1: /* $Id: imach.c,v 1.66 2003/01/28 17:23:35 brouard Exp $
2: Interpolated Markov Chain
3:
4: Short summary of the programme:
5:
6: This program computes Healthy Life Expectancies from
7: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
8: first survey ("cross") where individuals from different ages are
9: interviewed on their health status or degree of disability (in the
10: case of a health survey which is our main interest) -2- at least a
11: second wave of interviews ("longitudinal") which measure each change
12: (if any) in individual health status. Health expectancies are
13: computed from the time spent in each health state according to a
14: model. More health states you consider, more time is necessary to reach the
15: Maximum Likelihood of the parameters involved in the model. The
16: simplest model is the multinomial logistic model where pij is the
17: probability to be observed in state j at the second wave
18: conditional to be observed in state i at the first wave. Therefore
19: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
20: 'age' is age and 'sex' is a covariate. If you want to have a more
21: complex model than "constant and age", you should modify the program
22: where the markup *Covariates have to be included here again* invites
23: you to do it. More covariates you add, slower the
24: convergence.
25:
26: The advantage of this computer programme, compared to a simple
27: multinomial logistic model, is clear when the delay between waves is not
28: identical for each individual. Also, if a individual missed an
29: intermediate interview, the information is lost, but taken into
30: account using an interpolation or extrapolation.
31:
32: hPijx is the probability to be observed in state i at age x+h
33: conditional to the observed state i at age x. The delay 'h' can be
34: split into an exact number (nh*stepm) of unobserved intermediate
35: states. This elementary transition (by month, quarter,
36: semester or year) is modelled as a multinomial logistic. The hPx
37: matrix is simply the matrix product of nh*stepm elementary matrices
38: and the contribution of each individual to the likelihood is simply
39: hPijx.
40:
41: Also this programme outputs the covariance matrix of the parameters but also
42: of the life expectancies. It also computes the stable prevalence.
43:
44: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
45: Institut national d'études démographiques, Paris.
46: This software have been partly granted by Euro-REVES, a concerted action
47: from the European Union.
48: It is copyrighted identically to a GNU software product, ie programme and
49: software can be distributed freely for non commercial use. Latest version
50: can be accessed at http://euroreves.ined.fr/imach .
51: **********************************************************************/
52:
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;
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: 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 */
976: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
977: /*if(lli ==000.0)*/
978: /*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); */
979: ipmx +=1;
980: sw += weight[i];
981: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
982: } /* end of wave */
983: } /* end of individual */
984: } else if(mle==2){
985: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
986: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
987: for(mi=1; mi<= wav[i]-1; mi++){
988: for (ii=1;ii<=nlstate+ndeath;ii++)
989: for (j=1;j<=nlstate+ndeath;j++){
990: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
991: savm[ii][j]=(ii==j ? 1.0 : 0.0);
992: }
993: for(d=0; d<=dh[mi][i]; d++){
994: newm=savm;
995: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
996: for (kk=1; kk<=cptcovage;kk++) {
997: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
998: }
999: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1000: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1001: savm=oldm;
1002: oldm=newm;
1003: } /* end mult */
1004:
1005: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1006: /* But now since version 0.9 we anticipate for bias and large stepm.
1007: * If stepm is larger than one month (smallest stepm) and if the exact delay
1008: * (in months) between two waves is not a multiple of stepm, we rounded to
1009: * the nearest (and in case of equal distance, to the lowest) interval but now
1010: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1011: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1012: * probability in order to take into account the bias as a fraction of the way
1013: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1014: * -stepm/2 to stepm/2 .
1015: * For stepm=1 the results are the same as for previous versions of Imach.
1016: * For stepm > 1 the results are less biased than in previous versions.
1017: */
1018: s1=s[mw[mi][i]][i];
1019: s2=s[mw[mi+1][i]][i];
1020: bbh=(double)bh[mi][i]/(double)stepm;
1021: /* bias is positive if real duration
1022: * is higher than the multiple of stepm and negative otherwise.
1023: */
1024: 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 */
1025: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1026: /*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 */
1027: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1028: /*if(lli ==000.0)*/
1029: /*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); */
1030: ipmx +=1;
1031: sw += weight[i];
1032: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1033: } /* end of wave */
1034: } /* end of individual */
1035: } else if(mle==3){ /* exponential inter-extrapolation */
1036: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1037: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1038: for(mi=1; mi<= wav[i]-1; mi++){
1039: for (ii=1;ii<=nlstate+ndeath;ii++)
1040: for (j=1;j<=nlstate+ndeath;j++){
1041: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1042: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1043: }
1044: for(d=0; d<dh[mi][i]; d++){
1045: newm=savm;
1046: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1047: for (kk=1; kk<=cptcovage;kk++) {
1048: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1049: }
1050: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1051: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1052: savm=oldm;
1053: oldm=newm;
1054: } /* end mult */
1055:
1056: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1057: /* But now since version 0.9 we anticipate for bias and large stepm.
1058: * If stepm is larger than one month (smallest stepm) and if the exact delay
1059: * (in months) between two waves is not a multiple of stepm, we rounded to
1060: * the nearest (and in case of equal distance, to the lowest) interval but now
1061: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1062: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1063: * probability in order to take into account the bias as a fraction of the way
1064: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1065: * -stepm/2 to stepm/2 .
1066: * For stepm=1 the results are the same as for previous versions of Imach.
1067: * For stepm > 1 the results are less biased than in previous versions.
1068: */
1069: s1=s[mw[mi][i]][i];
1070: s2=s[mw[mi+1][i]][i];
1071: bbh=(double)bh[mi][i]/(double)stepm;
1072: /* bias is positive if real duration
1073: * is higher than the multiple of stepm and negative otherwise.
1074: */
1075: /* 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 */
1076: 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 */
1077: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1078: /*if(lli ==000.0)*/
1079: /*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); */
1080: ipmx +=1;
1081: sw += weight[i];
1082: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1083: } /* end of wave */
1084: } /* end of individual */
1085: }else{ /* ml=4 no inter-extrapolation */
1086: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1087: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1088: for(mi=1; mi<= wav[i]-1; mi++){
1089: for (ii=1;ii<=nlstate+ndeath;ii++)
1090: for (j=1;j<=nlstate+ndeath;j++){
1091: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1092: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1093: }
1094: for(d=0; d<dh[mi][i]; d++){
1095: newm=savm;
1096: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1097: for (kk=1; kk<=cptcovage;kk++) {
1098: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1099: }
1100:
1101: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1102: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1103: savm=oldm;
1104: oldm=newm;
1105: } /* end mult */
1106:
1107: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1108: ipmx +=1;
