1: /* $Id: imach.c,v 1.79 2003/06/05 15:17:23 brouard Exp $
2: Interpolated Markov Chain
3:
4: Short summary of the programme:
5:
6: This program computes Healthy Life Expectancies from
7: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
8: first survey ("cross") where individuals from different ages are
9: interviewed on their health status or degree of disability (in the
10: case of a health survey which is our main interest) -2- at least a
11: second wave of interviews ("longitudinal") which measure each change
12: (if any) in individual health status. Health expectancies are
13: computed from the time spent in each health state according to a
14: model. More health states you consider, more time is necessary to reach the
15: Maximum Likelihood of the parameters involved in the model. The
16: simplest model is the multinomial logistic model where pij is the
17: probability to be observed in state j at the second wave
18: conditional to be observed in state i at the first wave. Therefore
19: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
20: 'age' is age and 'sex' is a covariate. If you want to have a more
21: complex model than "constant and age", you should modify the program
22: where the markup *Covariates have to be included here again* invites
23: you to do it. More covariates you add, slower the
24: convergence.
25:
26: The advantage of this computer programme, compared to a simple
27: multinomial logistic model, is clear when the delay between waves is not
28: identical for each individual. Also, if a individual missed an
29: intermediate interview, the information is lost, but taken into
30: account using an interpolation or extrapolation.
31:
32: hPijx is the probability to be observed in state i at age x+h
33: conditional to the observed state i at age x. The delay 'h' can be
34: split into an exact number (nh*stepm) of unobserved intermediate
35: states. This elementary transition (by month, quarter,
36: semester or year) is modelled as a multinomial logistic. The hPx
37: matrix is simply the matrix product of nh*stepm elementary matrices
38: and the contribution of each individual to the likelihood is simply
39: hPijx.
40:
41: Also this programme outputs the covariance matrix of the parameters but also
42: of the life expectancies. It also computes the stable prevalence.
43:
44: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
45: Institut national d'études démographiques, Paris.
46: This software have been partly granted by Euro-REVES, a concerted action
47: from the European Union.
48: It is copyrighted identically to a GNU software product, ie programme and
49: software can be distributed freely for non commercial use. Latest version
50: can be accessed at http://euroreves.ined.fr/imach .
51:
52: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
53: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
54:
55: **********************************************************************/
56: /*
57: main
58: read parameterfile
59: read datafile
60: concatwav
61: if (mle >= 1)
62: mlikeli
63: print results files
64: if mle==1
65: computes hessian
66: read end of parameter file: agemin, agemax, bage, fage, estepm
67: begin-prev-date,...
68: open gnuplot file
69: open html file
70: stable prevalence
71: for age prevalim()
72: h Pij x
73: variance of p varprob
74: forecasting if prevfcast==1 prevforecast call prevalence()
75: health expectancies
76: Variance-covariance of DFLE
77: prevalence()
78: movingaverage()
79: varevsij()
80: if popbased==1 varevsij(,popbased)
81: total life expectancies
82: Variance of stable prevalence
83: end
84: */
85:
86:
87:
88:
89: #include <math.h>
90: #include <stdio.h>
91: #include <stdlib.h>
92: #include <unistd.h>
93:
94: #define MAXLINE 256
95: #define GNUPLOTPROGRAM "gnuplot"
96: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
97: #define FILENAMELENGTH 80
98: /*#define DEBUG*/
99: #define windows
100: #define GLOCK_ERROR_NOPATH -1 /* empty path */
101: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
102:
103: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
104: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
105:
106: #define NINTERVMAX 8
107: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
108: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
109: #define NCOVMAX 8 /* Maximum number of covariates */
110: #define MAXN 20000
111: #define YEARM 12. /* Number of months per year */
112: #define AGESUP 130
113: #define AGEBASE 40
114: #ifdef windows
115: #define DIRSEPARATOR '\\'
116: #define ODIRSEPARATOR '/'
117: #else
118: #define DIRSEPARATOR '/'
119: #define ODIRSEPARATOR '\\'
120: #endif
121:
122: /* $Id: imach.c,v 1.79 2003/06/05 15:17:23 brouard Exp $ */
123: /* $Log: imach.c,v $
124: /* Revision 1.79 2003/06/05 15:17:23 brouard
125: /* *** empty log message ***
126: /* */
127: char version[80]="Imach version 0.95a1, June 2003, INED-EUROREVES ";
128: int erreur; /* Error number */
129: int nvar;
130: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
131: int npar=NPARMAX;
132: int nlstate=2; /* Number of live states */
133: int ndeath=1; /* Number of dead states */
134: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
135: int popbased=0;
136:
137: int *wav; /* Number of waves for this individuual 0 is possible */
138: int maxwav; /* Maxim number of waves */
139: int jmin, jmax; /* min, max spacing between 2 waves */
140: int mle, weightopt;
141: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
142: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
143: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
144: * wave mi and wave mi+1 is not an exact multiple of stepm. */
145: double jmean; /* Mean space between 2 waves */
146: double **oldm, **newm, **savm; /* Working pointers to matrices */
147: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
148: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
149: FILE *ficlog, *ficrespow;
150: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
151: FILE *ficresprobmorprev;
152: FILE *fichtm; /* Html File */
153: FILE *ficreseij;
154: char filerese[FILENAMELENGTH];
155: FILE *ficresvij;
156: char fileresv[FILENAMELENGTH];
157: FILE *ficresvpl;
158: char fileresvpl[FILENAMELENGTH];
159: char title[MAXLINE];
160: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
161: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
162:
163: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
164: char filelog[FILENAMELENGTH]; /* Log file */
165: char filerest[FILENAMELENGTH];
166: char fileregp[FILENAMELENGTH];
167: char popfile[FILENAMELENGTH];
168:
169: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
170:
171: #define NR_END 1
172: #define FREE_ARG char*
173: #define FTOL 1.0e-10
174:
175: #define NRANSI
176: #define ITMAX 200
177:
178: #define TOL 2.0e-4
179:
180: #define CGOLD 0.3819660
181: #define ZEPS 1.0e-10
182: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
183:
184: #define GOLD 1.618034
185: #define GLIMIT 100.0
186: #define TINY 1.0e-20
187:
188: static double maxarg1,maxarg2;
189: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
190: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
191:
192: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
193: #define rint(a) floor(a+0.5)
194:
195: static double sqrarg;
196: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
197: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
198:
199: int imx;
200: int stepm;
201: /* Stepm, step in month: minimum step interpolation*/
202:
203: int estepm;
204: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
205:
206: int m,nb;
207: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
208: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
209: double **pmmij, ***probs;
210: double dateintmean=0;
211:
212: double *weight;
213: int **s; /* Status */
214: double *agedc, **covar, idx;
215: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
216:
217: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
218: double ftolhess; /* Tolerance for computing hessian */
219:
220: /**************** split *************************/
221: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
222: {
223: char *ss; /* pointer */
224: int l1, l2; /* length counters */
225:
226: l1 = strlen(path ); /* length of path */
227: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
228: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
229: if ( ss == NULL ) { /* no directory, so use current */
230: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
231: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
232: /* get current working directory */
233: /* extern char* getcwd ( char *buf , int len);*/
234: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
235: return( GLOCK_ERROR_GETCWD );
236: }
237: strcpy( name, path ); /* we've got it */
238: } else { /* strip direcotry from path */
239: ss++; /* after this, the filename */
240: l2 = strlen( ss ); /* length of filename */
241: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
242: strcpy( name, ss ); /* save file name */
243: strncpy( dirc, path, l1 - l2 ); /* now the directory */
244: dirc[l1-l2] = 0; /* add zero */
245: }
246: l1 = strlen( dirc ); /* length of directory */
247: #ifdef windows
248: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
249: #else
250: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
251: #endif
252: ss = strrchr( name, '.' ); /* find last / */
253: ss++;
254: strcpy(ext,ss); /* save extension */
255: l1= strlen( name);
256: l2= strlen(ss)+1;
257: strncpy( finame, name, l1-l2);
258: finame[l1-l2]= 0;
259: return( 0 ); /* we're done */
260: }
261:
262:
263: /******************************************/
264:
265: void replace(char *s, char*t)
266: {
267: int i;
268: int lg=20;
269: i=0;
270: lg=strlen(t);
271: for(i=0; i<= lg; i++) {
272: (s[i] = t[i]);
273: if (t[i]== '\\') s[i]='/';
274: }
275: }
276:
277: int nbocc(char *s, char occ)
278: {
279: int i,j=0;
280: int lg=20;
281: i=0;
282: lg=strlen(s);
283: for(i=0; i<= lg; i++) {
284: if (s[i] == occ ) j++;
285: }
286: return j;
287: }
288:
289: void cutv(char *u,char *v, char*t, char occ)
290: {
291: /* cuts string t into u and v where u is ended by char occ excluding it
292: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
293: gives u="abcedf" and v="ghi2j" */
294: int i,lg,j,p=0;
295: i=0;
296: for(j=0; j<=strlen(t)-1; j++) {
297: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
298: }
299:
300: lg=strlen(t);
301: for(j=0; j<p; j++) {
302: (u[j] = t[j]);
303: }
304: u[p]='\0';
305:
306: for(j=0; j<= lg; j++) {
307: if (j>=(p+1))(v[j-p-1] = t[j]);
308: }
309: }
310:
311: /********************** nrerror ********************/
312:
313: void nrerror(char error_text[])
314: {
315: fprintf(stderr,"ERREUR ...\n");
316: fprintf(stderr,"%s\n",error_text);
317: exit(EXIT_FAILURE);
318: }
319: /*********************** vector *******************/
320: double *vector(int nl, int nh)
321: {
322: double *v;
323: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
324: if (!v) nrerror("allocation failure in vector");
325: return v-nl+NR_END;
326: }
327:
328: /************************ free vector ******************/
329: void free_vector(double*v, int nl, int nh)
330: {
331: free((FREE_ARG)(v+nl-NR_END));
332: }
333:
334: /************************ivector *******************************/
335: char *cvector(long nl,long nh)
336: {
337: char *v;
338: v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
339: if (!v) nrerror("allocation failure in cvector");
340: return v-nl+NR_END;
341: }
342:
343: /******************free ivector **************************/
344: void free_cvector(char *v, long nl, long nh)
345: {
346: free((FREE_ARG)(v+nl-NR_END));
347: }
348:
349: /************************ivector *******************************/
350: int *ivector(long nl,long nh)
351: {
352: int *v;
353: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
354: if (!v) nrerror("allocation failure in ivector");
355: return v-nl+NR_END;
356: }
357:
358: /******************free ivector **************************/
359: void free_ivector(int *v, long nl, long nh)
360: {
361: free((FREE_ARG)(v+nl-NR_END));
362: }
363:
364: /******************* imatrix *******************************/
365: int **imatrix(long nrl, long nrh, long ncl, long nch)
366: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
367: {
368: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
369: int **m;
370:
371: /* allocate pointers to rows */
372: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
373: if (!m) nrerror("allocation failure 1 in matrix()");
374: m += NR_END;
375: m -= nrl;
376:
377:
378: /* allocate rows and set pointers to them */
379: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
380: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
381: m[nrl] += NR_END;
382: m[nrl] -= ncl;
383:
384: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
385:
386: /* return pointer to array of pointers to rows */
387: return m;
388: }
389:
390: /****************** free_imatrix *************************/
391: void free_imatrix(m,nrl,nrh,ncl,nch)
392: int **m;
393: long nch,ncl,nrh,nrl;
394: /* free an int matrix allocated by imatrix() */
395: {
396: free((FREE_ARG) (m[nrl]+ncl-NR_END));
397: free((FREE_ARG) (m+nrl-NR_END));
398: }
399:
400: /******************* matrix *******************************/
401: double **matrix(long nrl, long nrh, long ncl, long nch)
402: {
403: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
404: double **m;
405:
406: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
407: if (!m) nrerror("allocation failure 1 in matrix()");
408: m += NR_END;
409: m -= nrl;
410:
411: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
412: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
413: m[nrl] += NR_END;
414: m[nrl] -= ncl;
415:
416: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
417: return m;
418: /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1])
419: */
420: }
421:
422: /*************************free matrix ************************/
423: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
424: {
425: free((FREE_ARG)(m[nrl]+ncl-NR_END));
426: free((FREE_ARG)(m+nrl-NR_END));
427: }
428:
429: /******************* ma3x *******************************/
430: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
431: {
432: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
433: double ***m;
434:
435: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
436: if (!m) nrerror("allocation failure 1 in matrix()");
437: m += NR_END;
438: m -= nrl;
439:
440: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
441: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
442: m[nrl] += NR_END;
443: m[nrl] -= ncl;
444:
445: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
446:
447: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
448: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
449: m[nrl][ncl] += NR_END;
450: m[nrl][ncl] -= nll;
451: for (j=ncl+1; j<=nch; j++)
452: m[nrl][j]=m[nrl][j-1]+nlay;
453:
454: for (i=nrl+1; i<=nrh; i++) {
455: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
456: for (j=ncl+1; j<=nch; j++)
457: m[i][j]=m[i][j-1]+nlay;
458: }
459: return m;
460: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
461: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
462: */
463: }
464:
465: /*************************free ma3x ************************/
466: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
467: {
468: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
469: free((FREE_ARG)(m[nrl]+ncl-NR_END));
470: free((FREE_ARG)(m+nrl-NR_END));
471: }
472:
473: /***************** f1dim *************************/
474: extern int ncom;
475: extern double *pcom,*xicom;
476: extern double (*nrfunc)(double []);
477:
478: double f1dim(double x)
479: {
480: int j;
481: double f;
482: double *xt;
483:
484: xt=vector(1,ncom);
485: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
486: f=(*nrfunc)(xt);
487: free_vector(xt,1,ncom);
488: return f;
489: }
490:
491: /*****************brent *************************/
492: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
493: {
494: int iter;
495: double a,b,d,etemp;
496: double fu,fv,fw,fx;
497: double ftemp;
498: double p,q,r,tol1,tol2,u,v,w,x,xm;
499: double e=0.0;
500:
501: a=(ax < cx ? ax : cx);
502: b=(ax > cx ? ax : cx);
503: x=w=v=bx;
504: fw=fv=fx=(*f)(x);
505: for (iter=1;iter<=ITMAX;iter++) {
506: xm=0.5*(a+b);
507: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
508: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
509: printf(".");fflush(stdout);
510: fprintf(ficlog,".");fflush(ficlog);
511: #ifdef DEBUG
512: 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);
513: 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);
514: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
515: #endif
516: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
517: *xmin=x;
518: return fx;
519: }
520: ftemp=fu;
521: if (fabs(e) > tol1) {
522: r=(x-w)*(fx-fv);
523: q=(x-v)*(fx-fw);
524: p=(x-v)*q-(x-w)*r;
525: q=2.0*(q-r);
526: if (q > 0.0) p = -p;
527: q=fabs(q);
528: etemp=e;
529: e=d;
530: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
531: d=CGOLD*(e=(x >= xm ? a-x : b-x));
532: else {
533: d=p/q;
534: u=x+d;
535: if (u-a < tol2 || b-u < tol2)
536: d=SIGN(tol1,xm-x);
537: }
538: } else {
539: d=CGOLD*(e=(x >= xm ? a-x : b-x));
540: }
541: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
542: fu=(*f)(u);
543: if (fu <= fx) {
544: if (u >= x) a=x; else b=x;
545: SHFT(v,w,x,u)
546: SHFT(fv,fw,fx,fu)
547: } else {
548: if (u < x) a=u; else b=u;
549: if (fu <= fw || w == x) {
550: v=w;
551: w=u;
552: fv=fw;
553: fw=fu;
554: } else if (fu <= fv || v == x || v == w) {
555: v=u;
556: fv=fu;
557: }
558: }
559: }
560: nrerror("Too many iterations in brent");
561: *xmin=x;
562: return fx;
563: }
564:
565: /****************** mnbrak ***********************/
566:
567: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
568: double (*func)(double))
569: {
570: double ulim,u,r,q, dum;
571: double fu;
572:
573: *fa=(*func)(*ax);
574: *fb=(*func)(*bx);
575: if (*fb > *fa) {
576: SHFT(dum,*ax,*bx,dum)
577: SHFT(dum,*fb,*fa,dum)
578: }
579: *cx=(*bx)+GOLD*(*bx-*ax);
580: *fc=(*func)(*cx);
581: while (*fb > *fc) {
582: r=(*bx-*ax)*(*fb-*fc);
583: q=(*bx-*cx)*(*fb-*fa);
584: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
585: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
586: ulim=(*bx)+GLIMIT*(*cx-*bx);
587: if ((*bx-u)*(u-*cx) > 0.0) {
588: fu=(*func)(u);
589: } else if ((*cx-u)*(u-ulim) > 0.0) {
590: fu=(*func)(u);
