1: /* $Id: imach.c,v 1.68 2003/02/04 12:40:59 lievre 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:
53: #include <math.h>
54: #include <stdio.h>
55: #include <stdlib.h>
56: #include <unistd.h>
57:
58: #define MAXLINE 256
59: #define GNUPLOTPROGRAM "gnuplot"
60: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
61: #define FILENAMELENGTH 80
62: /*#define DEBUG*/
63: #define windows
64: #define GLOCK_ERROR_NOPATH -1 /* empty path */
65: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
66:
67: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
68: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
69:
70: #define NINTERVMAX 8
71: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
72: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
73: #define NCOVMAX 8 /* Maximum number of covariates */
74: #define MAXN 20000
75: #define YEARM 12. /* Number of months per year */
76: #define AGESUP 130
77: #define AGEBASE 40
78: #ifdef windows
79: #define DIRSEPARATOR '\\'
80: #define ODIRSEPARATOR '/'
81: #else
82: #define DIRSEPARATOR '/'
83: #define ODIRSEPARATOR '\\'
84: #endif
85:
86: char version[80]="Imach version 0.91, November 2002, INED-EUROREVES ";
87: int erreur; /* Error number */
88: int nvar;
89: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
90: int npar=NPARMAX;
91: int nlstate=2; /* Number of live states */
92: int ndeath=1; /* Number of dead states */
93: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
94: int popbased=0;
95:
96: int *wav; /* Number of waves for this individuual 0 is possible */
97: int maxwav; /* Maxim number of waves */
98: int jmin, jmax; /* min, max spacing between 2 waves */
99: int mle, weightopt;
100: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
101: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
102: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
103: * wave mi and wave mi+1 is not an exact multiple of stepm. */
104: double jmean; /* Mean space between 2 waves */
105: double **oldm, **newm, **savm; /* Working pointers to matrices */
106: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
107: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
108: FILE *ficlog;
109: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
110: FILE *ficresprobmorprev;
111: FILE *fichtm; /* Html File */
112: FILE *ficreseij;
113: char filerese[FILENAMELENGTH];
114: FILE *ficresvij;
115: char fileresv[FILENAMELENGTH];
116: FILE *ficresvpl;
117: char fileresvpl[FILENAMELENGTH];
118: char title[MAXLINE];
119: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
120: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
121:
122: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
123: char filelog[FILENAMELENGTH]; /* Log file */
124: char filerest[FILENAMELENGTH];
125: char fileregp[FILENAMELENGTH];
126: char popfile[FILENAMELENGTH];
127:
128: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
129:
130: #define NR_END 1
131: #define FREE_ARG char*
132: #define FTOL 1.0e-10
133:
134: #define NRANSI
135: #define ITMAX 200
136:
137: #define TOL 2.0e-4
138:
139: #define CGOLD 0.3819660
140: #define ZEPS 1.0e-10
141: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
142:
143: #define GOLD 1.618034
144: #define GLIMIT 100.0
145: #define TINY 1.0e-20
146:
147: static double maxarg1,maxarg2;
148: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
149: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
150:
151: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
152: #define rint(a) floor(a+0.5)
153:
154: static double sqrarg;
155: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
156: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
157:
158: int imx;
159: int stepm;
160: /* Stepm, step in month: minimum step interpolation*/
161:
162: int estepm;
163: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
164:
165: int m,nb;
166: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
167: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
168: double **pmmij, ***probs;
169: double dateintmean=0;
170:
171: double *weight;
172: int **s; /* Status */
173: double *agedc, **covar, idx;
174: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
175:
176: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
177: double ftolhess; /* Tolerance for computing hessian */
178:
179: /**************** split *************************/
180: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
181: {
182: char *ss; /* pointer */
183: int l1, l2; /* length counters */
184:
185: l1 = strlen(path ); /* length of path */
186: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
187: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
188: if ( ss == NULL ) { /* no directory, so use current */
189: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
190: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
191: #if defined(__bsd__) /* get current working directory */
192: extern char *getwd( );
193:
194: if ( getwd( dirc ) == NULL ) {
195: #else
196: extern char *getcwd( );
197:
198: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
199: #endif
200: return( GLOCK_ERROR_GETCWD );
201: }
202: strcpy( name, path ); /* we've got it */
203: } else { /* strip direcotry from path */
204: ss++; /* after this, the filename */
205: l2 = strlen( ss ); /* length of filename */
206: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
207: strcpy( name, ss ); /* save file name */
208: strncpy( dirc, path, l1 - l2 ); /* now the directory */
209: dirc[l1-l2] = 0; /* add zero */
210: }
211: l1 = strlen( dirc ); /* length of directory */
212: #ifdef windows
213: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
214: #else
215: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
216: #endif
217: ss = strrchr( name, '.' ); /* find last / */
218: ss++;
219: strcpy(ext,ss); /* save extension */
220: l1= strlen( name);
221: l2= strlen(ss)+1;
222: strncpy( finame, name, l1-l2);
223: finame[l1-l2]= 0;
224: return( 0 ); /* we're done */
225: }
226:
227:
228: /******************************************/
229:
230: void replace(char *s, char*t)
231: {
232: int i;
233: int lg=20;
234: i=0;
235: lg=strlen(t);
236: for(i=0; i<= lg; i++) {
237: (s[i] = t[i]);
238: if (t[i]== '\\') s[i]='/';
239: }
240: }
241:
242: int nbocc(char *s, char occ)
243: {
244: int i,j=0;
245: int lg=20;
246: i=0;
247: lg=strlen(s);
248: for(i=0; i<= lg; i++) {
249: if (s[i] == occ ) j++;
250: }
251: return j;
252: }
253:
254: void cutv(char *u,char *v, char*t, char occ)
255: {
256: /* cuts string t into u and v where u is ended by char occ excluding it
257: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
258: gives u="abcedf" and v="ghi2j" */
259: int i,lg,j,p=0;
260: i=0;
261: for(j=0; j<=strlen(t)-1; j++) {
262: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
263: }
264:
265: lg=strlen(t);
266: for(j=0; j<p; j++) {
267: (u[j] = t[j]);
268: }
269: u[p]='\0';
270:
271: for(j=0; j<= lg; j++) {
272: if (j>=(p+1))(v[j-p-1] = t[j]);
273: }
274: }
275:
276: /********************** nrerror ********************/
277:
278: void nrerror(char error_text[])
279: {
280: fprintf(stderr,"ERREUR ...\n");
281: fprintf(stderr,"%s\n",error_text);
282: exit(EXIT_FAILURE);
283: }
284: /*********************** vector *******************/
285: double *vector(int nl, int nh)
286: {
287: double *v;
288: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
289: if (!v) nrerror("allocation failure in vector");
290: return v-nl+NR_END;
291: }
292:
293: /************************ free vector ******************/
294: void free_vector(double*v, int nl, int nh)
295: {
296: free((FREE_ARG)(v+nl-NR_END));
297: }
298:
299: /************************ivector *******************************/
300: int *ivector(long nl,long nh)
301: {
302: int *v;
303: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
304: if (!v) nrerror("allocation failure in ivector");
305: return v-nl+NR_END;
306: }
307:
308: /******************free ivector **************************/
309: void free_ivector(int *v, long nl, long nh)
310: {
311: free((FREE_ARG)(v+nl-NR_END));
312: }
313:
314: /******************* imatrix *******************************/
315: int **imatrix(long nrl, long nrh, long ncl, long nch)
316: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
317: {
318: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
319: int **m;
320:
321: /* allocate pointers to rows */
322: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
323: if (!m) nrerror("allocation failure 1 in matrix()");
324: m += NR_END;
325: m -= nrl;
326:
327:
328: /* allocate rows and set pointers to them */
329: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
330: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
331: m[nrl] += NR_END;
332: m[nrl] -= ncl;
333:
334: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
335:
336: /* return pointer to array of pointers to rows */
337: return m;
338: }
339:
340: /****************** free_imatrix *************************/
341: void free_imatrix(m,nrl,nrh,ncl,nch)
342: int **m;
343: long nch,ncl,nrh,nrl;
344: /* free an int matrix allocated by imatrix() */
345: {
346: free((FREE_ARG) (m[nrl]+ncl-NR_END));
347: free((FREE_ARG) (m+nrl-NR_END));
348: }
349:
350: /******************* matrix *******************************/
351: double **matrix(long nrl, long nrh, long ncl, long nch)
352: {
353: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
354: double **m;
355:
356: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
357: if (!m) nrerror("allocation failure 1 in matrix()");
358: m += NR_END;
359: m -= nrl;
360:
361: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
362: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
363: m[nrl] += NR_END;
364: m[nrl] -= ncl;
365:
366: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
367: return m;
368: }
369:
370: /*************************free matrix ************************/
371: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
372: {
373: free((FREE_ARG)(m[nrl]+ncl-NR_END));
374: free((FREE_ARG)(m+nrl-NR_END));
375: }
376:
377: /******************* ma3x *******************************/
378: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
379: {
380: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
381: double ***m;
382:
383: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
384: if (!m) nrerror("allocation failure 1 in matrix()");
385: m += NR_END;
386: m -= nrl;
387:
388: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
389: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
390: m[nrl] += NR_END;
391: m[nrl] -= ncl;
392:
393: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
394:
395: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
396: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
397: m[nrl][ncl] += NR_END;
398: m[nrl][ncl] -= nll;
399: for (j=ncl+1; j<=nch; j++)
400: m[nrl][j]=m[nrl][j-1]+nlay;
401:
402: for (i=nrl+1; i<=nrh; i++) {
403: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
404: for (j=ncl+1; j<=nch; j++)
405: m[i][j]=m[i][j-1]+nlay;
406: }
407: return m;
408: }
409:
410: /*************************free ma3x ************************/
411: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
412: {
413: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
414: free((FREE_ARG)(m[nrl]+ncl-NR_END));
415: free((FREE_ARG)(m+nrl-NR_END));
416: }
417:
418: /***************** f1dim *************************/
419: extern int ncom;
420: extern double *pcom,*xicom;
421: extern double (*nrfunc)(double []);
422:
423: double f1dim(double x)
424: {
425: int j;
426: double f;
427: double *xt;
428:
429: xt=vector(1,ncom);
430: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
431: f=(*nrfunc)(xt);
432: free_vector(xt,1,ncom);
433: return f;
434: }
435:
436: /*****************brent *************************/
437: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
438: {
439: int iter;
440: double a,b,d,etemp;
441: double fu,fv,fw,fx;
442: double ftemp;
443: double p,q,r,tol1,tol2,u,v,w,x,xm;
444: double e=0.0;
445:
446: a=(ax < cx ? ax : cx);
447: b=(ax > cx ? ax : cx);
448: x=w=v=bx;
449: fw=fv=fx=(*f)(x);
450: for (iter=1;iter<=ITMAX;iter++) {
451: xm=0.5*(a+b);
452: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
453: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
454: printf(".");fflush(stdout);
455: fprintf(ficlog,".");fflush(ficlog);
456: #ifdef DEBUG
457: 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);
458: 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);
459: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
460: #endif
461: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
462: *xmin=x;
463: return fx;
464: }
465: ftemp=fu;
466: if (fabs(e) > tol1) {
467: r=(x-w)*(fx-fv);
468: q=(x-v)*(fx-fw);
469: p=(x-v)*q-(x-w)*r;
470: q=2.0*(q-r);
471: if (q > 0.0) p = -p;
472: q=fabs(q);
473: etemp=e;
474: e=d;
475: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
476: d=CGOLD*(e=(x >= xm ? a-x : b-x));
477: else {
478: d=p/q;
479: u=x+d;
480: if (u-a < tol2 || b-u < tol2)
481: d=SIGN(tol1,xm-x);
482: }
483: } else {
484: d=CGOLD*(e=(x >= xm ? a-x : b-x));
485: }
486: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
487: fu=(*f)(u);
488: if (fu <= fx) {
489: if (u >= x) a=x; else b=x;
490: SHFT(v,w,x,u)
491: SHFT(fv,fw,fx,fu)
492: } else {
493: if (u < x) a=u; else b=u;
494: if (fu <= fw || w == x) {
495: v=w;
496: w=u;
497: fv=fw;
498: fw=fu;
499: } else if (fu <= fv || v == x || v == w) {
500: v=u;
501: fv=fu;
502: }
503: }
504: }
505: nrerror("Too many iterations in brent");
506: *xmin=x;
507: return fx;
508: }
509:
510: /****************** mnbrak ***********************/
511:
512: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
513: double (*func)(double))
514: {
515: double ulim,u,r,q, dum;
516: double fu;
517:
518: *fa=(*func)(*ax);
519: *fb=(*func)(*bx);
520: if (*fb > *fa) {
521: SHFT(dum,*ax,*bx,dum)
522: SHFT(dum,*fb,*fa,dum)
523: }
524: *cx=(*bx)+GOLD*(*bx-*ax);
525: *fc=(*func)(*cx);
526: while (*fb > *fc) {
527: r=(*bx-*ax)*(*fb-*fc);
528: q=(*bx-*cx)*(*fb-*fa);
529: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
530: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
531: ulim=(*bx)+GLIMIT*(*cx-*bx);
532: if ((*bx-u)*(u-*cx) > 0.0) {
533: fu=(*func)(u);
534: } else if ((*cx-u)*(u-ulim) > 0.0) {
535: fu=(*func)(u);
536: if (fu < *fc) {
537: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
538: SHFT(*fb,*fc,fu,(*func)(u))
539: }
540: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
541: u=ulim;
542: fu=(*func)(u);
543: } else {
544: u=(*cx)+GOLD*(*cx-*bx);
545: fu=(*func)(u);
546: }
547: SHFT(*ax,*bx,*cx,u)
548: SHFT(*fa,*fb,*fc,fu)
549: }
550: }
551:
552: /*************** linmin ************************/
553:
554: int ncom;
555: double *pcom,*xicom;
556: double (*nrfunc)(double []);
557:
558: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
559: {
560: double brent(double ax, double bx, double cx,
561: double (*f)(double), double tol, double *xmin);
562: double f1dim(double x);
563: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
564: double *fc, double (*func)(double));
565: int j;
566: double xx,xmin,bx,ax;
567: double fx,fb,fa;
568:
569: ncom=n;
570: pcom=vector(1,n);
571: xicom=vector(1,n);
572: nrfunc=func;
573: for (j=1;j<=n;j++) {
574: pcom[j]=p[j];
575: xicom[j]=xi[j];
576: }
577: ax=0.0;
578: xx=1.0;
579: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
580: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
581: #ifdef DEBUG
582: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
583: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
584: #endif
585: for (j=1;j<=n;j++) {
586: xi[j] *= xmin;
587: p[j] += xi[j];
588: }
589: free_vector(xicom,1,n);
590: free_vector(pcom,1,n);
591: }
592:
593: /*************** powell ************************/
594: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
595: double (*func)(double []))
596: {
597: void linmin(double p[], double xi[], int n, double *fret,
598: double (*func)(double []));
599: int i,ibig,j;
600: double del,t,*pt,*ptt,*xit;
601: double fp,fptt;
602: double *xits;
603: pt=vector(1,n);
604: ptt=vector(1,n);
605: xit=vector(1,n);