1109: sw += weight[i];
1110: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1111: } /* end of wave */
1112: } /* end of individual */
1113: } /* End of if */
1114: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1115: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1116: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1117: return -l;
1118: }
1119:
1120:
1121: /*********** Maximum Likelihood Estimation ***************/
1122:
1123: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1124: {
1125: int i,j, iter;
1126: double **xi,*delti;
1127: double fret;
1128: xi=matrix(1,npar,1,npar);
1129: for (i=1;i<=npar;i++)
1130: for (j=1;j<=npar;j++)
1131: xi[i][j]=(i==j ? 1.0 : 0.0);
1132: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1133: powell(p,xi,npar,ftol,&iter,&fret,func);
1134:
1135: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1136: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1137: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1138:
1139: }
1140:
1141: /**** Computes Hessian and covariance matrix ***/
1142: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1143: {
1144: double **a,**y,*x,pd;
1145: double **hess;
1146: int i, j,jk;
1147: int *indx;
1148:
1149: double hessii(double p[], double delta, int theta, double delti[]);
1150: double hessij(double p[], double delti[], int i, int j);
1151: void lubksb(double **a, int npar, int *indx, double b[]) ;
1152: void ludcmp(double **a, int npar, int *indx, double *d) ;
1153:
1154: hess=matrix(1,npar,1,npar);
1155:
1156: printf("\nCalculation of the hessian matrix. Wait...\n");
1157: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1158: for (i=1;i<=npar;i++){
1159: printf("%d",i);fflush(stdout);
1160: fprintf(ficlog,"%d",i);fflush(ficlog);
1161: hess[i][i]=hessii(p,ftolhess,i,delti);
1162: /*printf(" %f ",p[i]);*/
1163: /*printf(" %lf ",hess[i][i]);*/
1164: }
1165:
1166: for (i=1;i<=npar;i++) {
1167: for (j=1;j<=npar;j++) {
1168: if (j>i) {
1169: printf(".%d%d",i,j);fflush(stdout);
1170: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1171: hess[i][j]=hessij(p,delti,i,j);
1172: hess[j][i]=hess[i][j];
1173: /*printf(" %lf ",hess[i][j]);*/
1174: }
1175: }
1176: }
1177: printf("\n");
1178: fprintf(ficlog,"\n");
1179:
1180: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1181: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1182:
1183: a=matrix(1,npar,1,npar);
1184: y=matrix(1,npar,1,npar);
1185: x=vector(1,npar);
1186: indx=ivector(1,npar);
1187: for (i=1;i<=npar;i++)
1188: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1189: ludcmp(a,npar,indx,&pd);
1190:
1191: for (j=1;j<=npar;j++) {
1192: for (i=1;i<=npar;i++) x[i]=0;
1193: x[j]=1;
1194: lubksb(a,npar,indx,x);
1195: for (i=1;i<=npar;i++){
1196: matcov[i][j]=x[i];
1197: }
1198: }
1199:
1200: printf("\n#Hessian matrix#\n");
1201: fprintf(ficlog,"\n#Hessian matrix#\n");
1202: for (i=1;i<=npar;i++) {
1203: for (j=1;j<=npar;j++) {
1204: printf("%.3e ",hess[i][j]);
1205: fprintf(ficlog,"%.3e ",hess[i][j]);
1206: }
1207: printf("\n");
1208: fprintf(ficlog,"\n");
1209: }
1210:
1211: /* Recompute Inverse */
1212: for (i=1;i<=npar;i++)
1213: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1214: ludcmp(a,npar,indx,&pd);
1215:
1216: /* printf("\n#Hessian matrix recomputed#\n");
1217:
1218: for (j=1;j<=npar;j++) {
1219: for (i=1;i<=npar;i++) x[i]=0;
1220: x[j]=1;
1221: lubksb(a,npar,indx,x);
1222: for (i=1;i<=npar;i++){
1223: y[i][j]=x[i];
1224: printf("%.3e ",y[i][j]);
1225: fprintf(ficlog,"%.3e ",y[i][j]);
1226: }
1227: printf("\n");
1228: fprintf(ficlog,"\n");
1229: }
1230: */
1231:
1232: free_matrix(a,1,npar,1,npar);
1233: free_matrix(y,1,npar,1,npar);
1234: free_vector(x,1,npar);
1235: free_ivector(indx,1,npar);
1236: free_matrix(hess,1,npar,1,npar);
1237:
1238:
1239: }
1240:
1241: /*************** hessian matrix ****************/
1242: double hessii( double x[], double delta, int theta, double delti[])
1243: {
1244: int i;
1245: int l=1, lmax=20;
1246: double k1,k2;
1247: double p2[NPARMAX+1];
1248: double res;
1249: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1250: double fx;
1251: int k=0,kmax=10;
1252: double l1;
1253:
1254: fx=func(x);
1255: for (i=1;i<=npar;i++) p2[i]=x[i];
1256: for(l=0 ; l <=lmax; l++){
1257: l1=pow(10,l);
1258: delts=delt;
1259: for(k=1 ; k <kmax; k=k+1){
1260: delt = delta*(l1*k);
1261: p2[theta]=x[theta] +delt;
1262: k1=func(p2)-fx;
1263: p2[theta]=x[theta]-delt;
1264: k2=func(p2)-fx;
1265: /*res= (k1-2.0*fx+k2)/delt/delt; */
1266: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1267:
1268: #ifdef DEBUG
1269: 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);
1270: 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);
1271: #endif
1272: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1273: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1274: k=kmax;
1275: }
1276: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1277: k=kmax; l=lmax*10.;
1278: }
1279: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1280: delts=delt;
1281: }
1282: }
1283: }
1284: delti[theta]=delts;
1285: return res;
1286:
1287: }
1288:
1289: double hessij( double x[], double delti[], int thetai,int thetaj)
1290: {
1291: int i;
1292: int l=1, l1, lmax=20;
1293: double k1,k2,k3,k4,res,fx;
1294: double p2[NPARMAX+1];
1295: int k;
1296:
1297: fx=func(x);
1298: for (k=1; k<=2; k++) {
1299: for (i=1;i<=npar;i++) p2[i]=x[i];
1300: p2[thetai]=x[thetai]+delti[thetai]/k;
1301: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1302: k1=func(p2)-fx;
1303:
1304: p2[thetai]=x[thetai]+delti[thetai]/k;
1305: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1306: k2=func(p2)-fx;
1307:
1308: p2[thetai]=x[thetai]-delti[thetai]/k;
1309: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1310: k3=func(p2)-fx;
1311:
1312: p2[thetai]=x[thetai]-delti[thetai]/k;
1313: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1314: k4=func(p2)-fx;
1315: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1316: #ifdef DEBUG
1317: 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);
1318: 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);
1319: #endif
1320: }
1321: return res;
1322: }
1323:
1324: /************** Inverse of matrix **************/
1325: void ludcmp(double **a, int n, int *indx, double *d)
1326: {
1327: int i,imax,j,k;
1328: double big,dum,sum,temp;
1329: double *vv;
1330:
1331: vv=vector(1,n);
1332: *d=1.0;
1333: for (i=1;i<=n;i++) {
1334: big=0.0;
1335: for (j=1;j<=n;j++)
1336: if ((temp=fabs(a[i][j])) > big) big=temp;
1337: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1338: vv[i]=1.0/big;
1339: }
1340: for (j=1;j<=n;j++) {
1341: for (i=1;i<j;i++) {
1342: sum=a[i][j];
1343: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1344: a[i][j]=sum;
1345: }
1346: big=0.0;
1347: for (i=j;i<=n;i++) {
1348: sum=a[i][j];
1349: for (k=1;k<j;k++)
1350: sum -= a[i][k]*a[k][j];
1351: a[i][j]=sum;
1352: if ( (dum=vv[i]*fabs(sum)) >= big) {
1353: big=dum;
1354: imax=i;
1355: }
1356: }
1357: if (j != imax) {
1358: for (k=1;k<=n;k++) {
1359: dum=a[imax][k];
1360: a[imax][k]=a[j][k];
1361: a[j][k]=dum;
1362: }
1363: *d = -(*d);
1364: vv[imax]=vv[j];
1365: }
1366: indx[j]=imax;
1367: if (a[j][j] == 0.0) a[j][j]=TINY;
1368: if (j != n) {
1369: dum=1.0/(a[j][j]);
1370: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1371: }
1372: }
1373: free_vector(vv,1,n); /* Doesn't work */
1374: ;
1375: }
1376:
1377: void lubksb(double **a, int n, int *indx, double b[])
1378: {
1379: int i,ii=0,ip,j;
1380: double sum;
1381:
1382: for (i=1;i<=n;i++) {
1383: ip=indx[i];
1384: sum=b[ip];
1385: b[ip]=b[i];
1386: if (ii)
1387: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1388: else if (sum) ii=i;
1389: b[i]=sum;
1390: }
1391: for (i=n;i>=1;i--) {
1392: sum=b[i];
1393: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1394: b[i]=sum/a[i][i];
1395: }
1396: }
1397:
1398: /************ Frequencies ********************/
1399: 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)
1400: { /* Some frequencies */
1401:
1402: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1403: int first;
1404: double ***freq; /* Frequencies */
1405: double *pp;
1406: double pos, k2, dateintsum=0,k2cpt=0;
1407: FILE *ficresp;
1408: char fileresp[FILENAMELENGTH];
1409:
1410: pp=vector(1,nlstate);
1411: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1412: strcpy(fileresp,"p");
1413: strcat(fileresp,fileres);
1414: if((ficresp=fopen(fileresp,"w"))==NULL) {
1415: printf("Problem with prevalence resultfile: %s\n", fileresp);
1416: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1417: exit(0);
1418: }
1419: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1420: j1=0;
1421:
1422: j=cptcoveff;