591: if (fu < *fc) {
592: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
593: SHFT(*fb,*fc,fu,(*func)(u))
594: }
595: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
596: u=ulim;
597: fu=(*func)(u);
598: } else {
599: u=(*cx)+GOLD*(*cx-*bx);
600: fu=(*func)(u);
601: }
602: SHFT(*ax,*bx,*cx,u)
603: SHFT(*fa,*fb,*fc,fu)
604: }
605: }
606:
607: /*************** linmin ************************/
608:
609: int ncom;
610: double *pcom,*xicom;
611: double (*nrfunc)(double []);
612:
613: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
614: {
615: double brent(double ax, double bx, double cx,
616: double (*f)(double), double tol, double *xmin);
617: double f1dim(double x);
618: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
619: double *fc, double (*func)(double));
620: int j;
621: double xx,xmin,bx,ax;
622: double fx,fb,fa;
623:
624: ncom=n;
625: pcom=vector(1,n);
626: xicom=vector(1,n);
627: nrfunc=func;
628: for (j=1;j<=n;j++) {
629: pcom[j]=p[j];
630: xicom[j]=xi[j];
631: }
632: ax=0.0;
633: xx=1.0;
634: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
635: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
636: #ifdef DEBUG
637: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
638: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
639: #endif
640: for (j=1;j<=n;j++) {
641: xi[j] *= xmin;
642: p[j] += xi[j];
643: }
644: free_vector(xicom,1,n);
645: free_vector(pcom,1,n);
646: }
647:
648: /*************** powell ************************/
649: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
650: double (*func)(double []))
651: {
652: void linmin(double p[], double xi[], int n, double *fret,
653: double (*func)(double []));
654: int i,ibig,j;
655: double del,t,*pt,*ptt,*xit;
656: double fp,fptt;
657: double *xits;
658: pt=vector(1,n);
659: ptt=vector(1,n);
660: xit=vector(1,n);
661: xits=vector(1,n);
662: *fret=(*func)(p);
663: for (j=1;j<=n;j++) pt[j]=p[j];
664: for (*iter=1;;++(*iter)) {
665: fp=(*fret);
666: ibig=0;
667: del=0.0;
668: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
669: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
670: fprintf(ficrespow,"%d %.12f",*iter,*fret);
671: for (i=1;i<=n;i++) {
672: printf(" %d %.12f",i, p[i]);
673: fprintf(ficlog," %d %.12lf",i, p[i]);
674: fprintf(ficrespow," %.12lf", p[i]);
675: }
676: printf("\n");
677: fprintf(ficlog,"\n");
678: fprintf(ficrespow,"\n");
679: for (i=1;i<=n;i++) {
680: for (j=1;j<=n;j++) xit[j]=xi[j][i];
681: fptt=(*fret);
682: #ifdef DEBUG
683: printf("fret=%lf \n",*fret);
684: fprintf(ficlog,"fret=%lf \n",*fret);
685: #endif
686: printf("%d",i);fflush(stdout);
687: fprintf(ficlog,"%d",i);fflush(ficlog);
688: linmin(p,xit,n,fret,func);
689: if (fabs(fptt-(*fret)) > del) {
690: del=fabs(fptt-(*fret));
691: ibig=i;
692: }
693: #ifdef DEBUG
694: printf("%d %.12e",i,(*fret));
695: fprintf(ficlog,"%d %.12e",i,(*fret));
696: for (j=1;j<=n;j++) {
697: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
698: printf(" x(%d)=%.12e",j,xit[j]);
699: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
700: }
701: for(j=1;j<=n;j++) {
702: printf(" p=%.12e",p[j]);
703: fprintf(ficlog," p=%.12e",p[j]);
704: }
705: printf("\n");
706: fprintf(ficlog,"\n");
707: #endif
708: }
709: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
710: #ifdef DEBUG
711: int k[2],l;
712: k[0]=1;
713: k[1]=-1;
714: printf("Max: %.12e",(*func)(p));
715: fprintf(ficlog,"Max: %.12e",(*func)(p));
716: for (j=1;j<=n;j++) {
717: printf(" %.12e",p[j]);
718: fprintf(ficlog," %.12e",p[j]);
719: }
720: printf("\n");
721: fprintf(ficlog,"\n");
722: for(l=0;l<=1;l++) {
723: for (j=1;j<=n;j++) {
724: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
725: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
726: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
727: }
728: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
729: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
730: }
731: #endif
732:
733:
734: free_vector(xit,1,n);
735: free_vector(xits,1,n);
736: free_vector(ptt,1,n);
737: free_vector(pt,1,n);
738: return;
739: }
740: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
741: for (j=1;j<=n;j++) {
742: ptt[j]=2.0*p[j]-pt[j];
743: xit[j]=p[j]-pt[j];
744: pt[j]=p[j];
745: }
746: fptt=(*func)(ptt);
747: if (fptt < fp) {
748: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
749: if (t < 0.0) {
750: linmin(p,xit,n,fret,func);
751: for (j=1;j<=n;j++) {
752: xi[j][ibig]=xi[j][n];
753: xi[j][n]=xit[j];
754: }
755: #ifdef DEBUG
756: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
757: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
758: for(j=1;j<=n;j++){
759: printf(" %.12e",xit[j]);
760: fprintf(ficlog," %.12e",xit[j]);
761: }
762: printf("\n");
763: fprintf(ficlog,"\n");
764: #endif
765: }
766: }
767: }
768: }
769:
770: /**** Prevalence limit (stable prevalence) ****************/
771:
772: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
773: {
774: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
775: matrix by transitions matrix until convergence is reached */
776:
777: int i, ii,j,k;
778: double min, max, maxmin, maxmax,sumnew=0.;
779: double **matprod2();
780: double **out, cov[NCOVMAX], **pmij();
781: double **newm;
782: double agefin, delaymax=50 ; /* Max number of years to converge */
783:
784: for (ii=1;ii<=nlstate+ndeath;ii++)
785: for (j=1;j<=nlstate+ndeath;j++){
786: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
787: }
788:
789: cov[1]=1.;
790:
791: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
792: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
793: newm=savm;
794: /* Covariates have to be included here again */
795: cov[2]=agefin;
796:
797: for (k=1; k<=cptcovn;k++) {
798: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
799: /* 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]]);*/
800: }
801: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
802: for (k=1; k<=cptcovprod;k++)
803: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
804:
805: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
806: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
807: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
808: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
809:
810: savm=oldm;
811: oldm=newm;
812: maxmax=0.;
813: for(j=1;j<=nlstate;j++){
814: min=1.;
815: max=0.;
816: for(i=1; i<=nlstate; i++) {
817: sumnew=0;
818: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
819: prlim[i][j]= newm[i][j]/(1-sumnew);
820: max=FMAX(max,prlim[i][j]);
821: min=FMIN(min,prlim[i][j]);
822: }
823: maxmin=max-min;
824: maxmax=FMAX(maxmax,maxmin);
825: }
826: if(maxmax < ftolpl){
827: return prlim;
828: }
829: }
830: }
831:
832: /*************** transition probabilities ***************/
833:
834: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
835: {
836: double s1, s2;
837: /*double t34;*/
838: int i,j,j1, nc, ii, jj;
839:
840: for(i=1; i<= nlstate; i++){
841: for(j=1; j<i;j++){
842: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
843: /*s2 += param[i][j][nc]*cov[nc];*/
844: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
845: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
846: }
847: ps[i][j]=s2;
848: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
849: }
850: for(j=i+1; j<=nlstate+ndeath;j++){
851: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
852: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
853: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
854: }
855: ps[i][j]=s2;
856: }
857: }
858: /*ps[3][2]=1;*/
859:
860: for(i=1; i<= nlstate; i++){
861: s1=0;
862: for(j=1; j<i; j++)
863: s1+=exp(ps[i][j]);
864: for(j=i+1; j<=nlstate+ndeath; j++)
865: s1+=exp(ps[i][j]);
866: ps[i][i]=1./(s1+1.);
867: for(j=1; j<i; j++)
868: ps[i][j]= exp(ps[i][j])*ps[i][i];
869: for(j=i+1; j<=nlstate+ndeath; j++)
870: ps[i][j]= exp(ps[i][j])*ps[i][i];
871: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
872: } /* end i */
873:
874: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
875: for(jj=1; jj<= nlstate+ndeath; jj++){
876: ps[ii][jj]=0;
877: ps[ii][ii]=1;
878: }
879: }
880:
881:
882: /* for(ii=1; ii<= nlstate+ndeath; ii++){
883: for(jj=1; jj<= nlstate+ndeath; jj++){
884: printf("%lf ",ps[ii][jj]);
885: }
886: printf("\n ");
887: }
888: printf("\n ");printf("%lf ",cov[2]);*/
889: /*
890: for(i=1; i<= npar; i++) printf("%f ",x[i]);
891: goto end;*/
892: return ps;
893: }
894:
895: /**************** Product of 2 matrices ******************/
896:
897: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
898: {
899: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
900: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
901: /* in, b, out are matrice of pointers which should have been initialized
902: before: only the contents of out is modified. The function returns
903: a pointer to pointers identical to out */
904: long i, j, k;
905: for(i=nrl; i<= nrh; i++)
906: for(k=ncolol; k<=ncoloh; k++)
907: for(j=ncl,out[i][k]=0.; j<=nch; j++)
908: out[i][k] +=in[i][j]*b[j][k];
909:
910: return out;
911: }
912:
913:
914: /************* Higher Matrix Product ***************/
915:
916: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
917: {
918: /* Computes the transition matrix starting at age 'age' over
919: 'nhstepm*hstepm*stepm' months (i.e. until
920: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
921: nhstepm*hstepm matrices.
922: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
923: (typically every 2 years instead of every month which is too big
924: for the memory).
925: Model is determined by parameters x and covariates have to be
926: included manually here.
927:
928: */
929:
930: int i, j, d, h, k;
931: double **out, cov[NCOVMAX];
932: double **newm;
933:
934: /* Hstepm could be zero and should return the unit matrix */
935: for (i=1;i<=nlstate+ndeath;i++)
936: for (j=1;j<=nlstate+ndeath;j++){
937: oldm[i][j]=(i==j ? 1.0 : 0.0);
938: po[i][j][0]=(i==j ? 1.0 : 0.0);
939: }
940: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
941: for(h=1; h <=nhstepm; h++){
942: for(d=1; d <=hstepm; d++){
943: newm=savm;
944: /* Covariates have to be included here again */
945: cov[1]=1.;
946: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
947: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
948: for (k=1; k<=cptcovage;k++)
949: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
950: for (k=1; k<=cptcovprod;k++)
951: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
952:
953:
954: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
955: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
956: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
957: pmij(pmmij,cov,ncovmodel,x,nlstate));
958: savm=oldm;
959: oldm=newm;
960: }
961: for(i=1; i<=nlstate+ndeath; i++)
962: for(j=1;j<=nlstate+ndeath;j++) {
963: po[i][j][h]=newm[i][j];
964: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
965: */
966: }
967: } /* end h */
968: return po;
969: }
970:
971:
972: /*************** log-likelihood *************/
973: double func( double *x)
974: {
975: int i, ii, j, k, mi, d, kk;
976: double l, ll[NLSTATEMAX], cov[NCOVMAX];
977: double **out;
978: double sw; /* Sum of weights */
979: double lli; /* Individual log likelihood */
980: int s1, s2;
981: double bbh, survp;
982: long ipmx;
983: /*extern weight */
984: /* We are differentiating ll according to initial status */
985: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
986: /*for(i=1;i<imx;i++)
987: printf(" %d\n",s[4][i]);
988: */
989: cov[1]=1.;
990:
991: for(k=1; k<=nlstate; k++) ll[k]=0.;
992:
993: if(mle==1){
994: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
995: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
996: for(mi=1; mi<= wav[i]-1; mi++){
997: for (ii=1;ii<=nlstate+ndeath;ii++)
998: for (j=1;j<=nlstate+ndeath;j++){
999: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1000: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1001: }
1002: for(d=0; d<dh[mi][i]; d++){
1003: newm=savm;
1004: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1005: for (kk=1; kk<=cptcovage;kk++) {
1006: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1007: }
1008: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1009: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1010: savm=oldm;
1011: oldm=newm;
1012: } /* end mult */
1013:
1014: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1015: /* But now since version 0.9 we anticipate for bias and large stepm.
1016: * If stepm is larger than one month (smallest stepm) and if the exact delay
1017: * (in months) between two waves is not a multiple of stepm, we rounded to
1018: * the nearest (and in case of equal distance, to the lowest) interval but now
1019: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1020: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1021: * probability in order to take into account the bias as a fraction of the way
1022: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1023: * -stepm/2 to stepm/2 .
1024: * For stepm=1 the results are the same as for previous versions of Imach.
1025: * For stepm > 1 the results are less biased than in previous versions.
1026: */
1027: s1=s[mw[mi][i]][i];
1028: s2=s[mw[mi+1][i]][i];
1029: bbh=(double)bh[mi][i]/(double)stepm;
1030: /* bias is positive if real duration
1031: * is higher than the multiple of stepm and negative otherwise.
1032: */
1033: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1034: if( s2 > nlstate){
1035: /* i.e. if s2 is a death state and if the date of death is known then the contribution
1036: to the likelihood is the probability to die between last step unit time and current
1037: step unit time, which is also the differences between probability to die before dh
1038: and probability to die before dh-stepm .
1039: In version up to 0.92 likelihood was computed
1040: as if date of death was unknown. Death was treated as any other
1041: health state: the date of the interview describes the actual state
1042: and not the date of a change in health state. The former idea was
1043: to consider that at each interview the state was recorded
1044: (healthy, disable or death) and IMaCh was corrected; but when we
1045: introduced the exact date of death then we should have modified
1046: the contribution of an exact death to the likelihood. This new
1047: contribution is smaller and very dependent of the step unit
1048: stepm. It is no more the probability to die between last interview
1049: and month of death but the probability to survive from last
1050: interview up to one month before death multiplied by the
1051: probability to die within a month. Thanks to Chris
1052: Jackson for correcting this bug. Former versions increased
1053: mortality artificially. The bad side is that we add another loop
1054: which slows down the processing. The difference can be up to 10%
1055: lower mortality.
1056: */
1057: lli=log(out[s1][s2] - savm[s1][s2]);
1058: }else{
1059: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1060: /* 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 */
1061: }
1062: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1063: /*if(lli ==000.0)*/
1064: /*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); */
1065: ipmx +=1;
1066: sw += weight[i];
1067: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1068: } /* end of wave */
1069: } /* end of individual */
1070: } else if(mle==2){
1071: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1072: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1073: for(mi=1; mi<= wav[i]-1; mi++){
1074: for (ii=1;ii<=nlstate+ndeath;ii++)
1075: for (j=1;j<=nlstate+ndeath;j++){
1076: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1077: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1078: }
1079: for(d=0; d<=dh[mi][i]; d++){
1080: newm=savm;
1081: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1082: for (kk=1; kk<=cptcovage;kk++) {
1083: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1084: }
1085: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1086: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1087: savm=oldm;
1088: oldm=newm;
1089: } /* end mult */
1090:
1091: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1092: /* But now since version 0.9 we anticipate for bias and large stepm.
1093: * If stepm is larger than one month (smallest stepm) and if the exact delay
1094: * (in months) between two waves is not a multiple of stepm, we rounded to
1095: * the nearest (and in case of equal distance, to the lowest) interval but now
1096: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1097: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1098: * probability in order to take into account the bias as a fraction of the way
1099: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1100: * -stepm/2 to stepm/2 .
1101: * For stepm=1 the results are the same as for previous versions of Imach.
1102: * For stepm > 1 the results are less biased than in previous versions.
1103: */
1104: s1=s[mw[mi][i]][i];
1105: s2=s[mw[mi+1][i]][i];
1106: bbh=(double)bh[mi][i]/(double)stepm;
1107: /* bias is positive if real duration
1108: * is higher than the multiple of stepm and negative otherwise.
1109: */
1110: 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 */
1111: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1112: /*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 */
1113: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1114: /*if(lli ==000.0)*/
1115: /*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); */
1116: ipmx +=1;
1117: sw += weight[i];
1118: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1119: } /* end of wave */
1120: } /* end of individual */
1121: } else if(mle==3){ /* exponential inter-extrapolation */
1122: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1123: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1124: for(mi=1; mi<= wav[i]-1; mi++){
1125: for (ii=1;ii<=nlstate+ndeath;ii++)
1126: for (j=1;j<=nlstate+ndeath;j++){
1127: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1128: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1129: }
1130: for(d=0; d<dh[mi][i]; d++){
1131: newm=savm;
1132: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1133: for (kk=1; kk<=cptcovage;kk++) {
1134: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1135: }
1136: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1137: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1138: savm=oldm;
1139: oldm=newm;
1140: } /* end mult */
1141:
1142: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1143: /* But now since version 0.9 we anticipate for bias and large stepm.