606: xits=vector(1,n);
607: *fret=(*func)(p);
608: for (j=1;j<=n;j++) pt[j]=p[j];
609: for (*iter=1;;++(*iter)) {
610: fp=(*fret);
611: ibig=0;
612: del=0.0;
613: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
614: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
615: for (i=1;i<=n;i++)
616: printf(" %d %.12f",i, p[i]);
617: fprintf(ficlog," %d %.12f",i, p[i]);
618: printf("\n");
619: fprintf(ficlog,"\n");
620: for (i=1;i<=n;i++) {
621: for (j=1;j<=n;j++) xit[j]=xi[j][i];
622: fptt=(*fret);
623: #ifdef DEBUG
624: printf("fret=%lf \n",*fret);
625: fprintf(ficlog,"fret=%lf \n",*fret);
626: #endif
627: printf("%d",i);fflush(stdout);
628: fprintf(ficlog,"%d",i);fflush(ficlog);
629: linmin(p,xit,n,fret,func);
630: if (fabs(fptt-(*fret)) > del) {
631: del=fabs(fptt-(*fret));
632: ibig=i;
633: }
634: #ifdef DEBUG
635: printf("%d %.12e",i,(*fret));
636: fprintf(ficlog,"%d %.12e",i,(*fret));
637: for (j=1;j<=n;j++) {
638: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
639: printf(" x(%d)=%.12e",j,xit[j]);
640: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
641: }
642: for(j=1;j<=n;j++) {
643: printf(" p=%.12e",p[j]);
644: fprintf(ficlog," p=%.12e",p[j]);
645: }
646: printf("\n");
647: fprintf(ficlog,"\n");
648: #endif
649: }
650: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
651: #ifdef DEBUG
652: int k[2],l;
653: k[0]=1;
654: k[1]=-1;
655: printf("Max: %.12e",(*func)(p));
656: fprintf(ficlog,"Max: %.12e",(*func)(p));
657: for (j=1;j<=n;j++) {
658: printf(" %.12e",p[j]);
659: fprintf(ficlog," %.12e",p[j]);
660: }
661: printf("\n");
662: fprintf(ficlog,"\n");
663: for(l=0;l<=1;l++) {
664: for (j=1;j<=n;j++) {
665: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
666: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
667: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
668: }
669: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
670: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
671: }
672: #endif
673:
674:
675: free_vector(xit,1,n);
676: free_vector(xits,1,n);
677: free_vector(ptt,1,n);
678: free_vector(pt,1,n);
679: return;
680: }
681: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
682: for (j=1;j<=n;j++) {
683: ptt[j]=2.0*p[j]-pt[j];
684: xit[j]=p[j]-pt[j];
685: pt[j]=p[j];
686: }
687: fptt=(*func)(ptt);
688: if (fptt < fp) {
689: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
690: if (t < 0.0) {
691: linmin(p,xit,n,fret,func);
692: for (j=1;j<=n;j++) {
693: xi[j][ibig]=xi[j][n];
694: xi[j][n]=xit[j];
695: }
696: #ifdef DEBUG
697: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
698: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
699: for(j=1;j<=n;j++){
700: printf(" %.12e",xit[j]);
701: fprintf(ficlog," %.12e",xit[j]);
702: }
703: printf("\n");
704: fprintf(ficlog,"\n");
705: #endif
706: }
707: }
708: }
709: }
710:
711: /**** Prevalence limit (stable prevalence) ****************/
712:
713: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
714: {
715: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
716: matrix by transitions matrix until convergence is reached */
717:
718: int i, ii,j,k;
719: double min, max, maxmin, maxmax,sumnew=0.;
720: double **matprod2();
721: double **out, cov[NCOVMAX], **pmij();
722: double **newm;
723: double agefin, delaymax=50 ; /* Max number of years to converge */
724:
725: for (ii=1;ii<=nlstate+ndeath;ii++)
726: for (j=1;j<=nlstate+ndeath;j++){
727: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
728: }
729:
730: cov[1]=1.;
731:
732: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
733: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
734: newm=savm;
735: /* Covariates have to be included here again */
736: cov[2]=agefin;
737:
738: for (k=1; k<=cptcovn;k++) {
739: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
740: /* 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]]);*/
741: }
742: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
743: for (k=1; k<=cptcovprod;k++)
744: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
745:
746: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
747: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
748: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
749: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
750:
751: savm=oldm;
752: oldm=newm;
753: maxmax=0.;
754: for(j=1;j<=nlstate;j++){
755: min=1.;
756: max=0.;
757: for(i=1; i<=nlstate; i++) {
758: sumnew=0;
759: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
760: prlim[i][j]= newm[i][j]/(1-sumnew);
761: max=FMAX(max,prlim[i][j]);
762: min=FMIN(min,prlim[i][j]);
763: }
764: maxmin=max-min;
765: maxmax=FMAX(maxmax,maxmin);
766: }
767: if(maxmax < ftolpl){
768: return prlim;
769: }
770: }
771: }
772:
773: /*************** transition probabilities ***************/
774:
775: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
776: {
777: double s1, s2;
778: /*double t34;*/
779: int i,j,j1, nc, ii, jj;
780:
781: for(i=1; i<= nlstate; i++){
782: for(j=1; j<i;j++){
783: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
784: /*s2 += param[i][j][nc]*cov[nc];*/
785: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
786: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
787: }
788: ps[i][j]=s2;
789: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
790: }
791: for(j=i+1; j<=nlstate+ndeath;j++){
792: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
793: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
794: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
795: }
796: ps[i][j]=s2;
797: }
798: }
799: /*ps[3][2]=1;*/
800:
801: for(i=1; i<= nlstate; i++){
802: s1=0;
803: for(j=1; j<i; j++)
804: s1+=exp(ps[i][j]);
805: for(j=i+1; j<=nlstate+ndeath; j++)
806: s1+=exp(ps[i][j]);
807: ps[i][i]=1./(s1+1.);
808: for(j=1; j<i; j++)
809: ps[i][j]= exp(ps[i][j])*ps[i][i];
810: for(j=i+1; j<=nlstate+ndeath; j++)
811: ps[i][j]= exp(ps[i][j])*ps[i][i];
812: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
813: } /* end i */
814:
815: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
816: for(jj=1; jj<= nlstate+ndeath; jj++){
817: ps[ii][jj]=0;
818: ps[ii][ii]=1;
819: }
820: }
821:
822:
823: /* for(ii=1; ii<= nlstate+ndeath; ii++){
824: for(jj=1; jj<= nlstate+ndeath; jj++){
825: printf("%lf ",ps[ii][jj]);
826: }
827: printf("\n ");
828: }
829: printf("\n ");printf("%lf ",cov[2]);*/
830: /*
831: for(i=1; i<= npar; i++) printf("%f ",x[i]);
832: goto end;*/
833: return ps;
834: }
835:
836: /**************** Product of 2 matrices ******************/
837:
838: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
839: {
840: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
841: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
842: /* in, b, out are matrice of pointers which should have been initialized
843: before: only the contents of out is modified. The function returns
844: a pointer to pointers identical to out */
845: long i, j, k;
846: for(i=nrl; i<= nrh; i++)
847: for(k=ncolol; k<=ncoloh; k++)
848: for(j=ncl,out[i][k]=0.; j<=nch; j++)
849: out[i][k] +=in[i][j]*b[j][k];
850:
851: return out;
852: }
853:
854:
855: /************* Higher Matrix Product ***************/
856:
857: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
858: {
859: /* Computes the transition matrix starting at age 'age' over
860: 'nhstepm*hstepm*stepm' months (i.e. until
861: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
862: nhstepm*hstepm matrices.
863: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
864: (typically every 2 years instead of every month which is too big
865: for the memory).
866: Model is determined by parameters x and covariates have to be
867: included manually here.
868:
869: */
870:
871: int i, j, d, h, k;
872: double **out, cov[NCOVMAX];
873: double **newm;
874:
875: /* Hstepm could be zero and should return the unit matrix */
876: for (i=1;i<=nlstate+ndeath;i++)
877: for (j=1;j<=nlstate+ndeath;j++){
878: oldm[i][j]=(i==j ? 1.0 : 0.0);
879: po[i][j][0]=(i==j ? 1.0 : 0.0);
880: }
881: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
882: for(h=1; h <=nhstepm; h++){
883: for(d=1; d <=hstepm; d++){
884: newm=savm;
885: /* Covariates have to be included here again */
886: cov[1]=1.;
887: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
888: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
889: for (k=1; k<=cptcovage;k++)
890: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
891: for (k=1; k<=cptcovprod;k++)
892: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
893:
894:
895: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
896: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
897: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
898: pmij(pmmij,cov,ncovmodel,x,nlstate));
899: savm=oldm;
900: oldm=newm;
901: }
902: for(i=1; i<=nlstate+ndeath; i++)
903: for(j=1;j<=nlstate+ndeath;j++) {
904: po[i][j][h]=newm[i][j];
905: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
906: */
907: }
908: } /* end h */
909: return po;
910: }
911:
912:
913: /*************** log-likelihood *************/
914: double func( double *x)
915: {
916: int i, ii, j, k, mi, d, kk;
917: double l, ll[NLSTATEMAX], cov[NCOVMAX];
918: double **out;
919: double sw; /* Sum of weights */
920: double lli; /* Individual log likelihood */
921: int s1, s2;
922: double bbh, survp;
923: long ipmx;
924: /*extern weight */
925: /* We are differentiating ll according to initial status */
926: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
927: /*for(i=1;i<imx;i++)
928: printf(" %d\n",s[4][i]);
929: */
930: cov[1]=1.;
931:
932: for(k=1; k<=nlstate; k++) ll[k]=0.;
933:
934: if(mle==1){
935: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
936: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
937: for(mi=1; mi<= wav[i]-1; mi++){
938: for (ii=1;ii<=nlstate+ndeath;ii++)
939: for (j=1;j<=nlstate+ndeath;j++){
940: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
941: savm[ii][j]=(ii==j ? 1.0 : 0.0);
942: }
943: for(d=0; d<dh[mi][i]; d++){
944: newm=savm;
945: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
946: for (kk=1; kk<=cptcovage;kk++) {
947: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
948: }
949: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
950: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
951: savm=oldm;
952: oldm=newm;
953: } /* end mult */
954:
955: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
956: /* But now since version 0.9 we anticipate for bias and large stepm.
957: * If stepm is larger than one month (smallest stepm) and if the exact delay
958: * (in months) between two waves is not a multiple of stepm, we rounded to
959: * the nearest (and in case of equal distance, to the lowest) interval but now
960: * we keep into memory the bias bh[mi][i] and also the previous matrix product
961: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
962: * probability in order to take into account the bias as a fraction of the way
963: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
964: * -stepm/2 to stepm/2 .
965: * For stepm=1 the results are the same as for previous versions of Imach.
966: * For stepm > 1 the results are less biased than in previous versions.
967: */
968: s1=s[mw[mi][i]][i];
969: s2=s[mw[mi+1][i]][i];
970: bbh=(double)bh[mi][i]/(double)stepm;
971: /* bias is positive if real duration
972: * is higher than the multiple of stepm and negative otherwise.
973: */
974: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
975: /* if s2=-2 lli=out[1][1]+out[1][2];*/
976: if (s2==-2) {
977: for (j=1,survp=0. ; j<=nlstate; j++)
978: survp += out[s1][j];
979: lli= survp;
980: }
981:
982: else
983: 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 */
984: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
985: /*if(lli ==000.0)*/
986: /*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); */
987: ipmx +=1;
988: sw += weight[i];
989: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
990: } /* end of wave */
991: } /* end of individual */
992: } else if(mle==2){
993: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
994: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
995: for(mi=1; mi<= wav[i]-1; mi++){
996: for (ii=1;ii<=nlstate+ndeath;ii++)
997: for (j=1;j<=nlstate+ndeath;j++){
998: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
999: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1000: }
1001: for(d=0; d<=dh[mi][i]; d++){
1002: newm=savm;
1003: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1004: for (kk=1; kk<=cptcovage;kk++) {
1005: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1006: }
1007: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1008: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1009: savm=oldm;
1010: oldm=newm;
1011: } /* end mult */
1012:
1013: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1014: /* But now since version 0.9 we anticipate for bias and large stepm.
1015: * If stepm is larger than one month (smallest stepm) and if the exact delay
1016: * (in months) between two waves is not a multiple of stepm, we rounded to
1017: * the nearest (and in case of equal distance, to the lowest) interval but now
1018: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1019: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1020: * probability in order to take into account the bias as a fraction of the way
1021: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1022: * -stepm/2 to stepm/2 .
1023: * For stepm=1 the results are the same as for previous versions of Imach.
1024: * For stepm > 1 the results are less biased than in previous versions.
1025: */
1026: s1=s[mw[mi][i]][i];
1027: s2=s[mw[mi+1][i]][i];
1028: bbh=(double)bh[mi][i]/(double)stepm;
1029: /* bias is positive if real duration
1030: * is higher than the multiple of stepm and negative otherwise.
1031: */
1032: 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 */
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: /*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 */
1035: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1036: /*if(lli ==000.0)*/
1037: /*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); */
1038: ipmx +=1;
1039: sw += weight[i];
1040: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1041: } /* end of wave */
1042: } /* end of individual */
1043: } else if(mle==3){ /* exponential inter-extrapolation */
1044: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1045: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1046: for(mi=1; mi<= wav[i]-1; mi++){
1047: for (ii=1;ii<=nlstate+ndeath;ii++)
1048: for (j=1;j<=nlstate+ndeath;j++){
1049: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1050: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1051: }
1052: for(d=0; d<dh[mi][i]; d++){
1053: newm=savm;
1054: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1055: for (kk=1; kk<=cptcovage;kk++) {
1056: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1057: }
1058: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1059: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1060: savm=oldm;
1061: oldm=newm;
1062: } /* end mult */
1063:
1064: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1065: /* But now since version 0.9 we anticipate for bias and large stepm.
1066: * If stepm is larger than one month (smallest stepm) and if the exact delay
1067: * (in months) between two waves is not a multiple of stepm, we rounded to
1068: * the nearest (and in case of equal distance, to the lowest) interval but now
1069: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1070: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1071: * probability in order to take into account the bias as a fraction of the way
1072: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1073: * -stepm/2 to stepm/2 .
1074: * For stepm=1 the results are the same as for previous versions of Imach.
1075: * For stepm > 1 the results are less biased than in previous versions.
1076: */
1077: s1=s[mw[mi][i]][i];
1078: s2=s[mw[mi+1][i]][i];
1079: bbh=(double)bh[mi][i]/(double)stepm;
1080: /* bias is positive if real duration
1081: * is higher than the multiple of stepm and negative otherwise.