1423: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1424:
1425: first=1;
1426:
1427: for(k1=1; k1<=j;k1++){
1428: for(i1=1; i1<=ncodemax[k1];i1++){
1429: j1++;
1430: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1431: scanf("%d", i);*/
1432: for (i=-1; i<=nlstate+ndeath; i++)
1433: for (jk=-1; jk<=nlstate+ndeath; jk++)
1434: for(m=agemin; m <= agemax+3; m++)
1435: freq[i][jk][m]=0;
1436:
1437: dateintsum=0;
1438: k2cpt=0;
1439: for (i=1; i<=imx; i++) {
1440: bool=1;
1441: if (cptcovn>0) {
1442: for (z1=1; z1<=cptcoveff; z1++)
1443: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1444: bool=0;
1445: }
1446: if (bool==1){
1447: for(m=firstpass; m<=lastpass; m++){
1448: k2=anint[m][i]+(mint[m][i]/12.);
1449: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1450: if(agev[m][i]==0) agev[m][i]=agemax+1;
1451: if(agev[m][i]==1) agev[m][i]=agemax+2;
1452: if (m<lastpass) {
1453: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1454: freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
1455: }
1456:
1457: if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
1458: dateintsum=dateintsum+k2;
1459: k2cpt++;
1460: }
1461: }
1462: }
1463: }
1464: }
1465:
1466: fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1467:
1468: if (cptcovn>0) {
1469: fprintf(ficresp, "\n#********** Variable ");
1470: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1471: fprintf(ficresp, "**********\n#");
1472: }
1473: for(i=1; i<=nlstate;i++)
1474: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1475: fprintf(ficresp, "\n");
1476:
1477: for(i=(int)agemin; i <= (int)agemax+3; i++){
1478: if(i==(int)agemax+3){
1479: fprintf(ficlog,"Total");
1480: }else{
1481: if(first==1){
1482: first=0;
1483: printf("See log file for details...\n");
1484: }
1485: fprintf(ficlog,"Age %d", i);
1486: }
1487: for(jk=1; jk <=nlstate ; jk++){
1488: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1489: pp[jk] += freq[jk][m][i];
1490: }
1491: for(jk=1; jk <=nlstate ; jk++){
1492: for(m=-1, pos=0; m <=0 ; m++)
1493: pos += freq[jk][m][i];
1494: if(pp[jk]>=1.e-10){
1495: if(first==1){
1496: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1497: }
1498: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1499: }else{
1500: if(first==1)
1501: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1502: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1503: }
1504: }
1505:
1506: for(jk=1; jk <=nlstate ; jk++){
1507: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1508: pp[jk] += freq[jk][m][i];
1509: }
1510:
1511: for(jk=1,pos=0; jk <=nlstate ; jk++)
1512: pos += pp[jk];
1513: for(jk=1; jk <=nlstate ; jk++){
1514: if(pos>=1.e-5){
1515: if(first==1)
1516: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1517: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1518: }else{
1519: if(first==1)
1520: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1521: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1522: }
1523: if( i <= (int) agemax){
1524: if(pos>=1.e-5){
1525: fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
1526: probs[i][jk][j1]= pp[jk]/pos;
1527: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1528: }
1529: else
1530: fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
1531: }
1532: }
1533:
1534: for(jk=-1; jk <=nlstate+ndeath; jk++)
1535: for(m=-1; m <=nlstate+ndeath; m++)
1536: if(freq[jk][m][i] !=0 ) {
1537: if(first==1)
1538: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1539: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1540: }
1541: if(i <= (int) agemax)
1542: fprintf(ficresp,"\n");
1543: if(first==1)
1544: printf("Others in log...\n");
1545: fprintf(ficlog,"\n");
1546: }
1547: }
1548: }
1549: dateintmean=dateintsum/k2cpt;
1550:
1551: fclose(ficresp);
1552: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1553: free_vector(pp,1,nlstate);
1554:
1555: /* End of Freq */
1556: }
1557:
1558: /************ Prevalence ********************/
1559: 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)
1560: { /* Some frequencies */
1561:
1562: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1563: double ***freq; /* Frequencies */
1564: double *pp;
1565: double pos, k2;
1566:
1567: pp=vector(1,nlstate);
1568:
1569: freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1570: j1=0;
1571:
1572: j=cptcoveff;
1573: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1574:
1575: for(k1=1; k1<=j;k1++){
1576: for(i1=1; i1<=ncodemax[k1];i1++){
1577: j1++;
1578:
1579: for (i=-1; i<=nlstate+ndeath; i++)
1580: for (jk=-1; jk<=nlstate+ndeath; jk++)
1581: for(m=agemin; m <= agemax+3; m++)
1582: freq[i][jk][m]=0;
1583:
1584: for (i=1; i<=imx; i++) {
1585: bool=1;
1586: if (cptcovn>0) {
1587: for (z1=1; z1<=cptcoveff; z1++)
1588: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1589: bool=0;
1590: }
1591: if (bool==1) {
1592: for(m=firstpass; m<=lastpass; m++){
1593: k2=anint[m][i]+(mint[m][i]/12.);
1594: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1595: if(agev[m][i]==0) agev[m][i]=agemax+1;
1596: if(agev[m][i]==1) agev[m][i]=agemax+2;
1597: if (m<lastpass) {
1598: if (calagedate>0)
1599: freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
1600: else
1601: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1602: freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];
1603: }
1604: }
1605: }
1606: }
1607: }
1608: for(i=(int)agemin; i <= (int)agemax+3; i++){
1609: for(jk=1; jk <=nlstate ; jk++){
1610: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1611: pp[jk] += freq[jk][m][i];
1612: }
1613: for(jk=1; jk <=nlstate ; jk++){
1614: for(m=-1, pos=0; m <=0 ; m++)
1615: pos += freq[jk][m][i];
1616: }
1617:
1618: for(jk=1; jk <=nlstate ; jk++){
1619: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1620: pp[jk] += freq[jk][m][i];
1621: }
1622:
1623: for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
1624:
1625: for(jk=1; jk <=nlstate ; jk++){
1626: if( i <= (int) agemax){
1627: if(pos>=1.e-5){
1628: probs[i][jk][j1]= pp[jk]/pos;
1629: }
1630: }
1631: }/* end jk */
1632: }/* end i */
1633: } /* end i1 */
1634: } /* end k1 */
1635:
1636:
1637: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1638: free_vector(pp,1,nlstate);
1639:
1640: } /* End of Freq */
1641:
1642: /************* Waves Concatenation ***************/
1643:
1644: 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)
1645: {
1646: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1647: Death is a valid wave (if date is known).
1648: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1649: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1650: and mw[mi+1][i]. dh depends on stepm.
1651: */
1652:
1653: int i, mi, m;
1654: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1655: double sum=0., jmean=0.;*/
1656: int first;
1657: int j, k=0,jk, ju, jl;
1658: double sum=0.;
1659: first=0;
1660: jmin=1e+5;
1661: jmax=-1;
1662: jmean=0.;
1663: for(i=1; i<=imx; i++){
1664: mi=0;
1665: m=firstpass;
1666: while(s[m][i] <= nlstate){
1667: if(s[m][i]>=1)
1668: mw[++mi][i]=m;
1669: if(m >=lastpass)
1670: break;
1671: else
1672: m++;
1673: }/* end while */
1674: if (s[m][i] > nlstate){
1675: mi++; /* Death is another wave */
1676: /* if(mi==0) never been interviewed correctly before death */
1677: /* Only death is a correct wave */
1678: mw[mi][i]=m;
1679: }
1680:
1681: wav[i]=mi;
1682: if(mi==0){
1683: if(first==0){
1684: printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
1685: first=1;
1686: }
1687: if(first==1){
1688: fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
1689: }
1690: } /* end mi==0 */
1691: }
1692:
1693: for(i=1; i<=imx; i++){
1694: for(mi=1; mi<wav[i];mi++){
1695: if (stepm <=0)
1696: dh[mi][i]=1;
1697: else{
1698: if (s[mw[mi+1][i]][i] > nlstate) {
1699: if (agedc[i] < 2*AGESUP) {
1700: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1701: if(j==0) j=1; /* Survives at least one month after exam */
1702: k=k+1;
1703: if (j >= jmax) jmax=j;
1704: if (j <= jmin) jmin=j;
1705: sum=sum+j;
1706: /*if (j<0) printf("j=%d num=%d \n",j,i); */
1707: }
1708: }
1709: else{
1710: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1711: k=k+1;
1712: if (j >= jmax) jmax=j;
1713: else if (j <= jmin)jmin=j;
1714: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1715: sum=sum+j;
1716: }
1717: jk= j/stepm;
1718: jl= j -jk*stepm;
1719: ju= j -(jk+1)*stepm;
1720: if(mle <=1){
1721: if(jl==0){
1722: dh[mi][i]=jk;
1723: bh[mi][i]=0;
1724: }else{ /* We want a negative bias in order to only have interpolation ie
1725: * at the price of an extra matrix product in likelihood */
1726: dh[mi][i]=jk+1;
1727: bh[mi][i]=ju;
1728: }
1729: }else{
1730: if(jl <= -ju){
1731: dh[mi][i]=jk;
1732: bh[mi][i]=jl; /* bias is positive if real duration
1733: * is higher than the multiple of stepm and negative otherwise.