1144: * If stepm is larger than one month (smallest stepm) and if the exact delay
1145: * (in months) between two waves is not a multiple of stepm, we rounded to
1146: * the nearest (and in case of equal distance, to the lowest) interval but now
1147: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1148: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1149: * probability in order to take into account the bias as a fraction of the way
1150: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1151: * -stepm/2 to stepm/2 .
1152: * For stepm=1 the results are the same as for previous versions of Imach.
1153: * For stepm > 1 the results are less biased than in previous versions.
1154: */
1155: s1=s[mw[mi][i]][i];
1156: s2=s[mw[mi+1][i]][i];
1157: bbh=(double)bh[mi][i]/(double)stepm;
1158: /* bias is positive if real duration
1159: * is higher than the multiple of stepm and negative otherwise.
1160: */
1161: /* 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 */
1162: 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 */
1163: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1164: /*if(lli ==000.0)*/
1165: /*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); */
1166: ipmx +=1;
1167: sw += weight[i];
1168: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1169: } /* end of wave */
1170: } /* end of individual */
1171: }else{ /* ml=4 no inter-extrapolation */
1172: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1173: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1174: for(mi=1; mi<= wav[i]-1; mi++){
1175: for (ii=1;ii<=nlstate+ndeath;ii++)
1176: for (j=1;j<=nlstate+ndeath;j++){
1177: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1178: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1179: }
1180: for(d=0; d<dh[mi][i]; d++){
1181: newm=savm;
1182: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1183: for (kk=1; kk<=cptcovage;kk++) {
1184: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1185: }
1186:
1187: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1188: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1189: savm=oldm;
1190: oldm=newm;
1191: } /* end mult */
1192:
1193: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1194: ipmx +=1;
1195: sw += weight[i];
1196: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1197: } /* end of wave */
1198: } /* end of individual */
1199: } /* End of if */
1200: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1201: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1202: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1203: return -l;
1204: }
1205:
1206:
1207: /*********** Maximum Likelihood Estimation ***************/
1208:
1209: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1210: {
1211: int i,j, iter;
1212: double **xi;
1213: double fret;
1214: char filerespow[FILENAMELENGTH];
1215: xi=matrix(1,npar,1,npar);
1216: for (i=1;i<=npar;i++)
1217: for (j=1;j<=npar;j++)
1218: xi[i][j]=(i==j ? 1.0 : 0.0);
1219: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1220: strcpy(filerespow,"pow");
1221: strcat(filerespow,fileres);
1222: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1223: printf("Problem with resultfile: %s\n", filerespow);
1224: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1225: }
1226: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1227: for (i=1;i<=nlstate;i++)
1228: for(j=1;j<=nlstate+ndeath;j++)
1229: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1230: fprintf(ficrespow,"\n");
1231: powell(p,xi,npar,ftol,&iter,&fret,func);
1232:
1233: fclose(ficrespow);
1234: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1235: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1236: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1237:
1238: }
1239:
1240: /**** Computes Hessian and covariance matrix ***/
1241: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1242: {
1243: double **a,**y,*x,pd;
1244: double **hess;
1245: int i, j,jk;
1246: int *indx;
1247:
1248: double hessii(double p[], double delta, int theta, double delti[]);
1249: double hessij(double p[], double delti[], int i, int j);
1250: void lubksb(double **a, int npar, int *indx, double b[]) ;
1251: void ludcmp(double **a, int npar, int *indx, double *d) ;
1252:
1253: hess=matrix(1,npar,1,npar);
1254:
1255: printf("\nCalculation of the hessian matrix. Wait...\n");
1256: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1257: for (i=1;i<=npar;i++){
1258: printf("%d",i);fflush(stdout);
1259: fprintf(ficlog,"%d",i);fflush(ficlog);
1260: hess[i][i]=hessii(p,ftolhess,i,delti);
1261: /*printf(" %f ",p[i]);*/
1262: /*printf(" %lf ",hess[i][i]);*/
1263: }
1264:
1265: for (i=1;i<=npar;i++) {
1266: for (j=1;j<=npar;j++) {
1267: if (j>i) {
1268: printf(".%d%d",i,j);fflush(stdout);
1269: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1270: hess[i][j]=hessij(p,delti,i,j);
1271: hess[j][i]=hess[i][j];
1272: /*printf(" %lf ",hess[i][j]);*/
1273: }
1274: }
1275: }
1276: printf("\n");
1277: fprintf(ficlog,"\n");
1278:
1279: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1280: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1281:
1282: a=matrix(1,npar,1,npar);
1283: y=matrix(1,npar,1,npar);
1284: x=vector(1,npar);
1285: indx=ivector(1,npar);
1286: for (i=1;i<=npar;i++)
1287: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1288: ludcmp(a,npar,indx,&pd);
1289:
1290: for (j=1;j<=npar;j++) {
1291: for (i=1;i<=npar;i++) x[i]=0;
1292: x[j]=1;
1293: lubksb(a,npar,indx,x);
1294: for (i=1;i<=npar;i++){
1295: matcov[i][j]=x[i];
1296: }
1297: }
1298:
1299: printf("\n#Hessian matrix#\n");
1300: fprintf(ficlog,"\n#Hessian matrix#\n");
1301: for (i=1;i<=npar;i++) {
1302: for (j=1;j<=npar;j++) {
1303: printf("%.3e ",hess[i][j]);
1304: fprintf(ficlog,"%.3e ",hess[i][j]);
1305: }
1306: printf("\n");
1307: fprintf(ficlog,"\n");
1308: }
1309:
1310: /* Recompute Inverse */
1311: for (i=1;i<=npar;i++)
1312: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1313: ludcmp(a,npar,indx,&pd);
1314:
1315: /* printf("\n#Hessian matrix recomputed#\n");
1316:
1317: for (j=1;j<=npar;j++) {
1318: for (i=1;i<=npar;i++) x[i]=0;
1319: x[j]=1;
1320: lubksb(a,npar,indx,x);
1321: for (i=1;i<=npar;i++){
1322: y[i][j]=x[i];
1323: printf("%.3e ",y[i][j]);
1324: fprintf(ficlog,"%.3e ",y[i][j]);
1325: }
1326: printf("\n");
1327: fprintf(ficlog,"\n");
1328: }
1329: */
1330:
1331: free_matrix(a,1,npar,1,npar);
1332: free_matrix(y,1,npar,1,npar);
1333: free_vector(x,1,npar);
1334: free_ivector(indx,1,npar);
1335: free_matrix(hess,1,npar,1,npar);
1336:
1337:
1338: }
1339:
1340: /*************** hessian matrix ****************/
1341: double hessii( double x[], double delta, int theta, double delti[])
1342: {
1343: int i;
1344: int l=1, lmax=20;
1345: double k1,k2;
1346: double p2[NPARMAX+1];
1347: double res;
1348: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1349: double fx;
1350: int k=0,kmax=10;
1351: double l1;
1352:
1353: fx=func(x);
1354: for (i=1;i<=npar;i++) p2[i]=x[i];
1355: for(l=0 ; l <=lmax; l++){
1356: l1=pow(10,l);
1357: delts=delt;
1358: for(k=1 ; k <kmax; k=k+1){
1359: delt = delta*(l1*k);
1360: p2[theta]=x[theta] +delt;
1361: k1=func(p2)-fx;
1362: p2[theta]=x[theta]-delt;
1363: k2=func(p2)-fx;
1364: /*res= (k1-2.0*fx+k2)/delt/delt; */
1365: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1366:
1367: #ifdef DEBUG
1368: 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);
1369: 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);
1370: #endif
1371: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1372: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1373: k=kmax;
1374: }
1375: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1376: k=kmax; l=lmax*10.;
1377: }
1378: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1379: delts=delt;
1380: }
1381: }
1382: }
1383: delti[theta]=delts;
1384: return res;
1385:
1386: }
1387:
1388: double hessij( double x[], double delti[], int thetai,int thetaj)
1389: {
1390: int i;
1391: int l=1, l1, lmax=20;
1392: double k1,k2,k3,k4,res,fx;
1393: double p2[NPARMAX+1];
1394: int k;
1395:
1396: fx=func(x);
1397: for (k=1; k<=2; k++) {
1398: for (i=1;i<=npar;i++) p2[i]=x[i];
1399: p2[thetai]=x[thetai]+delti[thetai]/k;
1400: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1401: k1=func(p2)-fx;
1402:
1403: p2[thetai]=x[thetai]+delti[thetai]/k;
1404: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1405: k2=func(p2)-fx;
1406:
1407: p2[thetai]=x[thetai]-delti[thetai]/k;
1408: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1409: k3=func(p2)-fx;
1410:
1411: p2[thetai]=x[thetai]-delti[thetai]/k;
1412: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1413: k4=func(p2)-fx;
1414: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1415: #ifdef DEBUG
1416: 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);
1417: 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);
1418: #endif
1419: }
1420: return res;
1421: }
1422:
1423: /************** Inverse of matrix **************/
1424: void ludcmp(double **a, int n, int *indx, double *d)
1425: {
1426: int i,imax,j,k;
1427: double big,dum,sum,temp;
1428: double *vv;
1429:
1430: vv=vector(1,n);
1431: *d=1.0;
1432: for (i=1;i<=n;i++) {
1433: big=0.0;
1434: for (j=1;j<=n;j++)
1435: if ((temp=fabs(a[i][j])) > big) big=temp;
1436: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1437: vv[i]=1.0/big;
1438: }
1439: for (j=1;j<=n;j++) {
1440: for (i=1;i<j;i++) {
1441: sum=a[i][j];
1442: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1443: a[i][j]=sum;
1444: }
1445: big=0.0;
1446: for (i=j;i<=n;i++) {
1447: sum=a[i][j];
1448: for (k=1;k<j;k++)
1449: sum -= a[i][k]*a[k][j];
1450: a[i][j]=sum;
1451: if ( (dum=vv[i]*fabs(sum)) >= big) {
1452: big=dum;
1453: imax=i;
1454: }
1455: }
1456: if (j != imax) {
1457: for (k=1;k<=n;k++) {
1458: dum=a[imax][k];
1459: a[imax][k]=a[j][k];
1460: a[j][k]=dum;
1461: }
1462: *d = -(*d);
1463: vv[imax]=vv[j];
1464: }
1465: indx[j]=imax;
1466: if (a[j][j] == 0.0) a[j][j]=TINY;
1467: if (j != n) {
1468: dum=1.0/(a[j][j]);
1469: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1470: }
1471: }
1472: free_vector(vv,1,n); /* Doesn't work */
1473: ;
1474: }
1475:
1476: void lubksb(double **a, int n, int *indx, double b[])
1477: {
1478: int i,ii=0,ip,j;
1479: double sum;
1480:
1481: for (i=1;i<=n;i++) {
1482: ip=indx[i];
1483: sum=b[ip];
1484: b[ip]=b[i];
1485: if (ii)
1486: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1487: else if (sum) ii=i;
1488: b[i]=sum;
1489: }
1490: for (i=n;i>=1;i--) {
1491: sum=b[i];
1492: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1493: b[i]=sum/a[i][i];
1494: }
1495: }
1496:
1497: /************ Frequencies ********************/
1498: 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, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
1499: { /* Some frequencies */
1500:
1501: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1502: int first;
1503: double ***freq; /* Frequencies */
1504: double *pp, **prop;
1505: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1506: FILE *ficresp;
1507: char fileresp[FILENAMELENGTH];
1508:
1509: pp=vector(1,nlstate);
1510: prop=matrix(1,nlstate,iagemin,iagemax+3);
1511: strcpy(fileresp,"p");
1512: strcat(fileresp,fileres);
1513: if((ficresp=fopen(fileresp,"w"))==NULL) {
1514: printf("Problem with prevalence resultfile: %s\n", fileresp);
1515: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1516: exit(0);
1517: }
1518: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
1519: j1=0;
1520:
1521: j=cptcoveff;
1522: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1523:
1524: first=1;
1525:
1526: for(k1=1; k1<=j;k1++){
1527: for(i1=1; i1<=ncodemax[k1];i1++){
1528: j1++;
1529: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1530: scanf("%d", i);*/
1531: for (i=-1; i<=nlstate+ndeath; i++)
1532: for (jk=-1; jk<=nlstate+ndeath; jk++)
1533: for(m=iagemin; m <= iagemax+3; m++)
1534: freq[i][jk][m]=0;
1535:
1536: for (i=1; i<=nlstate; i++)
1537: for(m=iagemin; m <= iagemax+3; m++)
1538: prop[i][m]=0;
1539:
1540: dateintsum=0;
1541: k2cpt=0;
1542: for (i=1; i<=imx; i++) {
1543: bool=1;
1544: if (cptcovn>0) {
1545: for (z1=1; z1<=cptcoveff; z1++)
1546: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1547: bool=0;
1548: }
1549: if (bool==1){
1550: for(m=firstpass; m<=lastpass; m++){
1551: k2=anint[m][i]+(mint[m][i]/12.);
1552: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1553: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1554: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1555: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1556: if (m<lastpass) {
1557: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1558: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1559: }
1560:
1561: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1562: dateintsum=dateintsum+k2;
1563: k2cpt++;
1564: }
1565: }
1566: }
1567: }
1568: }
1569:
1570: fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1571:
1572: if (cptcovn>0) {
1573: fprintf(ficresp, "\n#********** Variable ");
1574: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1575: fprintf(ficresp, "**********\n#");
1576: }
1577: for(i=1; i<=nlstate;i++)
1578: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1579: fprintf(ficresp, "\n");
1580:
1581: for(i=iagemin; i <= iagemax+3; i++){
1582: if(i==iagemax+3){
1583: fprintf(ficlog,"Total");
1584: }else{
1585: if(first==1){
1586: first=0;
1587: printf("See log file for details...\n");
1588: }
1589: fprintf(ficlog,"Age %d", i);
1590: }
1591: for(jk=1; jk <=nlstate ; jk++){
1592: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1593: pp[jk] += freq[jk][m][i];
1594: }
1595: for(jk=1; jk <=nlstate ; jk++){
1596: for(m=-1, pos=0; m <=0 ; m++)
1597: pos += freq[jk][m][i];
1598: if(pp[jk]>=1.e-10){
1599: if(first==1){
1600: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1601: }
1602: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1603: }else{
1604: if(first==1)
1605: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1606: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1607: }
1608: }
1609:
1610: for(jk=1; jk <=nlstate ; jk++){
1611: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1612: pp[jk] += freq[jk][m][i];
1613: }
1614: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
1615: pos += pp[jk];
1616: posprop += prop[jk][i];
1617: }
1618: for(jk=1; jk <=nlstate ; jk++){
1619: if(pos>=1.e-5){
1620: if(first==1)
1621: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1622: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1623: }else{
1624: if(first==1)
1625: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1626: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1627: }
1628: if( i <= iagemax){
1629: if(pos>=1.e-5){
1630: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1631: probs[i][jk][j1]= pp[jk]/pos;
1632: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1633: }
1634: else
1635: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1636: }
1637: }
1638:
1639: for(jk=-1; jk <=nlstate+ndeath; jk++)
1640: for(m=-1; m <=nlstate+ndeath; m++)
1641: if(freq[jk][m][i] !=0 ) {
1642: if(first==1)
1643: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1644: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1645: }
1646: if(i <= iagemax)
1647: fprintf(ficresp,"\n");
1648: if(first==1)
1649: printf("Others in log...\n");
1650: fprintf(ficlog,"\n");
1651: }
1652: }
1653: }
1654: dateintmean=dateintsum/k2cpt;
1655:
1656: fclose(ficresp);
1657: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
1658: free_vector(pp,1,nlstate);
1659: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1660: /* End of Freq */
1661: }
1662:
1663: /************ Prevalence ********************/
1664: void prevalence(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)
1665: {
1666: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
1667: in each health status at the date of interview (if between dateprev1 and dateprev2).
1668: We still use firstpass and lastpass as another selection.
