }
1442:
1443: /**** Computes Hessian and covariance matrix ***/
1444: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1445: {
1446: double **a,**y,*x,pd;
1447: double **hess;
1448: int i, j,jk;
1449: int *indx;
1450:
1451: double hessii(double p[], double delta, int theta, double delti[]);
1452: double hessij(double p[], double delti[], int i, int j);
1453: void lubksb(double **a, int npar, int *indx, double b[]) ;
1454: void ludcmp(double **a, int npar, int *indx, double *d) ;
1455:
1456: hess=matrix(1,npar,1,npar);
1457:
1458: printf("\nCalculation of the hessian matrix. Wait...\n");
1459: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1460: for (i=1;i<=npar;i++){
1461: printf("%d",i);fflush(stdout);
1462: fprintf(ficlog,"%d",i);fflush(ficlog);
1463: hess[i][i]=hessii(p,ftolhess,i,delti);
1464: /*printf(" %f ",p[i]);*/
1465: /*printf(" %lf ",hess[i][i]);*/
1466: }
1467:
1468: for (i=1;i<=npar;i++) {
1469: for (j=1;j<=npar;j++) {
1470: if (j>i) {
1471: printf(".%d%d",i,j);fflush(stdout);
1472: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1473: hess[i][j]=hessij(p,delti,i,j);
1474: hess[j][i]=hess[i][j];
1475: /*printf(" %lf ",hess[i][j]);*/
1476: }
1477: }
1478: }
1479: printf("\n");
1480: fprintf(ficlog,"\n");
1481:
1482: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1483: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1484:
1485: a=matrix(1,npar,1,npar);
1486: y=matrix(1,npar,1,npar);
1487: x=vector(1,npar);
1488: indx=ivector(1,npar);
1489: for (i=1;i<=npar;i++)
1490: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1491: ludcmp(a,npar,indx,&pd);
1492:
1493: for (j=1;j<=npar;j++) {
1494: for (i=1;i<=npar;i++) x[i]=0;
1495: x[j]=1;
1496: lubksb(a,npar,indx,x);
1497: for (i=1;i<=npar;i++){
1498: matcov[i][j]=x[i];
1499: }
1500: }
1501:
1502: printf("\n#Hessian matrix#\n");
1503: fprintf(ficlog,"\n#Hessian matrix#\n");
1504: for (i=1;i<=npar;i++) {
1505: for (j=1;j<=npar;j++) {
1506: printf("%.3e ",hess[i][j]);
1507: fprintf(ficlog,"%.3e ",hess[i][j]);
1508: }
1509: printf("\n");
1510: fprintf(ficlog,"\n");
1511: }
1512:
1513: /* Recompute Inverse */
1514: for (i=1;i<=npar;i++)
1515: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1516: ludcmp(a,npar,indx,&pd);
1517:
1518: /* printf("\n#Hessian matrix recomputed#\n");
1519:
1520: for (j=1;j<=npar;j++) {
1521: for (i=1;i<=npar;i++) x[i]=0;
1522: x[j]=1;
1523: lubksb(a,npar,indx,x);
1524: for (i=1;i<=npar;i++){
1525: y[i][j]=x[i];
1526: printf("%.3e ",y[i][j]);
1527: fprintf(ficlog,"%.3e ",y[i][j]);
1528: }
1529: printf("\n");
1530: fprintf(ficlog,"\n");
1531: }
1532: */
1533:
1534: free_matrix(a,1,npar,1,npar);
1535: free_matrix(y,1,npar,1,npar);
1536: free_vector(x,1,npar);
1537: free_ivector(indx,1,npar);
1538: free_matrix(hess,1,npar,1,npar);
1539:
1540:
1541: }
1542:
1543: /*************** hessian matrix ****************/
1544: double hessii( double x[], double delta, int theta, double delti[])
1545: {
1546: int i;
1547: int l=1, lmax=20;
1548: double k1,k2;
1549: double p2[NPARMAX+1];
1550: double res;
1551: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1552: double fx;
1553: int k=0,kmax=10;
1554: double l1;
1555:
1556: fx=func(x);
1557: for (i=1;i<=npar;i++) p2[i]=x[i];
1558: for(l=0 ; l <=lmax; l++){
1559: l1=pow(10,l);
1560: delts=delt;
1561: for(k=1 ; k <kmax; k=k+1){
1562: delt = delta*(l1*k);
1563: p2[theta]=x[theta] +delt;
1564: k1=func(p2)-fx;
1565: p2[theta]=x[theta]-delt;
1566: k2=func(p2)-fx;
1567: /*res= (k1-2.0*fx+k2)/delt/delt; */
1568: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1569:
1570: #ifdef DEBUG
1571: 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);
1572: 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);
1573: #endif
1574: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1575: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1576: k=kmax;
1577: }
1578: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1579: k=kmax; l=lmax*10.;
1580: }
1581: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1582: delts=delt;
1583: }
1584: }
1585: }
1586: delti[theta]=delts;
1587: return res;
1588:
1589: }
1590:
1591: double hessij( double x[], double delti[], int thetai,int thetaj)
1592: {
1593: int i;
1594: int l=1, l1, lmax=20;
1595: double k1,k2,k3,k4,res,fx;
1596: double p2[NPARMAX+1];
1597: int k;
1598:
1599: fx=func(x);
1600: for (k=1; k<=2; k++) {
1601: for (i=1;i<=npar;i++) p2[i]=x[i];
1602: p2[thetai]=x[thetai]+delti[thetai]/k;
1603: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1604: k1=func(p2)-fx;
1605:
1606: p2[thetai]=x[thetai]+delti[thetai]/k;
1607: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1608: k2=func(p2)-fx;
1609:
1610: p2[thetai]=x[thetai]-delti[thetai]/k;
1611: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1612: k3=func(p2)-fx;
1613:
1614: p2[thetai]=x[thetai]-delti[thetai]/k;
1615: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1616: k4=func(p2)-fx;
1617: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1618: #ifdef DEBUG
1619: 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);
1620: 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);
1621: #endif
1622: }
1623: return res;
1624: }
1625:
1626: /************** Inverse of matrix **************/
1627: void ludcmp(double **a, int n, int *indx, double *d)
1628: {
1629: int i,imax,j,k;
1630: double big,dum,sum,temp;
1631: double *vv;
1632:
1633: vv=vector(1,n);
1634: *d=1.0;
1635: for (i=1;i<=n;i++) {
1636: big=0.0;
1637: for (j=1;j<=n;j++)
1638: if ((temp=fabs(a[i][j])) > big) big=temp;
1639: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1640: vv[i]=1.0/big;
1641: }
1642: for (j=1;j<=n;j++) {
1643: for (i=1;i<j;i++) {
1644: sum=a[i][j];
1645: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1646: a[i][j]=sum;
1647: }
1648: big=0.0;
1649: for (i=j;i<=n;i++) {
1650: sum=a[i][j];
1651: for (k=1;k<j;k++)
1652: sum -= a[i][k]*a[k][j];
1653: a[i][j]=sum;
1654: if ( (dum=vv[i]*fabs(sum)) >= big) {
1655: big=dum;
1656: imax=i;
1657: }
1658: }
1659: if (j != imax) {
1660: for (k=1;k<=n;k++) {
1661: dum=a[imax][k];
1662: a[imax][k]=a[j][k];
1663: a[j][k]=dum;
1664: }
1665: *d = -(*d);
1666: vv[imax]=vv[j];
1667: }
1668: indx[j]=imax;
1669: if (a[j][j] == 0.0) a[j][j]=TINY;
1670: if (j != n) {
1671: dum=1.0/(a[j][j]);
1672: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1673: }
1674: }
1675: free_vector(vv,1,n); /* Doesn't work */
1676: ;
1677: }
1678:
1679: void lubksb(double **a, int n, int *indx, double b[])
1680: {
1681: int i,ii=0,ip,j;
1682: double sum;
1683:
1684: for (i=1;i<=n;i++) {
1685: ip=indx[i];
1686: sum=b[ip];
1687: b[ip]=b[i];
1688: if (ii)
1689: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1690: else if (sum) ii=i;
1691: b[i]=sum;
1692: }
1693: for (i=n;i>=1;i--) {
1694: sum=b[i];
1695: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1696: b[i]=sum/a[i][i];
1697: }
1698: }
1699:
1700: /************ Frequencies ********************/
1701: 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)
1702: { /* Some frequencies */
1703:
1704: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1705: int first;
1706: double ***freq; /* Frequencies */
1707: double *pp, **prop;
1708: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1709: FILE *ficresp;
1710: char fileresp[FILENAMELENGTH];
1711:
1712: pp=vector(1,nlstate);
1713: prop=matrix(1,nlstate,iagemin,iagemax+3);
1714: strcpy(fileresp,"p");
1715: strcat(fileresp,fileres);
1716: if((ficresp=fopen(fileresp,"w"))==NULL) {
1717: printf("Problem with prevalence resultfile: %s\n", fileresp);
1718: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1719: exit(0);
1720: }
1721: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
1722: j1=0;
1723:
1724: j=cptcoveff;
1725: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1726:
1727: first=1;
1728:
1729: for(k1=1; k1<=j;k1++){
1730: for(i1=1; i1<=ncodemax[k1];i1++){
1731: j1++;
1732: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1733: scanf("%d", i);*/
1734: for (i=-1; i<=nlstate+ndeath; i++)
1735: for (jk=-1; jk<=nlstate+ndeath; jk++)
1736: for(m=iagemin; m <= iagemax+3; m++)
1737: freq[i][jk][m]=0;
1738:
1739: for (i=1; i<=nlstate; i++)
1740: for(m=iagemin; m <= iagemax+3; m++)
1741: prop[i][m]=0;
1742:
1743: dateintsum=0;
1744: k2cpt=0;
1745: for (i=1; i<=imx; i++) {
1746: bool=1;
1747: if (cptcovn>0) {
1748: for (z1=1; z1<=cptcoveff; z1++)
1749: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1750: bool=0;
1751: }
1752: if (bool==1){
1753: for(m=firstpass; m<=lastpass; m++){
1754: k2=anint[m][i]+(mint[m][i]/12.);
1755: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1756: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1757: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1758: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1759: if (m<lastpass) {
1760: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1761: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1762: }
1763:
1764: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1765: dateintsum=dateintsum+k2;
1766: k2cpt++;
1767: }
1768: /*}*/
1769: }
1770: }
1771: }
1772:
1773: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1774:
1775: if (cptcovn>0) {
1776: fprintf(ficresp, "\n#********** Variable ");
1777: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1778: fprintf(ficresp, "**********\n#");
1779: }
1780: for(i=1; i<=nlstate;i++)
1781: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1782: fprintf(ficresp, "\n");
1783:
1784: for(i=iagemin; i <= iagemax+3; i++){
1785: if(i==iagemax+3){
1786: fprintf(ficlog,"Total");
1787: }else{
1788: if(first==1){
1789: first=0;
1790: printf("See log file for details...\n");
1791: }
1792: fprintf(ficlog,"Age %d", i);
1793: }
1794: for(jk=1; jk <=nlstate ; jk++){
1795: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1796: pp[jk] += freq[jk][m][i];
1797: }
1798: for(jk=1; jk <=nlstate ; jk++){
1799: for(m=-1, pos=0; m <=0 ; m++)
1800: pos += freq[jk][m][i];
1801: if(pp[jk]>=1.e-10){
1802: if(first==1){
1803: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1804: }
1805: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1806: }else{
1807: if(first==1)
1808: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1809: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1810: }
1811: }
1812:
1813: for(jk=1; jk <=nlstate ; jk++){
1814: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1815: pp[jk] += freq[jk][m][i];
1816: }
1817: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
1818: pos += pp[jk];
1819: posprop += prop[jk][i];
1820: }
1821: for(jk=1; jk <=nlstate ; jk++){
1822: if(pos>=1.e-5){
1823: if(first==1)
1824: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1825: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1826: }else{
1827: if(first==1)
1828: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1829: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1830: }
1831: if( i <= iagemax){
1832: if(pos>=1.e-5){
1833: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1834: /*probs[i][jk][j1]= pp[jk]/pos;*/
1835: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1836: }
1837: else
1838: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1839: }
1840: }
1841:
1842: for(jk=-1; jk <=nlstate+ndeath; jk++)
1843: for(m=-1; m <=nlstate+ndeath; m++)
1844: if(freq[jk][m][i] !=0 ) {
1845: if(first==1)
1846: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1847: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1848: }
1849: if(i <= iagemax)
1850: fprintf(ficresp,"\n");
1851: if(first==1)
1852: printf("Others in log...\n");
1853: fprintf(ficlog,"\n");
1854: }
1855: }
1856: }
1857: dateintmean=dateintsum/k2cpt;
1858:
1859: fclose(ficresp);
1860: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
1861: free_vector(pp,1,nlstate);
1862: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1863: /* End of Freq */
1864: }
1865:
1866: /************ Prevalence ********************/
1867: 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)
1868: {
1869: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
1870: in each health status at the date of interview (if between dateprev1 and dateprev2).