1734: */
1735: }
1736: else{
1737: dh[mi][i]=jk+1;
1738: bh[mi][i]=ju;
1739: }
1740: if(dh[mi][i]==0){
1741: dh[mi][i]=1; /* At least one step */
1742: bh[mi][i]=ju; /* At least one step */
1743: 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);
1744: }
1745: if(i==298 || i==287 || i==763 ||i==1061)printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d",bh[mi][i],ju,jl,dh[mi][i],jk,stepm);
1746: }
1747: } /* end if mle */
1748: } /* end wave */
1749: }
1750: jmean=sum/k;
1751: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1752: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1753: }
1754:
1755: /*********** Tricode ****************************/
1756: void tricode(int *Tvar, int **nbcode, int imx)
1757: {
1758:
1759: int Ndum[20],ij=1, k, j, i, maxncov=19;
1760: int cptcode=0;
1761: cptcoveff=0;
1762:
1763: for (k=0; k<maxncov; k++) Ndum[k]=0;
1764: for (k=1; k<=7; k++) ncodemax[k]=0;
1765:
1766: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1767: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
1768: modality*/
1769: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
1770: Ndum[ij]++; /*store the modality */
1771: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1772: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
1773: Tvar[j]. If V=sex and male is 0 and
1774: female is 1, then cptcode=1.*/
1775: }
1776:
1777: for (i=0; i<=cptcode; i++) {
1778: 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 */
1779: }
1780:
1781: ij=1;
1782: for (i=1; i<=ncodemax[j]; i++) {
1783: for (k=0; k<= maxncov; k++) {
1784: if (Ndum[k] != 0) {
1785: nbcode[Tvar[j]][ij]=k;
1786: /* 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; */
1787:
1788: ij++;
1789: }
1790: if (ij > ncodemax[j]) break;
1791: }
1792: }
1793: }
1794:
1795: for (k=0; k< maxncov; k++) Ndum[k]=0;
1796:
1797: for (i=1; i<=ncovmodel-2; i++) {
1798: /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
1799: ij=Tvar[i];
1800: Ndum[ij]++;
1801: }
1802:
1803: ij=1;
1804: for (i=1; i<= maxncov; i++) {
1805: if((Ndum[i]!=0) && (i<=ncovcol)){
1806: Tvaraff[ij]=i; /*For printing */
1807: ij++;
1808: }
1809: }
1810:
1811: cptcoveff=ij-1; /*Number of simple covariates*/
1812: }
1813:
1814: /*********** Health Expectancies ****************/
1815:
1816: 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 )
1817:
1818: {
1819: /* Health expectancies */
1820: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
1821: double age, agelim, hf;
1822: double ***p3mat,***varhe;
1823: double **dnewm,**doldm;
1824: double *xp;
1825: double **gp, **gm;
1826: double ***gradg, ***trgradg;
1827: int theta;
1828:
1829: varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
1830: xp=vector(1,npar);
1831: dnewm=matrix(1,nlstate*2,1,npar);
1832: doldm=matrix(1,nlstate*2,1,nlstate*2);
1833:
1834: fprintf(ficreseij,"# Health expectancies\n");
1835: fprintf(ficreseij,"# Age");
1836: for(i=1; i<=nlstate;i++)
1837: for(j=1; j<=nlstate;j++)
1838: fprintf(ficreseij," %1d-%1d (SE)",i,j);
1839: fprintf(ficreseij,"\n");
1840:
1841: if(estepm < stepm){
1842: printf ("Problem %d lower than %d\n",estepm, stepm);
1843: }
1844: else hstepm=estepm;
1845: /* We compute the life expectancy from trapezoids spaced every estepm months
1846: * This is mainly to measure the difference between two models: for example
1847: * if stepm=24 months pijx are given only every 2 years and by summing them
1848: * we are calculating an estimate of the Life Expectancy assuming a linear
1849: * progression in between and thus overestimating or underestimating according
1850: * to the curvature of the survival function. If, for the same date, we
1851: * estimate the model with stepm=1 month, we can keep estepm to 24 months
1852: * to compare the new estimate of Life expectancy with the same linear
1853: * hypothesis. A more precise result, taking into account a more precise
1854: * curvature will be obtained if estepm is as small as stepm. */
1855:
1856: /* For example we decided to compute the life expectancy with the smallest unit */
1857: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
1858: nhstepm is the number of hstepm from age to agelim
1859: nstepm is the number of stepm from age to agelin.
1860: Look at hpijx to understand the reason of that which relies in memory size
1861: and note for a fixed period like estepm months */
1862: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
1863: survival function given by stepm (the optimization length). Unfortunately it
1864: means that if the survival funtion is printed only each two years of age and if
1865: you sum them up and add 1 year (area under the trapezoids) you won't get the same
1866: results. So we changed our mind and took the option of the best precision.
1867: */
1868: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
1869:
1870: agelim=AGESUP;
1871: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1872: /* nhstepm age range expressed in number of stepm */
1873: nstepm=(int) rint((agelim-age)*YEARM/stepm);
1874: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
1875: /* if (stepm >= YEARM) hstepm=1;*/
1876: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
1877: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1878: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
1879: gp=matrix(0,nhstepm,1,nlstate*2);
1880: gm=matrix(0,nhstepm,1,nlstate*2);
1881:
1882: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1883: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1884: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1885:
1886:
1887: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1888:
1889: /* Computing Variances of health expectancies */
1890:
1891: for(theta=1; theta <=npar; theta++){
1892: for(i=1; i<=npar; i++){
1893: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1894: }
1895: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1896:
1897: cptj=0;
1898: for(j=1; j<= nlstate; j++){
1899: for(i=1; i<=nlstate; i++){
1900: cptj=cptj+1;
1901: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
1902: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
1903: }
1904: }
1905: }
1906:
1907:
1908: for(i=1; i<=npar; i++)
1909: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1910: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1911:
1912: cptj=0;
1913: for(j=1; j<= nlstate; j++){
1914: for(i=1;i<=nlstate;i++){
1915: cptj=cptj+1;
1916: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1917: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
1918: }
1919: }
1920: }
1921: for(j=1; j<= nlstate*2; j++)
1922: for(h=0; h<=nhstepm-1; h++){
1923: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
1924: }
1925: }
1926:
1927: /* End theta */
1928:
1929: trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
1930:
1931: for(h=0; h<=nhstepm-1; h++)
1932: for(j=1; j<=nlstate*2;j++)
1933: for(theta=1; theta <=npar; theta++)
1934: trgradg[h][j][theta]=gradg[h][theta][j];
1935:
1936:
1937: for(i=1;i<=nlstate*2;i++)
1938: for(j=1;j<=nlstate*2;j++)
1939: varhe[i][j][(int)age] =0.;
1940:
1941: printf("%d|",(int)age);fflush(stdout);
1942: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
1943: for(h=0;h<=nhstepm-1;h++){
1944: for(k=0;k<=nhstepm-1;k++){
1945: matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
1946: matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
1947: for(i=1;i<=nlstate*2;i++)
1948: for(j=1;j<=nlstate*2;j++)
1949: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
1950: }
1951: }
1952: /* Computing expectancies */
1953: for(i=1; i<=nlstate;i++)
1954: for(j=1; j<=nlstate;j++)
1955: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
1956: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
1957:
1958: /* 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]);*/
1959:
1960: }
1961:
1962: fprintf(ficreseij,"%3.0f",age );
1963: cptj=0;
1964: for(i=1; i<=nlstate;i++)
1965: for(j=1; j<=nlstate;j++){
1966: cptj++;
1967: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
1968: }
1969: fprintf(ficreseij,"\n");
1970:
1971: free_matrix(gm,0,nhstepm,1,nlstate*2);
1972: free_matrix(gp,0,nhstepm,1,nlstate*2);
1973: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
1974: free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
1975: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1976: }
1977: printf("\n");
1978: fprintf(ficlog,"\n");
1979:
1980: free_vector(xp,1,npar);
1981: free_matrix(dnewm,1,nlstate*2,1,npar);
1982: free_matrix(doldm,1,nlstate*2,1,nlstate*2);
1983: free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
1984: }
1985:
1986: /************ Variance ******************/
1987: 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)
1988: {
1989: /* Variance of health expectancies */
1990: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1991: /* double **newm;*/
1992: double **dnewm,**doldm;
1993: double **dnewmp,**doldmp;