1082: */
1083: /* 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 */
1084: 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 */
1085: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1086: /*if(lli ==000.0)*/
1087: /*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); */
1088: ipmx +=1;
1089: sw += weight[i];
1090: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1091: } /* end of wave */
1092: } /* end of individual */
1093: }else{ /* ml=4 no inter-extrapolation */
1094: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1095: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1096: for(mi=1; mi<= wav[i]-1; mi++){
1097: for (ii=1;ii<=nlstate+ndeath;ii++)
1098: for (j=1;j<=nlstate+ndeath;j++){
1099: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1100: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1101: }
1102: for(d=0; d<dh[mi][i]; d++){
1103: newm=savm;
1104: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1105: for (kk=1; kk<=cptcovage;kk++) {
1106: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1107: }
1108:
1109: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1110: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1111: savm=oldm;
1112: oldm=newm;
1113: } /* end mult */
1114:
1115: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
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: } /* End of if */
1122: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1123: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1124: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1125: return -l;
1126: }
1127:
1128:
1129: /*********** Maximum Likelihood Estimation ***************/
1130:
1131: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1132: {
1133: int i,j, iter;
1134: double **xi,*delti;
1135: double fret;
1136: xi=matrix(1,npar,1,npar);
1137: for (i=1;i<=npar;i++)
1138: for (j=1;j<=npar;j++)
1139: xi[i][j]=(i==j ? 1.0 : 0.0);
1140: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1141: powell(p,xi,npar,ftol,&iter,&fret,func);
1142:
1143: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1144: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1145: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1146:
1147: }
1148:
1149: /**** Computes Hessian and covariance matrix ***/
1150: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1151: {
1152: double **a,**y,*x,pd;
1153: double **hess;
1154: int i, j,jk;
1155: int *indx;
1156:
1157: double hessii(double p[], double delta, int theta, double delti[]);
1158: double hessij(double p[], double delti[], int i, int j);
1159: void lubksb(double **a, int npar, int *indx, double b[]) ;
1160: void ludcmp(double **a, int npar, int *indx, double *d) ;
1161:
1162: hess=matrix(1,npar,1,npar);
1163:
1164: printf("\nCalculation of the hessian matrix. Wait...\n");
1165: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1166: for (i=1;i<=npar;i++){
1167: printf("%d",i);fflush(stdout);
1168: fprintf(ficlog,"%d",i);fflush(ficlog);
1169: hess[i][i]=hessii(p,ftolhess,i,delti);
1170: /*printf(" %f ",p[i]);*/
1171: /*printf(" %lf ",hess[i][i]);*/
1172: }
1173:
1174: for (i=1;i<=npar;i++) {
1175: for (j=1;j<=npar;j++) {
1176: if (j>i) {
1177: printf(".%d%d",i,j);fflush(stdout);
1178: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1179: hess[i][j]=hessij(p,delti,i,j);
1180: hess[j][i]=hess[i][j];
1181: /*printf(" %lf ",hess[i][j]);*/
1182: }
1183: }
1184: }
1185: printf("\n");
1186: fprintf(ficlog,"\n");
1187:
1188: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1189: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1190:
1191: a=matrix(1,npar,1,npar);
1192: y=matrix(1,npar,1,npar);
1193: x=vector(1,npar);
1194: indx=ivector(1,npar);
1195: for (i=1;i<=npar;i++)
1196: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1197: ludcmp(a,npar,indx,&pd);
1198:
1199: for (j=1;j<=npar;j++) {
1200: for (i=1;i<=npar;i++) x[i]=0;
1201: x[j]=1;
1202: lubksb(a,npar,indx,x);
1203: for (i=1;i<=npar;i++){
1204: matcov[i][j]=x[i];
1205: }
1206: }
1207:
1208: printf("\n#Hessian matrix#\n");
1209: fprintf(ficlog,"\n#Hessian matrix#\n");
1210: for (i=1;i<=npar;i++) {
1211: for (j=1;j<=npar;j++) {
1212: printf("%.3e ",hess[i][j]);
1213: fprintf(ficlog,"%.3e ",hess[i][j]);
1214: }
1215: printf("\n");
1216: fprintf(ficlog,"\n");
1217: }
1218:
1219: /* Recompute Inverse */
1220: for (i=1;i<=npar;i++)
1221: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1222: ludcmp(a,npar,indx,&pd);
1223:
1224: /* printf("\n#Hessian matrix recomputed#\n");
1225:
1226: for (j=1;j<=npar;j++) {
1227: for (i=1;i<=npar;i++) x[i]=0;
1228: x[j]=1;
1229: lubksb(a,npar,indx,x);
1230: for (i=1;i<=npar;i++){
1231: y[i][j]=x[i];
1232: printf("%.3e ",y[i][j]);
1233: fprintf(ficlog,"%.3e ",y[i][j]);
1234: }
1235: printf("\n");
1236: fprintf(ficlog,"\n");
1237: }
1238: */
1239:
1240: free_matrix(a,1,npar,1,npar);
1241: free_matrix(y,1,npar,1,npar);
1242: free_vector(x,1,npar);
1243: free_ivector(indx,1,npar);
1244: free_matrix(hess,1,npar,1,npar);
1245:
1246:
1247: }
1248:
1249: /*************** hessian matrix ****************/
1250: double hessii( double x[], double delta, int theta, double delti[])
1251: {
1252: int i;
1253: int l=1, lmax=20;
1254: double k1,k2;
1255: double p2[NPARMAX+1];
1256: double res;
1257: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1258: double fx;
1259: int k=0,kmax=10;
1260: double l1;
1261:
1262: fx=func(x);
1263: for (i=1;i<=npar;i++) p2[i]=x[i];
1264: for(l=0 ; l <=lmax; l++){
1265: l1=pow(10,l);
1266: delts=delt;
1267: for(k=1 ; k <kmax; k=k+1){
1268: delt = delta*(l1*k);
1269: p2[theta]=x[theta] +delt;
1270: k1=func(p2)-fx;
1271: p2[theta]=x[theta]-delt;
1272: k2=func(p2)-fx;
1273: /*res= (k1-2.0*fx+k2)/delt/delt; */
1274: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1275:
1276: #ifdef DEBUG
1277: 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);
1278: 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);
1279: #endif
1280: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1281: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1282: k=kmax;
1283: }
1284: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1285: k=kmax; l=lmax*10.;
1286: }
1287: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1288: delts=delt;
1289: }
1290: }
1291: }
1292: delti[theta]=delts;
1293: return res;
1294:
1295: }
1296:
1297: double hessij( double x[], double delti[], int thetai,int thetaj)
1298: {
1299: int i;
1300: int l=1, l1, lmax=20;
1301: double k1,k2,k3,k4,res,fx;
1302: double p2[NPARMAX+1];
1303: int k;
1304:
1305: fx=func(x);
1306: for (k=1; k<=2; k++) {
1307: for (i=1;i<=npar;i++) p2[i]=x[i];
1308: p2[thetai]=x[thetai]+delti[thetai]/k;
1309: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1310: k1=func(p2)-fx;
1311:
1312: p2[thetai]=x[thetai]+delti[thetai]/k;
1313: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1314: k2=func(p2)-fx;
1315:
1316: p2[thetai]=x[thetai]-delti[thetai]/k;
1317: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1318: k3=func(p2)-fx;
1319:
1320: p2[thetai]=x[thetai]-delti[thetai]/k;
1321: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1322: k4=func(p2)-fx;
1323: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1324: #ifdef DEBUG
1325: 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);
1326: 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);
1327: #endif
1328: }
1329: return res;
1330: }
1331:
1332: /************** Inverse of matrix **************/
1333: void ludcmp(double **a, int n, int *indx, double *d)
1334: {
1335: int i,imax,j,k;
1336: double big,dum,sum,temp;
1337: double *vv;
1338:
1339: vv=vector(1,n);
1340: *d=1.0;
1341: for (i=1;i<=n;i++) {
1342: big=0.0;
1343: for (j=1;j<=n;j++)
1344: if ((temp=fabs(a[i][j])) > big) big=temp;
1345: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1346: vv[i]=1.0/big;
1347: }
1348: for (j=1;j<=n;j++) {
1349: for (i=1;i<j;i++) {
1350: sum=a[i][j];
1351: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1352: a[i][j]=sum;
1353: }
1354: big=0.0;
1355: for (i=j;i<=n;i++) {
1356: sum=a[i][j];
1357: for (k=1;k<j;k++)
1358: sum -= a[i][k]*a[k][j];
1359: a[i][j]=sum;
1360: if ( (dum=vv[i]*fabs(sum)) >= big) {
1361: big=dum;
1362: imax=i;
1363: }
1364: }
1365: if (j != imax) {
1366: for (k=1;k<=n;k++) {
1367: dum=a[imax][k];
1368: a[imax][k]=a[j][k];
1369: a[j][k]=dum;
1370: }
1371: *d = -(*d);
1372: vv[imax]=vv[j];
1373: }
1374: indx[j]=imax;
1375: if (a[j][j] == 0.0) a[j][j]=TINY;
1376: if (j != n) {
1377: dum=1.0/(a[j][j]);
1378: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1379: }
1380: }
1381: free_vector(vv,1,n); /* Doesn't work */
1382: ;
1383: }
1384:
1385: void lubksb(double **a, int n, int *indx, double b[])
1386: {
1387: int i,ii=0,ip,j;
1388: double sum;
1389:
1390: for (i=1;i<=n;i++) {
1391: ip=indx[i];
1392: sum=b[ip];
1393: b[ip]=b[i];
1394: if (ii)
1395: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1396: else if (sum) ii=i;
1397: b[i]=sum;
1398: }
1399: for (i=n;i>=1;i--) {
1400: sum=b[i];
1401: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1402: b[i]=sum/a[i][i];
1403: }
1404: }
1405:
1406: /************ Frequencies ********************/
1407: void freqsummary(char fileres[], int agemin, int agemax, 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)
1408: { /* Some frequencies */
1409:
1410: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1411: int first;
1412: double ***freq; /* Frequencies */
1413: double *pp;
1414: double pos, k2, dateintsum=0,k2cpt=0;
1415: FILE *ficresp;
1416: char fileresp[FILENAMELENGTH];
1417:
1418: pp=vector(1,nlstate);
1419: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1420: strcpy(fileresp,"p");
1421: strcat(fileresp,fileres);
1422: if((ficresp=fopen(fileresp,"w"))==NULL) {
1423: printf("Problem with prevalence resultfile: %s\n", fileresp);
1424: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1425: exit(0);
1426: }
1427: freq= ma3x(-2,nlstate+ndeath,-2,nlstate+ndeath,agemin,agemax+3);
1428: j1=0;
1429:
1430: j=cptcoveff;
1431: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1432:
1433: first=1;
1434:
1435: for(k1=1; k1<=j;k1++){
1436: for(i1=1; i1<=ncodemax[k1];i1++){
1437: j1++;
1438: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1439: scanf("%d", i);*/
1440: for (i=-1; i<=nlstate+ndeath; i++)
1441: for (jk=-1; jk<=nlstate+ndeath; jk++)
1442: for(m=agemin; m <= agemax+3; m++)
1443: freq[i][jk][m]=0;
1444:
1445: dateintsum=0;
1446: k2cpt=0;
1447: for (i=1; i<=imx; i++) {
1448: bool=1;
1449: if (cptcovn>0) {
1450: for (z1=1; z1<=cptcoveff; z1++)
1451: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1452: bool=0;
1453: }
1454: if (bool==1){
1455: for(m=firstpass; m<=lastpass; m++){
1456: k2=anint[m][i]+(mint[m][i]/12.);
1457: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1458: if(agev[m][i]==0) agev[m][i]=agemax+1;
1459: if(agev[m][i]==1) agev[m][i]=agemax+2;
1460: if (m<lastpass) {
1461: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1462: freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
1463: }
1464:
1465: if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
1466: dateintsum=dateintsum+k2;
1467: k2cpt++;
1468: }
1469: }
1470: }
1471: }
1472: }
1473:
1474: fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1475:
1476: if (cptcovn>0) {
1477: fprintf(ficresp, "\n#********** Variable ");
1478: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1479: fprintf(ficresp, "**********\n#");
1480: }
1481: for(i=1; i<=nlstate;i++)
1482: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1483: fprintf(ficresp, "\n");
1484:
1485: for(i=(int)agemin; i <= (int)agemax+3; i++){
1486: if(i==(int)agemax+3){
1487: fprintf(ficlog,"Total");
1488: }else{
1489: if(first==1){
1490: first=0;
1491: printf("See log file for details...\n");
1492: }
1493: fprintf(ficlog,"Age %d", i);
1494: }
1495: for(jk=1; jk <=nlstate ; jk++){
1496: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1497: pp[jk] += freq[jk][m][i];
1498: }
1499: for(jk=1; jk <=nlstate ; jk++){
1500: for(m=-1, pos=0; m <=0 ; m++)
1501: pos += freq[jk][m][i];
1502: if(pp[jk]>=1.e-10){
1503: if(first==1){
1504: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1505: }
1506: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1507: }else{
1508: if(first==1)
1509: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1510: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1511: }
1512: }
1513:
1514: for(jk=1; jk <=nlstate ; jk++){
1515: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1516: pp[jk] += freq[jk][m][i];
1517: }
1518:
1519: for(jk=1,pos=0; jk <=nlstate ; jk++)
1520: pos += pp[jk];
1521: for(jk=1; jk <=nlstate ; jk++){
1522: if(pos>=1.e-5){
1523: if(first==1)
1524: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1525: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1526: }else{
1527: if(first==1)
1528: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1529: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1530: }
1531: if( i <= (int) agemax){
1532: if(pos>=1.e-5){
1533: fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
1534: probs[i][jk][j1]= pp[jk]/pos;
1535: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1536: }
1537: else
1538: fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
1539: }
1540: }
1541:
1542: for(jk=-2; jk <=nlstate+ndeath; jk++)
1543: for(m=-2; m <=nlstate+ndeath; m++)
1544: if(freq[jk][m][i] !=0 ) {
1545: if(first==1)
1546: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1547: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1548: }
1549: if(i <= (int) agemax)
1550: fprintf(ficresp,"\n");
1551: if(first==1)
1552: printf("Others in log...\n");
1553: fprintf(ficlog,"\n");
1554: }
1555: }
1556: }
1557: dateintmean=dateintsum/k2cpt;
1558:
1559: fclose(ficresp);
1560: free_ma3x(freq,-2,nlstate+ndeath,-2,nlstate+ndeath,(int) agemin,(int) agemax+3);
1561: free_vector(pp,1,nlstate);
1562:
1563: /* End of Freq */
1564: }
1565:
1566: /************ Prevalence ********************/
1567: void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
1568: { /* Some frequencies */
1569:
1570: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1571: double ***freq; /* Frequencies */
1572: double *pp;
1573: double pos, k2;
1574:
1575: pp=vector(1,nlstate);
1576:
1577: freq=ma3x(-2,nlstate+ndeath,-2,nlstate+ndeath,agemin,agemax+3);
1578: j1=0;
1579:
1580: j=cptcoveff;
1581: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1582:
1583: for(k1=1; k1<=j;k1++){
1584: for(i1=1; i1<=ncodemax[k1];i1++){
1585: j1++;
1586:
1587: for (i=-2; i<=nlstate+ndeath; i++)
1588: for (jk=-2; jk<=nlstate+ndeath; jk++)
1589: for(m=agemin; m <= agemax+3; m++)
1590: freq[i][jk][m]=0;
1591:
1592: for (i=1; i<=imx; i++) {
1593: bool=1;
1594: if (cptcovn>0) {
1595: for (z1=1; z1<=cptcoveff; z1++)
1596: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1597: bool=0;
1598: }
1599: if (bool==1) {
1600: for(m=firstpass; m<=lastpass; m++){
1601: k2=anint[m][i]+(mint[m][i]/12.);
1602: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1603: if(agev[m][i]==0) agev[m][i]=agemax+1;
1604: if(agev[m][i]==1) agev[m][i]=agemax+2;
1605: if (m<lastpass) {
1606: if (calagedate>0)
1607: freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
1608: else
1609: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1610: freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];
1611: }
1612: }
1613: }
1614: }
1615: }
1616: for(i=(int)agemin; i <= (int)agemax+3; i++){
1617: for(jk=1; jk <=nlstate ; jk++){
1618: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1619: pp[jk] += freq[jk][m][i];
1620: }
1621: for(jk=1; jk <=nlstate ; jk++){
1622: for(m=-1, pos=0; m <=0 ; m++)
1623: pos += freq[jk][m][i];
1624: }
1625:
1626: for(jk=1; jk <=nlstate ; jk++){
1627: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1628: pp[jk] += freq[jk][m][i];
1629: }
1630:
1631: for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
1632:
1633: for(jk=1; jk <=nlstate ; jk++){
1634: if( i <= (int) agemax){
1635: if(pos>=1.e-5){
1636: probs[i][jk][j1]= pp[jk]/pos;
1637: }
1638: }
1639: }/* end jk */
1640: }/* end i */
1641: } /* end i1 */
1642: } /* end k1 */
1643:
1644:
1645: free_ma3x(freq,-2,nlstate+ndeath,-2,nlstate+ndeath,(int) agemin,(int) agemax+3);
1646: free_vector(pp,1,nlstate);
1647:
1648: } /* End of Freq */
1649:
1650: /************* Waves Concatenation ***************/
1651:
1652: 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)
1653: {
1654: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1655: Death is a valid wave (if date is known).
1656: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1657: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1658: and mw[mi+1][i]. dh depends on stepm.