1871: We still use firstpass and lastpass as another selection.
1872: */
1873:
1874: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1875: double ***freq; /* Frequencies */
1876: double *pp, **prop;
1877: double pos,posprop;
1878: double y2; /* in fractional years */
1879: int iagemin, iagemax;
1880:
1881: iagemin= (int) agemin;
1882: iagemax= (int) agemax;
1883: /*pp=vector(1,nlstate);*/
1884: prop=matrix(1,nlstate,iagemin,iagemax+3);
1885: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1886: j1=0;
1887:
1888: j=cptcoveff;
1889: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1890:
1891: for(k1=1; k1<=j;k1++){
1892: for(i1=1; i1<=ncodemax[k1];i1++){
1893: j1++;
1894:
1895: for (i=1; i<=nlstate; i++)
1896: for(m=iagemin; m <= iagemax+3; m++)
1897: prop[i][m]=0.0;
1898:
1899: for (i=1; i<=imx; i++) { /* Each individual */
1900: bool=1;
1901: if (cptcovn>0) {
1902: for (z1=1; z1<=cptcoveff; z1++)
1903: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1904: bool=0;
1905: }
1906: if (bool==1) {
1907: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
1908: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
1909: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1910: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1911: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1912: 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);
1913: if (s[m][i]>0 && s[m][i]<=nlstate) {
1914: /*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]]);*/
1915: prop[s[m][i]][(int)agev[m][i]] += weight[i];
1916: prop[s[m][i]][iagemax+3] += weight[i];
1917: }
1918: }
1919: } /* end selection of waves */
1920: }
1921: }
1922: for(i=iagemin; i <= iagemax+3; i++){
1923:
1924: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
1925: posprop += prop[jk][i];
1926: }
1927:
1928: for(jk=1; jk <=nlstate ; jk++){
1929: if( i <= iagemax){
1930: if(posprop>=1.e-5){
1931: probs[i][jk][j1]= prop[jk][i]/posprop;
1932: }
1933: }
1934: }/* end jk */
1935: }/* end i */
1936: } /* end i1 */
1937: } /* end k1 */
1938:
1939: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
1940: /*free_vector(pp,1,nlstate);*/
1941: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
1942: } /* End of prevalence */
1943:
1944: /************* Waves Concatenation ***************/
1945:
1946: 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)
1947: {
1948: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1949: Death is a valid wave (if date is known).
1950: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1951: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1952: and mw[mi+1][i]. dh depends on stepm.
1953: */
1954:
1955: int i, mi, m;
1956: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1957: double sum=0., jmean=0.;*/
1958: int first;
1959: int j, k=0,jk, ju, jl;
1960: double sum=0.;
1961: first=0;
1962: jmin=1e+5;
1963: jmax=-1;
1964: jmean=0.;
1965: for(i=1; i<=imx; i++){
1966: mi=0;
1967: m=firstpass;
1968: while(s[m][i] <= nlstate){
1969: if(s[m][i]>=1)
1970: mw[++mi][i]=m;
1971: if(m >=lastpass)
1972: break;
1973: else
1974: m++;
1975: }/* end while */
1976: if (s[m][i] > nlstate){
1977: mi++; /* Death is another wave */
1978: /* if(mi==0) never been interviewed correctly before death */
1979: /* Only death is a correct wave */
1980: mw[mi][i]=m;
1981: }
1982:
1983: wav[i]=mi;
1984: if(mi==0){
1985: if(first==0){
1986: printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
1987: first=1;
1988: }
1989: if(first==1){
1990: fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
1991: }
1992: } /* end mi==0 */
1993: } /* End individuals */
1994:
1995: for(i=1; i<=imx; i++){
1996: for(mi=1; mi<wav[i];mi++){
1997: if (stepm <=0)
1998: dh[mi][i]=1;
1999: else{
2000: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2001: if (agedc[i] < 2*AGESUP) {
2002: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2003: if(j==0) j=1; /* Survives at least one month after exam */
2004: else if(j<0){
2005: 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]);
2006: j=1; /* Careful Patch */
2007: 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);
2008: 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]);
2009: 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);
2010: }
2011: k=k+1;
2012: if (j >= jmax) jmax=j;
2013: if (j <= jmin) jmin=j;
2014: sum=sum+j;
2015: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2016: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2017: }
2018: }
2019: else{
2020: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2021: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2022: k=k+1;
2023: if (j >= jmax) jmax=j;
2024: else if (j <= jmin)jmin=j;
2025: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2026: /*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]);*/
2027: if(j<0){
2028: 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]);
2029: 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]);
2030: }
2031: sum=sum+j;
2032: }
2033: jk= j/stepm;
2034: jl= j -jk*stepm;
2035: ju= j -(jk+1)*stepm;
2036: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2037: if(jl==0){
2038: dh[mi][i]=jk;
2039: bh[mi][i]=0;
2040: }else{ /* We want a negative bias in order to only have interpolation ie
2041: * at the price of an extra matrix product in likelihood */
2042: dh[mi][i]=jk+1;
2043: bh[mi][i]=ju;
2044: }
2045: }else{
2046: if(jl <= -ju){
2047: dh[mi][i]=jk;
2048: bh[mi][i]=jl; /* bias is positive if real duration
2049: * is higher than the multiple of stepm and negative otherwise.
2050: */
2051: }
2052: else{
2053: dh[mi][i]=jk+1;
2054: bh[mi][i]=ju;
2055: }
2056: if(dh[mi][i]==0){
2057: dh[mi][i]=1; /* At least one step */
2058: bh[mi][i]=ju; /* At least one step */
2059: /* 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);*/
2060: }
2061: } /* end if mle */
2062: }
2063: } /* end wave */
2064: }
2065: jmean=sum/k;
2066: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2067: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2068: }
2069:
2070: /*********** Tricode ****************************/
2071: void tricode(int *Tvar, int **nbcode, int imx)
2072: {
2073:
2074: int Ndum[20],ij=1, k, j, i, maxncov=19;
2075: int cptcode=0;
2076: cptcoveff=0;
2077:
2078: for (k=0; k<maxncov; k++) Ndum[k]=0;
2079: for (k=1; k<=7; k++) ncodemax[k]=0;
2080:
2081: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
2082: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2083: modality*/
2084: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2085: Ndum[ij]++; /*store the modality */
2086: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2087: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2088: Tvar[j]. If V=sex and male is 0 and
2089: female is 1, then cptcode=1.*/
2090: }
2091:
2092: for (i=0; i<=cptcode; i++) {
2093: 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 */
2094: }
2095:
2096: ij=1;
2097: for (i=1; i<=ncodemax[j]; i++) {
2098: for (k=0; k<= maxncov; k++) {
2099: if (Ndum[k] != 0) {
2100: nbcode[Tvar[j]][ij]=k;
2101: /* 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; */
2102:
2103: ij++;
2104: }
2105: if (ij > ncodemax[j]) break;
2106: }
2107: }
2108: }
2109:
2110: for (k=0; k< maxncov; k++) Ndum[k]=0;
2111:
2112: for (i=1; i<=ncovmodel-2; i++) {
2113: /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2114: ij=Tvar[i];
2115: Ndum[ij]++;
2116: }
2117:
2118: ij=1;
2119: for (i=1; i<= maxncov; i++) {
2120: if((Ndum[i]!=0) && (i<=ncovcol)){
2121: Tvaraff[ij]=i; /*For printing */
2122: ij++;
2123: }
2124: }
2125:
2126: cptcoveff=ij-1; /*Number of simple covariates*/
2127: }
2128:
2129: /*********** Health Expectancies ****************/
2130:
2131: 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 )
2132:
2133: {
2134: /* Health expectancies */
2135: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
2136: double age, agelim, hf;
2137: double ***p3mat,***varhe;
2138: double **dnewm,**doldm;
2139: double *xp;
2140: double **gp, **gm;
2141: double ***gradg, ***trgradg;
2142: int theta;
2143:
2144: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2145: xp=vector(1,npar);
2146: dnewm=matrix(1,nlstate*nlstate,1,npar);
2147: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2148:
2149: fprintf(ficreseij,"# Health expectancies\n");
2150: fprintf(ficreseij,"# Age");
2151: for(i=1; i<=nlstate;i++)
2152: for(j=1; j<=nlstate;j++)
2153: fprintf(ficreseij," %1d-%1d (SE)",i,j);
2154: fprintf(ficreseij,"\n");
2155:
2156: if(estepm < stepm){
2157: printf ("Problem %d lower than %d\n",estepm, stepm);
2158: }
2159: else hstepm=estepm;
2160: /* We compute the life expectancy from trapezoids spaced every estepm months
2161: * This is mainly to measure the difference between two models: for example
2162: * if stepm=24 months pijx are given only every 2 years and by summing them
2163: * we are calculating an estimate of the Life Expectancy assuming a linear
2164: * progression in between and thus overestimating or underestimating according
2165: * to the curvature of the survival function. If, for the same date, we
2166: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2167: * to compare the new estimate of Life expectancy with the same linear
2168: * hypothesis. A more precise result, taking into account a more precise
2169: * curvature will be obtained if estepm is as small as stepm. */
2170:
2171: /* For example we decided to compute the life expectancy with the smallest unit */
2172: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2173: nhstepm is the number of hstepm from age to agelim
2174: nstepm is the number of stepm from age to agelin.
2175: Look at hpijx to understand the reason of that which relies in memory size
2176: and note for a fixed period like estepm months */
2177: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2178: survival function given by stepm (the optimization length). Unfortunately it
2179: means that if the survival funtion is printed only each two years of age and if
2180: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2181: results. So we changed our mind and took the option of the best precision.