1994: int i, j, nhstepm, hstepm, h, nstepm ;
1995: int k, cptcode;
1996: double *xp;
1997: double **gp, **gm; /* for var eij */
1998: double ***gradg, ***trgradg; /*for var eij */
1999: double **gradgp, **trgradgp; /* for var p point j */
2000: double *gpp, *gmp; /* for var p point j */
2001: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2002: double ***p3mat;
2003: double age,agelim, hf;
2004: double ***mobaverage;
2005: int theta;
2006: char digit[4];
2007: char digitp[25];
2008:
2009: char fileresprobmorprev[FILENAMELENGTH];
2010:
2011: if(popbased==1){
2012: if(mobilav!=0)
2013: strcpy(digitp,"-populbased-mobilav-");
2014: else strcpy(digitp,"-populbased-nomobil-");
2015: }
2016: else
2017: strcpy(digitp,"-stablbased-");
2018:
2019: if (mobilav!=0) {
2020: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2021: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2022: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2023: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2024: }
2025: }
2026:
2027: strcpy(fileresprobmorprev,"prmorprev");
2028: sprintf(digit,"%-d",ij);
2029: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2030: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2031: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2032: strcat(fileresprobmorprev,fileres);
2033: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2034: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2035: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2036: }
2037: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2038: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2039: 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);
2040: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2041: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2042: fprintf(ficresprobmorprev," p.%-d SE",j);
2043: for(i=1; i<=nlstate;i++)
2044: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2045: }
2046: fprintf(ficresprobmorprev,"\n");
2047: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2048: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2049: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2050: exit(0);
2051: }
2052: else{
2053: fprintf(ficgp,"\n# Routine varevsij");
2054: }
2055: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2056: printf("Problem with html file: %s\n", optionfilehtm);
2057: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2058: exit(0);
2059: }
2060: else{
2061: fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
2062: fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
2063: }
2064: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2065:
2066: 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");
2067: fprintf(ficresvij,"# Age");
2068: for(i=1; i<=nlstate;i++)
2069: for(j=1; j<=nlstate;j++)
2070: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2071: fprintf(ficresvij,"\n");
2072:
2073: xp=vector(1,npar);
2074: dnewm=matrix(1,nlstate,1,npar);
2075: doldm=matrix(1,nlstate,1,nlstate);
2076: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2077: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2078:
2079: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2080: gpp=vector(nlstate+1,nlstate+ndeath);
2081: gmp=vector(nlstate+1,nlstate+ndeath);
2082: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2083:
2084: if(estepm < stepm){
2085: printf ("Problem %d lower than %d\n",estepm, stepm);
2086: }
2087: else hstepm=estepm;
2088: /* For example we decided to compute the life expectancy with the smallest unit */
2089: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2090: nhstepm is the number of hstepm from age to agelim
2091: nstepm is the number of stepm from age to agelin.
2092: Look at hpijx to understand the reason of that which relies in memory size
2093: and note for a fixed period like k years */
2094: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2095: survival function given by stepm (the optimization length). Unfortunately it
2096: means that if the survival funtion is printed every two years of age and if
2097: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2098: results. So we changed our mind and took the option of the best precision.
2099: */
2100: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2101: agelim = AGESUP;
2102: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2103: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2104: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2105: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2106: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2107: gp=matrix(0,nhstepm,1,nlstate);
2108: gm=matrix(0,nhstepm,1,nlstate);
2109:
2110:
2111: for(theta=1; theta <=npar; theta++){
2112: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2113: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2114: }
2115: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2116: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2117:
2118: if (popbased==1) {
2119: if(mobilav ==0){
2120: for(i=1; i<=nlstate;i++)
2121: prlim[i][i]=probs[(int)age][i][ij];
2122: }else{ /* mobilav */
2123: for(i=1; i<=nlstate;i++)
2124: prlim[i][i]=mobaverage[(int)age][i][ij];
2125: }
2126: }
2127:
2128: for(j=1; j<= nlstate; j++){
2129: for(h=0; h<=nhstepm; h++){
2130: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2131: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2132: }
2133: }
2134: /* This for computing probability of death (h=1 means
2135: computed over hstepm matrices product = hstepm*stepm months)
2136: as a weighted average of prlim.
2137: */
2138: for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
2139: for(i=1; i<= nlstate; i++)
2140: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2141: }
2142: /* end probability of death */
2143:
2144: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
2145: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2146: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2147: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2148:
2149: if (popbased==1) {
2150: if(mobilav ==0){
2151: for(i=1; i<=nlstate;i++)
2152: prlim[i][i]=probs[(int)age][i][ij];
2153: }else{ /* mobilav */
2154: for(i=1; i<=nlstate;i++)
2155: prlim[i][i]=mobaverage[(int)age][i][ij];
2156: }
2157: }
2158:
2159: for(j=1; j<= nlstate; j++){
2160: for(h=0; h<=nhstepm; h++){
2161: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2162: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2163: }
2164: }
2165: /* This for computing probability of death (h=1 means
2166: computed over hstepm matrices product = hstepm*stepm months)
2167: as a weighted average of prlim.
2168: */
2169: for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
2170: for(i=1; i<= nlstate; i++)
2171: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2172: }
2173: /* end probability of death */
2174:
2175: for(j=1; j<= nlstate; j++) /* vareij */
2176: for(h=0; h<=nhstepm; h++){
2177: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2178: }
2179: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2180: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2181: }
2182:
2183: } /* End theta */
2184:
2185: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2186:
2187: for(h=0; h<=nhstepm; h++) /* veij */
2188: for(j=1; j<=nlstate;j++)
2189: for(theta=1; theta <=npar; theta++)
2190: trgradg[h][j][theta]=gradg[h][theta][j];
2191:
2192: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
2193: for(theta=1; theta <=npar; theta++)
2194: trgradgp[j][theta]=gradgp[theta][j];
2195:
2196: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2197: for(i=1;i<=nlstate;i++)
2198: for(j=1;j<=nlstate;j++)
2199: vareij[i][j][(int)age] =0.;
2200:
2201: for(h=0;h<=nhstepm;h++){
2202: for(k=0;k<=nhstepm;k++){
2203: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2204: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2205: for(i=1;i<=nlstate;i++)
2206: for(j=1;j<=nlstate;j++)
2207: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2208: }
2209: }
2210:
2211: /* pptj */
2212: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2213: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
2214: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2215: for(i=nlstate+1;i<=nlstate+ndeath;i++)
2216: varppt[j][i]=doldmp[j][i];
2217: /* end ppptj */
2218: /* x centered again */
2219: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2220: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2221:
2222: if (popbased==1) {
2223: if(mobilav ==0){
2224: for(i=1; i<=nlstate;i++)
2225: prlim[i][i]=probs[(int)age][i][ij];
2226: }else{ /* mobilav */
2227: for(i=1; i<=nlstate;i++)
2228: prlim[i][i]=mobaverage[(int)age][i][ij];
2229: }
2230: }
2231:
2232: /* This for computing probability of death (h=1 means
2233: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2234: as a weighted average of prlim.