1659: */
1660:
1661: int i, mi, m;
1662: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1663: double sum=0., jmean=0.;*/
1664: int first;
1665: int j, k=0,jk, ju, jl;
1666: double sum=0.;
1667: first=0;
1668: jmin=1e+5;
1669: jmax=-1;
1670: jmean=0.;
1671: for(i=1; i<=imx; i++){
1672: mi=0;
1673: m=firstpass;
1674: while(s[m][i] <= nlstate){
1675: if(s[m][i]>=1 || s[m][i]==-2)
1676: mw[++mi][i]=m;
1677: if(m >=lastpass)
1678: break;
1679: else
1680: m++;
1681: }/* end while */
1682: if (s[m][i] > nlstate){
1683: mi++; /* Death is another wave */
1684: /* if(mi==0) never been interviewed correctly before death */
1685: /* Only death is a correct wave */
1686: mw[mi][i]=m;
1687: }
1688:
1689: wav[i]=mi;
1690: if(mi==0){
1691: if(first==0){
1692: printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
1693: first=1;
1694: }
1695: if(first==1){
1696: fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
1697: }
1698: } /* end mi==0 */
1699: }
1700:
1701: for(i=1; i<=imx; i++){
1702: for(mi=1; mi<wav[i];mi++){
1703: if (stepm <=0)
1704: dh[mi][i]=1;
1705: else{
1706: if (s[mw[mi+1][i]][i] > nlstate) {
1707: if (agedc[i] < 2*AGESUP) {
1708: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1709: if(j==0) j=1; /* Survives at least one month after exam */
1710: k=k+1;
1711: if (j >= jmax) jmax=j;
1712: if (j <= jmin) jmin=j;
1713: sum=sum+j;
1714: /*if (j<0) printf("j=%d num=%d \n",j,i); */
1715: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1716: }
1717: }
1718: else{
1719: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1720: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1721: k=k+1;
1722: if (j >= jmax) jmax=j;
1723: else if (j <= jmin)jmin=j;
1724: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1725: sum=sum+j;
1726: }
1727: jk= j/stepm;
1728: jl= j -jk*stepm;
1729: ju= j -(jk+1)*stepm;
1730: if(mle <=1){
1731: if(jl==0){
1732: dh[mi][i]=jk;
1733: bh[mi][i]=0;
1734: }else{ /* We want a negative bias in order to only have interpolation ie
1735: * at the price of an extra matrix product in likelihood */
1736: dh[mi][i]=jk+1;
1737: bh[mi][i]=ju;
1738: }
1739: }else{
1740: if(jl <= -ju){
1741: dh[mi][i]=jk;
1742: bh[mi][i]=jl; /* bias is positive if real duration
1743: * is higher than the multiple of stepm and negative otherwise.
1744: */
1745: }
1746: else{
1747: dh[mi][i]=jk+1;
1748: bh[mi][i]=ju;
1749: }
1750: if(dh[mi][i]==0){
1751: dh[mi][i]=1; /* At least one step */
1752: bh[mi][i]=ju; /* At least one step */
1753: 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);
1754: }
1755: }
1756: } /* end if mle */
1757: } /* end wave */
1758: }
1759: jmean=sum/k;
1760: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1761: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1762: }
1763:
1764: /*********** Tricode ****************************/
1765: void tricode(int *Tvar, int **nbcode, int imx)
1766: {
1767:
1768: int Ndum[20],ij=1, k, j, i, maxncov=19;
1769: int cptcode=0;
1770: cptcoveff=0;
1771:
1772: for (k=0; k<maxncov; k++) Ndum[k]=0;
1773: for (k=1; k<=7; k++) ncodemax[k]=0;
1774:
1775: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1776: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
1777: modality*/
1778: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
1779: Ndum[ij]++; /*store the modality */
1780: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1781: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
1782: Tvar[j]. If V=sex and male is 0 and
1783: female is 1, then cptcode=1.*/
1784: }
1785:
1786: for (i=0; i<=cptcode; i++) {
1787: 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 */
1788: }
1789:
1790: ij=1;
1791: for (i=1; i<=ncodemax[j]; i++) {
1792: for (k=0; k<= maxncov; k++) {
1793: if (Ndum[k] != 0) {
1794: nbcode[Tvar[j]][ij]=k;
1795: /* 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; */
1796:
1797: ij++;
1798: }
1799: if (ij > ncodemax[j]) break;
1800: }
1801: }
1802: }
1803:
1804: for (k=0; k< maxncov; k++) Ndum[k]=0;
1805:
1806: for (i=1; i<=ncovmodel-2; i++) {
1807: /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
1808: ij=Tvar[i];
1809: Ndum[ij]++;
1810: }
1811:
1812: ij=1;
1813: for (i=1; i<= maxncov; i++) {
1814: if((Ndum[i]!=0) && (i<=ncovcol)){
1815: Tvaraff[ij]=i; /*For printing */
1816: ij++;
1817: }
1818: }
1819:
1820: cptcoveff=ij-1; /*Number of simple covariates*/
1821: }
1822:
1823: /*********** Health Expectancies ****************/
1824:
1825: 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 )
1826:
1827: {
1828: /* Health expectancies */
1829: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
1830: double age, agelim, hf;
1831: double ***p3mat,***varhe;
1832: double **dnewm,**doldm;
1833: double *xp;
1834: double **gp, **gm;
1835: double ***gradg, ***trgradg;
1836: int theta;
1837:
1838: varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
1839: xp=vector(1,npar);
1840: dnewm=matrix(1,nlstate*2,1,npar);
1841: doldm=matrix(1,nlstate*2,1,nlstate*2);
1842:
1843: fprintf(ficreseij,"# Health expectancies\n");
1844: fprintf(ficreseij,"# Age");
1845: for(i=1; i<=nlstate;i++)
1846: for(j=1; j<=nlstate;j++)
1847: fprintf(ficreseij," %1d-%1d (SE)",i,j);
1848: fprintf(ficreseij,"\n");
1849:
1850: if(estepm < stepm){
1851: printf ("Problem %d lower than %d\n",estepm, stepm);
1852: }
1853: else hstepm=estepm;
1854: /* We compute the life expectancy from trapezoids spaced every estepm months
1855: * This is mainly to measure the difference between two models: for example
1856: * if stepm=24 months pijx are given only every 2 years and by summing them
1857: * we are calculating an estimate of the Life Expectancy assuming a linear
1858: * progression in between and thus overestimating or underestimating according
1859: * to the curvature of the survival function. If, for the same date, we
1860: * estimate the model with stepm=1 month, we can keep estepm to 24 months
1861: * to compare the new estimate of Life expectancy with the same linear
1862: * hypothesis. A more precise result, taking into account a more precise
1863: * curvature will be obtained if estepm is as small as stepm. */
1864:
1865: /* For example we decided to compute the life expectancy with the smallest unit */
1866: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
1867: nhstepm is the number of hstepm from age to agelim
1868: nstepm is the number of stepm from age to agelin.
1869: Look at hpijx to understand the reason of that which relies in memory size
1870: and note for a fixed period like estepm months */
1871: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
1872: survival function given by stepm (the optimization length). Unfortunately it
1873: means that if the survival funtion is printed only each two years of age and if
1874: you sum them up and add 1 year (area under the trapezoids) you won't get the same
1875: results. So we changed our mind and took the option of the best precision.
1876: */
1877: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
1878:
1879: agelim=AGESUP;
1880: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1881: /* nhstepm age range expressed in number of stepm */
1882: nstepm=(int) rint((agelim-age)*YEARM/stepm);
1883: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
1884: /* if (stepm >= YEARM) hstepm=1;*/
1885: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
1886: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1887: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
1888: gp=matrix(0,nhstepm,1,nlstate*2);
1889: gm=matrix(0,nhstepm,1,nlstate*2);
1890:
1891: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1892: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1893: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1894:
1895:
1896: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1897:
1898: /* Computing Variances of health expectancies */
1899:
1900: for(theta=1; theta <=npar; theta++){
1901: for(i=1; i<=npar; i++){
1902: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1903: }
1904: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1905:
1906: cptj=0;
1907: for(j=1; j<= nlstate; j++){
1908: for(i=1; i<=nlstate; i++){
1909: cptj=cptj+1;
1910: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
1911: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
1912: }
1913: }
1914: }
1915:
1916:
1917: for(i=1; i<=npar; i++)
1918: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1919: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1920:
1921: cptj=0;
1922: for(j=1; j<= nlstate; j++){
1923: for(i=1;i<=nlstate;i++){
1924: cptj=cptj+1;
1925: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1926: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
1927: }
1928: }
1929: }
1930: for(j=1; j<= nlstate*2; j++)
1931: for(h=0; h<=nhstepm-1; h++){
1932: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
1933: }
1934: }
1935:
1936: /* End theta */
1937:
1938: trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
1939:
1940: for(h=0; h<=nhstepm-1; h++)
1941: for(j=1; j<=nlstate*2;j++)
1942: for(theta=1; theta <=npar; theta++)
1943: trgradg[h][j][theta]=gradg[h][theta][j];
1944:
1945:
1946: for(i=1;i<=nlstate*2;i++)
1947: for(j=1;j<=nlstate*2;j++)
1948: varhe[i][j][(int)age] =0.;
1949:
1950: printf("%d|",(int)age);fflush(stdout);
1951: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
1952: for(h=0;h<=nhstepm-1;h++){
1953: for(k=0;k<=nhstepm-1;k++){
1954: matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
1955: matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
1956: for(i=1;i<=nlstate*2;i++)
1957: for(j=1;j<=nlstate*2;j++)
1958: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
1959: }
1960: }
1961: /* Computing expectancies */
1962: for(i=1; i<=nlstate;i++)
1963: for(j=1; j<=nlstate;j++)
1964: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
1965: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
1966:
1967: /* 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]);*/
1968:
1969: }
1970:
1971: fprintf(ficreseij,"%3.0f",age );
1972: cptj=0;
1973: for(i=1; i<=nlstate;i++)
1974: for(j=1; j<=nlstate;j++){
1975: cptj++;
1976: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
1977: }
1978: fprintf(ficreseij,"\n");
1979:
1980: free_matrix(gm,0,nhstepm,1,nlstate*2);
1981: free_matrix(gp,0,nhstepm,1,nlstate*2);
1982: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
1983: free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
1984: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1985: }
1986: printf("\n");
1987: fprintf(ficlog,"\n");
1988:
1989: free_vector(xp,1,npar);
1990: free_matrix(dnewm,1,nlstate*2,1,npar);
1991: free_matrix(doldm,1,nlstate*2,1,nlstate*2);
1992: free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
1993: }
1994:
1995: /************ Variance ******************/
1996: 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)
1997: {
1998: /* Variance of health expectancies */
1999: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2000: /* double **newm;*/
2001: double **dnewm,**doldm;
2002: double **dnewmp,**doldmp;
2003: int i, j, nhstepm, hstepm, h, nstepm ;
2004: int k, cptcode;
2005: double *xp;
2006: double **gp, **gm; /* for var eij */
2007: double ***gradg, ***trgradg; /*for var eij */
2008: double **gradgp, **trgradgp; /* for var p point j */
2009: double *gpp, *gmp; /* for var p point j */
2010: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2011: double ***p3mat;
2012: double age,agelim, hf;
2013: double ***mobaverage;
2014: int theta;
2015: char digit[4];
2016: char digitp[25];
2017:
2018: char fileresprobmorprev[FILENAMELENGTH];
2019:
2020: if(popbased==1){
2021: if(mobilav!=0)
2022: strcpy(digitp,"-populbased-mobilav-");
2023: else strcpy(digitp,"-populbased-nomobil-");
2024: }
2025: else
2026: strcpy(digitp,"-stablbased-");
2027:
2028: if (mobilav!=0) {
2029: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2030: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2031: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2032: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2033: }
2034: }
2035:
2036: strcpy(fileresprobmorprev,"prmorprev");
2037: sprintf(digit,"%-d",ij);
2038: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2039: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2040: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2041: strcat(fileresprobmorprev,fileres);
2042: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2043: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2044: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2045: }
2046: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2047: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2048: 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);
2049: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2050: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2051: fprintf(ficresprobmorprev," p.%-d SE",j);
2052: for(i=1; i<=nlstate;i++)
2053: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2054: }
2055: fprintf(ficresprobmorprev,"\n");
2056: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2057: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2058: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2059: exit(0);
2060: }
2061: else{
2062: fprintf(ficgp,"\n# Routine varevsij");
2063: }
2064: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2065: printf("Problem with html file: %s\n", optionfilehtm);
2066: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2067: exit(0);
2068: }
2069: else{
2070: 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");
2071: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2072: }
2073: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2074:
2075: 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");
2076: fprintf(ficresvij,"# Age");
2077: for(i=1; i<=nlstate;i++)
2078: for(j=1; j<=nlstate;j++)
2079: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2080: fprintf(ficresvij,"\n");
2081:
2082: xp=vector(1,npar);
2083: dnewm=matrix(1,nlstate,1,npar);
2084: doldm=matrix(1,nlstate,1,nlstate);
2085: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2086: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2087:
2088: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2089: gpp=vector(nlstate+1,nlstate+ndeath);
2090: gmp=vector(nlstate+1,nlstate+ndeath);
2091: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2092:
2093: if(estepm < stepm){
2094: printf ("Problem %d lower than %d\n",estepm, stepm);
2095: }
2096: else hstepm=estepm;
2097: /* For example we decided to compute the life expectancy with the smallest unit */
2098: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2099: nhstepm is the number of hstepm from age to agelim
2100: nstepm is the number of stepm from age to agelin.
2101: Look at hpijx to understand the reason of that which relies in memory size
2102: and note for a fixed period like k years */
2103: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2104: survival function given by stepm (the optimization length). Unfortunately it
2105: means that if the survival funtion is printed every two years of age and if
2106: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2107: results. So we changed our mind and took the option of the best precision.
2108: */
2109: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2110: agelim = AGESUP;
2111: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2112: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2113: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2114: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2115: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2116: gp=matrix(0,nhstepm,1,nlstate);
2117: gm=matrix(0,nhstepm,1,nlstate);
2118:
2119:
2120: for(theta=1; theta <=npar; theta++){
2121: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2122: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2123: }
2124: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2125: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2126:
2127: if (popbased==1) {
2128: if(mobilav ==0){
2129: for(i=1; i<=nlstate;i++)
2130: prlim[i][i]=probs[(int)age][i][ij];
2131: }else{ /* mobilav */
2132: for(i=1; i<=nlstate;i++)
2133: prlim[i][i]=mobaverage[(int)age][i][ij];
2134: }
2135: }
2136:
2137: for(j=1; j<= nlstate; j++){
2138: for(h=0; h<=nhstepm; h++){
2139: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2140: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2141: }
2142: }
2143: /* This for computing probability of death (h=1 means
2144: computed over hstepm matrices product = hstepm*stepm months)
2145: as a weighted average of prlim.
2146: */
2147: for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
2148: for(i=1,gpp[j]=0.; i<= nlstate; i++)
2149: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2150: }
2151: /* end probability of death */
2152:
2153: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
2154: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2155: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2156: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2157:
2158: if (popbased==1) {
2159: if(mobilav ==0){
2160: for(i=1; i<=nlstate;i++)
2161: prlim[i][i]=probs[(int)age][i][ij];
2162: }else{ /* mobilav */
2163: for(i=1; i<=nlstate;i++)
2164: prlim[i][i]=mobaverage[(int)age][i][ij];
2165: }
2166: }
2167:
2168: for(j=1; j<= nlstate; j++){
2169: for(h=0; h<=nhstepm; h++){
2170: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2171: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2172: }
2173: }
2174: /* This for computing probability of death (h=1 means
2175: computed over hstepm matrices product = hstepm*stepm months)
2176: as a weighted average of prlim.