2182: */
2183: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2184:
2185: agelim=AGESUP;
2186: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2187: /* nhstepm age range expressed in number of stepm */
2188: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2189: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2190: /* if (stepm >= YEARM) hstepm=1;*/
2191: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2192: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2193: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2194: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2195: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2196:
2197: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2198: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2199: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
2200:
2201:
2202: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2203:
2204: /* Computing Variances of health expectancies */
2205:
2206: for(theta=1; theta <=npar; theta++){
2207: for(i=1; i<=npar; i++){
2208: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2209: }
2210: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2211:
2212: cptj=0;
2213: for(j=1; j<= nlstate; j++){
2214: for(i=1; i<=nlstate; i++){
2215: cptj=cptj+1;
2216: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2217: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2218: }
2219: }
2220: }
2221:
2222:
2223: for(i=1; i<=npar; i++)
2224: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2225: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2226:
2227: cptj=0;
2228: for(j=1; j<= nlstate; j++){
2229: for(i=1;i<=nlstate;i++){
2230: cptj=cptj+1;
2231: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
2232:
2233: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2234: }
2235: }
2236: }
2237: for(j=1; j<= nlstate*nlstate; j++)
2238: for(h=0; h<=nhstepm-1; h++){
2239: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2240: }
2241: }
2242:
2243: /* End theta */
2244:
2245: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2246:
2247: for(h=0; h<=nhstepm-1; h++)
2248: for(j=1; j<=nlstate*nlstate;j++)
2249: for(theta=1; theta <=npar; theta++)
2250: trgradg[h][j][theta]=gradg[h][theta][j];
2251:
2252:
2253: for(i=1;i<=nlstate*nlstate;i++)
2254: for(j=1;j<=nlstate*nlstate;j++)
2255: varhe[i][j][(int)age] =0.;
2256:
2257: printf("%d|",(int)age);fflush(stdout);
2258: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2259: for(h=0;h<=nhstepm-1;h++){
2260: for(k=0;k<=nhstepm-1;k++){
2261: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2262: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2263: for(i=1;i<=nlstate*nlstate;i++)
2264: for(j=1;j<=nlstate*nlstate;j++)
2265: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2266: }
2267: }
2268: /* Computing expectancies */
2269: for(i=1; i<=nlstate;i++)
2270: for(j=1; j<=nlstate;j++)
2271: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2272: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2273:
2274: /* 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]);*/
2275:
2276: }
2277:
2278: fprintf(ficreseij,"%3.0f",age );
2279: cptj=0;
2280: for(i=1; i<=nlstate;i++)
2281: for(j=1; j<=nlstate;j++){
2282: cptj++;
2283: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2284: }
2285: fprintf(ficreseij,"\n");
2286:
2287: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2288: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2289: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2290: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2291: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2292: }
2293: printf("\n");
2294: fprintf(ficlog,"\n");
2295:
2296: free_vector(xp,1,npar);
2297: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2298: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2299: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2300: }
2301:
2302: /************ Variance ******************/
2303: 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)
2304: {
2305: /* Variance of health expectancies */
2306: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2307: /* double **newm;*/
2308: double **dnewm,**doldm;
2309: double **dnewmp,**doldmp;
2310: int i, j, nhstepm, hstepm, h, nstepm ;
2311: int k, cptcode;
2312: double *xp;
2313: double **gp, **gm; /* for var eij */
2314: double ***gradg, ***trgradg; /*for var eij */
2315: double **gradgp, **trgradgp; /* for var p point j */
2316: double *gpp, *gmp; /* for var p point j */
2317: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2318: double ***p3mat;
2319: double age,agelim, hf;
2320: double ***mobaverage;
2321: int theta;
2322: char digit[4];
2323: char digitp[25];
2324:
2325: char fileresprobmorprev[FILENAMELENGTH];
2326:
2327: if(popbased==1){
2328: if(mobilav!=0)
2329: strcpy(digitp,"-populbased-mobilav-");
2330: else strcpy(digitp,"-populbased-nomobil-");
2331: }
2332: else
2333: strcpy(digitp,"-stablbased-");
2334:
2335: if (mobilav!=0) {
2336: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2337: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2338: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2339: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2340: }
2341: }
2342:
2343: strcpy(fileresprobmorprev,"prmorprev");
2344: sprintf(digit,"%-d",ij);
2345: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2346: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2347: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2348: strcat(fileresprobmorprev,fileres);
2349: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2350: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2351: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2352: }
2353: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2354: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2355: 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);
2356: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2357: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2358: fprintf(ficresprobmorprev," p.%-d SE",j);
2359: for(i=1; i<=nlstate;i++)
2360: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2361: }
2362: fprintf(ficresprobmorprev,"\n");
2363: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2364: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2365: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2366: exit(0);
2367: }
2368: else{
2369: fprintf(ficgp,"\n# Routine varevsij");
2370: }
2371: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2372: printf("Problem with html file: %s\n", optionfilehtm);
2373: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2374: exit(0);
2375: }
2376: else{
2377: 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");
2378: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2379: }
2380: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2381:
2382: 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");
2383: fprintf(ficresvij,"# Age");
2384: for(i=1; i<=nlstate;i++)
2385: for(j=1; j<=nlstate;j++)
2386: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2387: fprintf(ficresvij,"\n");
2388:
2389: xp=vector(1,npar);
2390: dnewm=matrix(1,nlstate,1,npar);
2391: doldm=matrix(1,nlstate,1,nlstate);
2392: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2393: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2394:
2395: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2396: gpp=vector(nlstate+1,nlstate+ndeath);
2397: gmp=vector(nlstate+1,nlstate+ndeath);
2398: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2399:
2400: if(estepm < stepm){
2401: printf ("Problem %d lower than %d\n",estepm, stepm);
2402: }
2403: else hstepm=estepm;
2404: /* For example we decided to compute the life expectancy with the smallest unit */
2405: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2406: nhstepm is the number of hstepm from age to agelim
2407: nstepm is the number of stepm from age to agelin.
2408: Look at hpijx to understand the reason of that which relies in memory size
2409: and note for a fixed period like k years */
2410: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2411: survival function given by stepm (the optimization length). Unfortunately it
2412: means that if the survival funtion is printed every two years of age and if
2413: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2414: results. So we changed our mind and took the option of the best precision.
2415: */
2416: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2417: agelim = AGESUP;
2418: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2419: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2420: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2421: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2422: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2423: gp=matrix(0,nhstepm,1,nlstate);
2424: gm=matrix(0,nhstepm,1,nlstate);
2425:
2426:
2427: for(theta=1; theta <=npar; theta++){
2428: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2429: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2430: }
2431: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2432: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2433:
2434: if (popbased==1) {
2435: if(mobilav ==0){
2436: for(i=1; i<=nlstate;i++)
2437: prlim[i][i]=probs[(int)age][i][ij];
2438: }else{ /* mobilav */
2439: for(i=1; i<=nlstate;i++)
2440: prlim[i][i]=mobaverage[(int)age][i][ij];
2441: }
2442: }
2443:
2444: for(j=1; j<= nlstate; j++){
2445: for(h=0; h<=nhstepm; h++){
2446: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2447: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2448: }
2449: }
2450: /* This for computing probability of death (h=1 means
2451: computed over hstepm matrices product = hstepm*stepm months)
2452: as a weighted average of prlim.
2453: */
2454: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2455: for(i=1,gpp[j]=0.; i<= nlstate; i++)
2456: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2457: }
2458: /* end probability of death */
2459:
2460: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
2461: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2462: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2463: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2464:
2465: if (popbased==1) {
2466: if(mobilav ==0){
2467: for(i=1; i<=nlstate;i++)
2468: prlim[i][i]=probs[(int)age][i][ij];
2469: }else{ /* mobilav */
2470: for(i=1; i<=nlstate;i++)
2471: prlim[i][i]=mobaverage[(int)age][i][ij];
2472: }
2473: }
2474:
2475: for(j=1; j<= nlstate; j++){
2476: for(h=0; h<=nhstepm; h++){
2477: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2478: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2479: }
2480: }
2481: /* This for computing probability of death (h=1 means
2482: computed over hstepm matrices product = hstepm*stepm months)
2483: as a weighted average of prlim.
2484: */
2485: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2486: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2487: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2488: }
2489: /* end probability of death */
2490:
2491: for(j=1; j<= nlstate; j++) /* vareij */
2492: for(h=0; h<=nhstepm; h++){
2493: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2494: }
2495:
2496: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2497: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2498: }
2499:
2500: } /* End theta */
2501:
2502: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2503:
2504: for(h=0; h<=nhstepm; h++) /* veij */
2505: for(j=1; j<=nlstate;j++)
2506: for(theta=1; theta <=npar; theta++)
2507: trgradg[h][j][theta]=gradg[h][theta][j];
2508:
2509: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
2510: for(theta=1; theta <=npar; theta++)
2511: trgradgp[j][theta]=gradgp[theta][j];
2512:
2513:
2514: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2515: for(i=1;i<=nlstate;i++)
2516: for(j=1;j<=nlstate;j++)
2517: vareij[i][j][(int)age] =0.;
2518:
2519: for(h=0;h<=nhstepm;h++){
2520: for(k=0;k<=nhstepm;k++){
2521: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2522: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2523: for(i=1;i<=nlstate;i++)
2524: for(j=1;j<=nlstate;j++)
2525: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2526: }
2527: }
2528:
2529: /* pptj */
2530: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2531: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
2532: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2533: for(i=nlstate+1;i<=nlstate+ndeath;i++)
2534: varppt[j][i]=doldmp[j][i];
2535: /* end ppptj */
2536: /* x centered again */
2537: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2538: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2539:
2540: if (popbased==1) {
2541: if(mobilav ==0){
2542: for(i=1; i<=nlstate;i++)
2543: prlim[i][i]=probs[(int)age][i][ij];
2544: }else{ /* mobilav */
2545: for(i=1; i<=nlstate;i++)
2546: prlim[i][i]=mobaverage[(int)age][i][ij];
2547: }
2548: }
2549:
2550: /* This for computing probability of death (h=1 means
2551: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2552: as a weighted average of prlim.
2553: */
2554: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2555: for(i=1,gmp[j]=0.;i<= nlstate; i++)
2556: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2557: }
2558: /* end probability of death */
2559:
2560: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2561: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2562: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2563: for(i=1; i<=nlstate;i++){
2564: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2565: }
2566: }
2567: fprintf(ficresprobmorprev,"\n");
2568:
2569: fprintf(ficresvij,"%.0f ",age );
2570: for(i=1; i<=nlstate;i++)
2571: for(j=1; j<=nlstate;j++){
2572: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2573: }
2574: fprintf(ficresvij,"\n");
2575: free_matrix(gp,0,nhstepm,1,nlstate);
2576: free_matrix(gm,0,nhstepm,1,nlstate);
2577: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2578: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2579: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2580: } /* End age */
2581: free_vector(gpp,nlstate+1,nlstate+ndeath);
2582: free_vector(gmp,nlstate+1,nlstate+ndeath);
2583: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2584: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2585: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2586: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2587: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
2588: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2589: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2590: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
2591: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",fileresprobmorprev);
2592: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
2593: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
2594: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
2595: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
2596: /* 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);
2597: */
2598: fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
2599:
2600: free_vector(xp,1,npar);
2601: free_matrix(doldm,1,nlstate,1,nlstate);
2602: free_matrix(dnewm,1,nlstate,1,npar);
2603: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2604: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2605: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2606: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2607: fclose(ficresprobmorprev);
2608: fclose(ficgp);
2609: fclose(fichtm);
2610: } /* end varevsij */
2611:
2612: /************ Variance of prevlim ******************/
2613: 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)
2614: {
2615: /* Variance of prevalence limit */
2616: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
2617: double **newm;
2618: double **dnewm,**doldm;
2619: int i, j, nhstepm, hstepm;
2620: int k, cptcode;
2621: double *xp;
2622: double *gp, *gm;
2623: double **gradg, **trgradg;
2624: double age,agelim;
2625: int theta;
2626:
2627: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
2628: fprintf(ficresvpl,"# Age");
2629: for(i=1; i<=nlstate;i++)
2630: fprintf(ficresvpl," %1d-%1d",i,i);
2631: fprintf(ficresvpl,"\n");
2632:
2633: xp=vector(1,npar);
2634: dnewm=matrix(1,nlstate,1,npar);
2635: doldm=matrix(1,nlstate,1,nlstate);
2636:
2637: hstepm=1*YEARM; /* Every year of age */
2638: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2639: agelim = AGESUP;
2640: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2641: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2642: if (stepm >= YEARM) hstepm=1;
2643: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2644: gradg=matrix(1,npar,1,nlstate);
2645: gp=vector(1,nlstate);
2646: gm=vector(1,nlstate);
2647:
2648: for(theta=1; theta <=npar; theta++){
2649: for(i=1; i<=npar; i++){ /* Computes gradient */
2650: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2651: }
2652: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2653: for(i=1;i<=nlstate;i++)
2654: gp[i] = prlim[i][i];
2655:
2656: for(i=1; i<=npar; i++) /* Computes gradient */
2657: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2658: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2659: for(i=1;i<=nlstate;i++)
2660: gm[i] = prlim[i][i];
2661:
2662: for(i=1;i<=nlstate;i++)
2663: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2664: } /* End theta */
2665:
2666: trgradg =matrix(1,nlstate,1,npar);
2667:
2668: for(j=1; j<=nlstate;j++)
2669: for(theta=1; theta <=npar; theta++)
2670: trgradg[j][theta]=gradg[theta][j];
2671:
2672: for(i=1;i<=nlstate;i++)
2673: varpl[i][(int)age] =0.;
2674: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2675: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2676: for(i=1;i<=nlstate;i++)
2677: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2678:
2679: fprintf(ficresvpl,"%.0f ",age );
2680: for(i=1; i<=nlstate;i++)
2681: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2682: fprintf(ficresvpl,"\n");
2683: free_vector(gp,1,nlstate);
2684: free_vector(gm,1,nlstate);
2685: free_matrix(gradg,1,npar,1,nlstate);
2686: free_matrix(trgradg,1,nlstate,1,npar);
2687: } /* End age */
2688:
2689: free_vector(xp,1,npar);
2690: free_matrix(doldm,1,nlstate,1,npar);
2691: free_matrix(dnewm,1,nlstate,1,nlstate);
2692:
2693: }
2694:
2695: /************ Variance of one-step probabilities ******************/
2696: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2697: {
2698: int i, j=0, i1, k1, l1, t, tj;
2699: int k2, l2, j1, z1;
2700: int k=0,l, cptcode;
2701: int first=1, first1;
2702: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2703: double **dnewm,**doldm;
2704: double *xp;
2705: double *gp, *gm;
2706: double **gradg, **trgradg;
2707: double **mu;
2708: double age,agelim, cov[NCOVMAX];
2709: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2710: int theta;
2711: char fileresprob[FILENAMELENGTH];
2712: char fileresprobcov[FILENAMELENGTH];
2713: char fileresprobcor[FILENAMELENGTH];
2714:
2715: double ***varpij;
2716:
2717: strcpy(fileresprob,"prob");
2718: strcat(fileresprob,fileres);
2719: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2720: printf("Problem with resultfile: %s\n", fileresprob);
2721: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2722: }
2723: strcpy(fileresprobcov,"probcov");
2724: strcat(fileresprobcov,fileres);
2725: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2726: printf("Problem with resultfile: %s\n", fileresprobcov);
2727: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2728: }
2729: strcpy(fileresprobcor,"probcor");
2730: strcat(fileresprobcor,fileres);
2731: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2732: printf("Problem with resultfile: %s\n", fileresprobcor);
2733: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2734: }
2735: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2736: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2737: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2738: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2739: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2740: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2741:
2742: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2743: fprintf(ficresprob,"# Age");
2744: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2745: fprintf(ficresprobcov,"# Age");