2235: */
2236: for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
2237: for(i=1; i<= nlstate; i++)
2238: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2239: }
2240: /* end probability of death */
2241:
2242: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2243: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2244: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2245: for(i=1; i<=nlstate;i++){
2246: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2247: }
2248: }
2249: fprintf(ficresprobmorprev,"\n");
2250:
2251: fprintf(ficresvij,"%.0f ",age );
2252: for(i=1; i<=nlstate;i++)
2253: for(j=1; j<=nlstate;j++){
2254: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2255: }
2256: fprintf(ficresvij,"\n");
2257: free_matrix(gp,0,nhstepm,1,nlstate);
2258: free_matrix(gm,0,nhstepm,1,nlstate);
2259: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2260: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2261: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2262: } /* End age */
2263: free_vector(gpp,nlstate+1,nlstate+ndeath);
2264: free_vector(gmp,nlstate+1,nlstate+ndeath);
2265: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2266: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2267: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2268: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2269: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
2270: fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);
2271: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
2272: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
2273: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
2274: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", estepm,digitp,digit);
2275: /* 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);
2276: */
2277: fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
2278:
2279: free_vector(xp,1,npar);
2280: free_matrix(doldm,1,nlstate,1,nlstate);
2281: free_matrix(dnewm,1,nlstate,1,npar);
2282: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2283: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2284: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2285: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2286: fclose(ficresprobmorprev);
2287: fclose(ficgp);
2288: fclose(fichtm);
2289: }
2290:
2291: /************ Variance of prevlim ******************/
2292: 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)
2293: {
2294: /* Variance of prevalence limit */
2295: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
2296: double **newm;
2297: double **dnewm,**doldm;
2298: int i, j, nhstepm, hstepm;
2299: int k, cptcode;
2300: double *xp;
2301: double *gp, *gm;
2302: double **gradg, **trgradg;
2303: double age,agelim;
2304: int theta;
2305:
2306: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
2307: fprintf(ficresvpl,"# Age");
2308: for(i=1; i<=nlstate;i++)
2309: fprintf(ficresvpl," %1d-%1d",i,i);
2310: fprintf(ficresvpl,"\n");
2311:
2312: xp=vector(1,npar);
2313: dnewm=matrix(1,nlstate,1,npar);
2314: doldm=matrix(1,nlstate,1,nlstate);
2315:
2316: hstepm=1*YEARM; /* Every year of age */
2317: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2318: agelim = AGESUP;
2319: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2320: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2321: if (stepm >= YEARM) hstepm=1;
2322: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2323: gradg=matrix(1,npar,1,nlstate);
2324: gp=vector(1,nlstate);
2325: gm=vector(1,nlstate);
2326:
2327: for(theta=1; theta <=npar; theta++){
2328: for(i=1; i<=npar; i++){ /* Computes gradient */
2329: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2330: }
2331: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2332: for(i=1;i<=nlstate;i++)
2333: gp[i] = prlim[i][i];
2334:
2335: for(i=1; i<=npar; i++) /* Computes gradient */
2336: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2337: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2338: for(i=1;i<=nlstate;i++)
2339: gm[i] = prlim[i][i];
2340:
2341: for(i=1;i<=nlstate;i++)
2342: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2343: } /* End theta */
2344:
2345: trgradg =matrix(1,nlstate,1,npar);
2346:
2347: for(j=1; j<=nlstate;j++)
2348: for(theta=1; theta <=npar; theta++)
2349: trgradg[j][theta]=gradg[theta][j];
2350:
2351: for(i=1;i<=nlstate;i++)
2352: varpl[i][(int)age] =0.;
2353: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2354: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2355: for(i=1;i<=nlstate;i++)
2356: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2357:
2358: fprintf(ficresvpl,"%.0f ",age );
2359: for(i=1; i<=nlstate;i++)
2360: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2361: fprintf(ficresvpl,"\n");
2362: free_vector(gp,1,nlstate);
2363: free_vector(gm,1,nlstate);
2364: free_matrix(gradg,1,npar,1,nlstate);
2365: free_matrix(trgradg,1,nlstate,1,npar);
2366: } /* End age */
2367:
2368: free_vector(xp,1,npar);
2369: free_matrix(doldm,1,nlstate,1,npar);
2370: free_matrix(dnewm,1,nlstate,1,nlstate);
2371:
2372: }
2373:
2374: /************ Variance of one-step probabilities ******************/
2375: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2376: {
2377: int i, j=0, i1, k1, l1, t, tj;
2378: int k2, l2, j1, z1;
2379: int k=0,l, cptcode;
2380: int first=1, first1;
2381: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2382: double **dnewm,**doldm;
2383: double *xp;
2384: double *gp, *gm;
2385: double **gradg, **trgradg;
2386: double **mu;
2387: double age,agelim, cov[NCOVMAX];
2388: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2389: int theta;
2390: char fileresprob[FILENAMELENGTH];
2391: char fileresprobcov[FILENAMELENGTH];
2392: char fileresprobcor[FILENAMELENGTH];
2393:
2394: double ***varpij;
2395:
2396: strcpy(fileresprob,"prob");
2397: strcat(fileresprob,fileres);
2398: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2399: printf("Problem with resultfile: %s\n", fileresprob);
2400: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2401: }
2402: strcpy(fileresprobcov,"probcov");
2403: strcat(fileresprobcov,fileres);
2404: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2405: printf("Problem with resultfile: %s\n", fileresprobcov);
2406: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2407: }
2408: strcpy(fileresprobcor,"probcor");
2409: strcat(fileresprobcor,fileres);
2410: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2411: printf("Problem with resultfile: %s\n", fileresprobcor);
2412: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2413: }
2414: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2415: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2416: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2417: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2418: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2419: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2420:
2421: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2422: fprintf(ficresprob,"# Age");
2423: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2424: fprintf(ficresprobcov,"# Age");
2425: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2426: fprintf(ficresprobcov,"# Age");
2427:
2428:
2429: for(i=1; i<=nlstate;i++)
2430: for(j=1; j<=(nlstate+ndeath);j++){
2431: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2432: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2433: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2434: }
2435: fprintf(ficresprob,"\n");
2436: fprintf(ficresprobcov,"\n");
2437: fprintf(ficresprobcor,"\n");
2438: xp=vector(1,npar);
2439: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2440: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2441: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2442: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2443: first=1;
2444: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2445: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2446: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2447: exit(0);
2448: }
2449: else{
2450: fprintf(ficgp,"\n# Routine varprob");
2451: }
2452: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2453: printf("Problem with html file: %s\n", optionfilehtm);
2454: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2455: exit(0);
2456: }
2457: else{
2458: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2459: fprintf(fichtm,"\n");
2460:
2461: fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
2462: 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");
2463: 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");
2464:
2465: }
2466:
2467: cov[1]=1;
2468: tj=cptcoveff;
2469: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2470: j1=0;
2471: for(t=1; t<=tj;t++){
2472: for(i1=1; i1<=ncodemax[t];i1++){
2473: j1++;
2474: if (cptcovn>0) {
2475: fprintf(ficresprob, "\n#********** Variable ");
2476: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2477: fprintf(ficresprob, "**********\n#");
2478: fprintf(ficresprobcov, "\n#********** Variable ");
2479: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2480: fprintf(ficresprobcov, "**********\n#");
2481:
2482: fprintf(ficgp, "\n#********** Variable ");
2483: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2484: fprintf(ficgp, "**********\n#");
2485:
2486:
2487: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2488: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2489: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2490:
2491: fprintf(ficresprobcor, "\n#********** Variable ");
2492: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2493: fprintf(ficgp, "**********\n#");
2494: }
2495:
2496: for (age=bage; age<=fage; age ++){
2497: cov[2]=age;
2498: for (k=1; k<=cptcovn;k++) {
2499: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2500: }
2501: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2502: for (k=1; k<=cptcovprod;k++)
2503: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2504:
2505: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2506: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2507: gp=vector(1,(nlstate)*(nlstate+ndeath));
2508: gm=vector(1,(nlstate)*(nlstate+ndeath));
2509:
2510: for(theta=1; theta <=npar; theta++){
2511: for(i=1; i<=npar; i++)
2512: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2513:
2514: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2515:
2516: k=0;
2517: for(i=1; i<= (nlstate); i++){
2518: for(j=1; j<=(nlstate+ndeath);j++){
2519: k=k+1;
2520: gp[k]=pmmij[i][j];
2521: }
2522: }
2523:
2524: for(i=1; i<=npar; i++)
2525: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2526:
2527: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2528: k=0;
2529: for(i=1; i<=(nlstate); i++){
2530: for(j=1; j<=(nlstate+ndeath);j++){
2531: k=k+1;
2532: gm[k]=pmmij[i][j];
2533: }
2534: }
2535:
2536: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
2537: gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
2538: }
2539:
2540: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2541: for(theta=1; theta <=npar; theta++)
2542: trgradg[j][theta]=gradg[theta][j];
2543:
2544: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2545: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
2546: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2547: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2548: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2549: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2550:
2551: pmij(pmmij,cov,ncovmodel,x,nlstate);
2552:
2553: k=0;
2554: for(i=1; i<=(nlstate); i++){
2555: for(j=1; j<=(nlstate+ndeath);j++){
2556: k=k+1;
2557: mu[k][(int) age]=pmmij[i][j];
2558: }
2559: }
2560: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2561: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2562: varpij[i][j][(int)age] = doldm[i][j];
2563:
2564: /*printf("\n%d ",(int)age);
2565: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2566: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2567: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2568: }*/
2569:
2570: fprintf(ficresprob,"\n%d ",(int)age);
2571: fprintf(ficresprobcov,"\n%d ",(int)age);
2572: fprintf(ficresprobcor,"\n%d ",(int)age);
2573:
2574: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2575: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2576: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2577: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2578: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2579: }
2580: i=0;
2581: for (k=1; k<=(nlstate);k++){
2582: for (l=1; l<=(nlstate+ndeath);l++){
2583: i=i++;
2584: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2585: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2586: for (j=1; j<=i;j++){
2587: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2588: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
2589: }
2590: }
2591: }/* end of loop for state */
2592: } /* end of loop for age */
2593:
2594: /* Confidence intervalle of pij */
2595: /*
2596: fprintf(ficgp,"\nset noparametric;unset label");
2597: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
2598: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2599: 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);
2600: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
2601: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
2602: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
2603: */
2604:
2605: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
2606: first1=1;
2607: for (k2=1; k2<=(nlstate);k2++){
2608: for (l2=1; l2<=(nlstate+ndeath);l2++){
2609: if(l2==k2) continue;
2610: j=(k2-1)*(nlstate+ndeath)+l2;
2611: for (k1=1; k1<=(nlstate);k1++){