2177: */
2178: for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
2179: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2180: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2181: }
2182: /* end probability of death */
2183:
2184: for(j=1; j<= nlstate; j++) /* vareij */
2185: for(h=0; h<=nhstepm; h++){
2186: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2187: }
2188:
2189: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2190: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2191: }
2192:
2193: } /* End theta */
2194:
2195: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2196:
2197: for(h=0; h<=nhstepm; h++) /* veij */
2198: for(j=1; j<=nlstate;j++)
2199: for(theta=1; theta <=npar; theta++)
2200: trgradg[h][j][theta]=gradg[h][theta][j];
2201:
2202: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
2203: for(theta=1; theta <=npar; theta++) {
2204: trgradgp[j][theta]=gradgp[theta][j];
2205: }
2206:
2207: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2208: for(i=1;i<=nlstate;i++)
2209: for(j=1;j<=nlstate;j++)
2210: vareij[i][j][(int)age] =0.;
2211:
2212: for(h=0;h<=nhstepm;h++){
2213: for(k=0;k<=nhstepm;k++){
2214: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2215: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2216: for(i=1;i<=nlstate;i++)
2217: for(j=1;j<=nlstate;j++)
2218: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2219: }
2220: }
2221:
2222: /* pptj */
2223: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2224: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
2225:
2226: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2227: for(i=nlstate+1;i<=nlstate+ndeath;i++){
2228: varppt[j][i]=doldmp[j][i];
2229: }
2230:
2231: /* end ppptj */
2232: /* x centered again */
2233: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2234: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2235:
2236: if (popbased==1) {
2237: if(mobilav ==0){
2238: for(i=1; i<=nlstate;i++)
2239: prlim[i][i]=probs[(int)age][i][ij];
2240: }else{ /* mobilav */
2241: for(i=1; i<=nlstate;i++)
2242: prlim[i][i]=mobaverage[(int)age][i][ij];
2243: }
2244: }
2245:
2246: /* This for computing probability of death (h=1 means
2247: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2248: as a weighted average of prlim.
2249: */
2250: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2251: for(i=1,gmp[j]=0.;i<= nlstate; i++)
2252: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2253: }
2254: /* end probability of death */
2255:
2256: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2257: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2258: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2259: for(i=1; i<=nlstate;i++){
2260: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2261: }
2262: }
2263: fprintf(ficresprobmorprev,"\n");
2264:
2265: fprintf(ficresvij,"%.0f ",age );
2266: for(i=1; i<=nlstate;i++)
2267: for(j=1; j<=nlstate;j++){
2268: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2269: }
2270: fprintf(ficresvij,"\n");
2271: free_matrix(gp,0,nhstepm,1,nlstate);
2272: free_matrix(gm,0,nhstepm,1,nlstate);
2273: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2274: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2275: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2276: } /* End age */
2277: free_vector(gpp,nlstate+1,nlstate+ndeath);
2278: free_vector(gmp,nlstate+1,nlstate+ndeath);
2279: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2280: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2281: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2282: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2283: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
2284: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2285: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2286: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
2287: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",fileresprobmorprev);
2288: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
2289: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
2290: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
2291: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", estepm,digitp,digit);
2292: /* 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);
2293: */
2294: fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
2295:
2296: free_vector(xp,1,npar);
2297: free_matrix(doldm,1,nlstate,1,nlstate);
2298: free_matrix(dnewm,1,nlstate,1,npar);
2299: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2300: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2301: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2302: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2303: fclose(ficresprobmorprev);
2304: fclose(ficgp);
2305: fclose(fichtm);
2306: }
2307:
2308: /************ Variance of prevlim ******************/
2309: 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)
2310: {
2311: /* Variance of prevalence limit */
2312: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
2313: double **newm;
2314: double **dnewm,**doldm;
2315: int i, j, nhstepm, hstepm;
2316: int k, cptcode;
2317: double *xp;
2318: double *gp, *gm;
2319: double **gradg, **trgradg;
2320: double age,agelim;
2321: int theta;
2322:
2323: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
2324: fprintf(ficresvpl,"# Age");
2325: for(i=1; i<=nlstate;i++)
2326: fprintf(ficresvpl," %1d-%1d",i,i);
2327: fprintf(ficresvpl,"\n");
2328:
2329: xp=vector(1,npar);
2330: dnewm=matrix(1,nlstate,1,npar);
2331: doldm=matrix(1,nlstate,1,nlstate);
2332:
2333: hstepm=1*YEARM; /* Every year of age */
2334: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2335: agelim = AGESUP;
2336: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2337: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2338: if (stepm >= YEARM) hstepm=1;
2339: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2340: gradg=matrix(1,npar,1,nlstate);
2341: gp=vector(1,nlstate);
2342: gm=vector(1,nlstate);
2343:
2344: for(theta=1; theta <=npar; theta++){
2345: for(i=1; i<=npar; i++){ /* Computes gradient */
2346: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2347: }
2348: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2349: for(i=1;i<=nlstate;i++)
2350: gp[i] = prlim[i][i];
2351:
2352: for(i=1; i<=npar; i++) /* Computes gradient */
2353: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2354: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2355: for(i=1;i<=nlstate;i++)
2356: gm[i] = prlim[i][i];
2357:
2358: for(i=1;i<=nlstate;i++)
2359: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2360: } /* End theta */
2361:
2362: trgradg =matrix(1,nlstate,1,npar);
2363:
2364: for(j=1; j<=nlstate;j++)
2365: for(theta=1; theta <=npar; theta++)
2366: trgradg[j][theta]=gradg[theta][j];
2367:
2368: for(i=1;i<=nlstate;i++)
2369: varpl[i][(int)age] =0.;
2370: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2371: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2372: for(i=1;i<=nlstate;i++)
2373: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2374:
2375: fprintf(ficresvpl,"%.0f ",age );
2376: for(i=1; i<=nlstate;i++)
2377: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2378: fprintf(ficresvpl,"\n");
2379: free_vector(gp,1,nlstate);
2380: free_vector(gm,1,nlstate);
2381: free_matrix(gradg,1,npar,1,nlstate);
2382: free_matrix(trgradg,1,nlstate,1,npar);
2383: } /* End age */
2384:
2385: free_vector(xp,1,npar);
2386: free_matrix(doldm,1,nlstate,1,npar);
2387: free_matrix(dnewm,1,nlstate,1,nlstate);
2388:
2389: }
2390:
2391: /************ Variance of one-step probabilities ******************/
2392: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2393: {
2394: int i, j=0, i1, k1, l1, t, tj;
2395: int k2, l2, j1, z1;
2396: int k=0,l, cptcode;
2397: int first=1, first1;
2398: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2399: double **dnewm,**doldm;
2400: double *xp;
2401: double *gp, *gm;
2402: double **gradg, **trgradg;
2403: double **mu;
2404: double age,agelim, cov[NCOVMAX];
2405: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2406: int theta;
2407: char fileresprob[FILENAMELENGTH];
2408: char fileresprobcov[FILENAMELENGTH];
2409: char fileresprobcor[FILENAMELENGTH];
2410:
2411: double ***varpij;
2412:
2413: strcpy(fileresprob,"prob");
2414: strcat(fileresprob,fileres);
2415: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2416: printf("Problem with resultfile: %s\n", fileresprob);
2417: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2418: }
2419: strcpy(fileresprobcov,"probcov");
2420: strcat(fileresprobcov,fileres);
2421: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2422: printf("Problem with resultfile: %s\n", fileresprobcov);
2423: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2424: }
2425: strcpy(fileresprobcor,"probcor");
2426: strcat(fileresprobcor,fileres);
2427: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2428: printf("Problem with resultfile: %s\n", fileresprobcor);
2429: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2430: }
2431: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2432: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2433: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2434: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2435: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2436: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2437:
2438: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2439: fprintf(ficresprob,"# Age");
2440: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2441: fprintf(ficresprobcov,"# Age");
2442: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2443: fprintf(ficresprobcov,"# Age");
2444:
2445:
2446: for(i=1; i<=nlstate;i++)
2447: for(j=1; j<=(nlstate+ndeath);j++){
2448: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2449: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2450: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2451: }
2452: fprintf(ficresprob,"\n");
2453: fprintf(ficresprobcov,"\n");
2454: fprintf(ficresprobcor,"\n");
2455: xp=vector(1,npar);
2456: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2457: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2458: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2459: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2460: first=1;
2461: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2462: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2463: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2464: exit(0);
2465: }
2466: else{
2467: fprintf(ficgp,"\n# Routine varprob");
2468: }
2469: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2470: printf("Problem with html file: %s\n", optionfilehtm);
2471: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2472: exit(0);
2473: }
2474: else{
2475: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2476: fprintf(fichtm,"\n");
2477:
2478: fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
2479: 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");
2480: 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");
2481:
2482: }
2483:
2484: cov[1]=1;
2485: tj=cptcoveff;
2486: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2487: j1=0;
2488: for(t=1; t<=tj;t++){
2489: for(i1=1; i1<=ncodemax[t];i1++){
2490: j1++;
2491: if (cptcovn>0) {
2492: fprintf(ficresprob, "\n#********** Variable ");
2493: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2494: fprintf(ficresprob, "**********\n#");
2495: fprintf(ficresprobcov, "\n#********** Variable ");
2496: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2497: fprintf(ficresprobcov, "**********\n#");
2498:
2499: fprintf(ficgp, "\n#********** Variable ");
2500: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2501: fprintf(ficgp, "**********\n#");
2502:
2503:
2504: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2505: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2506: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2507:
2508: fprintf(ficresprobcor, "\n#********** Variable ");
2509: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2510: fprintf(ficgp, "**********\n#");
2511: }
2512:
2513: for (age=bage; age<=fage; age ++){
2514: cov[2]=age;
2515: for (k=1; k<=cptcovn;k++) {
2516: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2517: }
2518: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2519: for (k=1; k<=cptcovprod;k++)
2520: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2521:
2522: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2523: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2524: gp=vector(1,(nlstate)*(nlstate+ndeath));
2525: gm=vector(1,(nlstate)*(nlstate+ndeath));
2526:
2527: for(theta=1; theta <=npar; theta++){
2528: for(i=1; i<=npar; i++)
2529: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2530:
2531: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2532:
2533: k=0;
2534: for(i=1; i<= (nlstate); i++){
2535: for(j=1; j<=(nlstate+ndeath);j++){
2536: k=k+1;
2537: gp[k]=pmmij[i][j];
2538: }
2539: }
2540:
2541: for(i=1; i<=npar; i++)
2542: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2543:
2544: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2545: k=0;
2546: for(i=1; i<=(nlstate); i++){
2547: for(j=1; j<=(nlstate+ndeath);j++){
2548: k=k+1;
2549: gm[k]=pmmij[i][j];
2550: }
2551: }
2552:
2553: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
2554: gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
2555: }
2556:
2557: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2558: for(theta=1; theta <=npar; theta++)
2559: trgradg[j][theta]=gradg[theta][j];
2560:
2561: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2562: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
2563: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2564: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2565: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2566: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2567:
2568: pmij(pmmij,cov,ncovmodel,x,nlstate);
2569:
2570: k=0;
2571: for(i=1; i<=(nlstate); i++){
2572: for(j=1; j<=(nlstate+ndeath);j++){
2573: k=k+1;
2574: mu[k][(int) age]=pmmij[i][j];
2575: }
2576: }
2577: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2578: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2579: varpij[i][j][(int)age] = doldm[i][j];
2580:
2581: /*printf("\n%d ",(int)age);
2582: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2583: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2584: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2585: }*/
2586:
2587: fprintf(ficresprob,"\n%d ",(int)age);
2588: fprintf(ficresprobcov,"\n%d ",(int)age);
2589: fprintf(ficresprobcor,"\n%d ",(int)age);
2590:
2591: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2592: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2593: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2594: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2595: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2596: }
2597: i=0;
2598: for (k=1; k<=(nlstate);k++){
2599: for (l=1; l<=(nlstate+ndeath);l++){
2600: i=i++;
2601: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2602: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2603: for (j=1; j<=i;j++){
2604: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2605: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
2606: }
2607: }
2608: }/* end of loop for state */
2609: } /* end of loop for age */
2610:
2611: /* Confidence intervalle of pij */
2612: /*
2613: fprintf(ficgp,"\nset noparametric;unset label");
2614: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
2615: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2616: 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);
2617: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
2618: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
2619: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
2620: */
2621:
2622: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
2623: first1=1;
2624: for (k2=1; k2<=(nlstate);k2++){
2625: for (l2=1; l2<=(nlstate+ndeath);l2++){
2626: if(l2==k2) continue;
2627: j=(k2-1)*(nlstate+ndeath)+l2;
2628: for (k1=1; k1<=(nlstate);k1++){
2629: for (l1=1; l1<=(nlstate+ndeath);l1++){
2630: if(l1==k1) continue;
2631: i=(k1-1)*(nlstate+ndeath)+l1;
2632: if(i<=j) continue;
2633: for (age=bage; age<=fage; age ++){
2634: if ((int)age %5==0){
2635: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
2636: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
2637: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
2638: mu1=mu[i][(int) age]/stepm*YEARM ;
2639: mu2=mu[j][(int) age]/stepm*YEARM;
2640: c12=cv12/sqrt(v1*v2);
2641: /* Computing eigen value of matrix of covariance */
2642: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2643: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2644: /* Eigen vectors */
2645: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
2646: /*v21=sqrt(1.-v11*v11); *//* error */
2647: v21=(lc1-v1)/cv12*v11;
2648: v12=-v21;
2649: v22=v11;
2650: tnalp=v21/v11;
2651: if(first1==1){
2652: first1=0;
2653: 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);
2654: }
2655: 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);
2656: /*printf(fignu*/
2657: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
2658: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
2659: if(first==1){
2660: first=0;
2661: fprintf(ficgp,"\nset parametric;unset label");
2662: 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);
2663: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2664: 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);
2665: fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
2666: fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
2667: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
2668: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2669: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2670: 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",\
2671: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2672: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2673: }else{
2674: first=0;
2675: fprintf(fichtm," %d (%.3f),",(int) age, c12);
2676: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2677: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2678: 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",\
2679: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2680: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2681: }/* if first */
2682: } /* age mod 5 */
2683: } /* end loop age */
2684: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
2685: first=1;
2686: } /*l12 */
2687: } /* k12 */
2688: } /*l1 */