2746: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2747: fprintf(ficresprobcov,"# Age");
2748:
2749:
2750: for(i=1; i<=nlstate;i++)
2751: for(j=1; j<=(nlstate+ndeath);j++){
2752: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2753: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2754: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2755: }
2756: /* fprintf(ficresprob,"\n");
2757: fprintf(ficresprobcov,"\n");
2758: fprintf(ficresprobcor,"\n");
2759: */
2760: xp=vector(1,npar);
2761: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2762: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2763: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2764: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2765: first=1;
2766: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2767: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2768: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2769: exit(0);
2770: }
2771: else{
2772: fprintf(ficgp,"\n# Routine varprob");
2773: }
2774: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2775: printf("Problem with html file: %s\n", optionfilehtm);
2776: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2777: exit(0);
2778: }
2779: else{
2780: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2781: fprintf(fichtm,"\n");
2782:
2783: fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
2784: fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
2785: fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
2786:
2787: }
2788:
2789: cov[1]=1;
2790: tj=cptcoveff;
2791: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2792: j1=0;
2793: for(t=1; t<=tj;t++){
2794: for(i1=1; i1<=ncodemax[t];i1++){
2795: j1++;
2796: if (cptcovn>0) {
2797: fprintf(ficresprob, "\n#********** Variable ");
2798: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2799: fprintf(ficresprob, "**********\n#\n");
2800: fprintf(ficresprobcov, "\n#********** Variable ");
2801: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2802: fprintf(ficresprobcov, "**********\n#\n");
2803:
2804: fprintf(ficgp, "\n#********** Variable ");
2805: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2806: fprintf(ficgp, "**********\n#\n");
2807:
2808:
2809: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2810: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2811: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2812:
2813: fprintf(ficresprobcor, "\n#********** Variable ");
2814: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2815: fprintf(ficresprobcor, "**********\n#");
2816: }
2817:
2818: for (age=bage; age<=fage; age ++){
2819: cov[2]=age;
2820: for (k=1; k<=cptcovn;k++) {
2821: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2822: }
2823: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2824: for (k=1; k<=cptcovprod;k++)
2825: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2826:
2827: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2828: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2829: gp=vector(1,(nlstate)*(nlstate+ndeath));
2830: gm=vector(1,(nlstate)*(nlstate+ndeath));
2831:
2832: for(theta=1; theta <=npar; theta++){
2833: for(i=1; i<=npar; i++)
2834: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
2835:
2836: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2837:
2838: k=0;
2839: for(i=1; i<= (nlstate); i++){
2840: for(j=1; j<=(nlstate+ndeath);j++){
2841: k=k+1;
2842: gp[k]=pmmij[i][j];
2843: }
2844: }
2845:
2846: for(i=1; i<=npar; i++)
2847: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
2848:
2849: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2850: k=0;
2851: for(i=1; i<=(nlstate); i++){
2852: for(j=1; j<=(nlstate+ndeath);j++){
2853: k=k+1;
2854: gm[k]=pmmij[i][j];
2855: }
2856: }
2857:
2858: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
2859: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
2860: }
2861:
2862: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2863: for(theta=1; theta <=npar; theta++)
2864: trgradg[j][theta]=gradg[theta][j];
2865:
2866: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2867: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
2868: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2869: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2870: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2871: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2872:
2873: pmij(pmmij,cov,ncovmodel,x,nlstate);
2874:
2875: k=0;
2876: for(i=1; i<=(nlstate); i++){
2877: for(j=1; j<=(nlstate+ndeath);j++){
2878: k=k+1;
2879: mu[k][(int) age]=pmmij[i][j];
2880: }
2881: }
2882: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2883: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2884: varpij[i][j][(int)age] = doldm[i][j];
2885:
2886: /*printf("\n%d ",(int)age);
2887: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2888: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2889: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2890: }*/
2891:
2892: fprintf(ficresprob,"\n%d ",(int)age);
2893: fprintf(ficresprobcov,"\n%d ",(int)age);
2894: fprintf(ficresprobcor,"\n%d ",(int)age);
2895:
2896: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2897: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2898: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2899: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2900: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2901: }
2902: i=0;
2903: for (k=1; k<=(nlstate);k++){
2904: for (l=1; l<=(nlstate+ndeath);l++){
2905: i=i++;
2906: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2907: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2908: for (j=1; j<=i;j++){
2909: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2910: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
2911: }
2912: }
2913: }/* end of loop for state */
2914: } /* end of loop for age */
2915:
2916: /* Confidence intervalle of pij */
2917: /*
2918: fprintf(ficgp,"\nset noparametric;unset label");
2919: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
2920: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2921: 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);
2922: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
2923: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
2924: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
2925: */
2926:
2927: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
2928: first1=1;
2929: for (k2=1; k2<=(nlstate);k2++){
2930: for (l2=1; l2<=(nlstate+ndeath);l2++){
2931: if(l2==k2) continue;
2932: j=(k2-1)*(nlstate+ndeath)+l2;
2933: for (k1=1; k1<=(nlstate);k1++){
2934: for (l1=1; l1<=(nlstate+ndeath);l1++){
2935: if(l1==k1) continue;
2936: i=(k1-1)*(nlstate+ndeath)+l1;
2937: if(i<=j) continue;
2938: for (age=bage; age<=fage; age ++){
2939: if ((int)age %5==0){
2940: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
2941: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
2942: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
2943: mu1=mu[i][(int) age]/stepm*YEARM ;
2944: mu2=mu[j][(int) age]/stepm*YEARM;
2945: c12=cv12/sqrt(v1*v2);
2946: /* Computing eigen value of matrix of covariance */
2947: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2948: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2949: /* Eigen vectors */
2950: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
2951: /*v21=sqrt(1.-v11*v11); *//* error */
2952: v21=(lc1-v1)/cv12*v11;
2953: v12=-v21;
2954: v22=v11;
2955: tnalp=v21/v11;
2956: if(first1==1){
2957: first1=0;
2958: 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);
2959: }
2960: 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);
2961: /*printf(fignu*/
2962: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
2963: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
2964: if(first==1){
2965: first=0;
2966: fprintf(ficgp,"\nset parametric;unset label");
2967: 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);
2968: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2969: fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
2970: fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
2971: fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
2972: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
2973: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2974: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2975: 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",\
2976: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2977: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2978: }else{
2979: first=0;
2980: fprintf(fichtm," %d (%.3f),",(int) age, c12);
2981: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2982: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2983: 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",\
2984: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2985: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2986: }/* if first */
2987: } /* age mod 5 */
2988: } /* end loop age */
2989: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
2990: first=1;
2991: } /*l12 */
2992: } /* k12 */
2993: } /*l1 */
2994: }/* k1 */
2995: } /* loop covariates */
2996: }
2997: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
2998: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
2999: free_vector(xp,1,npar);
3000: fclose(ficresprob);
3001: fclose(ficresprobcov);
3002: fclose(ficresprobcor);
3003: fclose(ficgp);
3004: fclose(fichtm);
3005: }
3006:
3007:
3008: /******************* Printing html file ***********/
3009: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3010: int lastpass, int stepm, int weightopt, char model[],\
3011: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3012: int popforecast, int estepm ,\
3013: double jprev1, double mprev1,double anprev1, \
3014: double jprev2, double mprev2,double anprev2){
3015: int jj1, k1, i1, cpt;
3016: /*char optionfilehtm[FILENAMELENGTH];*/
3017: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
3018: printf("Problem with %s \n",optionfilehtm), exit(0);
3019: fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
3020: }
3021:
3022: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
3023: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n \
3024: - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n \
3025: - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n \
3026: - Life expectancies by age and initial health status (estepm=%2d months): \
3027: <a href=\"e%s\">e%s</a> <br>\n</li>", \
3028: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
3029:
3030: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3031:
3032: m=cptcoveff;
3033: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3034:
3035: jj1=0;
3036: for(k1=1; k1<=m;k1++){
3037: for(i1=1; i1<=ncodemax[k1];i1++){
3038: jj1++;
3039: if (cptcovn > 0) {
3040: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3041: for (cpt=1; cpt<=cptcoveff;cpt++)
3042: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3043: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3044: }
3045: /* Pij */
3046: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: pe%s%d1.png<br> \
3047: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
3048: /* Quasi-incidences */
3049: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3050: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br> \
3051: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
3052: /* Stable prevalence in each health state */
3053: for(cpt=1; cpt<nlstate;cpt++){
3054: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
3055: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
3056: }
3057: for(cpt=1; cpt<=nlstate;cpt++) {
3058: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br> \
3059: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
3060: }
3061: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3062: health expectancies in states (1) and (2): e%s%d.png<br>\
3063: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
3064: } /* end i1 */
3065: }/* End k1 */
3066: fprintf(fichtm,"</ul>");
3067:
3068:
3069: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
3070: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
3071: - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n\
3072: - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n\
3073: - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n\
3074: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n\
3075: - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n\
3076: - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
3077:
3078: /* if(popforecast==1) fprintf(fichtm,"\n */
3079: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3080: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3081: /* <br>",fileres,fileres,fileres,fileres); */
3082: /* else */
3083: /* 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); */
3084: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3085:
3086: m=cptcoveff;
3087: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3088:
3089: jj1=0;
3090: for(k1=1; k1<=m;k1++){
3091: for(i1=1; i1<=ncodemax[k1];i1++){
3092: jj1++;
3093: if (cptcovn > 0) {
3094: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3095: for (cpt=1; cpt<=cptcoveff;cpt++)
3096: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3097: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3098: }
3099: for(cpt=1; cpt<=nlstate;cpt++) {
3100: fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
3101: interval) in state (%d): v%s%d%d.png <br>\
3102: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
3103: }
3104: } /* end i1 */
3105: }/* End k1 */
3106: fprintf(fichtm,"</ul>");
3107: fclose(fichtm);
3108: }
3109:
3110: /******************* Gnuplot file **************/
3111: void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3112:
3113: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3114: int ng;
3115: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
3116: printf("Problem with file %s",optionfilegnuplot);
3117: fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
3118: }
3119:
3120: /*#ifdef windows */
3121: fprintf(ficgp,"cd \"%s\" \n",pathc);
3122: /*#endif */
3123: m=pow(2,cptcoveff);
3124:
3125: /* 1eme*/
3126: for (cpt=1; cpt<= nlstate ; cpt ++) {
3127: for (k1=1; k1<= m ; k1 ++) {
3128: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
3129: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
3130:
3131: for (i=1; i<= nlstate ; i ++) {
3132: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3133: else fprintf(ficgp," \%%*lf (\%%*lf)");
3134: }
3135: fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
3136: for (i=1; i<= nlstate ; i ++) {
3137: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3138: else fprintf(ficgp," \%%*lf (\%%*lf)");
3139: }
3140: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
3141: for (i=1; i<= nlstate ; i ++) {
3142: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3143: else fprintf(ficgp," \%%*lf (\%%*lf)");
3144: }
3145: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
3146: }
3147: }
3148: /*2 eme*/
3149:
3150: for (k1=1; k1<= m ; k1 ++) {
3151: fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
3152: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3153:
3154: for (i=1; i<= nlstate+1 ; i ++) {
3155: k=2*i;
3156: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
3157: for (j=1; j<= nlstate+1 ; j ++) {
3158: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3159: else fprintf(ficgp," \%%*lf (\%%*lf)");
3160: }
3161: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3162: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3163: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
3164: for (j=1; j<= nlstate+1 ; j ++) {
3165: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3166: else fprintf(ficgp," \%%*lf (\%%*lf)");
3167: }
3168: fprintf(ficgp,"\" t\"\" w l 0,");
3169: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
3170: for (j=1; j<= nlstate+1 ; j ++) {
3171: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3172: else fprintf(ficgp," \%%*lf (\%%*lf)");
3173: }
3174: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3175: else fprintf(ficgp,"\" t\"\" w l 0,");
3176: }
3177: }
3178:
3179: /*3eme*/
3180:
3181: for (k1=1; k1<= m ; k1 ++) {
3182: for (cpt=1; cpt<= nlstate ; cpt ++) {
3183: k=2+nlstate*(2*cpt-2);
3184: fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
3185: fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
3186: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3187: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3188: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3189: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3190: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3191: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3192:
3193: */
3194: for (i=1; i< nlstate ; i ++) {
3195: fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
3196:
3197: }
3198: }
3199: }
3200:
3201: /* CV preval stable (period) */
3202: for (k1=1; k1<= m ; k1 ++) {
3203: for (cpt=1; cpt<=nlstate ; cpt ++) {
3204: k=3;
3205: fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
3206: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
3207:
3208: for (i=1; i< nlstate ; i ++)
3209: fprintf(ficgp,"+$%d",k+i+1);
3210: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3211:
3212: l=3+(nlstate+ndeath)*cpt;
3213: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
3214: for (i=1; i< nlstate ; i ++) {
3215: l=3+(nlstate+ndeath)*cpt;
3216: fprintf(ficgp,"+$%d",l+i+1);
3217: }
3218: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3219: }
3220: }
3221:
3222: /* proba elementaires */
3223: for(i=1,jk=1; i <=nlstate; i++){
3224: for(k=1; k <=(nlstate+ndeath); k++){
3225: if (k != i) {
3226: for(j=1; j <=ncovmodel; j++){
3227: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3228: jk++;
3229: fprintf(ficgp,"\n");
3230: }
3231: }
3232: }
3233: }
3234:
3235: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3236: for(jk=1; jk <=m; jk++) {
3237: fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
3238: if (ng==2)
3239: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3240: else
3241: fprintf(ficgp,"\nset title \"Probability\"\n");
3242: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3243: i=1;
3244: for(k2=1; k2<=nlstate; k2++) {
3245: k3=i;
3246: for(k=1; k<=(nlstate+ndeath); k++) {
3247: if (k != k2){
3248: if(ng==2)
3249: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3250: else
3251: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3252: ij=1;
3253: for(j=3; j <=ncovmodel; j++) {
3254: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3255: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3256: ij++;
3257: }
3258: else
3259: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3260: }
3261: fprintf(ficgp,")/(1");
3262:
3263: for(k1=1; k1 <=nlstate; k1++){
3264: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3265: ij=1;
3266: for(j=3; j <=ncovmodel; j++){
3267: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3268: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3269: ij++;
3270: }
3271: else
3272: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3273: }
3274: fprintf(ficgp,")");
3275: }
3276: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3277: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3278: i=i+ncovmodel;
3279: }
3280: } /* end k */
3281: } /* end k2 */
3282: } /* end jk */
3283: } /* end ng */
3284: fclose(ficgp);
3285: } /* end gnuplot */
3286:
3287:
3288: /*************** Moving average **************/
3289: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3290:
3291: int i, cpt, cptcod;
3292: int modcovmax =1;
3293: int mobilavrange, mob;
3294: double age;
3295:
3296: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3297: a covariate has 2 modalities */
3298: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3299:
3300: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3301: if(mobilav==1) mobilavrange=5; /* default */
3302: else mobilavrange=mobilav;
3303: for (age=bage; age<=fage; age++)
3304: for (i=1; i<=nlstate;i++)
3305: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3306: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3307: /* We keep the original values on the extreme ages bage, fage and for
3308: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3309: we use a 5 terms etc. until the borders are no more concerned.