1669: */
1670:
1671: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1672: double ***freq; /* Frequencies */
1673: double *pp, **prop;
1674: double pos,posprop;
1675: double y2; /* in fractional years */
1676: int iagemin, iagemax;
1677:
1678: iagemin= (int) agemin;
1679: iagemax= (int) agemax;
1680: /*pp=vector(1,nlstate);*/
1681: prop=matrix(1,nlstate,iagemin,iagemax+3);
1682: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1683: j1=0;
1684:
1685: j=cptcoveff;
1686: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1687:
1688: for(k1=1; k1<=j;k1++){
1689: for(i1=1; i1<=ncodemax[k1];i1++){
1690: j1++;
1691:
1692: for (i=1; i<=nlstate; i++)
1693: for(m=iagemin; m <= iagemax+3; m++)
1694: prop[i][m]=0.0;
1695:
1696: for (i=1; i<=imx; i++) { /* Each individual */
1697: bool=1;
1698: if (cptcovn>0) {
1699: for (z1=1; z1<=cptcoveff; z1++)
1700: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1701: bool=0;
1702: }
1703: if (bool==1) {
1704: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
1705: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
1706: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1707: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1708: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1709: 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);
1710: if (s[m][i]>0 && s[m][i]<=nlstate) {
1711: /*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]]);*/
1712: prop[s[m][i]][(int)agev[m][i]] += weight[i];
1713: prop[s[m][i]][iagemax+3] += weight[i];
1714: }
1715: }
1716: } /* end selection of waves */
1717: }
1718: }
1719: for(i=iagemin; i <= iagemax+3; i++){
1720:
1721: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
1722: posprop += prop[jk][i];
1723: }
1724:
1725: for(jk=1; jk <=nlstate ; jk++){
1726: if( i <= iagemax){
1727: if(posprop>=1.e-5){
1728: probs[i][jk][j1]= prop[jk][i]/posprop;
1729: }
1730: }
1731: }/* end jk */
1732: }/* end i */
1733: } /* end i1 */
1734: } /* end k1 */
1735:
1736: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
1737: /*free_vector(pp,1,nlstate);*/
1738: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
1739: } /* End of prevalence */
1740:
1741: /************* Waves Concatenation ***************/
1742:
1743: 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)
1744: {
1745: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1746: Death is a valid wave (if date is known).
1747: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1748: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1749: and mw[mi+1][i]. dh depends on stepm.
1750: */
1751:
1752: int i, mi, m;
1753: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1754: double sum=0., jmean=0.;*/
1755: int first;
1756: int j, k=0,jk, ju, jl;
1757: double sum=0.;
1758: first=0;
1759: jmin=1e+5;
1760: jmax=-1;
1761: jmean=0.;
1762: for(i=1; i<=imx; i++){
1763: mi=0;
1764: m=firstpass;
1765: while(s[m][i] <= nlstate){
1766: if(s[m][i]>=1)
1767: mw[++mi][i]=m;
1768: if(m >=lastpass)
1769: break;
1770: else
1771: m++;
1772: }/* end while */
1773: if (s[m][i] > nlstate){
1774: mi++; /* Death is another wave */
1775: /* if(mi==0) never been interviewed correctly before death */
1776: /* Only death is a correct wave */
1777: mw[mi][i]=m;
1778: }
1779:
1780: wav[i]=mi;
1781: if(mi==0){
1782: if(first==0){
1783: printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
1784: first=1;
1785: }
1786: if(first==1){
1787: fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
1788: }
1789: } /* end mi==0 */
1790: } /* End individuals */
1791:
1792: for(i=1; i<=imx; i++){
1793: for(mi=1; mi<wav[i];mi++){
1794: if (stepm <=0)
1795: dh[mi][i]=1;
1796: else{
1797: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
1798: if (agedc[i] < 2*AGESUP) {
1799: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1800: if(j==0) j=1; /* Survives at least one month after exam */
1801: k=k+1;
1802: if (j >= jmax) jmax=j;
1803: if (j <= jmin) jmin=j;
1804: sum=sum+j;
1805: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
1806: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1807: if(j<0)printf("Error! Negative delay (%d to death) between waves %d and %d of individual %d 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]);
1808: }
1809: }
1810: else{
1811: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1812: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1813: k=k+1;
1814: if (j >= jmax) jmax=j;
1815: else if (j <= jmin)jmin=j;
1816: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1817: /*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]);*/
1818: if(j<0)printf("Error! Negative delay (%d) between waves %d and %d of individual %d 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]);
1819: sum=sum+j;
1820: }
1821: jk= j/stepm;
1822: jl= j -jk*stepm;
1823: ju= j -(jk+1)*stepm;
1824: if(mle <=1){
1825: if(jl==0){
1826: dh[mi][i]=jk;
1827: bh[mi][i]=0;
1828: }else{ /* We want a negative bias in order to only have interpolation ie
1829: * at the price of an extra matrix product in likelihood */
1830: dh[mi][i]=jk+1;
1831: bh[mi][i]=ju;
1832: }
1833: }else{
1834: if(jl <= -ju){
1835: dh[mi][i]=jk;
1836: bh[mi][i]=jl; /* bias is positive if real duration
1837: * is higher than the multiple of stepm and negative otherwise.
1838: */
1839: }
1840: else{
1841: dh[mi][i]=jk+1;
1842: bh[mi][i]=ju;
1843: }
1844: if(dh[mi][i]==0){
1845: dh[mi][i]=1; /* At least one step */
1846: bh[mi][i]=ju; /* At least one step */
1847: /* 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);*/
1848: }
1849: }
1850: } /* end if mle */
1851: } /* end wave */
1852: }
1853: jmean=sum/k;
1854: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1855: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1856: }
1857:
1858: /*********** Tricode ****************************/
1859: void tricode(int *Tvar, int **nbcode, int imx)
1860: {
1861:
1862: int Ndum[20],ij=1, k, j, i, maxncov=19;
1863: int cptcode=0;
1864: cptcoveff=0;
1865:
1866: for (k=0; k<maxncov; k++) Ndum[k]=0;
1867: for (k=1; k<=7; k++) ncodemax[k]=0;
1868:
1869: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1870: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
1871: modality*/
1872: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
1873: Ndum[ij]++; /*store the modality */
1874: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1875: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
1876: Tvar[j]. If V=sex and male is 0 and
1877: female is 1, then cptcode=1.*/
1878: }
1879:
1880: for (i=0; i<=cptcode; i++) {
1881: 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 */
1882: }
1883:
1884: ij=1;
1885: for (i=1; i<=ncodemax[j]; i++) {
1886: for (k=0; k<= maxncov; k++) {
1887: if (Ndum[k] != 0) {
1888: nbcode[Tvar[j]][ij]=k;
1889: /* 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; */
1890:
1891: ij++;
1892: }
1893: if (ij > ncodemax[j]) break;
1894: }
1895: }
1896: }
1897:
1898: for (k=0; k< maxncov; k++) Ndum[k]=0;
1899:
1900: for (i=1; i<=ncovmodel-2; i++) {
1901: /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
1902: ij=Tvar[i];
1903: Ndum[ij]++;
1904: }
1905:
1906: ij=1;
1907: for (i=1; i<= maxncov; i++) {
1908: if((Ndum[i]!=0) && (i<=ncovcol)){
1909: Tvaraff[ij]=i; /*For printing */
1910: ij++;
1911: }
1912: }
1913:
1914: cptcoveff=ij-1; /*Number of simple covariates*/
1915: }
1916:
1917: /*********** Health Expectancies ****************/
1918:
1919: 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 )
1920:
1921: {
1922: /* Health expectancies */
1923: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
1924: double age, agelim, hf;
1925: double ***p3mat,***varhe;
1926: double **dnewm,**doldm;
1927: double *xp;
1928: double **gp, **gm;
1929: double ***gradg, ***trgradg;
1930: int theta;
1931:
1932: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1933: xp=vector(1,npar);
1934: dnewm=matrix(1,nlstate*nlstate,1,npar);
1935: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1936:
1937: fprintf(ficreseij,"# Health expectancies\n");
1938: fprintf(ficreseij,"# Age");
1939: for(i=1; i<=nlstate;i++)
1940: for(j=1; j<=nlstate;j++)
1941: fprintf(ficreseij," %1d-%1d (SE)",i,j);
1942: fprintf(ficreseij,"\n");
1943:
1944: if(estepm < stepm){
1945: printf ("Problem %d lower than %d\n",estepm, stepm);
1946: }
1947: else hstepm=estepm;
1948: /* We compute the life expectancy from trapezoids spaced every estepm months
1949: * This is mainly to measure the difference between two models: for example
1950: * if stepm=24 months pijx are given only every 2 years and by summing them
1951: * we are calculating an estimate of the Life Expectancy assuming a linear
1952: * progression in between and thus overestimating or underestimating according
1953: * to the curvature of the survival function. If, for the same date, we
1954: * estimate the model with stepm=1 month, we can keep estepm to 24 months
1955: * to compare the new estimate of Life expectancy with the same linear
1956: * hypothesis. A more precise result, taking into account a more precise
1957: * curvature will be obtained if estepm is as small as stepm. */
1958:
1959: /* For example we decided to compute the life expectancy with the smallest unit */
1960: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
1961: nhstepm is the number of hstepm from age to agelim
1962: nstepm is the number of stepm from age to agelin.
1963: Look at hpijx to understand the reason of that which relies in memory size
1964: and note for a fixed period like estepm months */
1965: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
1966: survival function given by stepm (the optimization length). Unfortunately it
1967: means that if the survival funtion is printed only each two years of age and if
1968: you sum them up and add 1 year (area under the trapezoids) you won't get the same
1969: results. So we changed our mind and took the option of the best precision.
1970: */
1971: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
1972:
1973: agelim=AGESUP;
1974: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1975: /* nhstepm age range expressed in number of stepm */
1976: nstepm=(int) rint((agelim-age)*YEARM/stepm);
1977: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
1978: /* if (stepm >= YEARM) hstepm=1;*/
1979: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
1980: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1981: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
1982: gp=matrix(0,nhstepm,1,nlstate*nlstate);
1983: gm=matrix(0,nhstepm,1,nlstate*nlstate);
1984:
1985: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1986: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1987: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1988:
1989:
1990: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1991:
1992: /* Computing Variances of health expectancies */
1993:
1994: for(theta=1; theta <=npar; theta++){
1995: for(i=1; i<=npar; i++){
1996: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1997: }
1998: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1999:
2000: cptj=0;
2001: for(j=1; j<= nlstate; j++){
2002: for(i=1; i<=nlstate; i++){
2003: cptj=cptj+1;
2004: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2005: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2006: }
2007: }
2008: }
2009:
2010:
2011: for(i=1; i<=npar; i++)
2012: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2013: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2014:
2015: cptj=0;
2016: for(j=1; j<= nlstate; j++){
2017: for(i=1;i<=nlstate;i++){
2018: cptj=cptj+1;
2019: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
2020:
2021: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2022: }
2023: }
2024: }
2025: for(j=1; j<= nlstate*nlstate; j++)
2026: for(h=0; h<=nhstepm-1; h++){
2027: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2028: }
2029: }
2030:
2031: /* End theta */
2032:
2033: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2034:
2035: for(h=0; h<=nhstepm-1; h++)
2036: for(j=1; j<=nlstate*nlstate;j++)
2037: for(theta=1; theta <=npar; theta++)
2038: trgradg[h][j][theta]=gradg[h][theta][j];
2039:
2040:
2041: for(i=1;i<=nlstate*nlstate;i++)
2042: for(j=1;j<=nlstate*nlstate;j++)
2043: varhe[i][j][(int)age] =0.;
2044:
2045: printf("%d|",(int)age);fflush(stdout);
2046: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2047: for(h=0;h<=nhstepm-1;h++){
2048: for(k=0;k<=nhstepm-1;k++){
2049: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2050: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2051: for(i=1;i<=nlstate*nlstate;i++)
2052: for(j=1;j<=nlstate*nlstate;j++)
2053: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2054: }
2055: }
2056: /* Computing expectancies */
2057: for(i=1; i<=nlstate;i++)
2058: for(j=1; j<=nlstate;j++)
2059: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2060: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2061:
2062: /* 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]);*/
2063:
2064: }
2065:
2066: fprintf(ficreseij,"%3.0f",age );
2067: cptj=0;
2068: for(i=1; i<=nlstate;i++)
2069: for(j=1; j<=nlstate;j++){
2070: cptj++;
2071: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2072: }
2073: fprintf(ficreseij,"\n");
2074:
2075: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2076: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2077: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2078: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2079: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2080: }
2081: printf("\n");
2082: fprintf(ficlog,"\n");
2083:
2084: free_vector(xp,1,npar);
2085: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2086: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2087: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2088: }
2089:
2090: /************ Variance ******************/
2091: 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)
2092: {
2093: /* Variance of health expectancies */
2094: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2095: /* double **newm;*/
2096: double **dnewm,**doldm;
2097: double **dnewmp,**doldmp;
2098: int i, j, nhstepm, hstepm, h, nstepm ;
2099: int k, cptcode;
2100: double *xp;
2101: double **gp, **gm; /* for var eij */
2102: double ***gradg, ***trgradg; /*for var eij */
2103: double **gradgp, **trgradgp; /* for var p point j */
2104: double *gpp, *gmp; /* for var p point j */
2105: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2106: double ***p3mat;
2107: double age,agelim, hf;
2108: double ***mobaverage;
2109: int theta;
2110: char digit[4];
2111: char digitp[25];
2112:
2113: char fileresprobmorprev[FILENAMELENGTH];
2114:
2115: if(popbased==1){
2116: if(mobilav!=0)
2117: strcpy(digitp,"-populbased-mobilav-");
2118: else strcpy(digitp,"-populbased-nomobil-");
2119: }
2120: else
2121: strcpy(digitp,"-stablbased-");
2122:
2123: if (mobilav!=0) {
2124: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2125: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2126: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2127: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2128: }
2129: }
2130:
2131: strcpy(fileresprobmorprev,"prmorprev");
2132: sprintf(digit,"%-d",ij);
2133: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2134: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2135: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2136: strcat(fileresprobmorprev,fileres);
2137: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2138: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2139: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2140: }
2141: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2142: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2143: 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);
2144: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2145: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2146: fprintf(ficresprobmorprev," p.%-d SE",j);
2147: for(i=1; i<=nlstate;i++)
2148: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2149: }
2150: fprintf(ficresprobmorprev,"\n");
2151: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2152: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2153: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2154: exit(0);
2155: }
2156: else{
2157: fprintf(ficgp,"\n# Routine varevsij");
2158: }
2159: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2160: printf("Problem with html file: %s\n", optionfilehtm);
2161: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2162: exit(0);
2163: }
2164: else{
2165: 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");
2166: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2167: }
2168: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2169:
2170: 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");
2171: fprintf(ficresvij,"# Age");
2172: for(i=1; i<=nlstate;i++)
2173: for(j=1; j<=nlstate;j++)
2174: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2175: fprintf(ficresvij,"\n");
2176:
2177: xp=vector(1,npar);
2178: dnewm=matrix(1,nlstate,1,npar);
2179: doldm=matrix(1,nlstate,1,nlstate);
2180: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2181: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2182:
2183: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2184: gpp=vector(nlstate+1,nlstate+ndeath);
2185: gmp=vector(nlstate+1,nlstate+ndeath);
2186: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2187:
2188: if(estepm < stepm){
2189: printf ("Problem %d lower than %d\n",estepm, stepm);
2190: }
2191: else hstepm=estepm;
2192: /* For example we decided to compute the life expectancy with the smallest unit */
2193: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2194: nhstepm is the number of hstepm from age to agelim
2195: nstepm is the number of stepm from age to agelin.
2196: Look at hpijx to understand the reason of that which relies in memory size
2197: and note for a fixed period like k years */
2198: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2199: survival function given by stepm (the optimization length). Unfortunately it
2200: means that if the survival funtion is printed every two years of age and if
2201: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2202: results. So we changed our mind and took the option of the best precision.
2203: */
2204: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2205: agelim = AGESUP;
2206: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2207: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2208: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2209: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2210: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2211: gp=matrix(0,nhstepm,1,nlstate);
2212: gm=matrix(0,nhstepm,1,nlstate);
2213:
2214:
2215: for(theta=1; theta <=npar; theta++){
2216: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2217: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2218: }
2219: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2220: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2221:
2222: if (popbased==1) {
2223: if(mobilav ==0){
2224: for(i=1; i<=nlstate;i++)
2225: prlim[i][i]=probs[(int)age][i][ij];
2226: }else{ /* mobilav */
2227: for(i=1; i<=nlstate;i++)
2228: prlim[i][i]=mobaverage[(int)age][i][ij];
2229: }
2230: }
2231:
2232: for(j=1; j<= nlstate; j++){
2233: for(h=0; h<=nhstepm; h++){
2234: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2235: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2236: }
2237: }
2238: /* This for computing probability of death (h=1 means
2239: computed over hstepm matrices product = hstepm*stepm months)
2240: as a weighted average of prlim.
2241: */
2242: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2243: for(i=1,gpp[j]=0.; i<= nlstate; i++)
2244: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2245: }
2246: /* end probability of death */
2247:
2248: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
2249: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2250: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2251: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2252:
2253: if (popbased==1) {
2254: if(mobilav ==0){
2255: for(i=1; i<=nlstate;i++)
2256: prlim[i][i]=probs[(int)age][i][ij];
2257: }else{ /* mobilav */
2258: for(i=1; i<=nlstate;i++)
2259: prlim[i][i]=mobaverage[(int)age][i][ij];
2260: }
2261: }
2262:
2263: for(j=1; j<= nlstate; j++){
2264: for(h=0; h<=nhstepm; h++){
2265: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2266: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2267: }
2268: }
2269: /* This for computing probability of death (h=1 means
2270: computed over hstepm matrices product = hstepm*stepm months)
2271: as a weighted average of prlim.