2689: }/* k1 */
2690: } /* loop covariates */
2691: }
2692: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
2693: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
2694: free_vector(xp,1,npar);
2695: fclose(ficresprob);
2696: fclose(ficresprobcov);
2697: fclose(ficresprobcor);
2698: fclose(ficgp);
2699: fclose(fichtm);
2700: }
2701:
2702:
2703: /******************* Printing html file ***********/
2704: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
2705: int lastpass, int stepm, int weightopt, char model[],\
2706: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
2707: int popforecast, int estepm ,\
2708: double jprev1, double mprev1,double anprev1, \
2709: double jprev2, double mprev2,double anprev2){
2710: int jj1, k1, i1, cpt;
2711: /*char optionfilehtm[FILENAMELENGTH];*/
2712: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2713: printf("Problem with %s \n",optionfilehtm), exit(0);
2714: fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
2715: }
2716:
2717: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
2718: - 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
2719: - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
2720: - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
2721: - Life expectancies by age and initial health status (estepm=%2d months):
2722: <a href=\"e%s\">e%s</a> <br>\n</li>", \
2723: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
2724:
2725: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
2726:
2727: m=cptcoveff;
2728: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2729:
2730: jj1=0;
2731: for(k1=1; k1<=m;k1++){
2732: for(i1=1; i1<=ncodemax[k1];i1++){
2733: jj1++;
2734: if (cptcovn > 0) {
2735: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2736: for (cpt=1; cpt<=cptcoveff;cpt++)
2737: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2738: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2739: }
2740: /* Pij */
2741: 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>
2742: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2743: /* Quasi-incidences */
2744: 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>
2745: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2746: /* Stable prevalence in each health state */
2747: for(cpt=1; cpt<nlstate;cpt++){
2748: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
2749: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2750: }
2751: for(cpt=1; cpt<=nlstate;cpt++) {
2752: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
2753: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2754: }
2755: fprintf(fichtm,"\n<br>- Total life expectancy by age and
2756: health expectancies in states (1) and (2): e%s%d.png<br>
2757: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2758: } /* end i1 */
2759: }/* End k1 */
2760: fprintf(fichtm,"</ul>");
2761:
2762:
2763: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
2764: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
2765: - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
2766: - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
2767: - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
2768: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
2769: - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
2770: - 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);
2771:
2772: if(popforecast==1) fprintf(fichtm,"\n
2773: - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
2774: - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
2775: <br>",fileres,fileres,fileres,fileres);
2776: else
2777: 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);
2778: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
2779:
2780: m=cptcoveff;
2781: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2782:
2783: jj1=0;
2784: for(k1=1; k1<=m;k1++){
2785: for(i1=1; i1<=ncodemax[k1];i1++){
2786: jj1++;
2787: if (cptcovn > 0) {
2788: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2789: for (cpt=1; cpt<=cptcoveff;cpt++)
2790: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2791: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2792: }
2793: for(cpt=1; cpt<=nlstate;cpt++) {
2794: fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
2795: interval) in state (%d): v%s%d%d.png <br>
2796: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2797: }
2798: } /* end i1 */
2799: }/* End k1 */
2800: fprintf(fichtm,"</ul>");
2801: fclose(fichtm);
2802: }
2803:
2804: /******************* Gnuplot file **************/
2805: void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
2806:
2807: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
2808: int ng;
2809: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2810: printf("Problem with file %s",optionfilegnuplot);
2811: fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
2812: }
2813:
2814: /*#ifdef windows */
2815: fprintf(ficgp,"cd \"%s\" \n",pathc);
2816: /*#endif */
2817: m=pow(2,cptcoveff);
2818:
2819: /* 1eme*/
2820: for (cpt=1; cpt<= nlstate ; cpt ++) {
2821: for (k1=1; k1<= m ; k1 ++) {
2822: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2823: 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);
2824:
2825: for (i=1; i<= nlstate ; i ++) {
2826: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2827: else fprintf(ficgp," \%%*lf (\%%*lf)");
2828: }
2829: fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
2830: for (i=1; i<= nlstate ; i ++) {
2831: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2832: else fprintf(ficgp," \%%*lf (\%%*lf)");
2833: }
2834: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
2835: for (i=1; i<= nlstate ; i ++) {
2836: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2837: else fprintf(ficgp," \%%*lf (\%%*lf)");
2838: }
2839: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2840: }
2841: }
2842: /*2 eme*/
2843:
2844: for (k1=1; k1<= m ; k1 ++) {
2845: fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
2846: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
2847:
2848: for (i=1; i<= nlstate+1 ; i ++) {
2849: k=2*i;
2850: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2851: for (j=1; j<= nlstate+1 ; j ++) {
2852: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2853: else fprintf(ficgp," \%%*lf (\%%*lf)");
2854: }
2855: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2856: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2857: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2858: for (j=1; j<= nlstate+1 ; j ++) {
2859: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2860: else fprintf(ficgp," \%%*lf (\%%*lf)");
2861: }
2862: fprintf(ficgp,"\" t\"\" w l 0,");
2863: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
2864: for (j=1; j<= nlstate+1 ; j ++) {
2865: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2866: else fprintf(ficgp," \%%*lf (\%%*lf)");
2867: }
2868: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2869: else fprintf(ficgp,"\" t\"\" w l 0,");
2870: }
2871: }
2872:
2873: /*3eme*/
2874:
2875: for (k1=1; k1<= m ; k1 ++) {
2876: for (cpt=1; cpt<= nlstate ; cpt ++) {
2877: k=2+nlstate*(2*cpt-2);
2878: fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2879: fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
2880: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2881: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2882: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2883: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2884: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2885: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2886:
2887: */
2888: for (i=1; i< nlstate ; i ++) {
2889: 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);
2890:
2891: }
2892: }
2893: }
2894:
2895: /* CV preval stat */
2896: for (k1=1; k1<= m ; k1 ++) {
2897: for (cpt=1; cpt<nlstate ; cpt ++) {
2898: k=3;
2899: fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2900: 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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
2901:
2902: for (i=1; i< nlstate ; i ++)
2903: fprintf(ficgp,"+$%d",k+i+1);
2904: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
2905:
2906: l=3+(nlstate+ndeath)*cpt;
2907: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
2908: for (i=1; i< nlstate ; i ++) {
2909: l=3+(nlstate+ndeath)*cpt;
2910: fprintf(ficgp,"+$%d",l+i+1);
2911: }
2912: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
2913: }
2914: }
2915:
2916: /* proba elementaires */
2917: for(i=1,jk=1; i <=nlstate; i++){
2918: for(k=1; k <=(nlstate+ndeath); k++){
2919: if (k != i) {
2920: for(j=1; j <=ncovmodel; j++){
2921: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
2922: jk++;
2923: fprintf(ficgp,"\n");
2924: }
2925: }
2926: }
2927: }
2928:
2929: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
2930: for(jk=1; jk <=m; jk++) {
2931: fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
2932: if (ng==2)
2933: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
2934: else
2935: fprintf(ficgp,"\nset title \"Probability\"\n");
2936: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
2937: i=1;
2938: for(k2=1; k2<=nlstate; k2++) {
2939: k3=i;
2940: for(k=1; k<=(nlstate+ndeath); k++) {
2941: if (k != k2){
2942: if(ng==2)
2943: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
2944: else
2945: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
2946: ij=1;
2947: for(j=3; j <=ncovmodel; j++) {
2948: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2949: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2950: ij++;
2951: }
2952: else
2953: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2954: }
2955: fprintf(ficgp,")/(1");
2956:
2957: for(k1=1; k1 <=nlstate; k1++){
2958: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
2959: ij=1;
2960: for(j=3; j <=ncovmodel; j++){
2961: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2962: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2963: ij++;
2964: }
2965: else
2966: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2967: }
2968: fprintf(ficgp,")");
2969: }
2970: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
2971: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
2972: i=i+ncovmodel;
2973: }
2974: } /* end k */
2975: } /* end k2 */
2976: } /* end jk */
2977: } /* end ng */
2978: fclose(ficgp);
2979: } /* end gnuplot */
2980:
2981:
2982: /*************** Moving average **************/
2983: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
2984:
2985: int i, cpt, cptcod;
2986: int modcovmax =1;
2987: int mobilavrange, mob;
2988: double age;
2989:
2990: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
2991: a covariate has 2 modalities */
2992: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
2993:
2994: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
2995: if(mobilav==1) mobilavrange=5; /* default */
2996: else mobilavrange=mobilav;
2997: for (age=bage; age<=fage; age++)
2998: for (i=1; i<=nlstate;i++)
2999: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3000: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3001: /* We keep the original values on the extreme ages bage, fage and for
3002: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3003: we use a 5 terms etc. until the borders are no more concerned.
3004: */
3005: for (mob=3;mob <=mobilavrange;mob=mob+2){
3006: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3007: for (i=1; i<=nlstate;i++){
3008: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3009: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3010: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3011: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3012: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3013: }
3014: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3015: }
3016: }
3017: }/* end age */
3018: }/* end mob */
3019: }else return -1;
3020: return 0;
3021: }/* End movingaverage */
3022:
3023:
3024: /************** Forecasting ******************/
3025: prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
3026:
3027: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3028: int *popage;
3029: double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3030: double *popeffectif,*popcount;
3031: double ***p3mat;
3032: double ***mobaverage;
3033: char fileresf[FILENAMELENGTH];
3034:
3035: agelim=AGESUP;
3036: calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
3037:
3038: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
3039:
3040:
3041: strcpy(fileresf,"f");
3042: strcat(fileresf,fileres);
3043: if((ficresf=fopen(fileresf,"w"))==NULL) {
3044: printf("Problem with forecast resultfile: %s\n", fileresf);
3045: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3046: }
3047: printf("Computing forecasting: result on file '%s' \n", fileresf);
3048: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3049:
3050: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3051:
3052: if (mobilav!=0) {
3053: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3054: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3055: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3056: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3057: }
3058: }
3059:
3060: stepsize=(int) (stepm+YEARM-1)/YEARM;
3061: if (stepm<=12) stepsize=1;
3062:
3063: agelim=AGESUP;
3064:
3065: hstepm=1;
3066: hstepm=hstepm/stepm;
3067: yp1=modf(dateintmean,&yp);
3068: anprojmean=yp;
3069: yp2=modf((yp1*12),&yp);
3070: mprojmean=yp;
3071: yp1=modf((yp2*30.5),&yp);
3072: jprojmean=yp;
3073: if(jprojmean==0) jprojmean=1;
3074: if(mprojmean==0) jprojmean=1;
3075:
3076: fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);
3077:
3078: for(cptcov=1;cptcov<=i2;cptcov++){
3079: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3080: k=k+1;
3081: fprintf(ficresf,"\n#******");
3082: for(j=1;j<=cptcoveff;j++) {
3083: fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3084: }
3085: fprintf(ficresf,"******\n");
3086: fprintf(ficresf,"# StartingAge FinalAge");
3087: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
3088:
3089:
3090: for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {
3091: fprintf(ficresf,"\n");
3092: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);
3093:
3094: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
3095: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3096: nhstepm = nhstepm/hstepm;
3097:
3098: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3099: oldm=oldms;savm=savms;
3100: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3101:
3102: for (h=0; h<=nhstepm; h++){
3103: if (h==(int) (calagedate+YEARM*cpt)) {
3104: fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
3105: }
3106: for(j=1; j<=nlstate+ndeath;j++) {
3107: kk1=0.;kk2=0;
3108: for(i=1; i<=nlstate;i++) {
3109: if (mobilav==1)
3110: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3111: else {
3112: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3113: }
3114:
3115: }
3116: if (h==(int)(calagedate+12*cpt)){
3117: fprintf(ficresf," %.3f", kk1);
3118:
3119: }
3120: }
3121: }
3122: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3123: }
3124: }
3125: }
3126: }
3127:
3128: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3129:
3130: fclose(ficresf);
3131: }
3132: /************** Forecasting ******************/
3133: 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){
3134:
3135: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3136: int *popage;
3137: double calagedate, agelim, kk1, kk2;
3138: double *popeffectif,*popcount;
3139: double ***p3mat,***tabpop,***tabpopprev;
3140: double ***mobaverage;
3141: char filerespop[FILENAMELENGTH];
3142:
3143: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3144: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3145: agelim=AGESUP;
3146: calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
3147:
3148: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
3149:
3150:
3151: strcpy(filerespop,"pop");
3152: strcat(filerespop,fileres);
3153: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3154: printf("Problem with forecast resultfile: %s\n", filerespop);
3155: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3156: }
3157: printf("Computing forecasting: result on file '%s' \n", filerespop);
3158: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3159:
3160: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3161:
3162: if (mobilav!=0) {
3163: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3164: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3165: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3166: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3167: }
3168: }
3169:
3170: stepsize=(int) (stepm+YEARM-1)/YEARM;
3171: if (stepm<=12) stepsize=1;
3172:
3173: agelim=AGESUP;
3174:
3175: hstepm=1;
3176: hstepm=hstepm/stepm;
3177:
3178: if (popforecast==1) {
3179: if((ficpop=fopen(popfile,"r"))==NULL) {
3180: printf("Problem with population file : %s\n",popfile);exit(0);
3181: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3182: }
3183: popage=ivector(0,AGESUP);
3184: popeffectif=vector(0,AGESUP);
3185: popcount=vector(0,AGESUP);
3186:
3187: i=1;
3188: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3189:
3190: imx=i;
3191: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3192: }
3193:
3194: for(cptcov=1;cptcov<=i2;cptcov++){
3195: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3196: k=k+1;
3197: fprintf(ficrespop,"\n#******");
3198: for(j=1;j<=cptcoveff;j++) {
3199: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3200: }
3201: fprintf(ficrespop,"******\n");
3202: fprintf(ficrespop,"# Age");
3203: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3204: if (popforecast==1) fprintf(ficrespop," [Population]");
3205:
3206: for (cpt=0; cpt<=0;cpt++) {
3207: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3208:
3209: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
3210: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3211: nhstepm = nhstepm/hstepm;
3212:
3213: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3214: oldm=oldms;savm=savms;
3215: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3216:
3217: for (h=0; h<=nhstepm; h++){
3218: if (h==(int) (calagedate+YEARM*cpt)) {
3219: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3220: }
3221: for(j=1; j<=nlstate+ndeath;j++) {
3222: kk1=0.;kk2=0;
3223: for(i=1; i<=nlstate;i++) {
3224: if (mobilav==1)
3225: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3226: else {
3227: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3228: }
3229: }
3230: if (h==(int)(calagedate+12*cpt)){
3231: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3232: /*fprintf(ficrespop," %.3f", kk1);