3310: */
3311: for (mob=3;mob <=mobilavrange;mob=mob+2){
3312: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3313: for (i=1; i<=nlstate;i++){
3314: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3315: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3316: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3317: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3318: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3319: }
3320: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3321: }
3322: }
3323: }/* end age */
3324: }/* end mob */
3325: }else return -1;
3326: return 0;
3327: }/* End movingaverage */
3328:
3329:
3330: /************** Forecasting ******************/
3331: 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){
3332: /* proj1, year, month, day of starting projection
3333: agemin, agemax range of age
3334: dateprev1 dateprev2 range of dates during which prevalence is computed
3335: anproj2 year of en of projection (same day and month as proj1).
3336: */
3337: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
3338: int *popage;
3339: double agec; /* generic age */
3340: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3341: double *popeffectif,*popcount;
3342: double ***p3mat;
3343: double ***mobaverage;
3344: char fileresf[FILENAMELENGTH];
3345:
3346: agelim=AGESUP;
3347: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3348:
3349: strcpy(fileresf,"f");
3350: strcat(fileresf,fileres);
3351: if((ficresf=fopen(fileresf,"w"))==NULL) {
3352: printf("Problem with forecast resultfile: %s\n", fileresf);
3353: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3354: }
3355: printf("Computing forecasting: result on file '%s' \n", fileresf);
3356: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3357:
3358: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3359:
3360: if (mobilav!=0) {
3361: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3362: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3363: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3364: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3365: }
3366: }
3367:
3368: stepsize=(int) (stepm+YEARM-1)/YEARM;
3369: if (stepm<=12) stepsize=1;
3370: if(estepm < stepm){
3371: printf ("Problem %d lower than %d\n",estepm, stepm);
3372: }
3373: else hstepm=estepm;
3374:
3375: hstepm=hstepm/stepm;
3376: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3377: fractional in yp1 */
3378: anprojmean=yp;
3379: yp2=modf((yp1*12),&yp);
3380: mprojmean=yp;
3381: yp1=modf((yp2*30.5),&yp);
3382: jprojmean=yp;
3383: if(jprojmean==0) jprojmean=1;
3384: if(mprojmean==0) jprojmean=1;
3385:
3386: i1=cptcoveff;
3387: if (cptcovn < 1){i1=1;}
3388:
3389: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
3390:
3391: fprintf(ficresf,"#****** Routine prevforecast **\n");
3392:
3393: /* if (h==(int)(YEARM*yearp)){ */
3394: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
3395: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3396: k=k+1;
3397: fprintf(ficresf,"\n#******");
3398: for(j=1;j<=cptcoveff;j++) {
3399: 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]]);
3400: }
3401: fprintf(ficresf,"******\n");
3402: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3403: for(j=1; j<=nlstate+ndeath;j++){
3404: for(i=1; i<=nlstate;i++)
3405: fprintf(ficresf," p%d%d",i,j);
3406: fprintf(ficresf," p.%d",j);
3407: }
3408: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
3409: fprintf(ficresf,"\n");
3410: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
3411:
3412: for (agec=fage; agec>=(ageminpar-1); agec--){
3413: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
3414: nhstepm = nhstepm/hstepm;
3415: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3416: oldm=oldms;savm=savms;
3417: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
3418:
3419: for (h=0; h<=nhstepm; h++){
3420: if (h*hstepm/YEARM*stepm ==yearp) {
3421: fprintf(ficresf,"\n");
3422: for(j=1;j<=cptcoveff;j++)
3423: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3424: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
3425: }
3426: for(j=1; j<=nlstate+ndeath;j++) {
3427: ppij=0.;
3428: for(i=1; i<=nlstate;i++) {
3429: if (mobilav==1)
3430: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
3431: else {
3432: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
3433: }
3434: if (h*hstepm/YEARM*stepm== yearp) {
3435: fprintf(ficresf," %.3f", p3mat[i][j][h]);
3436: }
3437: } /* end i */
3438: if (h*hstepm/YEARM*stepm==yearp) {
3439: fprintf(ficresf," %.3f", ppij);
3440: }
3441: }/* end j */
3442: } /* end h */
3443: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3444: } /* end agec */
3445: } /* end yearp */
3446: } /* end cptcod */
3447: } /* end cptcov */
3448:
3449: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3450:
3451: fclose(ficresf);
3452: }
3453:
3454: /************** Forecasting *****not tested NB*************/
3455: 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){
3456:
3457: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3458: int *popage;
3459: double calagedatem, agelim, kk1, kk2;
3460: double *popeffectif,*popcount;
3461: double ***p3mat,***tabpop,***tabpopprev;
3462: double ***mobaverage;
3463: char filerespop[FILENAMELENGTH];
3464:
3465: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3466: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3467: agelim=AGESUP;
3468: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
3469:
3470: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3471:
3472:
3473: strcpy(filerespop,"pop");
3474: strcat(filerespop,fileres);
3475: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3476: printf("Problem with forecast resultfile: %s\n", filerespop);
3477: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3478: }
3479: printf("Computing forecasting: result on file '%s' \n", filerespop);
3480: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3481:
3482: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3483:
3484: if (mobilav!=0) {
3485: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3486: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3487: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3488: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3489: }
3490: }
3491:
3492: stepsize=(int) (stepm+YEARM-1)/YEARM;
3493: if (stepm<=12) stepsize=1;
3494:
3495: agelim=AGESUP;
3496:
3497: hstepm=1;
3498: hstepm=hstepm/stepm;
3499:
3500: if (popforecast==1) {
3501: if((ficpop=fopen(popfile,"r"))==NULL) {
3502: printf("Problem with population file : %s\n",popfile);exit(0);
3503: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3504: }
3505: popage=ivector(0,AGESUP);
3506: popeffectif=vector(0,AGESUP);
3507: popcount=vector(0,AGESUP);
3508:
3509: i=1;
3510: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3511:
3512: imx=i;
3513: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3514: }
3515:
3516: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
3517: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3518: k=k+1;
3519: fprintf(ficrespop,"\n#******");
3520: for(j=1;j<=cptcoveff;j++) {
3521: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3522: }
3523: fprintf(ficrespop,"******\n");
3524: fprintf(ficrespop,"# Age");
3525: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3526: if (popforecast==1) fprintf(ficrespop," [Population]");
3527:
3528: for (cpt=0; cpt<=0;cpt++) {
3529: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3530:
3531: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3532: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3533: nhstepm = nhstepm/hstepm;
3534:
3535: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3536: oldm=oldms;savm=savms;
3537: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3538:
3539: for (h=0; h<=nhstepm; h++){
3540: if (h==(int) (calagedatem+YEARM*cpt)) {
3541: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3542: }
3543: for(j=1; j<=nlstate+ndeath;j++) {
3544: kk1=0.;kk2=0;
3545: for(i=1; i<=nlstate;i++) {
3546: if (mobilav==1)
3547: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3548: else {
3549: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3550: }
3551: }
3552: if (h==(int)(calagedatem+12*cpt)){
3553: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3554: /*fprintf(ficrespop," %.3f", kk1);
3555: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3556: }
3557: }
3558: for(i=1; i<=nlstate;i++){
3559: kk1=0.;
3560: for(j=1; j<=nlstate;j++){
3561: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3562: }
3563: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
3564: }
3565:
3566: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
3567: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3568: }
3569: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3570: }
3571: }
3572:
3573: /******/
3574:
3575: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3576: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3577: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3578: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3579: nhstepm = nhstepm/hstepm;
3580:
3581: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3582: oldm=oldms;savm=savms;
3583: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3584: for (h=0; h<=nhstepm; h++){
3585: if (h==(int) (calagedatem+YEARM*cpt)) {
3586: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3587: }
3588: for(j=1; j<=nlstate+ndeath;j++) {
3589: kk1=0.;kk2=0;
3590: for(i=1; i<=nlstate;i++) {
3591: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3592: }
3593: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
3594: }
3595: }
3596: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3597: }
3598: }
3599: }
3600: }
3601:
3602: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3603:
3604: if (popforecast==1) {
3605: free_ivector(popage,0,AGESUP);
3606: free_vector(popeffectif,0,AGESUP);
3607: free_vector(popcount,0,AGESUP);
3608: }
3609: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3610: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3611: fclose(ficrespop);
3612: } /* End of popforecast */
3613:
3614: int fileappend(FILE *fichier, char *optionfile)
3615: {
3616: if((fichier=fopen(optionfile,"a"))==NULL) {
3617: printf("Problem with file: %s\n", optionfile);
3618: fprintf(ficlog,"Problem with file: %s\n", optionfile);
3619: return (1);
3620: }
3621:
3622: }
3623: /***********************************************/
3624: /**************** Main Program *****************/
3625: /***********************************************/
3626:
3627: int main(int argc, char *argv[])
3628: {
3629: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
3630: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
3631: int jj;
3632: int numlinepar=0; /* Current linenumber of parameter file */
3633: double agedeb, agefin,hf;
3634: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3635:
3636: double fret;
3637: double **xi,tmp,delta;
3638:
3639: double dum; /* Dummy variable */
3640: double ***p3mat;
3641: double ***mobaverage;
3642: int *indx;
3643: char line[MAXLINE], linepar[MAXLINE];
3644: char path[132],pathc[132],pathcd[132],pathtot[132],model[132];
3645: int firstobs=1, lastobs=10;
3646: int sdeb, sfin; /* Status at beginning and end */
3647: int c, h , cpt,l;
3648: int ju,jl, mi;
3649: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
3650: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
3651: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
3652: int mobilav=0,popforecast=0;
3653: int hstepm, nhstepm;
3654: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
3655: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
3656:
3657: double bage, fage, age, agelim, agebase;
3658: double ftolpl=FTOL;
3659: double **prlim;
3660: double *severity;
3661: double ***param; /* Matrix of parameters */
3662: double *p;
3663: double **matcov; /* Matrix of covariance */
3664: double ***delti3; /* Scale */
3665: double *delti; /* Scale */
3666: double ***eij, ***vareij;
3667: double **varpl; /* Variances of prevalence limits by age */
3668: double *epj, vepp;
3669: double kk1, kk2;
3670: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
3671:
3672: char *alph[]={"a","a","b","c","d","e"}, str[4];
3673:
3674:
3675: char z[1]="c", occ;
3676:
3677: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
3678: char *strt, *strtend;
3679: char *stratrunc;
3680: int lstra;
3681:
3682: long total_usecs;
3683: struct timeval start_time, end_time, curr_time;
3684: struct timezone tzp;
3685: extern int gettimeofday();
3686: struct tm tmg, tm, *gmtime(), *localtime();
3687: long time_value;
3688: extern long time();
3689:
3690: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
3691: (void) gettimeofday(&start_time,&tzp);
3692: tm = *localtime(&start_time.tv_sec);
3693: tmg = *gmtime(&start_time.tv_sec);
3694: strt=asctime(&tm);
3695:
3696: /* printf("Localtime (at start)=%s",strt); */
3697: /* tp.tv_sec = tp.tv_sec +86400; */
3698: /* tm = *localtime(&start_time.tv_sec); */