2272: */
2273: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2274: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2275: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2276: }
2277: /* end probability of death */
2278:
2279: for(j=1; j<= nlstate; j++) /* vareij */
2280: for(h=0; h<=nhstepm; h++){
2281: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2282: }
2283:
2284: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2285: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2286: }
2287:
2288: } /* End theta */
2289:
2290: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2291:
2292: for(h=0; h<=nhstepm; h++) /* veij */
2293: for(j=1; j<=nlstate;j++)
2294: for(theta=1; theta <=npar; theta++)
2295: trgradg[h][j][theta]=gradg[h][theta][j];
2296:
2297: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
2298: for(theta=1; theta <=npar; theta++)
2299: trgradgp[j][theta]=gradgp[theta][j];
2300:
2301:
2302: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2303: for(i=1;i<=nlstate;i++)
2304: for(j=1;j<=nlstate;j++)
2305: vareij[i][j][(int)age] =0.;
2306:
2307: for(h=0;h<=nhstepm;h++){
2308: for(k=0;k<=nhstepm;k++){
2309: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2310: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2311: for(i=1;i<=nlstate;i++)
2312: for(j=1;j<=nlstate;j++)
2313: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2314: }
2315: }
2316:
2317: /* pptj */
2318: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2319: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
2320: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2321: for(i=nlstate+1;i<=nlstate+ndeath;i++)
2322: varppt[j][i]=doldmp[j][i];
2323: /* end ppptj */
2324: /* x centered again */
2325: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2326: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2327:
2328: if (popbased==1) {
2329: if(mobilav ==0){
2330: for(i=1; i<=nlstate;i++)
2331: prlim[i][i]=probs[(int)age][i][ij];
2332: }else{ /* mobilav */
2333: for(i=1; i<=nlstate;i++)
2334: prlim[i][i]=mobaverage[(int)age][i][ij];
2335: }
2336: }
2337:
2338: /* This for computing probability of death (h=1 means
2339: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2340: as a weighted average of prlim.
2341: */
2342: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2343: for(i=1,gmp[j]=0.;i<= nlstate; i++)
2344: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2345: }
2346: /* end probability of death */
2347:
2348: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2349: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2350: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2351: for(i=1; i<=nlstate;i++){
2352: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2353: }
2354: }
2355: fprintf(ficresprobmorprev,"\n");
2356:
2357: fprintf(ficresvij,"%.0f ",age );
2358: for(i=1; i<=nlstate;i++)
2359: for(j=1; j<=nlstate;j++){
2360: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2361: }
2362: fprintf(ficresvij,"\n");
2363: free_matrix(gp,0,nhstepm,1,nlstate);
2364: free_matrix(gm,0,nhstepm,1,nlstate);
2365: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2366: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2367: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2368: } /* End age */
2369: free_vector(gpp,nlstate+1,nlstate+ndeath);
2370: free_vector(gmp,nlstate+1,nlstate+ndeath);
2371: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2372: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2373: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2374: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2375: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
2376: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2377: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2378: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
2379: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",fileresprobmorprev);
2380: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
2381: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
2382: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
2383: 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);
2384: /* 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);
2385: */
2386: fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
2387:
2388: free_vector(xp,1,npar);
2389: free_matrix(doldm,1,nlstate,1,nlstate);
2390: free_matrix(dnewm,1,nlstate,1,npar);
2391: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2392: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2393: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2394: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2395: fclose(ficresprobmorprev);
2396: fclose(ficgp);
2397: fclose(fichtm);
2398: }
2399:
2400: /************ Variance of prevlim ******************/
2401: 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)
2402: {
2403: /* Variance of prevalence limit */
2404: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
2405: double **newm;
2406: double **dnewm,**doldm;
2407: int i, j, nhstepm, hstepm;
2408: int k, cptcode;
2409: double *xp;
2410: double *gp, *gm;
2411: double **gradg, **trgradg;
2412: double age,agelim;
2413: int theta;
2414:
2415: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
2416: fprintf(ficresvpl,"# Age");
2417: for(i=1; i<=nlstate;i++)
2418: fprintf(ficresvpl," %1d-%1d",i,i);
2419: fprintf(ficresvpl,"\n");
2420:
2421: xp=vector(1,npar);
2422: dnewm=matrix(1,nlstate,1,npar);
2423: doldm=matrix(1,nlstate,1,nlstate);
2424:
2425: hstepm=1*YEARM; /* Every year of age */
2426: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2427: agelim = AGESUP;
2428: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2429: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2430: if (stepm >= YEARM) hstepm=1;
2431: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2432: gradg=matrix(1,npar,1,nlstate);
2433: gp=vector(1,nlstate);
2434: gm=vector(1,nlstate);
2435:
2436: for(theta=1; theta <=npar; theta++){
2437: for(i=1; i<=npar; i++){ /* Computes gradient */
2438: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2439: }
2440: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2441: for(i=1;i<=nlstate;i++)
2442: gp[i] = prlim[i][i];
2443:
2444: for(i=1; i<=npar; i++) /* Computes gradient */
2445: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2446: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2447: for(i=1;i<=nlstate;i++)
2448: gm[i] = prlim[i][i];
2449:
2450: for(i=1;i<=nlstate;i++)
2451: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2452: } /* End theta */
2453:
2454: trgradg =matrix(1,nlstate,1,npar);
2455:
2456: for(j=1; j<=nlstate;j++)
2457: for(theta=1; theta <=npar; theta++)
2458: trgradg[j][theta]=gradg[theta][j];
2459:
2460: for(i=1;i<=nlstate;i++)
2461: varpl[i][(int)age] =0.;
2462: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2463: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2464: for(i=1;i<=nlstate;i++)
2465: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2466:
2467: fprintf(ficresvpl,"%.0f ",age );
2468: for(i=1; i<=nlstate;i++)
2469: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2470: fprintf(ficresvpl,"\n");
2471: free_vector(gp,1,nlstate);
2472: free_vector(gm,1,nlstate);
2473: free_matrix(gradg,1,npar,1,nlstate);
2474: free_matrix(trgradg,1,nlstate,1,npar);
2475: } /* End age */
2476:
2477: free_vector(xp,1,npar);
2478: free_matrix(doldm,1,nlstate,1,npar);
2479: free_matrix(dnewm,1,nlstate,1,nlstate);
2480:
2481: }
2482:
2483: /************ Variance of one-step probabilities ******************/
2484: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2485: {
2486: int i, j=0, i1, k1, l1, t, tj;
2487: int k2, l2, j1, z1;
2488: int k=0,l, cptcode;
2489: int first=1, first1;
2490: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2491: double **dnewm,**doldm;
2492: double *xp;
2493: double *gp, *gm;
2494: double **gradg, **trgradg;
2495: double **mu;
2496: double age,agelim, cov[NCOVMAX];
2497: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2498: int theta;
2499: char fileresprob[FILENAMELENGTH];
2500: char fileresprobcov[FILENAMELENGTH];
2501: char fileresprobcor[FILENAMELENGTH];
2502:
2503: double ***varpij;
2504:
2505: strcpy(fileresprob,"prob");
2506: strcat(fileresprob,fileres);
2507: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2508: printf("Problem with resultfile: %s\n", fileresprob);
2509: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2510: }
2511: strcpy(fileresprobcov,"probcov");
2512: strcat(fileresprobcov,fileres);
2513: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2514: printf("Problem with resultfile: %s\n", fileresprobcov);
2515: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2516: }
2517: strcpy(fileresprobcor,"probcor");
2518: strcat(fileresprobcor,fileres);
2519: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2520: printf("Problem with resultfile: %s\n", fileresprobcor);
2521: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2522: }
2523: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2524: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2525: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2526: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2527: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2528: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2529:
2530: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2531: fprintf(ficresprob,"# Age");
2532: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2533: fprintf(ficresprobcov,"# Age");
2534: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2535: fprintf(ficresprobcov,"# Age");
2536:
2537:
2538: for(i=1; i<=nlstate;i++)
2539: for(j=1; j<=(nlstate+ndeath);j++){
2540: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2541: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2542: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2543: }
2544: /* fprintf(ficresprob,"\n");
2545: fprintf(ficresprobcov,"\n");
2546: fprintf(ficresprobcor,"\n");
2547: */
2548: xp=vector(1,npar);
2549: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2550: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2551: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2552: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2553: first=1;
2554: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2555: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2556: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2557: exit(0);
2558: }
2559: else{
2560: fprintf(ficgp,"\n# Routine varprob");
2561: }
2562: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2563: printf("Problem with html file: %s\n", optionfilehtm);
2564: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2565: exit(0);
2566: }
2567: else{
2568: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2569: fprintf(fichtm,"\n");
2570:
2571: fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
2572: 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");
2573: 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");
2574:
2575: }
2576:
2577: cov[1]=1;
2578: tj=cptcoveff;
2579: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2580: j1=0;
2581: for(t=1; t<=tj;t++){
2582: for(i1=1; i1<=ncodemax[t];i1++){
2583: j1++;
2584: if (cptcovn>0) {
2585: fprintf(ficresprob, "\n#********** Variable ");
2586: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2587: fprintf(ficresprob, "**********\n#\n");
2588: fprintf(ficresprobcov, "\n#********** Variable ");
2589: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2590: fprintf(ficresprobcov, "**********\n#\n");
2591:
2592: fprintf(ficgp, "\n#********** Variable ");
2593: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2594: fprintf(ficgp, "**********\n#\n");
2595:
2596:
2597: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2598: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2599: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2600:
2601: fprintf(ficresprobcor, "\n#********** Variable ");
2602: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2603: fprintf(ficresprobcor, "**********\n#");
2604: }
2605:
2606: for (age=bage; age<=fage; age ++){
2607: cov[2]=age;
2608: for (k=1; k<=cptcovn;k++) {
2609: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2610: }
2611: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2612: for (k=1; k<=cptcovprod;k++)
2613: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2614:
2615: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2616: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2617: gp=vector(1,(nlstate)*(nlstate+ndeath));
2618: gm=vector(1,(nlstate)*(nlstate+ndeath));
2619:
2620: for(theta=1; theta <=npar; theta++){
2621: for(i=1; i<=npar; i++)
2622: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
2623:
2624: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2625:
2626: k=0;
2627: for(i=1; i<= (nlstate); i++){
2628: for(j=1; j<=(nlstate+ndeath);j++){
2629: k=k+1;
2630: gp[k]=pmmij[i][j];
2631: }
2632: }
2633:
2634: for(i=1; i<=npar; i++)
2635: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
2636:
2637: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2638: k=0;
2639: for(i=1; i<=(nlstate); i++){
2640: for(j=1; j<=(nlstate+ndeath);j++){
2641: k=k+1;
2642: gm[k]=pmmij[i][j];
2643: }
2644: }
2645:
2646: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
2647: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
2648: }
2649:
2650: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2651: for(theta=1; theta <=npar; theta++)
2652: trgradg[j][theta]=gradg[theta][j];
2653:
2654: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2655: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
2656: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2657: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2658: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2659: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2660:
2661: pmij(pmmij,cov,ncovmodel,x,nlstate);
2662:
2663: k=0;
2664: for(i=1; i<=(nlstate); i++){
2665: for(j=1; j<=(nlstate+ndeath);j++){
2666: k=k+1;
2667: mu[k][(int) age]=pmmij[i][j];
2668: }
2669: }
2670: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2671: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2672: varpij[i][j][(int)age] = doldm[i][j];
2673:
2674: /*printf("\n%d ",(int)age);
2675: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2676: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2677: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2678: }*/
2679:
2680: fprintf(ficresprob,"\n%d ",(int)age);
2681: fprintf(ficresprobcov,"\n%d ",(int)age);
2682: fprintf(ficresprobcor,"\n%d ",(int)age);
2683:
2684: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2685: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2686: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2687: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2688: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2689: }
2690: i=0;
2691: for (k=1; k<=(nlstate);k++){
2692: for (l=1; l<=(nlstate+ndeath);l++){
2693: i=i++;
2694: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2695: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2696: for (j=1; j<=i;j++){
2697: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2698: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
2699: }
2700: }
2701: }/* end of loop for state */
2702: } /* end of loop for age */
2703:
2704: /* Confidence intervalle of pij */
2705: /*
2706: fprintf(ficgp,"\nset noparametric;unset label");
2707: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
2708: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2709: 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);
2710: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
2711: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
2712: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
2713: */
2714:
2715: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
2716: first1=1;
2717: for (k2=1; k2<=(nlstate);k2++){
2718: for (l2=1; l2<=(nlstate+ndeath);l2++){
2719: if(l2==k2) continue;
2720: j=(k2-1)*(nlstate+ndeath)+l2;
2721: for (k1=1; k1<=(nlstate);k1++){
2722: for (l1=1; l1<=(nlstate+ndeath);l1++){
2723: if(l1==k1) continue;
2724: i=(k1-1)*(nlstate+ndeath)+l1;
2725: if(i<=j) continue;
2726: for (age=bage; age<=fage; age ++){
2727: if ((int)age %5==0){
2728: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
2729: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
2730: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
2731: mu1=mu[i][(int) age]/stepm*YEARM ;
2732: mu2=mu[j][(int) age]/stepm*YEARM;
2733: c12=cv12/sqrt(v1*v2);
2734: /* Computing eigen value of matrix of covariance */
2735: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2736: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2737: /* Eigen vectors */
2738: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
2739: /*v21=sqrt(1.-v11*v11); *//* error */
2740: v21=(lc1-v1)/cv12*v11;
2741: v12=-v21;
2742: v22=v11;
2743: tnalp=v21/v11;
2744: if(first1==1){
2745: first1=0;
2746: 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);
2747: }
2748: 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);
2749: /*printf(fignu*/
2750: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
2751: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
2752: if(first==1){
2753: first=0;
2754: fprintf(ficgp,"\nset parametric;unset label");
2755: 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);
2756: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2757: 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);
2758: fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
2759: fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
2760: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
2761: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2762: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2763: 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",\
2764: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2765: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2766: }else{
2767: first=0;
2768: fprintf(fichtm," %d (%.3f),",(int) age, c12);
2769: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2770: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2771: 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",\
2772: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2773: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2774: }/* if first */
2775: } /* age mod 5 */
2776: } /* end loop age */
2777: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
2778: first=1;
2779: } /*l12 */
2780: } /* k12 */
2781: } /*l1 */
2782: }/* k1 */
2783: } /* loop covariates */
2784: }
2785: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
2786: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
2787: free_vector(xp,1,npar);
2788: fclose(ficresprob);
2789: fclose(ficresprobcov);
2790: fclose(ficresprobcor);
2791: fclose(ficgp);
2792: fclose(fichtm);
2793: }
2794:
2795:
2796: /******************* Printing html file ***********/
2797: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
2798: int lastpass, int stepm, int weightopt, char model[],\
2799: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
2800: int popforecast, int estepm ,\
2801: double jprev1, double mprev1,double anprev1, \
2802: double jprev2, double mprev2,double anprev2){
2803: int jj1, k1, i1, cpt;
2804: /*char optionfilehtm[FILENAMELENGTH];*/