3233: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3234: }
3235: }
3236: for(i=1; i<=nlstate;i++){
3237: kk1=0.;
3238: for(j=1; j<=nlstate;j++){
3239: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3240: }
3241: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
3242: }
3243:
3244: if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)
3245: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3246: }
3247: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3248: }
3249: }
3250:
3251: /******/
3252:
3253: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3254: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3255: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
3256: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3257: nhstepm = nhstepm/hstepm;
3258:
3259: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3260: oldm=oldms;savm=savms;
3261: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3262: for (h=0; h<=nhstepm; h++){
3263: if (h==(int) (calagedate+YEARM*cpt)) {
3264: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3265: }
3266: for(j=1; j<=nlstate+ndeath;j++) {
3267: kk1=0.;kk2=0;
3268: for(i=1; i<=nlstate;i++) {
3269: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3270: }
3271: if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);
3272: }
3273: }
3274: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3275: }
3276: }
3277: }
3278: }
3279:
3280: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3281:
3282: if (popforecast==1) {
3283: free_ivector(popage,0,AGESUP);
3284: free_vector(popeffectif,0,AGESUP);
3285: free_vector(popcount,0,AGESUP);
3286: }
3287: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3288: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3289: fclose(ficrespop);
3290: }
3291:
3292: /***********************************************/
3293: /**************** Main Program *****************/
3294: /***********************************************/
3295:
3296: int main(int argc, char *argv[])
3297: {
3298: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
3299: int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
3300: double agedeb, agefin,hf;
3301: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3302:
3303: double fret;
3304: double **xi,tmp,delta;
3305:
3306: double dum; /* Dummy variable */
3307: double ***p3mat;
3308: double ***mobaverage;
3309: int *indx;
3310: char line[MAXLINE], linepar[MAXLINE];
3311: char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
3312: int firstobs=1, lastobs=10;
3313: int sdeb, sfin; /* Status at beginning and end */
3314: int c, h , cpt,l;
3315: int ju,jl, mi;
3316: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
3317: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
3318: int mobilav=0,popforecast=0;
3319: int hstepm, nhstepm;
3320: double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
3321:
3322: double bage, fage, age, agelim, agebase;
3323: double ftolpl=FTOL;
3324: double **prlim;
3325: double *severity;
3326: double ***param; /* Matrix of parameters */
3327: double *p;
3328: double **matcov; /* Matrix of covariance */
3329: double ***delti3; /* Scale */
3330: double *delti; /* Scale */
3331: double ***eij, ***vareij;
3332: double **varpl; /* Variances of prevalence limits by age */
3333: double *epj, vepp;
3334: double kk1, kk2;
3335: double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
3336:
3337: char *alph[]={"a","a","b","c","d","e"}, str[4];
3338:
3339:
3340: char z[1]="c", occ;
3341: #include <sys/time.h>
3342: #include <time.h>
3343: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
3344:
3345: /* long total_usecs;
3346: struct timeval start_time, end_time;
3347:
3348: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
3349: getcwd(pathcd, size);
3350:
3351: printf("\n%s",version);
3352: if(argc <=1){
3353: printf("\nEnter the parameter file name: ");
3354: scanf("%s",pathtot);
3355: }
3356: else{
3357: strcpy(pathtot,argv[1]);
3358: }
3359: /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
3360: /*cygwin_split_path(pathtot,path,optionfile);
3361: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3362: /* cutv(path,optionfile,pathtot,'\\');*/
3363:
3364: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
3365: printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3366: chdir(path);
3367: replace(pathc,path);
3368:
3369: /*-------- arguments in the command line --------*/
3370:
3371: /* Log file */
3372: strcat(filelog, optionfilefiname);
3373: strcat(filelog,".log"); /* */
3374: if((ficlog=fopen(filelog,"w"))==NULL) {
3375: printf("Problem with logfile %s\n",filelog);
3376: goto end;
3377: }
3378: fprintf(ficlog,"Log filename:%s\n",filelog);
3379: fprintf(ficlog,"\n%s",version);
3380: fprintf(ficlog,"\nEnter the parameter file name: ");
3381: fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3382: fflush(ficlog);
3383:
3384: /* */
3385: strcpy(fileres,"r");
3386: strcat(fileres, optionfilefiname);
3387: strcat(fileres,".txt"); /* Other files have txt extension */
3388:
3389: /*---------arguments file --------*/
3390:
3391: if((ficpar=fopen(optionfile,"r"))==NULL) {
3392: printf("Problem with optionfile %s\n",optionfile);
3393: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
3394: goto end;
3395: }
3396:
3397: strcpy(filereso,"o");
3398: strcat(filereso,fileres);
3399: if((ficparo=fopen(filereso,"w"))==NULL) {
3400: printf("Problem with Output resultfile: %s\n", filereso);
3401: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
3402: goto end;
3403: }
3404:
3405: /* Reads comments: lines beginning with '#' */
3406: while((c=getc(ficpar))=='#' && c!= EOF){
3407: ungetc(c,ficpar);
3408: fgets(line, MAXLINE, ficpar);
3409: puts(line);
3410: fputs(line,ficparo);
3411: }
3412: ungetc(c,ficpar);
3413:
3414: 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);
3415: 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);
3416: 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);
3417: while((c=getc(ficpar))=='#' && c!= EOF){
3418: ungetc(c,ficpar);
3419: fgets(line, MAXLINE, ficpar);
3420: puts(line);
3421: fputs(line,ficparo);
3422: }
3423: ungetc(c,ficpar);
3424:
3425:
3426: covar=matrix(0,NCOVMAX,1,n);
3427: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
3428: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
3429:
3430: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
3431: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
3432:
3433: /* Read guess parameters */
3434: /* Reads comments: lines beginning with '#' */
3435: while((c=getc(ficpar))=='#' && c!= EOF){
3436: ungetc(c,ficpar);
3437: fgets(line, MAXLINE, ficpar);
3438: puts(line);
3439: fputs(line,ficparo);
3440: }
3441: ungetc(c,ficpar);
3442:
3443: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
3444: for(i=1; i <=nlstate; i++)
3445: for(j=1; j <=nlstate+ndeath-1; j++){
3446: fscanf(ficpar,"%1d%1d",&i1,&j1);
3447: fprintf(ficparo,"%1d%1d",i1,j1);
3448: if(mle==1)
3449: printf("%1d%1d",i,j);
3450: fprintf(ficlog,"%1d%1d",i,j);
3451: for(k=1; k<=ncovmodel;k++){
3452: fscanf(ficpar," %lf",¶m[i][j][k]);
3453: if(mle==1){
3454: printf(" %lf",param[i][j][k]);
3455: fprintf(ficlog," %lf",param[i][j][k]);
3456: }
3457: else
3458: fprintf(ficlog," %lf",param[i][j][k]);
3459: fprintf(ficparo," %lf",param[i][j][k]);
3460: }
3461: fscanf(ficpar,"\n");
3462: if(mle==1)
3463: printf("\n");
3464: fprintf(ficlog,"\n");
3465: fprintf(ficparo,"\n");
3466: }
3467:
3468: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
3469:
3470: p=param[1][1];
3471:
3472: /* Reads comments: lines beginning with '#' */
3473: while((c=getc(ficpar))=='#' && c!= EOF){
3474: ungetc(c,ficpar);
3475: fgets(line, MAXLINE, ficpar);
3476: puts(line);
3477: fputs(line,ficparo);
3478: }
3479: ungetc(c,ficpar);
3480:
3481: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
3482: delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
3483: for(i=1; i <=nlstate; i++){
3484: for(j=1; j <=nlstate+ndeath-1; j++){
3485: fscanf(ficpar,"%1d%1d",&i1,&j1);
3486: printf("%1d%1d",i,j);
3487: fprintf(ficparo,"%1d%1d",i1,j1);
3488: for(k=1; k<=ncovmodel;k++){
3489: fscanf(ficpar,"%le",&delti3[i][j][k]);
3490: printf(" %le",delti3[i][j][k]);
3491: fprintf(ficparo," %le",delti3[i][j][k]);
3492: }
3493: fscanf(ficpar,"\n");
3494: printf("\n");
3495: fprintf(ficparo,"\n");
3496: }
3497: }
3498: delti=delti3[1][1];
3499:
3500: /* Reads comments: lines beginning with '#' */
3501: while((c=getc(ficpar))=='#' && c!= EOF){
3502: ungetc(c,ficpar);
3503: fgets(line, MAXLINE, ficpar);
3504: puts(line);
3505: fputs(line,ficparo);
3506: }
3507: ungetc(c,ficpar);
3508:
3509: matcov=matrix(1,npar,1,npar);
3510: for(i=1; i <=npar; i++){
3511: fscanf(ficpar,"%s",&str);
3512: if(mle==1)
3513: printf("%s",str);
3514: fprintf(ficlog,"%s",str);
3515: fprintf(ficparo,"%s",str);
3516: for(j=1; j <=i; j++){
3517: fscanf(ficpar," %le",&matcov[i][j]);
3518: if(mle==1){
3519: printf(" %.5le",matcov[i][j]);
3520: fprintf(ficlog," %.5le",matcov[i][j]);
3521: }
3522: else
3523: fprintf(ficlog," %.5le",matcov[i][j]);
3524: fprintf(ficparo," %.5le",matcov[i][j]);
3525: }
3526: fscanf(ficpar,"\n");
3527: if(mle==1)
3528: printf("\n");
3529: fprintf(ficlog,"\n");
3530: fprintf(ficparo,"\n");
3531: }
3532: for(i=1; i <=npar; i++)
3533: for(j=i+1;j<=npar;j++)
3534: matcov[i][j]=matcov[j][i];
3535:
3536: if(mle==1)
3537: printf("\n");
3538: fprintf(ficlog,"\n");
3539:
3540:
3541: /*-------- Rewriting paramater file ----------*/
3542: strcpy(rfileres,"r"); /* "Rparameterfile */
3543: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
3544: strcat(rfileres,"."); /* */
3545: strcat(rfileres,optionfilext); /* Other files have txt extension */
3546: if((ficres =fopen(rfileres,"w"))==NULL) {
3547: printf("Problem writing new parameter file: %s\n", fileres);goto end;
3548: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
3549: }
3550: fprintf(ficres,"#%s\n",version);
3551:
3552: /*-------- data file ----------*/
3553: if((fic=fopen(datafile,"r"))==NULL) {
3554: printf("Problem with datafile: %s\n", datafile);goto end;
3555: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
3556: }
3557:
3558: n= lastobs;
3559: severity = vector(1,maxwav);
3560: outcome=imatrix(1,maxwav+1,1,n);
3561: num=ivector(1,n);
3562: moisnais=vector(1,n);
3563: annais=vector(1,n);
3564: moisdc=vector(1,n);
3565: andc=vector(1,n);
3566: agedc=vector(1,n);
3567: cod=ivector(1,n);
3568: weight=vector(1,n);
3569: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
3570: mint=matrix(1,maxwav,1,n);
3571: anint=matrix(1,maxwav,1,n);
3572: s=imatrix(1,maxwav+1,1,n);
3573: tab=ivector(1,NCOVMAX);
3574: ncodemax=ivector(1,8);
3575:
3576: i=1;
3577: while (fgets(line, MAXLINE, fic) != NULL) {
3578: if ((i >= firstobs) && (i <=lastobs)) {
3579:
3580: for (j=maxwav;j>=1;j--){
3581: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
3582: strcpy(line,stra);
3583: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3584: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3585: }
3586:
3587: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
3588: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
3589:
3590: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
3591: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
3592:
3593: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
3594: for (j=ncovcol;j>=1;j--){
3595: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3596: }
3597: num[i]=atol(stra);
3598:
3599: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
3600: 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;}*/
3601:
3602: i=i+1;
3603: }
3604: }
3605: /* printf("ii=%d", ij);
3606: scanf("%d",i);*/
3607: imx=i-1; /* Number of individuals */
3608:
3609: /* for (i=1; i<=imx; i++){
3610: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
3611: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
3612: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
3613: }*/
3614: /* for (i=1; i<=imx; i++){
3615: if (s[4][i]==9) s[4][i]=-1;
3616: 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]));}*/
3617:
3618:
3619: /* Calculation of the number of parameter from char model*/
3620: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
3621: Tprod=ivector(1,15);
3622: Tvaraff=ivector(1,15);
3623: Tvard=imatrix(1,15,1,2);
3624: Tage=ivector(1,15);
3625:
3626: if (strlen(model) >1){ /* If there is at least 1 covariate */
3627: j=0, j1=0, k1=1, k2=1;
3628: j=nbocc(model,'+'); /* j=Number of '+' */
3629: j1=nbocc(model,'*'); /* j1=Number of '*' */
3630: cptcovn=j+1;
3631: cptcovprod=j1; /*Number of products */
3632:
3633: strcpy(modelsav,model);
3634: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
3635: printf("Error. Non available option model=%s ",model);
3636: fprintf(ficlog,"Error. Non available option model=%s ",model);
3637: goto end;
3638: }
3639:
3640: /* This loop fills the array Tvar from the string 'model'.*/
3641:
3642: for(i=(j+1); i>=1;i--){
3643: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
3644: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
3645: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
3646: /*scanf("%d",i);*/
3647: if (strchr(strb,'*')) { /* Model includes a product */
3648: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
3649: if (strcmp(strc,"age")==0) { /* Vn*age */
3650: cptcovprod--;
3651: cutv(strb,stre,strd,'V');
3652: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
3653: cptcovage++;
3654: Tage[cptcovage]=i;
3655: /*printf("stre=%s ", stre);*/
3656: }
3657: else if (strcmp(strd,"age")==0) { /* or age*Vn */
3658: cptcovprod--;
3659: cutv(strb,stre,strc,'V');
3660: Tvar[i]=atoi(stre);
3661: cptcovage++;
3662: Tage[cptcovage]=i;
3663: }
3664: else { /* Age is not in the model */
3665: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
3666: Tvar[i]=ncovcol+k1;
3667: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
3668: Tprod[k1]=i;
3669: Tvard[k1][1]=atoi(strc); /* m*/
3670: Tvard[k1][2]=atoi(stre); /* n */
3671: Tvar[cptcovn+k2]=Tvard[k1][1];
3672: Tvar[cptcovn+k2+1]=Tvard[k1][2];
3673: for (k=1; k<=lastobs;k++)
3674: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
3675: k1++;
3676: k2=k2+2;
3677: }
3678: }
3679: else { /* no more sum */
3680: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
3681: /* scanf("%d",i);*/
3682: cutv(strd,strc,strb,'V');
3683: Tvar[i]=atoi(strc);
3684: }
3685: strcpy(modelsav,stra);
3686: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
3687: scanf("%d",i);*/
3688: } /* end of loop + */
3689: } /* end model */
3690:
3691: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
3692: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
3693:
3694: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
3695: printf("cptcovprod=%d ", cptcovprod);
3696: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
3697:
3698: scanf("%d ",i);
3699: fclose(fic);*/
3700:
3701: /* if(mle==1){*/
3702: if (weightopt != 1) { /* Maximisation without weights*/
3703: for(i=1;i<=n;i++) weight[i]=1.0;
3704: }
3705: /*-calculation of age at interview from date of interview and age at death -*/
3706: agev=matrix(1,maxwav,1,imx);
3707:
3708: for (i=1; i<=imx; i++) {
3709: for(m=2; (m<= maxwav); m++) {
3710: if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
3711: anint[m][i]=9999;
3712: s[m][i]=-1;
3713: }
3714: if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
3715: }
3716: }
3717:
3718: for (i=1; i<=imx; i++) {
3719: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
3720: for(m=1; (m<= maxwav); m++){
3721: if(s[m][i] >0 || s[m][i]==-2){
3722: if (s[m][i] >= nlstate+1) {
3723: if(agedc[i]>0)
3724: if(moisdc[i]!=99 && andc[i]!=9999) agev[m][i]=agedc[i];
3725: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
3726: else {
3727: if (andc[i]!=9999){
3728: printf("Warning negative age at death: %d line:%d\n",num[i],i);
3729: fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
3730: agev[m][i]=-1;
3731: }
3732: }
3733: }
3734: else if(s[m][i] !=9){ /* Should no more exist */
3735: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
3736: if(mint[m][i]==99 || anint[m][i]==9999)
3737: agev[m][i]=1;
3738: else if(agev[m][i] <agemin){
3739: agemin=agev[m][i];
3740: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
3741: }
3742: else if(agev[m][i] >agemax){
3743: agemax=agev[m][i];
3744: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
3745: }
3746: /*agev[m][i]=anint[m][i]-annais[i];*/
3747: /* agev[m][i] = age[i]+2*m;*/
3748: }
3749: else { /* =9 */
3750: agev[m][i]=1;
3751: s[m][i]=-1;
3752: }
3753: }
3754: else /*= 0 Unknown */
3755: agev[m][i]=1;
3756: }
3757:
3758: }
3759: for (i=1; i<=imx; i++) {
3760: for(m=1; (m<= maxwav); m++){
3761: if (s[m][i] > (nlstate+ndeath)) {
3762: 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);
3763: 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);
3764: goto end;
3765: }
3766: }
3767: }
3768:
3769: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3770: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3771:
3772: free_vector(severity,1,maxwav);
3773: free_imatrix(outcome,1,maxwav+1,1,n);
3774: free_vector(moisnais,1,n);
3775: free_vector(annais,1,n);
3776: /* free_matrix(mint,1,maxwav,1,n);
3777: free_matrix(anint,1,maxwav,1,n);*/
3778: free_vector(moisdc,1,n);
3779: free_vector(andc,1,n);
3780:
3781:
3782: wav=ivector(1,imx);
3783: dh=imatrix(1,lastpass-firstpass+1,1,imx);
3784: bh=imatrix(1,lastpass-firstpass+1,1,imx);
3785: mw=imatrix(1,lastpass-firstpass+1,1,imx);
3786:
3787:
3788: /* Concatenates waves */
3789: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
3790:
3791: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
3792:
3793: Tcode=ivector(1,100);
3794: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
3795: ncodemax[1]=1;
3796: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
3797:
3798: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
3799: the estimations*/
3800: h=0;
3801: m=pow(2,cptcoveff);
3802:
3803: for(k=1;k<=cptcoveff; k++){
3804: for(i=1; i <=(m/pow(2,k));i++){
3805: for(j=1; j <= ncodemax[k]; j++){
3806: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
3807: h++;
3808: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
3809: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
3810: }
3811: }
3812: }
3813: }
3814: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
3815: codtab[1][2]=1;codtab[2][2]=2; */
3816: /* for(i=1; i <=m ;i++){
3817: for(k=1; k <=cptcovn; k++){
3818: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
3819: }
3820: printf("\n");
3821: }
3822: scanf("%d",i);*/
3823:
3824: /* Calculates basic frequencies. Computes observed prevalence at single age