3699: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
3700: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
3701: /* tmg.tm_hour=tmg.tm_hour + 1; */
3702: /* tp.tv_sec = mktime(&tmg); */
3703: /* strt=asctime(&tmg); */
3704: /* printf("Time(after) =%s",strt); */
3705: /* (void) time (&time_value);
3706: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
3707: * tm = *localtime(&time_value);
3708: * strt=asctime(&tm);
3709: * printf("tim_value=%d,asctime=%s\n",time_value,strt);
3710: */
3711:
3712: getcwd(pathcd, size);
3713:
3714: printf("\n%s\n%s",version,fullversion);
3715: if(argc <=1){
3716: printf("\nEnter the parameter file name: ");
3717: scanf("%s",pathtot);
3718: }
3719: else{
3720: strcpy(pathtot,argv[1]);
3721: }
3722: /*if(getcwd(pathcd, 132)!= NULL)printf ("Error pathcd\n");*/
3723: /*cygwin_split_path(pathtot,path,optionfile);
3724: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3725: /* cutv(path,optionfile,pathtot,'\\');*/
3726:
3727: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
3728: printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3729: chdir(path);
3730: replace(pathc,path);
3731:
3732: /*-------- arguments in the command line --------*/
3733:
3734: /* Log file */
3735: strcat(filelog, optionfilefiname);
3736: strcat(filelog,".log"); /* */
3737: if((ficlog=fopen(filelog,"w"))==NULL) {
3738: printf("Problem with logfile %s\n",filelog);
3739: goto end;
3740: }
3741: fprintf(ficlog,"Log filename:%s\n",filelog);
3742: fprintf(ficlog,"\n%s\n%s",version,fullversion);
3743: fprintf(ficlog,"\nEnter the parameter file name: ");
3744: fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3745:
3746: printf("Localtime (at start)=%s",strt);
3747: fprintf(ficlog,"Localtime (at start)=%s",strt);
3748: fflush(ficlog);
3749:
3750: /* */
3751: strcpy(fileres,"r");
3752: strcat(fileres, optionfilefiname);
3753: strcat(fileres,".txt"); /* Other files have txt extension */
3754:
3755: /*---------arguments file --------*/
3756:
3757: if((ficpar=fopen(optionfile,"r"))==NULL) {
3758: printf("Problem with optionfile %s\n",optionfile);
3759: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
3760: fflush(ficlog);
3761: goto end;
3762: }
3763:
3764: strcpy(filereso,"o");
3765: strcat(filereso,fileres);
3766: if((ficparo=fopen(filereso,"w"))==NULL) {
3767: printf("Problem with Output resultfile: %s\n", filereso);
3768: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
3769: fflush(ficlog);
3770: goto end;
3771: }
3772:
3773: /* Reads comments: lines beginning with '#' */
3774: numlinepar=0;
3775: while((c=getc(ficpar))=='#' && c!= EOF){
3776: ungetc(c,ficpar);
3777: fgets(line, MAXLINE, ficpar);
3778: numlinepar++;
3779: puts(line);
3780: fputs(line,ficparo);
3781: fputs(line,ficlog);
3782: }
3783: ungetc(c,ficpar);
3784:
3785: 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);
3786: numlinepar++;
3787: 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);
3788: 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);
3789: 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);
3790: fflush(ficlog);
3791: while((c=getc(ficpar))=='#' && c!= EOF){
3792: ungetc(c,ficpar);
3793: fgets(line, MAXLINE, ficpar);
3794: numlinepar++;
3795: puts(line);
3796: fputs(line,ficparo);
3797: fputs(line,ficlog);
3798: }
3799: ungetc(c,ficpar);
3800:
3801:
3802: covar=matrix(0,NCOVMAX,1,n);
3803: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
3804: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
3805:
3806: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
3807: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
3808:
3809: /* Read guess parameters */
3810: /* Reads comments: lines beginning with '#' */
3811: while((c=getc(ficpar))=='#' && c!= EOF){
3812: ungetc(c,ficpar);
3813: fgets(line, MAXLINE, ficpar);
3814: numlinepar++;
3815: puts(line);
3816: fputs(line,ficparo);
3817: fputs(line,ficlog);
3818: }
3819: ungetc(c,ficpar);
3820:
3821: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
3822: for(i=1; i <=nlstate; i++){
3823: j=0;
3824: for(jj=1; jj <=nlstate+ndeath; jj++){
3825: if(jj==i) continue;
3826: j++;
3827: fscanf(ficpar,"%1d%1d",&i1,&j1);
3828: if ((i1 != i) && (j1 != j)){
3829: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
3830: exit(1);
3831: }
3832: fprintf(ficparo,"%1d%1d",i1,j1);
3833: if(mle==1)
3834: printf("%1d%1d",i,j);
3835: fprintf(ficlog,"%1d%1d",i,j);
3836: for(k=1; k<=ncovmodel;k++){
3837: fscanf(ficpar," %lf",¶m[i][j][k]);
3838: if(mle==1){
3839: printf(" %lf",param[i][j][k]);
3840: fprintf(ficlog," %lf",param[i][j][k]);
3841: }
3842: else
3843: fprintf(ficlog," %lf",param[i][j][k]);
3844: fprintf(ficparo," %lf",param[i][j][k]);
3845: }
3846: fscanf(ficpar,"\n");
3847: numlinepar++;
3848: if(mle==1)
3849: printf("\n");
3850: fprintf(ficlog,"\n");
3851: fprintf(ficparo,"\n");
3852: }
3853: }
3854: fflush(ficlog);
3855:
3856: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
3857:
3858: p=param[1][1];
3859:
3860: /* Reads comments: lines beginning with '#' */
3861: while((c=getc(ficpar))=='#' && c!= EOF){
3862: ungetc(c,ficpar);
3863: fgets(line, MAXLINE, ficpar);
3864: numlinepar++;
3865: puts(line);
3866: fputs(line,ficparo);
3867: fputs(line,ficlog);
3868: }
3869: ungetc(c,ficpar);
3870:
3871: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
3872: /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
3873: for(i=1; i <=nlstate; i++){
3874: for(j=1; j <=nlstate+ndeath-1; j++){
3875: fscanf(ficpar,"%1d%1d",&i1,&j1);
3876: if ((i1-i)*(j1-j)!=0){
3877: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
3878: exit(1);
3879: }
3880: printf("%1d%1d",i,j);
3881: fprintf(ficparo,"%1d%1d",i1,j1);
3882: fprintf(ficlog,"%1d%1d",i1,j1);
3883: for(k=1; k<=ncovmodel;k++){
3884: fscanf(ficpar,"%le",&delti3[i][j][k]);
3885: printf(" %le",delti3[i][j][k]);
3886: fprintf(ficparo," %le",delti3[i][j][k]);
3887: fprintf(ficlog," %le",delti3[i][j][k]);
3888: }
3889: fscanf(ficpar,"\n");
3890: numlinepar++;
3891: printf("\n");
3892: fprintf(ficparo,"\n");
3893: fprintf(ficlog,"\n");
3894: }
3895: }
3896: fflush(ficlog);
3897:
3898: delti=delti3[1][1];
3899:
3900:
3901: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
3902:
3903: /* Reads comments: lines beginning with '#' */
3904: while((c=getc(ficpar))=='#' && c!= EOF){
3905: ungetc(c,ficpar);
3906: fgets(line, MAXLINE, ficpar);
3907: numlinepar++;
3908: puts(line);
3909: fputs(line,ficparo);
3910: fputs(line,ficlog);
3911: }
3912: ungetc(c,ficpar);
3913:
3914: matcov=matrix(1,npar,1,npar);
3915: for(i=1; i <=npar; i++){
3916: fscanf(ficpar,"%s",&str);
3917: if(mle==1)
3918: printf("%s",str);
3919: fprintf(ficlog,"%s",str);
3920: fprintf(ficparo,"%s",str);
3921: for(j=1; j <=i; j++){
3922: fscanf(ficpar," %le",&matcov[i][j]);
3923: if(mle==1){
3924: printf(" %.5le",matcov[i][j]);
3925: }
3926: fprintf(ficlog," %.5le",matcov[i][j]);
3927: fprintf(ficparo," %.5le",matcov[i][j]);
3928: }
3929: fscanf(ficpar,"\n");
3930: numlinepar++;
3931: if(mle==1)
3932: printf("\n");
3933: fprintf(ficlog,"\n");
3934: fprintf(ficparo,"\n");
3935: }
3936: for(i=1; i <=npar; i++)
3937: for(j=i+1;j<=npar;j++)
3938: matcov[i][j]=matcov[j][i];
3939:
3940: if(mle==1)
3941: printf("\n");
3942: fprintf(ficlog,"\n");
3943:
3944: fflush(ficlog);
3945:
3946: /*-------- Rewriting paramater file ----------*/
3947: strcpy(rfileres,"r"); /* "Rparameterfile */
3948: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
3949: strcat(rfileres,"."); /* */
3950: strcat(rfileres,optionfilext); /* Other files have txt extension */
3951: if((ficres =fopen(rfileres,"w"))==NULL) {
3952: printf("Problem writing new parameter file: %s\n", fileres);goto end;
3953: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
3954: }
3955: fprintf(ficres,"#%s\n",version);
3956:
3957: /*-------- data file ----------*/
3958: if((fic=fopen(datafile,"r"))==NULL) {
3959: printf("Problem with datafile: %s\n", datafile);goto end;
3960: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
3961: }
3962:
3963: n= lastobs;
3964: severity = vector(1,maxwav);
3965: outcome=imatrix(1,maxwav+1,1,n);
3966: num=lvector(1,n);
3967: moisnais=vector(1,n);
3968: annais=vector(1,n);
3969: moisdc=vector(1,n);
3970: andc=vector(1,n);
3971: agedc=vector(1,n);
3972: cod=ivector(1,n);
3973: weight=vector(1,n);
3974: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
3975: mint=matrix(1,maxwav,1,n);
3976: anint=matrix(1,maxwav,1,n);
3977: s=imatrix(1,maxwav+1,1,n);
3978: tab=ivector(1,NCOVMAX);
3979: ncodemax=ivector(1,8);
3980:
3981: i=1;
3982: while (fgets(line, MAXLINE, fic) != NULL) {
3983: if ((i >= firstobs) && (i <=lastobs)) {
3984:
3985: for (j=maxwav;j>=1;j--){
3986: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
3987: strcpy(line,stra);
3988: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3989: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3990: }
3991:
3992: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
3993: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
3994:
3995: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
3996: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
3997:
3998: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
3999: for (j=ncovcol;j>=1;j--){
4000: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4001: }
4002: lstra=strlen(stra);
4003: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4004: stratrunc = &(stra[lstra-9]);
4005: num[i]=atol(stratrunc);
4006: }
4007: else
4008: num[i]=atol(stra);
4009:
4010: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4011: 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;}*/
4012:
4013: i=i+1;
4014: }
4015: }
4016: /* printf("ii=%d", ij);
4017: scanf("%d",i);*/
4018: imx=i-1; /* Number of individuals */
4019:
4020: /* for (i=1; i<=imx; i++){
4021: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4022: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4023: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4024: }*/
4025: /* for (i=1; i<=imx; i++){
4026: if (s[4][i]==9) s[4][i]=-1;
4027: 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]));}*/
4028:
4029: for (i=1; i<=imx; i++)
4030:
4031: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4032: else weight[i]=1;*/
4033:
4034: /* Calculation of the number of parameter from char model*/
4035: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4036: Tprod=ivector(1,15);
4037: Tvaraff=ivector(1,15);
4038: Tvard=imatrix(1,15,1,2);
4039: Tage=ivector(1,15);
4040:
4041: if (strlen(model) >1){ /* If there is at least 1 covariate */
4042: j=0, j1=0, k1=1, k2=1;
4043: j=nbocc(model,'+'); /* j=Number of '+' */
4044: j1=nbocc(model,'*'); /* j1=Number of '*' */
4045: cptcovn=j+1;
4046: cptcovprod=j1; /*Number of products */
4047:
4048: strcpy(modelsav,model);
4049: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4050: printf("Error. Non available option model=%s ",model);
4051: fprintf(ficlog,"Error. Non available option model=%s ",model);
4052: goto end;
4053: }
4054:
4055: /* This loop fills the array Tvar from the string 'model'.*/
4056:
4057: for(i=(j+1); i>=1;i--){
4058: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
4059: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
4060: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4061: /*scanf("%d",i);*/
4062: if (strchr(strb,'*')) { /* Model includes a product */
4063: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4064: if (strcmp(strc,"age")==0) { /* Vn*age */
4065: cptcovprod--;
4066: cutv(strb,stre,strd,'V');
4067: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4068: cptcovage++;
4069: Tage[cptcovage]=i;
4070: /*printf("stre=%s ", stre);*/
4071: }
4072: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4073: cptcovprod--;
4074: cutv(strb,stre,strc,'V');
4075: Tvar[i]=atoi(stre);
4076: cptcovage++;
4077: Tage[cptcovage]=i;
4078: }
4079: else { /* Age is not in the model */
4080: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4081: Tvar[i]=ncovcol+k1;
4082: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4083: Tprod[k1]=i;
4084: Tvard[k1][1]=atoi(strc); /* m*/
4085: Tvard[k1][2]=atoi(stre); /* n */
4086: Tvar[cptcovn+k2]=Tvard[k1][1];
4087: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4088: for (k=1; k<=lastobs;k++)
4089: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4090: k1++;
4091: k2=k2+2;
4092: }
4093: }
4094: else { /* no more sum */
4095: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4096: /* scanf("%d",i);*/
4097: cutv(strd,strc,strb,'V');
4098: Tvar[i]=atoi(strc);
4099: }
4100: strcpy(modelsav,stra);
4101: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4102: scanf("%d",i);*/
4103: } /* end of loop + */
4104: } /* end model */
4105:
4106: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4107: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4108:
4109: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4110: printf("cptcovprod=%d ", cptcovprod);
4111: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
4112:
4113: scanf("%d ",i);
4114: fclose(fic);*/
4115:
4116: /* if(mle==1){*/