2805: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2806: printf("Problem with %s \n",optionfilehtm), exit(0);
2807: fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
2808: }
2809:
2810: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
2811: - 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
2812: - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
2813: - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
2814: - Life expectancies by age and initial health status (estepm=%2d months):
2815: <a href=\"e%s\">e%s</a> <br>\n</li>", \
2816: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
2817:
2818: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
2819:
2820: m=cptcoveff;
2821: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2822:
2823: jj1=0;
2824: for(k1=1; k1<=m;k1++){
2825: for(i1=1; i1<=ncodemax[k1];i1++){
2826: jj1++;
2827: if (cptcovn > 0) {
2828: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2829: for (cpt=1; cpt<=cptcoveff;cpt++)
2830: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2831: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2832: }
2833: /* Pij */
2834: 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>
2835: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2836: /* Quasi-incidences */
2837: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
2838: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2839: /* Stable prevalence in each health state */
2840: for(cpt=1; cpt<nlstate;cpt++){
2841: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
2842: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2843: }
2844: for(cpt=1; cpt<=nlstate;cpt++) {
2845: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
2846: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2847: }
2848: fprintf(fichtm,"\n<br>- Total life expectancy by age and
2849: health expectancies in states (1) and (2): e%s%d.png<br>
2850: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2851: } /* end i1 */
2852: }/* End k1 */
2853: fprintf(fichtm,"</ul>");
2854:
2855:
2856: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
2857: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
2858: - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
2859: - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
2860: - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
2861: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
2862: - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
2863: - 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);
2864:
2865: /* if(popforecast==1) fprintf(fichtm,"\n */
2866: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
2867: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
2868: /* <br>",fileres,fileres,fileres,fileres); */
2869: /* else */
2870: /* 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); */
2871: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
2872:
2873: m=cptcoveff;
2874: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2875:
2876: jj1=0;
2877: for(k1=1; k1<=m;k1++){
2878: for(i1=1; i1<=ncodemax[k1];i1++){
2879: jj1++;
2880: if (cptcovn > 0) {
2881: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2882: for (cpt=1; cpt<=cptcoveff;cpt++)
2883: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2884: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2885: }
2886: for(cpt=1; cpt<=nlstate;cpt++) {
2887: fprintf(fichtm,"<br>- Observed and period prevalence (with confident
2888: interval) in state (%d): v%s%d%d.png <br>
2889: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2890: }
2891: } /* end i1 */
2892: }/* End k1 */
2893: fprintf(fichtm,"</ul>");
2894: fclose(fichtm);
2895: }
2896:
2897: /******************* Gnuplot file **************/
2898: void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
2899:
2900: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
2901: int ng;
2902: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2903: printf("Problem with file %s",optionfilegnuplot);
2904: fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
2905: }
2906:
2907: /*#ifdef windows */
2908: fprintf(ficgp,"cd \"%s\" \n",pathc);
2909: /*#endif */
2910: m=pow(2,cptcoveff);
2911:
2912: /* 1eme*/
2913: for (cpt=1; cpt<= nlstate ; cpt ++) {
2914: for (k1=1; k1<= m ; k1 ++) {
2915: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2916: 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);
2917:
2918: for (i=1; i<= nlstate ; i ++) {
2919: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2920: else fprintf(ficgp," \%%*lf (\%%*lf)");
2921: }
2922: 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);
2923: for (i=1; i<= nlstate ; i ++) {
2924: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2925: else fprintf(ficgp," \%%*lf (\%%*lf)");
2926: }
2927: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
2928: for (i=1; i<= nlstate ; i ++) {
2929: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2930: else fprintf(ficgp," \%%*lf (\%%*lf)");
2931: }
2932: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2933: }
2934: }
2935: /*2 eme*/
2936:
2937: for (k1=1; k1<= m ; k1 ++) {
2938: fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
2939: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
2940:
2941: for (i=1; i<= nlstate+1 ; i ++) {
2942: k=2*i;
2943: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2944: for (j=1; j<= nlstate+1 ; j ++) {
2945: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2946: else fprintf(ficgp," \%%*lf (\%%*lf)");
2947: }
2948: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2949: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2950: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2951: for (j=1; j<= nlstate+1 ; j ++) {
2952: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2953: else fprintf(ficgp," \%%*lf (\%%*lf)");
2954: }
2955: fprintf(ficgp,"\" t\"\" w l 0,");
2956: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
2957: for (j=1; j<= nlstate+1 ; j ++) {
2958: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2959: else fprintf(ficgp," \%%*lf (\%%*lf)");
2960: }
2961: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2962: else fprintf(ficgp,"\" t\"\" w l 0,");
2963: }
2964: }
2965:
2966: /*3eme*/
2967:
2968: for (k1=1; k1<= m ; k1 ++) {
2969: for (cpt=1; cpt<= nlstate ; cpt ++) {
2970: k=2+nlstate*(2*cpt-2);
2971: fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2972: fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
2973: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2974: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2975: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2976: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2977: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2978: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2979:
2980: */
2981: for (i=1; i< nlstate ; i ++) {
2982: 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);
2983:
2984: }
2985: }
2986: }
2987:
2988: /* CV preval stable (period) */
2989: for (k1=1; k1<= m ; k1 ++) {
2990: for (cpt=1; cpt<=nlstate ; cpt ++) {
2991: k=3;
2992: fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2993: 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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
2994:
2995: for (i=1; i<= nlstate ; i ++)
2996: fprintf(ficgp,"+$%d",k+i+1);
2997: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
2998:
2999: l=3+(nlstate+ndeath)*cpt;
3000: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
3001: for (i=1; i< nlstate ; i ++) {
3002: l=3+(nlstate+ndeath)*cpt;
3003: fprintf(ficgp,"+$%d",l+i+1);
3004: }
3005: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3006: }
3007: }
3008:
3009: /* proba elementaires */
3010: for(i=1,jk=1; i <=nlstate; i++){
3011: for(k=1; k <=(nlstate+ndeath); k++){
3012: if (k != i) {
3013: for(j=1; j <=ncovmodel; j++){
3014: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3015: jk++;
3016: fprintf(ficgp,"\n");
3017: }
3018: }
3019: }
3020: }
3021:
3022: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3023: for(jk=1; jk <=m; jk++) {
3024: fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
3025: if (ng==2)
3026: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3027: else
3028: fprintf(ficgp,"\nset title \"Probability\"\n");
3029: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3030: i=1;
3031: for(k2=1; k2<=nlstate; k2++) {
3032: k3=i;
3033: for(k=1; k<=(nlstate+ndeath); k++) {
3034: if (k != k2){
3035: if(ng==2)
3036: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3037: else
3038: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3039: ij=1;
3040: for(j=3; j <=ncovmodel; j++) {
3041: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3042: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3043: ij++;
3044: }
3045: else
3046: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3047: }
3048: fprintf(ficgp,")/(1");
3049:
3050: for(k1=1; k1 <=nlstate; k1++){
3051: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3052: ij=1;
3053: for(j=3; j <=ncovmodel; j++){
3054: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3055: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3056: ij++;
3057: }
3058: else
3059: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3060: }
3061: fprintf(ficgp,")");
3062: }
3063: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3064: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3065: i=i+ncovmodel;
3066: }
3067: } /* end k */
3068: } /* end k2 */
3069: } /* end jk */
3070: } /* end ng */
3071: fclose(ficgp);
3072: } /* end gnuplot */
3073:
3074:
3075: /*************** Moving average **************/
3076: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3077:
3078: int i, cpt, cptcod;
3079: int modcovmax =1;
3080: int mobilavrange, mob;
3081: double age;
3082:
3083: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3084: a covariate has 2 modalities */
3085: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3086:
3087: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3088: if(mobilav==1) mobilavrange=5; /* default */
3089: else mobilavrange=mobilav;
3090: for (age=bage; age<=fage; age++)
3091: for (i=1; i<=nlstate;i++)
3092: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3093: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3094: /* We keep the original values on the extreme ages bage, fage and for
3095: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3096: we use a 5 terms etc. until the borders are no more concerned.
3097: */
3098: for (mob=3;mob <=mobilavrange;mob=mob+2){
3099: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3100: for (i=1; i<=nlstate;i++){
3101: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3102: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3103: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3104: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3105: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3106: }
3107: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3108: }
3109: }
3110: }/* end age */
3111: }/* end mob */
3112: }else return -1;
3113: return 0;
3114: }/* End movingaverage */
3115:
3116:
3117: /************** Forecasting ******************/
3118: 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){
3119: /* proj1, year, month, day of starting projection
3120: agemin, agemax range of age
3121: dateprev1 dateprev2 range of dates during which prevalence is computed
3122: anproj2 year of en of projection (same day and month as proj1).
3123: */
3124: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
3125: int *popage;
3126: double agec; /* generic age */
3127: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3128: double *popeffectif,*popcount;
3129: double ***p3mat;
3130: double ***mobaverage;
3131: char fileresf[FILENAMELENGTH];
3132:
3133: agelim=AGESUP;
3134: prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3135:
3136: strcpy(fileresf,"f");
3137: strcat(fileresf,fileres);
3138: if((ficresf=fopen(fileresf,"w"))==NULL) {
3139: printf("Problem with forecast resultfile: %s\n", fileresf);
3140: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3141: }
3142: printf("Computing forecasting: result on file '%s' \n", fileresf);
3143: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3144:
3145: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3146:
3147: if (mobilav!=0) {
3148: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3149: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3150: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3151: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3152: }
3153: }
3154:
3155: stepsize=(int) (stepm+YEARM-1)/YEARM;
3156: if (stepm<=12) stepsize=1;
3157: if(estepm < stepm){
3158: printf ("Problem %d lower than %d\n",estepm, stepm);
3159: }
3160: else hstepm=estepm;
3161:
3162: hstepm=hstepm/stepm;
3163: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3164: fractional in yp1 */
3165: anprojmean=yp;
3166: yp2=modf((yp1*12),&yp);
3167: mprojmean=yp;
3168: yp1=modf((yp2*30.5),&yp);
3169: jprojmean=yp;
3170: if(jprojmean==0) jprojmean=1;
3171: if(mprojmean==0) jprojmean=1;
3172:
3173: i1=cptcoveff;
3174: if (cptcovn < 1){i1=1;}
3175:
3176: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
3177:
3178: fprintf(ficresf,"#****** Routine prevforecast **\n");
3179:
3180: /* if (h==(int)(YEARM*yearp)){ */
3181: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
3182: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3183: k=k+1;
3184: fprintf(ficresf,"\n#******");
3185: for(j=1;j<=cptcoveff;j++) {
3186: 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]]);
3187: }
3188: fprintf(ficresf,"******\n");
3189: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3190: for(j=1; j<=nlstate+ndeath;j++){
3191: for(i=1; i<=nlstate;i++)
3192: fprintf(ficresf," p%d%d",i,j);
3193: fprintf(ficresf," p.%d",j);
3194: }
3195: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
3196: fprintf(ficresf,"\n");
3197: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
3198:
3199: for (agec=fage; agec>=(ageminpar-1); agec--){
3200: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
3201: nhstepm = nhstepm/hstepm;
3202: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3203: oldm=oldms;savm=savms;
3204: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
3205:
3206: for (h=0; h<=nhstepm; h++){
3207: if (h*hstepm/YEARM*stepm ==yearp) {
3208: fprintf(ficresf,"\n");
3209: for(j=1;j<=cptcoveff;j++)
3210: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3211: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
3212: }
3213: for(j=1; j<=nlstate+ndeath;j++) {
3214: ppij=0.;
3215: for(i=1; i<=nlstate;i++) {
3216: if (mobilav==1)
3217: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
3218: else {
3219: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
3220: }
3221: if (h*hstepm/YEARM*stepm== yearp) {
3222: fprintf(ficresf," %.3f", p3mat[i][j][h]);
3223: }
3224: } /* end i */
3225: if (h*hstepm/YEARM*stepm==yearp) {
3226: fprintf(ficresf," %.3f", ppij);
3227: }
3228: }/* end j */
3229: } /* end h */
3230: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3231: } /* end agec */
3232: } /* end yearp */
3233: } /* end cptcod */
3234: } /* end cptcov */
3235:
3236: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3237:
3238: fclose(ficresf);
3239: }
3240:
3241: /************** Forecasting *****not tested NB*************/
3242: 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){
3243:
3244: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3245: int *popage;
3246: double calagedatem, agelim, kk1, kk2;
3247: double *popeffectif,*popcount;
3248: double ***p3mat,***tabpop,***tabpopprev;
3249: double ***mobaverage;
3250: char filerespop[FILENAMELENGTH];
3251:
3252: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3253: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3254: agelim=AGESUP;
3255: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
3256:
3257: prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3258:
3259:
3260: strcpy(filerespop,"pop");
3261: strcat(filerespop,fileres);
3262: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3263: printf("Problem with forecast resultfile: %s\n", filerespop);
3264: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3265: }
3266: printf("Computing forecasting: result on file '%s' \n", filerespop);
3267: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3268:
3269: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3270:
3271: if (mobilav!=0) {
3272: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3273: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3274: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3275: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3276: }
3277: }
3278:
3279: stepsize=(int) (stepm+YEARM-1)/YEARM;
3280: if (stepm<=12) stepsize=1;
3281:
3282: agelim=AGESUP;
3283:
3284: hstepm=1;
3285: hstepm=hstepm/stepm;
3286:
3287: if (popforecast==1) {
3288: if((ficpop=fopen(popfile,"r"))==NULL) {
3289: printf("Problem with population file : %s\n",popfile);exit(0);
3290: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3291: }
3292: popage=ivector(0,AGESUP);
3293: popeffectif=vector(0,AGESUP);
3294: popcount=vector(0,AGESUP);
3295:
3296: i=1;
3297: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3298:
3299: imx=i;
3300: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3301: }
3302:
3303: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
3304: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3305: k=k+1;
3306: fprintf(ficrespop,"\n#******");
3307: for(j=1;j<=cptcoveff;j++) {
3308: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3309: }
3310: fprintf(ficrespop,"******\n");
3311: fprintf(ficrespop,"# Age");
3312: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3313: if (popforecast==1) fprintf(ficrespop," [Population]");
3314:
3315: for (cpt=0; cpt<=0;cpt++) {
3316: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3317:
3318: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3319: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3320: nhstepm = nhstepm/hstepm;
3321:
3322: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3323: oldm=oldms;savm=savms;
3324: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3325:
3326: for (h=0; h<=nhstepm; h++){
3327: if (h==(int) (calagedatem+YEARM*cpt)) {
3328: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3329: }
3330: for(j=1; j<=nlstate+ndeath;j++) {
3331: kk1=0.;kk2=0;
3332: for(i=1; i<=nlstate;i++) {
3333: if (mobilav==1)
3334: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3335: else {
3336: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3337: }
3338: }
3339: if (h==(int)(calagedatem+12*cpt)){
3340: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3341: /*fprintf(ficrespop," %.3f", kk1);
3342: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3343: }
3344: }
3345: for(i=1; i<=nlstate;i++){
3346: kk1=0.;
3347: for(j=1; j<=nlstate;j++){
3348: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3349: }
3350: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
3351: }
3352:
3353: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
3354: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3355: }
3356: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3357: }
3358: }
3359:
3360: /******/
3361:
3362: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3363: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3364: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3365: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3366: nhstepm = nhstepm/hstepm;