3825: and prints on file fileres'p'. */
3826:
3827: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3828: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3829: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3830: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3831: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
3832:
3833:
3834: /* For Powell, parameters are in a vector p[] starting at p[1]
3835: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
3836: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
3837:
3838: if(mle>=1){ /* Could be 1 or 2 */
3839: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
3840: }
3841:
3842: /*--------- results files --------------*/
3843: 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);
3844:
3845:
3846: jk=1;
3847: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3848: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3849: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3850: for(i=1,jk=1; i <=nlstate; i++){
3851: for(k=1; k <=(nlstate+ndeath); k++){
3852: if (k != i)
3853: {
3854: printf("%d%d ",i,k);
3855: fprintf(ficlog,"%d%d ",i,k);
3856: fprintf(ficres,"%1d%1d ",i,k);
3857: for(j=1; j <=ncovmodel; j++){
3858: printf("%f ",p[jk]);
3859: fprintf(ficlog,"%f ",p[jk]);
3860: fprintf(ficres,"%f ",p[jk]);
3861: jk++;
3862: }
3863: printf("\n");
3864: fprintf(ficlog,"\n");
3865: fprintf(ficres,"\n");
3866: }
3867: }
3868: }
3869: if(mle==1){
3870: /* Computing hessian and covariance matrix */
3871: ftolhess=ftol; /* Usually correct */
3872: hesscov(matcov, p, npar, delti, ftolhess, func);
3873: }
3874: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
3875: printf("# Scales (for hessian or gradient estimation)\n");
3876: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
3877: for(i=1,jk=1; i <=nlstate; i++){
3878: for(j=1; j <=nlstate+ndeath; j++){
3879: if (j!=i) {
3880: fprintf(ficres,"%1d%1d",i,j);
3881: printf("%1d%1d",i,j);
3882: fprintf(ficlog,"%1d%1d",i,j);
3883: for(k=1; k<=ncovmodel;k++){
3884: printf(" %.5e",delti[jk]);
3885: fprintf(ficlog," %.5e",delti[jk]);
3886: fprintf(ficres," %.5e",delti[jk]);
3887: jk++;
3888: }
3889: printf("\n");
3890: fprintf(ficlog,"\n");
3891: fprintf(ficres,"\n");
3892: }
3893: }
3894: }
3895:
3896: 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");
3897: if(mle==1)
3898: 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");
3899: 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");
3900: for(i=1,k=1;i<=npar;i++){
3901: /* if (k>nlstate) k=1;
3902: i1=(i-1)/(ncovmodel*nlstate)+1;
3903: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
3904: printf("%s%d%d",alph[k],i1,tab[i]);
3905: */
3906: fprintf(ficres,"%3d",i);
3907: if(mle==1)
3908: printf("%3d",i);
3909: fprintf(ficlog,"%3d",i);
3910: for(j=1; j<=i;j++){
3911: fprintf(ficres," %.5e",matcov[i][j]);
3912: if(mle==1)
3913: printf(" %.5e",matcov[i][j]);
3914: fprintf(ficlog," %.5e",matcov[i][j]);
3915: }
3916: fprintf(ficres,"\n");
3917: if(mle==1)
3918: printf("\n");
3919: fprintf(ficlog,"\n");
3920: k++;
3921: }
3922:
3923: while((c=getc(ficpar))=='#' && c!= EOF){
3924: ungetc(c,ficpar);
3925: fgets(line, MAXLINE, ficpar);
3926: puts(line);
3927: fputs(line,ficparo);
3928: }
3929: ungetc(c,ficpar);
3930:
3931: estepm=0;
3932: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
3933: if (estepm==0 || estepm < stepm) estepm=stepm;
3934: if (fage <= 2) {
3935: bage = ageminpar;
3936: fage = agemaxpar;
3937: }
3938:
3939: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
3940: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
3941: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
3942:
3943: while((c=getc(ficpar))=='#' && c!= EOF){
3944: ungetc(c,ficpar);
3945: fgets(line, MAXLINE, ficpar);
3946: puts(line);
3947: fputs(line,ficparo);
3948: }
3949: ungetc(c,ficpar);
3950:
3951: 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);
3952: 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);
3953: 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);
3954:
3955: while((c=getc(ficpar))=='#' && c!= EOF){
3956: ungetc(c,ficpar);
3957: fgets(line, MAXLINE, ficpar);
3958: puts(line);
3959: fputs(line,ficparo);
3960: }
3961: ungetc(c,ficpar);
3962:
3963:
3964: dateprev1=anprev1+mprev1/12.+jprev1/365.;
3965: dateprev2=anprev2+mprev2/12.+jprev2/365.;
3966:
3967: fscanf(ficpar,"pop_based=%d\n",&popbased);
3968: fprintf(ficparo,"pop_based=%d\n",popbased);
3969: fprintf(ficres,"pop_based=%d\n",popbased);
3970:
3971: while((c=getc(ficpar))=='#' && c!= EOF){
3972: ungetc(c,ficpar);
3973: fgets(line, MAXLINE, ficpar);
3974: puts(line);
3975: fputs(line,ficparo);
3976: }
3977: ungetc(c,ficpar);
3978:
3979: fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
3980: fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
3981: fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
3982:
3983:
3984: while((c=getc(ficpar))=='#' && c!= EOF){
3985: ungetc(c,ficpar);
3986: fgets(line, MAXLINE, ficpar);
3987: puts(line);
3988: fputs(line,ficparo);
3989: }
3990: ungetc(c,ficpar);
3991:
3992: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
3993: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
3994: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
3995:
3996:
3997: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
3998:
3999: /*------------ gnuplot -------------*/
4000: strcpy(optionfilegnuplot,optionfilefiname);
4001: strcat(optionfilegnuplot,".gp");
4002: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4003: printf("Problem with file %s",optionfilegnuplot);
4004: }
4005: else{
4006: fprintf(ficgp,"\n# %s\n", version);
4007: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4008: fprintf(ficgp,"set missing 'NaNq'\n");
4009: }
4010: fclose(ficgp);
4011: printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
4012: /*--------- index.htm --------*/
4013:
4014: strcpy(optionfilehtm,optionfile);
4015: strcat(optionfilehtm,".htm");
4016: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4017: printf("Problem with %s \n",optionfilehtm), exit(0);
4018: }
4019:
4020: fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
4021: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
4022: \n
4023: Total number of observations=%d <br>\n
4024: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
4025: <hr size=\"2\" color=\"#EC5E5E\">
4026: <ul><li><h4>Parameter files</h4>\n
4027: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
4028: - Log file of the run: <a href=\"%s\">%s</a><br>\n
4029: - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
4030: fclose(fichtm);
4031:
4032: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
4033:
4034: /*------------ free_vector -------------*/
4035: chdir(path);
4036:
4037: free_ivector(wav,1,imx);
4038: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
4039: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
4040: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
4041: free_ivector(num,1,n);
4042: free_vector(agedc,1,n);
4043: /*free_matrix(covar,0,NCOVMAX,1,n);*/
4044: /*free_matrix(covar,1,NCOVMAX,1,n);*/
4045: fclose(ficparo);
4046: fclose(ficres);
4047:
4048:
4049: /*--------------- Prevalence limit (stable prevalence) --------------*/
4050:
4051: strcpy(filerespl,"pl");
4052: strcat(filerespl,fileres);
4053: if((ficrespl=fopen(filerespl,"w"))==NULL) {
4054: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4055: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4056: }
4057: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
4058: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
4059: fprintf(ficrespl,"#Stable prevalence \n");
4060: fprintf(ficrespl,"#Age ");
4061: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
4062: fprintf(ficrespl,"\n");
4063:
4064: prlim=matrix(1,nlstate,1,nlstate);
4065:
4066: agebase=ageminpar;
4067: agelim=agemaxpar;
4068: ftolpl=1.e-10;
4069: i1=cptcoveff;
4070: if (cptcovn < 1){i1=1;}
4071:
4072: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4073: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4074: k=k+1;
4075: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
4076: fprintf(ficrespl,"\n#******");
4077: printf("\n#******");
4078: fprintf(ficlog,"\n#******");
4079: for(j=1;j<=cptcoveff;j++) {
4080: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4081: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4082: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4083: }
4084: fprintf(ficrespl,"******\n");
4085: printf("******\n");
4086: fprintf(ficlog,"******\n");
4087:
4088: for (age=agebase; age<=agelim; age++){
4089: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4090: fprintf(ficrespl,"%.0f",age );
4091: for(i=1; i<=nlstate;i++)
4092: fprintf(ficrespl," %.5f", prlim[i][i]);
4093: fprintf(ficrespl,"\n");
4094: }
4095: }
4096: }
4097: fclose(ficrespl);
4098:
4099: /*------------- h Pij x at various ages ------------*/
4100:
4101: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
4102: if((ficrespij=fopen(filerespij,"w"))==NULL) {
4103: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
4104: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
4105: }
4106: printf("Computing pij: result on file '%s' \n", filerespij);
4107: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
4108:
4109: stepsize=(int) (stepm+YEARM-1)/YEARM;
4110: /*if (stepm<=24) stepsize=2;*/
4111:
4112: agelim=AGESUP;
4113: hstepm=stepsize*YEARM; /* Every year of age */
4114: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
4115:
4116: /* hstepm=1; aff par mois*/
4117:
4118: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4119: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4120: k=k+1;
4121: fprintf(ficrespij,"\n#****** ");
4122: for(j=1;j<=cptcoveff;j++)
4123: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4124: fprintf(ficrespij,"******\n");
4125:
4126: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
4127: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4128: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4129:
4130: /* nhstepm=nhstepm*YEARM; aff par mois*/
4131:
4132: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4133: oldm=oldms;savm=savms;
4134: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4135: fprintf(ficrespij,"# Age");
4136: for(i=1; i<=nlstate;i++)
4137: for(j=1; j<=nlstate+ndeath;j++)
4138: fprintf(ficrespij," %1d-%1d",i,j);
4139: fprintf(ficrespij,"\n");
4140: for (h=0; h<=nhstepm; h++){
4141: fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
4142: for(i=1; i<=nlstate;i++)
4143: for(j=1; j<=nlstate+ndeath;j++)
4144: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
4145: fprintf(ficrespij,"\n");
4146: }
4147: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4148: fprintf(ficrespij,"\n");
4149: }
4150: }
4151: }
4152:
4153: varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
4154:
4155: fclose(ficrespij);
4156:
4157:
4158: /*---------- Forecasting ------------------*/
4159: if((stepm == 1) && (strcmp(model,".")==0)){
4160: prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
4161: if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
4162: }
4163: else{
4164: erreur=108;
4165: 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);
4166: 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);
4167: }
4168:
4169:
4170: /*---------- Health expectancies and variances ------------*/
4171:
4172: strcpy(filerest,"t");
4173: strcat(filerest,fileres);
4174: if((ficrest=fopen(filerest,"w"))==NULL) {
4175: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
4176: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
4177: }
4178: printf("Computing Total LEs with variances: file '%s' \n", filerest);
4179: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
4180:
4181:
4182: strcpy(filerese,"e");
4183: strcat(filerese,fileres);
4184: if((ficreseij=fopen(filerese,"w"))==NULL) {
4185: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4186: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4187: }
4188: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
4189: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
4190:
4191:
4192: strcpy(fileresv,"v");
4193: strcat(fileresv,fileres);
4194: if((ficresvij=fopen(fileresv,"w"))==NULL) {
4195: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
4196: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
4197: }
4198: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4199: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4200:
4201: calagedate=-1;
4202:
4203: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
4204:
4205: if (mobilav!=0) {
4206: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4207: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4208: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4209: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4210: }
4211: }
4212:
4213: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4214: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4215: k=k+1;
4216: fprintf(ficrest,"\n#****** ");
4217: for(j=1;j<=cptcoveff;j++)
4218: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4219: fprintf(ficrest,"******\n");
4220:
4221: fprintf(ficreseij,"\n#****** ");
4222: for(j=1;j<=cptcoveff;j++)
4223: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4224: fprintf(ficreseij,"******\n");
4225:
4226: fprintf(ficresvij,"\n#****** ");
4227: for(j=1;j<=cptcoveff;j++)
4228: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4229: fprintf(ficresvij,"******\n");
4230:
4231: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4232: oldm=oldms;savm=savms;
4233: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
4234:
4235: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4236: oldm=oldms;savm=savms;
4237: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
4238: if(popbased==1){
4239: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
4240: }
4241:
4242:
4243: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
4244: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
4245: fprintf(ficrest,"\n");
4246:
4247: epj=vector(1,nlstate+1);
4248: for(age=bage; age <=fage ;age++){
4249: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4250: if (popbased==1) {
4251: if(mobilav ==0){
4252: for(i=1; i<=nlstate;i++)
4253: prlim[i][i]=probs[(int)age][i][k];
4254: }else{ /* mobilav */
4255: for(i=1; i<=nlstate;i++)
4256: prlim[i][i]=mobaverage[(int)age][i][k];
4257: }
4258: }
4259:
4260: fprintf(ficrest," %4.0f",age);
4261: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
4262: for(i=1, epj[j]=0.;i <=nlstate;i++) {
4263: epj[j] += prlim[i][i]*eij[i][j][(int)age];
4264: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
4265: }
4266: epj[nlstate+1] +=epj[j];
4267: }
4268:
4269: for(i=1, vepp=0.;i <=nlstate;i++)
4270: for(j=1;j <=nlstate;j++)
4271: vepp += vareij[i][j][(int)age];
4272: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
4273: for(j=1;j <=nlstate;j++){
4274: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
4275: }
4276: fprintf(ficrest,"\n");
4277: }
4278: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4279: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4280: free_vector(epj,1,nlstate+1);
4281: }
4282: }
4283: free_vector(weight,1,n);
4284: free_imatrix(Tvard,1,15,1,2);
4285: free_imatrix(s,1,maxwav+1,1,n);
4286: free_matrix(anint,1,maxwav,1,n);
4287: free_matrix(mint,1,maxwav,1,n);
4288: free_ivector(cod,1,n);
4289: free_ivector(tab,1,NCOVMAX);
4290: fclose(ficreseij);
4291: fclose(ficresvij);
4292: fclose(ficrest);
4293: fclose(ficpar);
4294:
4295: /*------- Variance of stable prevalence------*/
4296:
4297: strcpy(fileresvpl,"vpl");
4298: strcat(fileresvpl,fileres);
4299: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
4300: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
4301: exit(0);
4302: }
4303: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
4304:
4305: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4306: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4307: k=k+1;
4308: fprintf(ficresvpl,"\n#****** ");
4309: for(j=1;j<=cptcoveff;j++)
4310: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4311: fprintf(ficresvpl,"******\n");
4312:
4313: varpl=matrix(1,nlstate,(int) bage, (int) fage);
4314: oldm=oldms;savm=savms;
4315: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
4316: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
4317: }
4318: }
4319:
4320: fclose(ficresvpl);
4321:
4322: /*---------- End : free ----------------*/
4323: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
4324: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
4325: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
4326: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
4327:
4328: free_matrix(covar,0,NCOVMAX,1,n);
4329: free_matrix(matcov,1,npar,1,npar);
4330: free_vector(delti,1,npar);
4331: free_matrix(agev,1,maxwav,1,imx);
4332: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4333: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4334: free_ivector(ncodemax,1,8);
4335: free_ivector(Tvar,1,15);
4336: free_ivector(Tprod,1,15);
4337: free_ivector(Tvaraff,1,15);
4338: free_ivector(Tage,1,15);
4339: free_ivector(Tcode,1,100);
4340:
4341: fprintf(fichtm,"\n</body>");
4342: fclose(fichtm);
4343: fclose(ficgp);
4344:
4345:
4346: if(erreur >0){
4347: printf("End of Imach with error or warning %d\n",erreur);
4348: fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
4349: }else{
4350: printf("End of Imach\n");
4351: fprintf(ficlog,"End of Imach\n");
4352: }
4353: printf("See log file on %s\n",filelog);
4354: fclose(ficlog);
4355: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
4356:
4357: /* 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);*/
4358: /*printf("Total time was %d uSec.\n", total_usecs);*/
4359: /*------ End -----------*/
4360:
4361: end:
4362: #ifdef windows
4363: /* chdir(pathcd);*/
4364: #endif
4365: /*system("wgnuplot graph.plt");*/
4366: /*system("../gp37mgw/wgnuplot graph.plt");*/
4367: /*system("cd ../gp37mgw");*/
4368: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
4369: strcpy(plotcmd,GNUPLOTPROGRAM);
4370: strcat(plotcmd," ");
4371: strcat(plotcmd,optionfilegnuplot);
4372: printf("Starting: %s\n",plotcmd);fflush(stdout);
4373: system(plotcmd);
4374:
4375: /*#ifdef windows*/
4376: while (z[0] != 'q') {
4377: /* chdir(path); */
4378: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
4379: scanf("%s",z);
4380: if (z[0] == 'c') system("./imach");
4381: else if (z[0] == 'e') system(optionfilehtm);
4382: else if (z[0] == 'g') system(plotcmd);
4383: else if (z[0] == 'q') exit(0);
4384: }
4385: /*#endif */
4386: }
4387:
4388:
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