4117: if (weightopt != 1) { /* Maximisation without weights*/
4118: for(i=1;i<=n;i++) weight[i]=1.0;
4119: }
4120: /*-calculation of age at interview from date of interview and age at death -*/
4121: agev=matrix(1,maxwav,1,imx);
4122:
4123: for (i=1; i<=imx; i++) {
4124: for(m=2; (m<= maxwav); m++) {
4125: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
4126: anint[m][i]=9999;
4127: s[m][i]=-1;
4128: }
4129: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
4130: 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);
4131: 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);
4132: s[m][i]=-1;
4133: }
4134: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
4135: 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]);
4136: 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]);
4137: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
4138: }
4139: }
4140: }
4141:
4142: for (i=1; i<=imx; i++) {
4143: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
4144: for(m=firstpass; (m<= lastpass); m++){
4145: if(s[m][i] >0){
4146: if (s[m][i] >= nlstate+1) {
4147: if(agedc[i]>0)
4148: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
4149: agev[m][i]=agedc[i];
4150: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4151: else {
4152: if ((int)andc[i]!=9999){
4153: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4154: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
4155: agev[m][i]=-1;
4156: }
4157: }
4158: }
4159: else if(s[m][i] !=9){ /* Standard case, age in fractional
4160: years but with the precision of a
4161: month */
4162: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
4163: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
4164: agev[m][i]=1;
4165: else if(agev[m][i] <agemin){
4166: agemin=agev[m][i];
4167: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
4168: }
4169: else if(agev[m][i] >agemax){
4170: agemax=agev[m][i];
4171: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
4172: }
4173: /*agev[m][i]=anint[m][i]-annais[i];*/
4174: /* agev[m][i] = age[i]+2*m;*/
4175: }
4176: else { /* =9 */
4177: agev[m][i]=1;
4178: s[m][i]=-1;
4179: }
4180: }
4181: else /*= 0 Unknown */
4182: agev[m][i]=1;
4183: }
4184:
4185: }
4186: for (i=1; i<=imx; i++) {
4187: for(m=firstpass; (m<=lastpass); m++){
4188: if (s[m][i] > (nlstate+ndeath)) {
4189: 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);
4190: 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);
4191: goto end;
4192: }
4193: }
4194: }
4195:
4196: /*for (i=1; i<=imx; i++){
4197: for (m=firstpass; (m<lastpass); m++){
4198: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
4199: }
4200:
4201: }*/
4202:
4203: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4204: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4205:
4206: free_vector(severity,1,maxwav);
4207: free_imatrix(outcome,1,maxwav+1,1,n);
4208: free_vector(moisnais,1,n);
4209: free_vector(annais,1,n);
4210: /* free_matrix(mint,1,maxwav,1,n);
4211: free_matrix(anint,1,maxwav,1,n);*/
4212: free_vector(moisdc,1,n);
4213: free_vector(andc,1,n);
4214:
4215:
4216: wav=ivector(1,imx);
4217: dh=imatrix(1,lastpass-firstpass+1,1,imx);
4218: bh=imatrix(1,lastpass-firstpass+1,1,imx);
4219: mw=imatrix(1,lastpass-firstpass+1,1,imx);
4220:
4221: /* Concatenates waves */
4222: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
4223:
4224: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
4225:
4226: Tcode=ivector(1,100);
4227: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
4228: ncodemax[1]=1;
4229: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
4230:
4231: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
4232: the estimations*/
4233: h=0;
4234: m=pow(2,cptcoveff);
4235:
4236: for(k=1;k<=cptcoveff; k++){
4237: for(i=1; i <=(m/pow(2,k));i++){
4238: for(j=1; j <= ncodemax[k]; j++){
4239: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
4240: h++;
4241: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
4242: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
4243: }
4244: }
4245: }
4246: }
4247: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
4248: codtab[1][2]=1;codtab[2][2]=2; */
4249: /* for(i=1; i <=m ;i++){
4250: for(k=1; k <=cptcovn; k++){
4251: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
4252: }
4253: printf("\n");
4254: }
4255: scanf("%d",i);*/
4256:
4257: /*------------ gnuplot -------------*/
4258: strcpy(optionfilegnuplot,optionfilefiname);
4259: strcat(optionfilegnuplot,".gp");
4260: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4261: printf("Problem with file %s",optionfilegnuplot);
4262: }
4263: else{
4264: fprintf(ficgp,"\n# %s\n", version);
4265: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4266: fprintf(ficgp,"set missing 'NaNq'\n");
4267: }
4268: fclose(ficgp);
4269: /*--------- index.htm --------*/
4270:
4271: strcpy(optionfilehtm,optionfile);
4272: strcat(optionfilehtm,".htm");
4273: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4274: printf("Problem with %s \n",optionfilehtm), exit(0);
4275: }
4276:
4277: fprintf(fichtm,"<body> <font size=\"2\">%s <br> %s</font> \
4278: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4279: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
4280: \n\
4281: <hr size=\"2\" color=\"#EC5E5E\">\
4282: <ul><li><h4>Parameter files</h4>\n\
4283: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
4284: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
4285: - Gnuplot file name: <a href=\"%s\">%s</a>\n\
4286: - Date and time at start: %s</ul>\n",\
4287: version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt,\
4288: model,fileres,fileres,\
4289: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strt);
4290: fclose(fichtm);
4291:
4292: /* Calculates basic frequencies. Computes observed prevalence at single age
4293: and prints on file fileres'p'. */
4294: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
4295:
4296: if(fileappend(fichtm, optionfilehtm)){
4297: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
4298: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
4299: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
4300: imx,agemin,agemax,jmin,jmax,jmean);
4301: fclose(fichtm);
4302: }
4303: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4304: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4305: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4306: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4307: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
4308:
4309:
4310: /* For Powell, parameters are in a vector p[] starting at p[1]
4311: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
4312: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
4313:
4314: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
4315: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4316: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4317: for (k=1; k<=npar;k++)
4318: printf(" %d %8.5f",k,p[k]);
4319: printf("\n");
4320: globpr=1; /* to print the contributions */
4321: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4322: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4323: for (k=1; k<=npar;k++)
4324: printf(" %d %8.5f",k,p[k]);
4325: printf("\n");
4326: if(mle>=1){ /* Could be 1 or 2 */
4327: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
4328: }
4329:
4330: /*--------- results files --------------*/
4331: 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);
4332:
4333:
4334: jk=1;
4335: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4336: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4337: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4338: for(i=1,jk=1; i <=nlstate; i++){
4339: for(k=1; k <=(nlstate+ndeath); k++){
4340: if (k != i)
4341: {
4342: printf("%d%d ",i,k);
4343: fprintf(ficlog,"%d%d ",i,k);
4344: fprintf(ficres,"%1d%1d ",i,k);
4345: for(j=1; j <=ncovmodel; j++){
4346: printf("%f ",p[jk]);
4347: fprintf(ficlog,"%f ",p[jk]);
4348: fprintf(ficres,"%f ",p[jk]);
4349: jk++;
4350: }
4351: printf("\n");
4352: fprintf(ficlog,"\n");
4353: fprintf(ficres,"\n");
4354: }
4355: }
4356: }
4357: if(mle!=0){
4358: /* Computing hessian and covariance matrix */
4359: ftolhess=ftol; /* Usually correct */
4360: hesscov(matcov, p, npar, delti, ftolhess, func);
4361: }
4362: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
4363: printf("# Scales (for hessian or gradient estimation)\n");
4364: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
4365: for(i=1,jk=1; i <=nlstate; i++){
4366: for(j=1; j <=nlstate+ndeath; j++){
4367: if (j!=i) {
4368: fprintf(ficres,"%1d%1d",i,j);
4369: printf("%1d%1d",i,j);
4370: fprintf(ficlog,"%1d%1d",i,j);
4371: for(k=1; k<=ncovmodel;k++){
4372: printf(" %.5e",delti[jk]);
4373: fprintf(ficlog," %.5e",delti[jk]);
4374: fprintf(ficres," %.5e",delti[jk]);
4375: jk++;
4376: }
4377: printf("\n");
4378: fprintf(ficlog,"\n");
4379: fprintf(ficres,"\n");
4380: }
4381: }
4382: }
4383:
4384: 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");
4385: if(mle==1)
4386: 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");
4387: 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");
4388: for(i=1,k=1;i<=npar;i++){
4389: /* if (k>nlstate) k=1;
4390: i1=(i-1)/(ncovmodel*nlstate)+1;
4391: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
4392: printf("%s%d%d",alph[k],i1,tab[i]);
4393: */
4394: fprintf(ficres,"%3d",i);
4395: if(mle==1)
4396: printf("%3d",i);
4397: fprintf(ficlog,"%3d",i);
4398: for(j=1; j<=i;j++){
4399: fprintf(ficres," %.5e",matcov[i][j]);
4400: if(mle==1)
4401: printf(" %.5e",matcov[i][j]);
4402: fprintf(ficlog," %.5e",matcov[i][j]);
4403: }
4404: fprintf(ficres,"\n");
4405: if(mle==1)
4406: printf("\n");
4407: fprintf(ficlog,"\n");
4408: k++;
4409: }
4410:
4411: while((c=getc(ficpar))=='#' && c!= EOF){
4412: ungetc(c,ficpar);
4413: fgets(line, MAXLINE, ficpar);
4414: puts(line);
4415: fputs(line,ficparo);
4416: }
4417: ungetc(c,ficpar);
4418:
4419: estepm=0;
4420: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
4421: if (estepm==0 || estepm < stepm) estepm=stepm;
4422: if (fage <= 2) {
4423: bage = ageminpar;
4424: fage = agemaxpar;
4425: }
4426:
4427: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
4428: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
4429: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
4430:
4431: while((c=getc(ficpar))=='#' && c!= EOF){
4432: ungetc(c,ficpar);
4433: fgets(line, MAXLINE, ficpar);
4434: puts(line);
4435: fputs(line,ficparo);
4436: }
4437: ungetc(c,ficpar);
4438:
4439: 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);
4440: 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);
4441: 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);
4442: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
4443: 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);
4444:
4445: while((c=getc(ficpar))=='#' && c!= EOF){
4446: ungetc(c,ficpar);
4447: fgets(line, MAXLINE, ficpar);
4448: puts(line);
4449: fputs(line,ficparo);
4450: }
4451: ungetc(c,ficpar);
4452:
4453:
4454: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
4455: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
4456:
4457: fscanf(ficpar,"pop_based=%d\n",&popbased);
4458: fprintf(ficparo,"pop_based=%d\n",popbased);
4459: fprintf(ficres,"pop_based=%d\n",popbased);
4460:
4461: while((c=getc(ficpar))=='#' && c!= EOF){
4462: ungetc(c,ficpar);
4463: fgets(line, MAXLINE, ficpar);
4464: puts(line);
4465: fputs(line,ficparo);
4466: }
4467: ungetc(c,ficpar);
4468:
4469: 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);
4470: 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);
4471: 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);
4472: 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);
4473: 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);
4474: /* day and month of proj2 are not used but only year anproj2.*/
4475:
4476: while((c=getc(ficpar))=='#' && c!= EOF){
4477: ungetc(c,ficpar);
4478: fgets(line, MAXLINE, ficpar);
4479: puts(line);
4480: fputs(line,ficparo);
4481: }
4482: ungetc(c,ficpar);
4483:
4484: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
4485: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4486: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4487:
4488: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
4489: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
4490:
4491: printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
4492:
4493: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
4494: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
4495: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
4496:
4497: /*------------ free_vector -------------*/
4498: chdir(path);
4499:
4500: free_ivector(wav,1,imx);
4501: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
4502: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
4503: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
4504: free_lvector(num,1,n);
4505: free_vector(agedc,1,n);
4506: /*free_matrix(covar,0,NCOVMAX,1,n);*/
4507: /*free_matrix(covar,1,NCOVMAX,1,n);*/