2612: for (l1=1; l1<=(nlstate+ndeath);l1++){
2613: if(l1==k1) continue;
2614: i=(k1-1)*(nlstate+ndeath)+l1;
2615: if(i<=j) continue;
2616: for (age=bage; age<=fage; age ++){
2617: if ((int)age %5==0){
2618: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
2619: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
2620: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
2621: mu1=mu[i][(int) age]/stepm*YEARM ;
2622: mu2=mu[j][(int) age]/stepm*YEARM;
2623: c12=cv12/sqrt(v1*v2);
2624: /* Computing eigen value of matrix of covariance */
2625: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2626: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2627: /* Eigen vectors */
2628: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
2629: /*v21=sqrt(1.-v11*v11); *//* error */
2630: v21=(lc1-v1)/cv12*v11;
2631: v12=-v21;
2632: v22=v11;
2633: tnalp=v21/v11;
2634: if(first1==1){
2635: first1=0;
2636: 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);
2637: }
2638: 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);
2639: /*printf(fignu*/
2640: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
2641: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
2642: if(first==1){
2643: first=0;
2644: fprintf(ficgp,"\nset parametric;unset label");
2645: 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);
2646: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2647: 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);
2648: fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
2649: fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
2650: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
2651: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2652: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2653: 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",\
2654: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2655: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2656: }else{
2657: first=0;
2658: fprintf(fichtm," %d (%.3f),",(int) age, c12);
2659: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2660: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2661: 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",\
2662: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2663: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2664: }/* if first */
2665: } /* age mod 5 */
2666: } /* end loop age */
2667: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
2668: first=1;
2669: } /*l12 */
2670: } /* k12 */
2671: } /*l1 */
2672: }/* k1 */
2673: } /* loop covariates */
2674: }
2675: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
2676: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
2677: free_vector(xp,1,npar);
2678: fclose(ficresprob);
2679: fclose(ficresprobcov);
2680: fclose(ficresprobcor);
2681: fclose(ficgp);
2682: fclose(fichtm);
2683: }
2684:
2685:
2686: /******************* Printing html file ***********/
2687: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
2688: int lastpass, int stepm, int weightopt, char model[],\
2689: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
2690: int popforecast, int estepm ,\
2691: double jprev1, double mprev1,double anprev1, \
2692: double jprev2, double mprev2,double anprev2){
2693: int jj1, k1, i1, cpt;
2694: /*char optionfilehtm[FILENAMELENGTH];*/
2695: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2696: printf("Problem with %s \n",optionfilehtm), exit(0);
2697: fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
2698: }
2699:
2700: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
2701: - 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
2702: - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
2703: - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
2704: - Life expectancies by age and initial health status (estepm=%2d months):
2705: <a href=\"e%s\">e%s</a> <br>\n</li>", \
2706: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
2707:
2708: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
2709:
2710: m=cptcoveff;
2711: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2712:
2713: jj1=0;
2714: for(k1=1; k1<=m;k1++){
2715: for(i1=1; i1<=ncodemax[k1];i1++){
2716: jj1++;
2717: if (cptcovn > 0) {
2718: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2719: for (cpt=1; cpt<=cptcoveff;cpt++)
2720: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2721: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2722: }
2723: /* Pij */
2724: 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>
2725: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2726: /* Quasi-incidences */
2727: 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>
2728: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2729: /* Stable prevalence in each health state */
2730: for(cpt=1; cpt<nlstate;cpt++){
2731: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
2732: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2733: }
2734: for(cpt=1; cpt<=nlstate;cpt++) {
2735: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
2736: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2737: }
2738: fprintf(fichtm,"\n<br>- Total life expectancy by age and
2739: health expectancies in states (1) and (2): e%s%d.png<br>
2740: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2741: } /* end i1 */
2742: }/* End k1 */
2743: fprintf(fichtm,"</ul>");
2744:
2745:
2746: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
2747: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
2748: - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
2749: - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
2750: - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
2751: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
2752: - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
2753: - 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);
2754:
2755: if(popforecast==1) fprintf(fichtm,"\n
2756: - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
2757: - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
2758: <br>",fileres,fileres,fileres,fileres);
2759: else
2760: 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);
2761: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
2762:
2763: m=cptcoveff;
2764: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2765:
2766: jj1=0;
2767: for(k1=1; k1<=m;k1++){
2768: for(i1=1; i1<=ncodemax[k1];i1++){
2769: jj1++;
2770: if (cptcovn > 0) {
2771: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2772: for (cpt=1; cpt<=cptcoveff;cpt++)
2773: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2774: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2775: }
2776: for(cpt=1; cpt<=nlstate;cpt++) {
2777: fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
2778: interval) in state (%d): v%s%d%d.png <br>
2779: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2780: }
2781: } /* end i1 */
2782: }/* End k1 */
2783: fprintf(fichtm,"</ul>");
2784: fclose(fichtm);
2785: }
2786:
2787: /******************* Gnuplot file **************/
2788: void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
2789:
2790: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
2791: int ng;
2792: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2793: printf("Problem with file %s",optionfilegnuplot);
2794: fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
2795: }
2796:
2797: /*#ifdef windows */
2798: fprintf(ficgp,"cd \"%s\" \n",pathc);
2799: /*#endif */
2800: m=pow(2,cptcoveff);
2801:
2802: /* 1eme*/
2803: for (cpt=1; cpt<= nlstate ; cpt ++) {
2804: for (k1=1; k1<= m ; k1 ++) {
2805: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2806: 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);
2807:
2808: for (i=1; i<= nlstate ; i ++) {
2809: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2810: else fprintf(ficgp," \%%*lf (\%%*lf)");
2811: }
2812: fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
2813: for (i=1; i<= nlstate ; i ++) {
2814: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2815: else fprintf(ficgp," \%%*lf (\%%*lf)");
2816: }
2817: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
2818: for (i=1; i<= nlstate ; i ++) {
2819: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2820: else fprintf(ficgp," \%%*lf (\%%*lf)");
2821: }
2822: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2823: }
2824: }
2825: /*2 eme*/
2826:
2827: for (k1=1; k1<= m ; k1 ++) {
2828: fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
2829: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
2830:
2831: for (i=1; i<= nlstate+1 ; i ++) {
2832: k=2*i;
2833: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2834: for (j=1; j<= nlstate+1 ; j ++) {
2835: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2836: else fprintf(ficgp," \%%*lf (\%%*lf)");
2837: }
2838: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2839: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2840: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2841: for (j=1; j<= nlstate+1 ; j ++) {
2842: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2843: else fprintf(ficgp," \%%*lf (\%%*lf)");
2844: }
2845: fprintf(ficgp,"\" t\"\" w l 0,");
2846: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
2847: for (j=1; j<= nlstate+1 ; j ++) {
2848: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2849: else fprintf(ficgp," \%%*lf (\%%*lf)");
2850: }
2851: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2852: else fprintf(ficgp,"\" t\"\" w l 0,");
2853: }
2854: }
2855:
2856: /*3eme*/
2857:
2858: for (k1=1; k1<= m ; k1 ++) {
2859: for (cpt=1; cpt<= nlstate ; cpt ++) {
2860: k=2+nlstate*(2*cpt-2);
2861: fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2862: fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
2863: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2864: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2865: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2866: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2867: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2868: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2869:
2870: */
2871: for (i=1; i< nlstate ; i ++) {
2872: 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);
2873:
2874: }
2875: }
2876: }
2877:
2878: /* CV preval stat */
2879: for (k1=1; k1<= m ; k1 ++) {
2880: for (cpt=1; cpt<nlstate ; cpt ++) {
2881: k=3;
2882: fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2883: 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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
2884:
2885: for (i=1; i< nlstate ; i ++)
2886: fprintf(ficgp,"+$%d",k+i+1);
2887: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
2888:
2889: l=3+(nlstate+ndeath)*cpt;
2890: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
2891: for (i=1; i< nlstate ; i ++) {
2892: l=3+(nlstate+ndeath)*cpt;
2893: fprintf(ficgp,"+$%d",l+i+1);
2894: }
2895: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
2896: }
2897: }
2898:
2899: /* proba elementaires */
2900: for(i=1,jk=1; i <=nlstate; i++){
2901: for(k=1; k <=(nlstate+ndeath); k++){
2902: if (k != i) {
2903: for(j=1; j <=ncovmodel; j++){
2904: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
2905: jk++;
2906: fprintf(ficgp,"\n");
2907: }
2908: }
2909: }
2910: }
2911:
2912: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
2913: for(jk=1; jk <=m; jk++) {
2914: fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
2915: if (ng==2)
2916: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
2917: else
2918: fprintf(ficgp,"\nset title \"Probability\"\n");
2919: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
2920: i=1;
2921: for(k2=1; k2<=nlstate; k2++) {
2922: k3=i;
2923: for(k=1; k<=(nlstate+ndeath); k++) {
2924: if (k != k2){
2925: if(ng==2)
2926: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
2927: else
2928: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
2929: ij=1;
2930: for(j=3; j <=ncovmodel; j++) {
2931: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2932: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2933: ij++;
2934: }
2935: else
2936: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2937: }
2938: fprintf(ficgp,")/(1");
2939:
2940: for(k1=1; k1 <=nlstate; k1++){
2941: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
2942: ij=1;
2943: for(j=3; j <=ncovmodel; j++){
2944: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2945: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2946: ij++;
2947: }
2948: else
2949: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2950: }
2951: fprintf(ficgp,")");
2952: }
2953: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
2954: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
2955: i=i+ncovmodel;
2956: }
2957: } /* end k */
2958: } /* end k2 */
2959: } /* end jk */
2960: } /* end ng */
2961: fclose(ficgp);
2962: } /* end gnuplot */
2963:
2964:
2965: /*************** Moving average **************/
2966: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
2967:
2968: int i, cpt, cptcod;
2969: int modcovmax =1;
2970: int mobilavrange, mob;
2971: double age;
2972:
2973: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
2974: a covariate has 2 modalities */
2975: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
2976:
2977: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
2978: if(mobilav==1) mobilavrange=5; /* default */
2979: else mobilavrange=mobilav;
2980: for (age=bage; age<=fage; age++)
2981: for (i=1; i<=nlstate;i++)
2982: for (cptcod=1;cptcod<=modcovmax;cptcod++)
2983: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
2984: /* We keep the original values on the extreme ages bage, fage and for
2985: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
2986: we use a 5 terms etc. until the borders are no more concerned.