3367:
3368: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3369: oldm=oldms;savm=savms;
3370: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3371: for (h=0; h<=nhstepm; h++){
3372: if (h==(int) (calagedatem+YEARM*cpt)) {
3373: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3374: }
3375: for(j=1; j<=nlstate+ndeath;j++) {
3376: kk1=0.;kk2=0;
3377: for(i=1; i<=nlstate;i++) {
3378: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3379: }
3380: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
3381: }
3382: }
3383: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3384: }
3385: }
3386: }
3387: }
3388:
3389: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3390:
3391: if (popforecast==1) {
3392: free_ivector(popage,0,AGESUP);
3393: free_vector(popeffectif,0,AGESUP);
3394: free_vector(popcount,0,AGESUP);
3395: }
3396: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3397: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3398: fclose(ficrespop);
3399: }
3400:
3401: /***********************************************/
3402: /**************** Main Program *****************/
3403: /***********************************************/
3404:
3405: int main(int argc, char *argv[])
3406: {
3407: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
3408: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
3409: double agedeb, agefin,hf;
3410: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3411:
3412: double fret;
3413: double **xi,tmp,delta;
3414:
3415: double dum; /* Dummy variable */
3416: double ***p3mat;
3417: double ***mobaverage;
3418: int *indx;
3419: char line[MAXLINE], linepar[MAXLINE];
3420: char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
3421: int firstobs=1, lastobs=10;
3422: int sdeb, sfin; /* Status at beginning and end */
3423: int c, h , cpt,l;
3424: int ju,jl, mi;
3425: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
3426: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
3427: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
3428: int mobilav=0,popforecast=0;
3429: int hstepm, nhstepm;
3430: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
3431: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
3432:
3433: double bage, fage, age, agelim, agebase;
3434: double ftolpl=FTOL;
3435: double **prlim;
3436: double *severity;
3437: double ***param; /* Matrix of parameters */
3438: double *p;
3439: double **matcov; /* Matrix of covariance */
3440: double ***delti3; /* Scale */
3441: double *delti; /* Scale */
3442: double ***eij, ***vareij;
3443: double **varpl; /* Variances of prevalence limits by age */
3444: double *epj, vepp;
3445: double kk1, kk2;
3446: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
3447:
3448: char *alph[]={"a","a","b","c","d","e"}, str[4];
3449:
3450:
3451: char z[1]="c", occ;
3452: #include <sys/time.h>
3453: #include <time.h>
3454: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
3455:
3456: /* long total_usecs;
3457: struct timeval start_time, end_time;
3458:
3459: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
3460: getcwd(pathcd, size);
3461:
3462: printf("\n%s",version);
3463: if(argc <=1){
3464: printf("\nEnter the parameter file name: ");
3465: scanf("%s",pathtot);
3466: }
3467: else{
3468: strcpy(pathtot,argv[1]);
3469: }
3470: /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
3471: /*cygwin_split_path(pathtot,path,optionfile);
3472: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3473: /* cutv(path,optionfile,pathtot,'\\');*/
3474:
3475: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
3476: printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3477: chdir(path);
3478: replace(pathc,path);
3479:
3480: /*-------- arguments in the command line --------*/
3481:
3482: /* Log file */
3483: strcat(filelog, optionfilefiname);
3484: strcat(filelog,".log"); /* */
3485: if((ficlog=fopen(filelog,"w"))==NULL) {
3486: printf("Problem with logfile %s\n",filelog);
3487: goto end;
3488: }
3489: fprintf(ficlog,"Log filename:%s\n",filelog);
3490: fprintf(ficlog,"\n%s",version);
3491: fprintf(ficlog,"\nEnter the parameter file name: ");
3492: fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3493: fflush(ficlog);
3494:
3495: /* */
3496: strcpy(fileres,"r");
3497: strcat(fileres, optionfilefiname);
3498: strcat(fileres,".txt"); /* Other files have txt extension */
3499:
3500: /*---------arguments file --------*/
3501:
3502: if((ficpar=fopen(optionfile,"r"))==NULL) {
3503: printf("Problem with optionfile %s\n",optionfile);
3504: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
3505: goto end;
3506: }
3507:
3508: strcpy(filereso,"o");
3509: strcat(filereso,fileres);
3510: if((ficparo=fopen(filereso,"w"))==NULL) {
3511: printf("Problem with Output resultfile: %s\n", filereso);
3512: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
3513: goto end;
3514: }
3515:
3516: /* Reads comments: lines beginning with '#' */
3517: while((c=getc(ficpar))=='#' && c!= EOF){
3518: ungetc(c,ficpar);
3519: fgets(line, MAXLINE, ficpar);
3520: puts(line);
3521: fputs(line,ficparo);
3522: }
3523: ungetc(c,ficpar);
3524:
3525: 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);
3526: 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);
3527: 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);
3528: while((c=getc(ficpar))=='#' && c!= EOF){
3529: ungetc(c,ficpar);
3530: fgets(line, MAXLINE, ficpar);
3531: puts(line);
3532: fputs(line,ficparo);
3533: }
3534: ungetc(c,ficpar);
3535:
3536:
3537: covar=matrix(0,NCOVMAX,1,n);
3538: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
3539: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
3540:
3541: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
3542: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
3543:
3544: /* Read guess parameters */
3545: /* Reads comments: lines beginning with '#' */
3546: while((c=getc(ficpar))=='#' && c!= EOF){
3547: ungetc(c,ficpar);
3548: fgets(line, MAXLINE, ficpar);
3549: puts(line);
3550: fputs(line,ficparo);
3551: }
3552: ungetc(c,ficpar);
3553:
3554: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
3555: for(i=1; i <=nlstate; i++)
3556: for(j=1; j <=nlstate+ndeath-1; j++){
3557: fscanf(ficpar,"%1d%1d",&i1,&j1);
3558: fprintf(ficparo,"%1d%1d",i1,j1);
3559: if(mle==1)
3560: printf("%1d%1d",i,j);
3561: fprintf(ficlog,"%1d%1d",i,j);
3562: for(k=1; k<=ncovmodel;k++){
3563: fscanf(ficpar," %lf",¶m[i][j][k]);
3564: if(mle==1){
3565: printf(" %lf",param[i][j][k]);
3566: fprintf(ficlog," %lf",param[i][j][k]);
3567: }
3568: else
3569: fprintf(ficlog," %lf",param[i][j][k]);
3570: fprintf(ficparo," %lf",param[i][j][k]);
3571: }
3572: fscanf(ficpar,"\n");
3573: if(mle==1)
3574: printf("\n");
3575: fprintf(ficlog,"\n");
3576: fprintf(ficparo,"\n");
3577: }
3578:
3579: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
3580:
3581: p=param[1][1];
3582:
3583: /* Reads comments: lines beginning with '#' */
3584: while((c=getc(ficpar))=='#' && c!= EOF){
3585: ungetc(c,ficpar);
3586: fgets(line, MAXLINE, ficpar);
3587: puts(line);
3588: fputs(line,ficparo);
3589: }
3590: ungetc(c,ficpar);
3591:
3592: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
3593: /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
3594: for(i=1; i <=nlstate; i++){
3595: for(j=1; j <=nlstate+ndeath-1; j++){
3596: fscanf(ficpar,"%1d%1d",&i1,&j1);
3597: printf("%1d%1d",i,j);
3598: fprintf(ficparo,"%1d%1d",i1,j1);
3599: for(k=1; k<=ncovmodel;k++){
3600: fscanf(ficpar,"%le",&delti3[i][j][k]);
3601: printf(" %le",delti3[i][j][k]);
3602: fprintf(ficparo," %le",delti3[i][j][k]);
3603: }
3604: fscanf(ficpar,"\n");
3605: printf("\n");
3606: fprintf(ficparo,"\n");
3607: }
3608: }
3609: delti=delti3[1][1];
3610:
3611:
3612: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
3613:
3614: /* Reads comments: lines beginning with '#' */
3615: while((c=getc(ficpar))=='#' && c!= EOF){
3616: ungetc(c,ficpar);
3617: fgets(line, MAXLINE, ficpar);
3618: puts(line);
3619: fputs(line,ficparo);
3620: }
3621: ungetc(c,ficpar);
3622:
3623: matcov=matrix(1,npar,1,npar);
3624: for(i=1; i <=npar; i++){
3625: fscanf(ficpar,"%s",&str);
3626: if(mle==1)
3627: printf("%s",str);
3628: fprintf(ficlog,"%s",str);
3629: fprintf(ficparo,"%s",str);
3630: for(j=1; j <=i; j++){
3631: fscanf(ficpar," %le",&matcov[i][j]);
3632: if(mle==1){
3633: printf(" %.5le",matcov[i][j]);
3634: fprintf(ficlog," %.5le",matcov[i][j]);
3635: }
3636: else
3637: fprintf(ficlog," %.5le",matcov[i][j]);
3638: fprintf(ficparo," %.5le",matcov[i][j]);
3639: }
3640: fscanf(ficpar,"\n");
3641: if(mle==1)
3642: printf("\n");
3643: fprintf(ficlog,"\n");
3644: fprintf(ficparo,"\n");
3645: }
3646: for(i=1; i <=npar; i++)
3647: for(j=i+1;j<=npar;j++)
3648: matcov[i][j]=matcov[j][i];
3649:
3650: if(mle==1)
3651: printf("\n");
3652: fprintf(ficlog,"\n");
3653:
3654:
3655: /*-------- Rewriting paramater file ----------*/
3656: strcpy(rfileres,"r"); /* "Rparameterfile */
3657: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
3658: strcat(rfileres,"."); /* */
3659: strcat(rfileres,optionfilext); /* Other files have txt extension */
3660: if((ficres =fopen(rfileres,"w"))==NULL) {
3661: printf("Problem writing new parameter file: %s\n", fileres);goto end;
3662: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
3663: }
3664: fprintf(ficres,"#%s\n",version);
3665:
3666: /*-------- data file ----------*/
3667: if((fic=fopen(datafile,"r"))==NULL) {
3668: printf("Problem with datafile: %s\n", datafile);goto end;
3669: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
3670: }
3671:
3672: n= lastobs;
3673: severity = vector(1,maxwav);
3674: outcome=imatrix(1,maxwav+1,1,n);
3675: num=ivector(1,n);
3676: moisnais=vector(1,n);
3677: annais=vector(1,n);
3678: moisdc=vector(1,n);
3679: andc=vector(1,n);
3680: agedc=vector(1,n);
3681: cod=ivector(1,n);
3682: weight=vector(1,n);
3683: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
3684: mint=matrix(1,maxwav,1,n);
3685: anint=matrix(1,maxwav,1,n);
3686: s=imatrix(1,maxwav+1,1,n);
3687: tab=ivector(1,NCOVMAX);
3688: ncodemax=ivector(1,8);
3689:
3690: i=1;
3691: while (fgets(line, MAXLINE, fic) != NULL) {
3692: if ((i >= firstobs) && (i <=lastobs)) {
3693:
3694: for (j=maxwav;j>=1;j--){
3695: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
3696: strcpy(line,stra);
3697: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3698: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3699: }
3700:
3701: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
3702: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
3703:
3704: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
3705: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
3706:
3707: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
3708: for (j=ncovcol;j>=1;j--){
3709: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3710: }
3711: num[i]=atol(stra);
3712:
3713: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
3714: printf("%d %.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;}*/
3715:
3716: i=i+1;
3717: }
3718: }
3719: /* printf("ii=%d", ij);
3720: scanf("%d",i);*/
3721: imx=i-1; /* Number of individuals */
3722:
3723: /* for (i=1; i<=imx; i++){
3724: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
3725: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
3726: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
3727: }*/
3728: /* for (i=1; i<=imx; i++){
3729: if (s[4][i]==9) s[4][i]=-1;
3730: printf("%d %.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]));}*/
3731:
3732: for (i=1; i<=imx; i++)
3733:
3734: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
3735: else weight[i]=1;*/
3736:
3737: /* Calculation of the number of parameter from char model*/
3738: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
3739: Tprod=ivector(1,15);
3740: Tvaraff=ivector(1,15);
3741: Tvard=imatrix(1,15,1,2);
3742: Tage=ivector(1,15);
3743:
3744: if (strlen(model) >1){ /* If there is at least 1 covariate */
3745: j=0, j1=0, k1=1, k2=1;
3746: j=nbocc(model,'+'); /* j=Number of '+' */
3747: j1=nbocc(model,'*'); /* j1=Number of '*' */
3748: cptcovn=j+1;
3749: cptcovprod=j1; /*Number of products */
3750:
3751: strcpy(modelsav,model);
3752: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
3753: printf("Error. Non available option model=%s ",model);
3754: fprintf(ficlog,"Error. Non available option model=%s ",model);
3755: goto end;
3756: }
3757:
3758: /* This loop fills the array Tvar from the string 'model'.*/
3759:
3760: for(i=(j+1); i>=1;i--){
3761: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
3762: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
3763: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
3764: /*scanf("%d",i);*/
3765: if (strchr(strb,'*')) { /* Model includes a product */
3766: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
3767: if (strcmp(strc,"age")==0) { /* Vn*age */
3768: cptcovprod--;
3769: cutv(strb,stre,strd,'V');
3770: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
3771: cptcovage++;
3772: Tage[cptcovage]=i;
3773: /*printf("stre=%s ", stre);*/
3774: }
3775: else if (strcmp(strd,"age")==0) { /* or age*Vn */
3776: cptcovprod--;
3777: cutv(strb,stre,strc,'V');
3778: Tvar[i]=atoi(stre);
3779: cptcovage++;
3780: Tage[cptcovage]=i;
3781: }
3782: else { /* Age is not in the model */
3783: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
3784: Tvar[i]=ncovcol+k1;
3785: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
3786: Tprod[k1]=i;
3787: Tvard[k1][1]=atoi(strc); /* m*/
3788: Tvard[k1][2]=atoi(stre); /* n */
3789: Tvar[cptcovn+k2]=Tvard[k1][1];
3790: Tvar[cptcovn+k2+1]=Tvard[k1][2];
3791: for (k=1; k<=lastobs;k++)
3792: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
3793: k1++;
3794: k2=k2+2;
3795: }
3796: }
3797: else { /* no more sum */
3798: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
3799: /* scanf("%d",i);*/
3800: cutv(strd,strc,strb,'V');
3801: Tvar[i]=atoi(strc);
3802: }
3803: strcpy(modelsav,stra);
3804: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
3805: scanf("%d",i);*/
3806: } /* end of loop + */
3807: } /* end model */
3808:
3809: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
3810: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
3811:
3812: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
3813: printf("cptcovprod=%d ", cptcovprod);
3814: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
3815:
3816: scanf("%d ",i);
3817: fclose(fic);*/
3818:
3819: /* if(mle==1){*/
3820: if (weightopt != 1) { /* Maximisation without weights*/
3821: for(i=1;i<=n;i++) weight[i]=1.0;
3822: }
3823: /*-calculation of age at interview from date of interview and age at death -*/
3824: agev=matrix(1,maxwav,1,imx);
3825:
3826: for (i=1; i<=imx; i++) {
3827: for(m=2; (m<= maxwav); m++) {
3828: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
3829: anint[m][i]=9999;
3830: s[m][i]=-1;
3831: }
3832: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
3833: printf("Error! Date of death (month %2d and year %4d) of individual %d 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);
3834: fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d 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);
3835: s[m][i]=-1;
3836: }
3837: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
3838: printf("Error! Month of death of individual %d 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]);
3839: fprintf(ficlog,"Error! Month of death of individual %d 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]);
3840: s[m][i]=-1;
3841: }
3842: }
3843: }
3844:
3845: for (i=1; i<=imx; i++) {
3846: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
3847: for(m=firstpass; (m<= lastpass); m++){
3848: if(s[m][i] >0){
3849: if (s[m][i] >= nlstate+1) {
3850: if(agedc[i]>0)
3851: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
3852: agev[m][i]=agedc[i];
3853: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
3854: else {
3855: if ((int)andc[i]!=9999){
3856: printf("Warning negative age at death: %d line:%d\n",num[i],i);
3857: fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
3858: agev[m][i]=-1;
3859: }
3860: }
3861: }
3862: else if(s[m][i] !=9){ /* Standard case, age in fractional
3863: years but with the precision of a
3864: month */
3865: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
3866: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
3867: agev[m][i]=1;
3868: else if(agev[m][i] <agemin){
3869: agemin=agev[m][i];
3870: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
3871: }
3872: else if(agev[m][i] >agemax){
3873: agemax=agev[m][i];
3874: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
3875: }
3876: /*agev[m][i]=anint[m][i]-annais[i];*/
3877: /* agev[m][i] = age[i]+2*m;*/
3878: }
3879: else { /* =9 */
3880: agev[m][i]=1;
3881: s[m][i]=-1;
3882: }
3883: }
3884: else /*= 0 Unknown */
3885: agev[m][i]=1;
3886: }
3887:
3888: }
3889: for (i=1; i<=imx; i++) {
3890: for(m=firstpass; (m<=lastpass); m++){
3891: if (s[m][i] > (nlstate+ndeath)) {
3892: 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);
3893: 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);
3894: goto end;
3895: }
3896: }
3897: }
3898:
3899: /*for (i=1; i<=imx; i++){
3900: for (m=firstpass; (m<lastpass); m++){
3901: printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
3902: }
3903:
3904: }*/
3905:
3906: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3907: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3908:
3909: free_vector(severity,1,maxwav);
3910: free_imatrix(outcome,1,maxwav+1,1,n);
3911: free_vector(moisnais,1,n);
3912: free_vector(annais,1,n);
3913: /* free_matrix(mint,1,maxwav,1,n);
3914: free_matrix(anint,1,maxwav,1,n);*/
3915: free_vector(moisdc,1,n);
3916: free_vector(andc,1,n);
3917:
3918:
3919: wav=ivector(1,imx);
3920: dh=imatrix(1,lastpass-firstpass+1,1,imx);
3921: bh=imatrix(1,lastpass-firstpass+1,1,imx);
3922: mw=imatrix(1,lastpass-firstpass+1,1,imx);
3923:
3924: /* Concatenates waves */
3925: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
3926:
3927: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
3928:
3929: Tcode=ivector(1,100);
3930: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
3931: ncodemax[1]=1;
3932: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
3933:
3934: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
3935: the estimations*/
3936: h=0;
3937: m=pow(2,cptcoveff);
3938:
3939: for(k=1;k<=cptcoveff; k++){
3940: for(i=1; i <=(m/pow(2,k));i++){
3941: for(j=1; j <= ncodemax[k]; j++){
3942: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
3943: h++;
3944: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
3945: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
3946: }
3947: }
3948: }
3949: }
3950: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
3951: codtab[1][2]=1;codtab[2][2]=2; */
3952: /* for(i=1; i <=m ;i++){
3953: for(k=1; k <=cptcovn; k++){
3954: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
3955: }
3956: printf("\n");
3957: }
3958: scanf("%d",i);*/
3959:
3960: /* Calculates basic frequencies. Computes observed prevalence at single age
3961: and prints on file fileres'p'. */
3962:
3963: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3964: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3965: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3966: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3967: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