4508: fclose(ficparo);
4509: fclose(ficres);
4510:
4511:
4512: /*--------------- Prevalence limit (stable prevalence) --------------*/
4513:
4514: strcpy(filerespl,"pl");
4515: strcat(filerespl,fileres);
4516: if((ficrespl=fopen(filerespl,"w"))==NULL) {
4517: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4518: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4519: }
4520: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
4521: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
4522: fprintf(ficrespl,"#Stable prevalence \n");
4523: fprintf(ficrespl,"#Age ");
4524: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
4525: fprintf(ficrespl,"\n");
4526:
4527: prlim=matrix(1,nlstate,1,nlstate);
4528:
4529: agebase=ageminpar;
4530: agelim=agemaxpar;
4531: ftolpl=1.e-10;
4532: i1=cptcoveff;
4533: if (cptcovn < 1){i1=1;}
4534:
4535: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4536: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4537: k=k+1;
4538: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
4539: fprintf(ficrespl,"\n#******");
4540: printf("\n#******");
4541: fprintf(ficlog,"\n#******");
4542: for(j=1;j<=cptcoveff;j++) {
4543: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4544: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4545: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4546: }
4547: fprintf(ficrespl,"******\n");
4548: printf("******\n");
4549: fprintf(ficlog,"******\n");
4550:
4551: for (age=agebase; age<=agelim; age++){
4552: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4553: fprintf(ficrespl,"%.0f ",age );
4554: for(j=1;j<=cptcoveff;j++)
4555: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4556: for(i=1; i<=nlstate;i++)
4557: fprintf(ficrespl," %.5f", prlim[i][i]);
4558: fprintf(ficrespl,"\n");
4559: }
4560: }
4561: }
4562: fclose(ficrespl);
4563:
4564: /*------------- h Pij x at various ages ------------*/
4565:
4566: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
4567: if((ficrespij=fopen(filerespij,"w"))==NULL) {
4568: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
4569: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
4570: }
4571: printf("Computing pij: result on file '%s' \n", filerespij);
4572: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
4573:
4574: stepsize=(int) (stepm+YEARM-1)/YEARM;
4575: /*if (stepm<=24) stepsize=2;*/
4576:
4577: agelim=AGESUP;
4578: hstepm=stepsize*YEARM; /* Every year of age */
4579: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
4580:
4581: /* hstepm=1; aff par mois*/
4582:
4583: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
4584: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4585: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4586: k=k+1;
4587: fprintf(ficrespij,"\n#****** ");
4588: for(j=1;j<=cptcoveff;j++)
4589: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4590: fprintf(ficrespij,"******\n");
4591:
4592: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
4593: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4594: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4595:
4596: /* nhstepm=nhstepm*YEARM; aff par mois*/
4597:
4598: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4599: oldm=oldms;savm=savms;
4600: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4601: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
4602: for(i=1; i<=nlstate;i++)
4603: for(j=1; j<=nlstate+ndeath;j++)
4604: fprintf(ficrespij," %1d-%1d",i,j);
4605: fprintf(ficrespij,"\n");
4606: for (h=0; h<=nhstepm; h++){
4607: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
4608: for(i=1; i<=nlstate;i++)
4609: for(j=1; j<=nlstate+ndeath;j++)
4610: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
4611: fprintf(ficrespij,"\n");
4612: }
4613: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4614: fprintf(ficrespij,"\n");
4615: }
4616: }
4617: }
4618:
4619: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
4620:
4621: fclose(ficrespij);
4622:
4623: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
4624:
4625: /*---------- Forecasting ------------------*/
4626: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
4627: if(prevfcast==1){
4628: /* if(stepm ==1){*/
4629: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
4630: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
4631: /* } */
4632: /* else{ */
4633: /* erreur=108; */
4634: /* 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); */
4635: /* 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); */
4636: /* } */
4637: }
4638:
4639:
4640: /*---------- Health expectancies and variances ------------*/
4641:
4642: strcpy(filerest,"t");
4643: strcat(filerest,fileres);
4644: if((ficrest=fopen(filerest,"w"))==NULL) {
4645: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
4646: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
4647: }
4648: printf("Computing Total LEs with variances: file '%s' \n", filerest);
4649: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
4650:
4651:
4652: strcpy(filerese,"e");
4653: strcat(filerese,fileres);
4654: if((ficreseij=fopen(filerese,"w"))==NULL) {
4655: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4656: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4657: }
4658: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
4659: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
4660:
4661: strcpy(fileresv,"v");
4662: strcat(fileresv,fileres);
4663: if((ficresvij=fopen(fileresv,"w"))==NULL) {
4664: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
4665: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
4666: }
4667: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4668: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4669:
4670: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
4671: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4672: /* 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",\
4673: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
4674: */
4675:
4676: if (mobilav!=0) {
4677: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4678: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4679: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4680: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4681: }
4682: }
4683:
4684: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4685: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4686: k=k+1;
4687: fprintf(ficrest,"\n#****** ");
4688: for(j=1;j<=cptcoveff;j++)
4689: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4690: fprintf(ficrest,"******\n");
4691:
4692: fprintf(ficreseij,"\n#****** ");
4693: for(j=1;j<=cptcoveff;j++)
4694: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4695: fprintf(ficreseij,"******\n");
4696:
4697: fprintf(ficresvij,"\n#****** ");
4698: for(j=1;j<=cptcoveff;j++)
4699: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4700: fprintf(ficresvij,"******\n");
4701:
4702: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4703: oldm=oldms;savm=savms;
4704: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
4705:
4706: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4707: oldm=oldms;savm=savms;
4708: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
4709: if(popbased==1){
4710: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
4711: }
4712:
4713:
4714: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
4715: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
4716: fprintf(ficrest,"\n");
4717:
4718: epj=vector(1,nlstate+1);
4719: for(age=bage; age <=fage ;age++){
4720: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4721: if (popbased==1) {
4722: if(mobilav ==0){
4723: for(i=1; i<=nlstate;i++)
4724: prlim[i][i]=probs[(int)age][i][k];
4725: }else{ /* mobilav */
4726: for(i=1; i<=nlstate;i++)
4727: prlim[i][i]=mobaverage[(int)age][i][k];
4728: }
4729: }
4730:
4731: fprintf(ficrest," %4.0f",age);
4732: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
4733: for(i=1, epj[j]=0.;i <=nlstate;i++) {
4734: epj[j] += prlim[i][i]*eij[i][j][(int)age];
4735: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
4736: }
4737: epj[nlstate+1] +=epj[j];
4738: }
4739:
4740: for(i=1, vepp=0.;i <=nlstate;i++)
4741: for(j=1;j <=nlstate;j++)
4742: vepp += vareij[i][j][(int)age];
4743: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
4744: for(j=1;j <=nlstate;j++){
4745: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
4746: }
4747: fprintf(ficrest,"\n");
4748: }
4749: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4750: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4751: free_vector(epj,1,nlstate+1);
4752: }
4753: }
4754: free_vector(weight,1,n);
4755: free_imatrix(Tvard,1,15,1,2);
4756: free_imatrix(s,1,maxwav+1,1,n);
4757: free_matrix(anint,1,maxwav,1,n);
4758: free_matrix(mint,1,maxwav,1,n);
4759: free_ivector(cod,1,n);
4760: free_ivector(tab,1,NCOVMAX);
4761: fclose(ficreseij);
4762: fclose(ficresvij);
4763: fclose(ficrest);
4764: fclose(ficpar);
4765:
4766: /*------- Variance of stable prevalence------*/
4767:
4768: strcpy(fileresvpl,"vpl");
4769: strcat(fileresvpl,fileres);
4770: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
4771: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
4772: exit(0);
4773: }
4774: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
4775:
4776: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4777: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4778: k=k+1;
4779: fprintf(ficresvpl,"\n#****** ");
4780: for(j=1;j<=cptcoveff;j++)
4781: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4782: fprintf(ficresvpl,"******\n");
4783:
4784: varpl=matrix(1,nlstate,(int) bage, (int) fage);
4785: oldm=oldms;savm=savms;
4786: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
4787: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
4788: }
4789: }
4790:
4791: fclose(ficresvpl);
4792:
4793: /*---------- End : free ----------------*/
4794: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
4795: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
4796: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
4797: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
4798:
4799: free_matrix(covar,0,NCOVMAX,1,n);
4800: free_matrix(matcov,1,npar,1,npar);
4801: /*free_vector(delti,1,npar);*/
4802: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4803: free_matrix(agev,1,maxwav,1,imx);
4804: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4805: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4806: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
4807:
4808: free_ivector(ncodemax,1,8);
4809: free_ivector(Tvar,1,15);
4810: free_ivector(Tprod,1,15);
4811: free_ivector(Tvaraff,1,15);
4812: free_ivector(Tage,1,15);
4813: free_ivector(Tcode,1,100);
4814:
4815: /* fclose(fichtm);*/
4816: /* fclose(ficgp);*/ /* ALready done */
4817:
4818:
4819: if(erreur >0){
4820: printf("End of Imach with error or warning %d\n",erreur);
4821: fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
4822: }else{
4823: printf("End of Imach\n");
4824: fprintf(ficlog,"End of Imach\n");
4825: }
4826: printf("See log file on %s\n",filelog);
4827: fclose(ficlog);
4828: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
4829: (void) gettimeofday(&end_time,&tzp);
4830: tm = *localtime(&end_time.tv_sec);
4831: tmg = *gmtime(&end_time.tv_sec);
4832: strtend=asctime(&tm);
4833: printf("Localtime at start %s and at end=%s",strt, strtend);
4834: fprintf(ficlog,"Localtime at start %s and at end=%s",strt, strtend);
4835: /* printf("Total time used %d Sec\n", asc_time(end_time.tv_sec -start_time.tv_sec);*/
4836:
4837: printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
4838: fprintf(ficlog,"Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
4839: /* printf("Total time was %d uSec.\n", total_usecs);*/
4840: if(fileappend(fichtm,optionfilehtm)){
4841: fprintf(fichtm,"<br>Localtime at start %s and at end=%s<br>",strt, strtend);
4842: fclose(fichtm);
4843: }
4844: /*------ End -----------*/
4845:
4846: end:
4847: #ifdef windows
4848: /* chdir(pathcd);*/
4849: #endif
4850: /*system("wgnuplot graph.plt");*/
4851: /*system("../gp37mgw/wgnuplot graph.plt");*/
4852: /*system("cd ../gp37mgw");*/
4853: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
4854: strcpy(plotcmd,GNUPLOTPROGRAM);
4855: strcat(plotcmd," ");
4856: strcat(plotcmd,optionfilegnuplot);
4857: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
4858: system(plotcmd);
4859: printf(" Wait...");
4860:
4861: /*#ifdef windows*/
4862: while (z[0] != 'q') {
4863: /* chdir(path); */
4864: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
4865: scanf("%s",z);
4866: if (z[0] == 'c') system("./imach");
4867: else if (z[0] == 'e') system(optionfilehtm);
4868: else if (z[0] == 'g') system(plotcmd);
4869: else if (z[0] == 'q') exit(0);
4870: }
4871: /*#endif */
4872: }
4873:
4874:
FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>
![[BACK]](/icons/small/back.gif){kind=icon}
Return to imach.c CVS log ![[TXT]](/icons/small/text.gif){kind=icon}
![[DIR]](/icons/small/dir.gif){kind=icon}
Up to [Local Repository] / imach / src