3968:
3969:
3970: /* For Powell, parameters are in a vector p[] starting at p[1]
3971: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
3972: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
3973:
3974: if(mle>=1){ /* Could be 1 or 2 */
3975: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
3976: }
3977:
3978: /*--------- results files --------------*/
3979: 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);
3980:
3981:
3982: jk=1;
3983: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3984: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3985: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3986: for(i=1,jk=1; i <=nlstate; i++){
3987: for(k=1; k <=(nlstate+ndeath); k++){
3988: if (k != i)
3989: {
3990: printf("%d%d ",i,k);
3991: fprintf(ficlog,"%d%d ",i,k);
3992: fprintf(ficres,"%1d%1d ",i,k);
3993: for(j=1; j <=ncovmodel; j++){
3994: printf("%f ",p[jk]);
3995: fprintf(ficlog,"%f ",p[jk]);
3996: fprintf(ficres,"%f ",p[jk]);
3997: jk++;
3998: }
3999: printf("\n");
4000: fprintf(ficlog,"\n");
4001: fprintf(ficres,"\n");
4002: }
4003: }
4004: }
4005: if(mle==1){
4006: /* Computing hessian and covariance matrix */
4007: ftolhess=ftol; /* Usually correct */
4008: hesscov(matcov, p, npar, delti, ftolhess, func);
4009: }
4010: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
4011: printf("# Scales (for hessian or gradient estimation)\n");
4012: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
4013: for(i=1,jk=1; i <=nlstate; i++){
4014: for(j=1; j <=nlstate+ndeath; j++){
4015: if (j!=i) {
4016: fprintf(ficres,"%1d%1d",i,j);
4017: printf("%1d%1d",i,j);
4018: fprintf(ficlog,"%1d%1d",i,j);
4019: for(k=1; k<=ncovmodel;k++){
4020: printf(" %.5e",delti[jk]);
4021: fprintf(ficlog," %.5e",delti[jk]);
4022: fprintf(ficres," %.5e",delti[jk]);
4023: jk++;
4024: }
4025: printf("\n");
4026: fprintf(ficlog,"\n");
4027: fprintf(ficres,"\n");
4028: }
4029: }
4030: }
4031:
4032: 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");
4033: if(mle==1)
4034: 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");
4035: 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");
4036: for(i=1,k=1;i<=npar;i++){
4037: /* if (k>nlstate) k=1;
4038: i1=(i-1)/(ncovmodel*nlstate)+1;
4039: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
4040: printf("%s%d%d",alph[k],i1,tab[i]);
4041: */
4042: fprintf(ficres,"%3d",i);
4043: if(mle==1)
4044: printf("%3d",i);
4045: fprintf(ficlog,"%3d",i);
4046: for(j=1; j<=i;j++){
4047: fprintf(ficres," %.5e",matcov[i][j]);
4048: if(mle==1)
4049: printf(" %.5e",matcov[i][j]);
4050: fprintf(ficlog," %.5e",matcov[i][j]);
4051: }
4052: fprintf(ficres,"\n");
4053: if(mle==1)
4054: printf("\n");
4055: fprintf(ficlog,"\n");
4056: k++;
4057: }
4058:
4059: while((c=getc(ficpar))=='#' && c!= EOF){
4060: ungetc(c,ficpar);
4061: fgets(line, MAXLINE, ficpar);
4062: puts(line);
4063: fputs(line,ficparo);
4064: }
4065: ungetc(c,ficpar);
4066:
4067: estepm=0;
4068: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
4069: if (estepm==0 || estepm < stepm) estepm=stepm;
4070: if (fage <= 2) {
4071: bage = ageminpar;
4072: fage = agemaxpar;
4073: }
4074:
4075: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
4076: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
4077: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
4078:
4079: while((c=getc(ficpar))=='#' && c!= EOF){
4080: ungetc(c,ficpar);
4081: fgets(line, MAXLINE, ficpar);
4082: puts(line);
4083: fputs(line,ficparo);
4084: }
4085: ungetc(c,ficpar);
4086:
4087: 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);
4088: 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);
4089: 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);
4090: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
4091: 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);
4092:
4093: while((c=getc(ficpar))=='#' && c!= EOF){
4094: ungetc(c,ficpar);
4095: fgets(line, MAXLINE, ficpar);
4096: puts(line);
4097: fputs(line,ficparo);
4098: }
4099: ungetc(c,ficpar);
4100:
4101:
4102: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
4103: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
4104:
4105: fscanf(ficpar,"pop_based=%d\n",&popbased);
4106: fprintf(ficparo,"pop_based=%d\n",popbased);
4107: fprintf(ficres,"pop_based=%d\n",popbased);
4108:
4109: while((c=getc(ficpar))=='#' && c!= EOF){
4110: ungetc(c,ficpar);
4111: fgets(line, MAXLINE, ficpar);
4112: puts(line);
4113: fputs(line,ficparo);
4114: }
4115: ungetc(c,ficpar);
4116:
4117: 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);
4118: 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);
4119: 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);
4120: 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);
4121: 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);
4122: /* day and month of proj2 are not used but only year anproj2.*/
4123:
4124: while((c=getc(ficpar))=='#' && c!= EOF){
4125: ungetc(c,ficpar);
4126: fgets(line, MAXLINE, ficpar);
4127: puts(line);
4128: fputs(line,ficparo);
4129: }
4130: ungetc(c,ficpar);
4131:
4132: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
4133: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4134: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4135:
4136: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
4137: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
4138:
4139: /*------------ gnuplot -------------*/
4140: strcpy(optionfilegnuplot,optionfilefiname);
4141: strcat(optionfilegnuplot,".gp");
4142: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4143: printf("Problem with file %s",optionfilegnuplot);
4144: }
4145: else{
4146: fprintf(ficgp,"\n# %s\n", version);
4147: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4148: fprintf(ficgp,"set missing 'NaNq'\n");
4149: }
4150: fclose(ficgp);
4151: printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
4152: /*--------- index.htm --------*/
4153:
4154: strcpy(optionfilehtm,optionfile);
4155: strcat(optionfilehtm,".htm");
4156: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4157: printf("Problem with %s \n",optionfilehtm), exit(0);
4158: }
4159:
4160: fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
4161: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
4162: \n
4163: Total number of observations=%d <br>\n
4164: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n
4165: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
4166: <hr size=\"2\" color=\"#EC5E5E\">
4167: <ul><li><h4>Parameter files</h4>\n
4168: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
4169: - Log file of the run: <a href=\"%s\">%s</a><br>\n
4170: - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
4171: fclose(fichtm);
4172:
4173: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
4174:
4175: /*------------ free_vector -------------*/
4176: chdir(path);
4177:
4178: free_ivector(wav,1,imx);
4179: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
4180: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
4181: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
4182: free_ivector(num,1,n);
4183: free_vector(agedc,1,n);
4184: /*free_matrix(covar,0,NCOVMAX,1,n);*/
4185: /*free_matrix(covar,1,NCOVMAX,1,n);*/
4186: fclose(ficparo);
4187: fclose(ficres);
4188:
4189:
4190: /*--------------- Prevalence limit (stable prevalence) --------------*/
4191:
4192: strcpy(filerespl,"pl");
4193: strcat(filerespl,fileres);
4194: if((ficrespl=fopen(filerespl,"w"))==NULL) {
4195: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4196: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4197: }
4198: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
4199: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
4200: fprintf(ficrespl,"#Stable prevalence \n");
4201: fprintf(ficrespl,"#Age ");
4202: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
4203: fprintf(ficrespl,"\n");
4204:
4205: prlim=matrix(1,nlstate,1,nlstate);
4206:
4207: agebase=ageminpar;
4208: agelim=agemaxpar;
4209: ftolpl=1.e-10;
4210: i1=cptcoveff;
4211: if (cptcovn < 1){i1=1;}
4212:
4213: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4214: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4215: k=k+1;
4216: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
4217: fprintf(ficrespl,"\n#******");
4218: printf("\n#******");
4219: fprintf(ficlog,"\n#******");
4220: for(j=1;j<=cptcoveff;j++) {
4221: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4222: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4223: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4224: }
4225: fprintf(ficrespl,"******\n");
4226: printf("******\n");
4227: fprintf(ficlog,"******\n");
4228:
4229: for (age=agebase; age<=agelim; age++){
4230: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4231: fprintf(ficrespl,"%.0f ",age );
4232: for(j=1;j<=cptcoveff;j++)
4233: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4234: for(i=1; i<=nlstate;i++)
4235: fprintf(ficrespl," %.5f", prlim[i][i]);
4236: fprintf(ficrespl,"\n");
4237: }
4238: }
4239: }
4240: fclose(ficrespl);
4241:
4242: /*------------- h Pij x at various ages ------------*/
4243:
4244: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
4245: if((ficrespij=fopen(filerespij,"w"))==NULL) {
4246: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
4247: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
4248: }
4249: printf("Computing pij: result on file '%s' \n", filerespij);
4250: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
4251:
4252: stepsize=(int) (stepm+YEARM-1)/YEARM;
4253: /*if (stepm<=24) stepsize=2;*/
4254:
4255: agelim=AGESUP;
4256: hstepm=stepsize*YEARM; /* Every year of age */
4257: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
4258:
4259: /* hstepm=1; aff par mois*/
4260:
4261: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
4262: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4263: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4264: k=k+1;
4265: fprintf(ficrespij,"\n#****** ");
4266: for(j=1;j<=cptcoveff;j++)
4267: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4268: fprintf(ficrespij,"******\n");
4269:
4270: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
4271: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4272: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4273:
4274: /* nhstepm=nhstepm*YEARM; aff par mois*/
4275:
4276: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4277: oldm=oldms;savm=savms;
4278: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4279: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
4280: for(i=1; i<=nlstate;i++)
4281: for(j=1; j<=nlstate+ndeath;j++)
4282: fprintf(ficrespij," %1d-%1d",i,j);
4283: fprintf(ficrespij,"\n");
4284: for (h=0; h<=nhstepm; h++){
4285: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
4286: for(i=1; i<=nlstate;i++)
4287: for(j=1; j<=nlstate+ndeath;j++)
4288: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
4289: fprintf(ficrespij,"\n");
4290: }
4291: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4292: fprintf(ficrespij,"\n");
4293: }
4294: }
4295: }
4296:
4297: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
4298:
4299: fclose(ficrespij);
4300:
4301:
4302: /*---------- Forecasting ------------------*/
4303: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
4304: if(prevfcast==1){
4305: /* if(stepm ==1){*/
4306: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
4307: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
4308: /* } */
4309: /* else{ */
4310: /* erreur=108; */
4311: /* 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); */
4312: /* 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); */
4313: /* } */
4314: }
4315:
4316:
4317: /*---------- Health expectancies and variances ------------*/
4318:
4319: strcpy(filerest,"t");
4320: strcat(filerest,fileres);
4321: if((ficrest=fopen(filerest,"w"))==NULL) {
4322: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
4323: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
4324: }
4325: printf("Computing Total LEs with variances: file '%s' \n", filerest);
4326: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
4327:
4328:
4329: strcpy(filerese,"e");
4330: strcat(filerese,fileres);
4331: if((ficreseij=fopen(filerese,"w"))==NULL) {
4332: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4333: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4334: }
4335: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
4336: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
4337:
4338: strcpy(fileresv,"v");
4339: strcat(fileresv,fileres);
4340: if((ficresvij=fopen(fileresv,"w"))==NULL) {
4341: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
4342: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
4343: }
4344: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4345: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4346:
4347: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
4348: prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4349: /* 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",\
4350: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
4351: */
4352:
4353: if (mobilav!=0) {
4354: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4355: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4356: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4357: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4358: }
4359: }
4360:
4361: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4362: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4363: k=k+1;
4364: fprintf(ficrest,"\n#****** ");
4365: for(j=1;j<=cptcoveff;j++)
4366: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4367: fprintf(ficrest,"******\n");
4368:
4369: fprintf(ficreseij,"\n#****** ");
4370: for(j=1;j<=cptcoveff;j++)
4371: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4372: fprintf(ficreseij,"******\n");
4373:
4374: fprintf(ficresvij,"\n#****** ");
4375: for(j=1;j<=cptcoveff;j++)
4376: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4377: fprintf(ficresvij,"******\n");
4378:
4379: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4380: oldm=oldms;savm=savms;
4381: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
4382:
4383: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4384: oldm=oldms;savm=savms;
4385: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
4386: if(popbased==1){
4387: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
4388: }
4389:
4390:
4391: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
4392: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
4393: fprintf(ficrest,"\n");
4394:
4395: epj=vector(1,nlstate+1);
4396: for(age=bage; age <=fage ;age++){
4397: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4398: if (popbased==1) {
4399: if(mobilav ==0){
4400: for(i=1; i<=nlstate;i++)
4401: prlim[i][i]=probs[(int)age][i][k];
4402: }else{ /* mobilav */
4403: for(i=1; i<=nlstate;i++)
4404: prlim[i][i]=mobaverage[(int)age][i][k];
4405: }
4406: }
4407:
4408: fprintf(ficrest," %4.0f",age);
4409: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
4410: for(i=1, epj[j]=0.;i <=nlstate;i++) {
4411: epj[j] += prlim[i][i]*eij[i][j][(int)age];
4412: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
4413: }
4414: epj[nlstate+1] +=epj[j];
4415: }
4416:
4417: for(i=1, vepp=0.;i <=nlstate;i++)
4418: for(j=1;j <=nlstate;j++)
4419: vepp += vareij[i][j][(int)age];
4420: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
4421: for(j=1;j <=nlstate;j++){
4422: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
4423: }
4424: fprintf(ficrest,"\n");
4425: }
4426: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4427: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4428: free_vector(epj,1,nlstate+1);
4429: }
4430: }
4431: free_vector(weight,1,n);
4432: free_imatrix(Tvard,1,15,1,2);
4433: free_imatrix(s,1,maxwav+1,1,n);
4434: free_matrix(anint,1,maxwav,1,n);
4435: free_matrix(mint,1,maxwav,1,n);
4436: free_ivector(cod,1,n);
4437: free_ivector(tab,1,NCOVMAX);
4438: fclose(ficreseij);
4439: fclose(ficresvij);
4440: fclose(ficrest);
4441: fclose(ficpar);
4442:
4443: /*------- Variance of stable prevalence------*/
4444:
4445: strcpy(fileresvpl,"vpl");
4446: strcat(fileresvpl,fileres);
4447: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
4448: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
4449: exit(0);
4450: }
4451: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
4452:
4453: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4454: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4455: k=k+1;
4456: fprintf(ficresvpl,"\n#****** ");
4457: for(j=1;j<=cptcoveff;j++)
4458: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4459: fprintf(ficresvpl,"******\n");
4460:
4461: varpl=matrix(1,nlstate,(int) bage, (int) fage);
4462: oldm=oldms;savm=savms;
4463: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
4464: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
4465: }
4466: }
4467:
4468: fclose(ficresvpl);
4469:
4470: /*---------- End : free ----------------*/
4471: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
4472: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
4473: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
4474: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
4475:
4476: free_matrix(covar,0,NCOVMAX,1,n);
4477: free_matrix(matcov,1,npar,1,npar);
4478: /*free_vector(delti,1,npar);*/
4479: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4480: free_matrix(agev,1,maxwav,1,imx);
4481: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4482: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4483: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
4484:
4485: free_ivector(ncodemax,1,8);
4486: free_ivector(Tvar,1,15);
4487: free_ivector(Tprod,1,15);
4488: free_ivector(Tvaraff,1,15);
4489: free_ivector(Tage,1,15);
4490: free_ivector(Tcode,1,100);
4491:
4492: /* fclose(fichtm);*/
4493: /* fclose(ficgp);*/ /* ALready done */
4494:
4495:
4496: if(erreur >0){
4497: printf("End of Imach with error or warning %d\n",erreur);
4498: fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
4499: }else{
4500: printf("End of Imach\n");
4501: fprintf(ficlog,"End of Imach\n");
4502: }
4503: printf("See log file on %s\n",filelog);
4504: fclose(ficlog);
4505: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
4506:
4507: /* 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);*/
4508: /*printf("Total time was %d uSec.\n", total_usecs);*/
4509: /*------ End -----------*/
4510:
4511: end:
4512: #ifdef windows
4513: /* chdir(pathcd);*/
4514: #endif
4515: /*system("wgnuplot graph.plt");*/
4516: /*system("../gp37mgw/wgnuplot graph.plt");*/
4517: /*system("cd ../gp37mgw");*/
4518: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
4519: strcpy(plotcmd,GNUPLOTPROGRAM);
4520: strcat(plotcmd," ");
4521: strcat(plotcmd,optionfilegnuplot);
4522: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
4523: system(plotcmd);
4524: printf(" Wait...");
4525:
4526: /*#ifdef windows*/
4527: while (z[0] != 'q') {
4528: /* chdir(path); */
4529: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
4530: scanf("%s",z);
4531: if (z[0] == 'c') system("./imach");
4532: else if (z[0] == 'e') system(optionfilehtm);
4533: else if (z[0] == 'g') system(plotcmd);
4534: else if (z[0] == 'q') exit(0);
4535: }
4536: /*#endif */
4537: }
4538:
4539:
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