2987: */
2988: for (mob=3;mob <=mobilavrange;mob=mob+2){
2989: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
2990: for (i=1; i<=nlstate;i++){
2991: for (cptcod=1;cptcod<=modcovmax;cptcod++){
2992: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
2993: for (cpt=1;cpt<=(mob-1)/2;cpt++){
2994: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
2995: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
2996: }
2997: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
2998: }
2999: }
3000: }/* end age */
3001: }/* end mob */
3002: }else return -1;
3003: return 0;
3004: }/* End movingaverage */
3005:
3006:
3007: /************** Forecasting ******************/
3008: 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){
3009:
3010: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3011: int *popage;
3012: double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3013: double *popeffectif,*popcount;
3014: double ***p3mat;
3015: double ***mobaverage;
3016: char fileresf[FILENAMELENGTH];
3017:
3018: agelim=AGESUP;
3019: calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
3020:
3021: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
3022:
3023:
3024: strcpy(fileresf,"f");
3025: strcat(fileresf,fileres);
3026: if((ficresf=fopen(fileresf,"w"))==NULL) {
3027: printf("Problem with forecast resultfile: %s\n", fileresf);
3028: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3029: }
3030: printf("Computing forecasting: result on file '%s' \n", fileresf);
3031: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3032:
3033: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3034:
3035: if (mobilav!=0) {
3036: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3037: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3038: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3039: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3040: }
3041: }
3042:
3043: stepsize=(int) (stepm+YEARM-1)/YEARM;
3044: if (stepm<=12) stepsize=1;
3045:
3046: agelim=AGESUP;
3047:
3048: hstepm=1;
3049: hstepm=hstepm/stepm;
3050: yp1=modf(dateintmean,&yp);
3051: anprojmean=yp;
3052: yp2=modf((yp1*12),&yp);
3053: mprojmean=yp;
3054: yp1=modf((yp2*30.5),&yp);
3055: jprojmean=yp;
3056: if(jprojmean==0) jprojmean=1;
3057: if(mprojmean==0) jprojmean=1;
3058:
3059: fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);
3060:
3061: for(cptcov=1;cptcov<=i2;cptcov++){
3062: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3063: k=k+1;
3064: fprintf(ficresf,"\n#******");
3065: for(j=1;j<=cptcoveff;j++) {
3066: fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3067: }
3068: fprintf(ficresf,"******\n");
3069: fprintf(ficresf,"# StartingAge FinalAge");
3070: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
3071:
3072:
3073: for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {
3074: fprintf(ficresf,"\n");
3075: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);
3076:
3077: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
3078: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3079: nhstepm = nhstepm/hstepm;
3080:
3081: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3082: oldm=oldms;savm=savms;
3083: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3084:
3085: for (h=0; h<=nhstepm; h++){
3086: if (h==(int) (calagedate+YEARM*cpt)) {
3087: fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
3088: }
3089: for(j=1; j<=nlstate+ndeath;j++) {
3090: kk1=0.;kk2=0;
3091: for(i=1; i<=nlstate;i++) {
3092: if (mobilav==1)
3093: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3094: else {
3095: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3096: }
3097:
3098: }
3099: if (h==(int)(calagedate+12*cpt)){
3100: fprintf(ficresf," %.3f", kk1);
3101:
3102: }
3103: }
3104: }
3105: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3106: }
3107: }
3108: }
3109: }
3110:
3111: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3112:
3113: fclose(ficresf);
3114: }
3115: /************** Forecasting ******************/
3116: 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){
3117:
3118: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3119: int *popage;
3120: double calagedate, agelim, kk1, kk2;
3121: double *popeffectif,*popcount;
3122: double ***p3mat,***tabpop,***tabpopprev;
3123: double ***mobaverage;
3124: char filerespop[FILENAMELENGTH];
3125:
3126: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3127: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3128: agelim=AGESUP;
3129: calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
3130:
3131: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
3132:
3133:
3134: strcpy(filerespop,"pop");
3135: strcat(filerespop,fileres);
3136: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3137: printf("Problem with forecast resultfile: %s\n", filerespop);
3138: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3139: }
3140: printf("Computing forecasting: result on file '%s' \n", filerespop);
3141: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3142:
3143: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3144:
3145: if (mobilav!=0) {
3146: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3147: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3148: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3149: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3150: }
3151: }
3152:
3153: stepsize=(int) (stepm+YEARM-1)/YEARM;
3154: if (stepm<=12) stepsize=1;
3155:
3156: agelim=AGESUP;
3157:
3158: hstepm=1;
3159: hstepm=hstepm/stepm;
3160:
3161: if (popforecast==1) {
3162: if((ficpop=fopen(popfile,"r"))==NULL) {
3163: printf("Problem with population file : %s\n",popfile);exit(0);
3164: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3165: }
3166: popage=ivector(0,AGESUP);
3167: popeffectif=vector(0,AGESUP);
3168: popcount=vector(0,AGESUP);
3169:
3170: i=1;
3171: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3172:
3173: imx=i;
3174: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3175: }
3176:
3177: for(cptcov=1;cptcov<=i2;cptcov++){
3178: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3179: k=k+1;
3180: fprintf(ficrespop,"\n#******");
3181: for(j=1;j<=cptcoveff;j++) {
3182: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3183: }
3184: fprintf(ficrespop,"******\n");
3185: fprintf(ficrespop,"# Age");
3186: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3187: if (popforecast==1) fprintf(ficrespop," [Population]");
3188:
3189: for (cpt=0; cpt<=0;cpt++) {
3190: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3191:
3192: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
3193: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3194: nhstepm = nhstepm/hstepm;
3195:
3196: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3197: oldm=oldms;savm=savms;
3198: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3199:
3200: for (h=0; h<=nhstepm; h++){
3201: if (h==(int) (calagedate+YEARM*cpt)) {
3202: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3203: }
3204: for(j=1; j<=nlstate+ndeath;j++) {
3205: kk1=0.;kk2=0;
3206: for(i=1; i<=nlstate;i++) {
3207: if (mobilav==1)
3208: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3209: else {
3210: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3211: }
3212: }
3213: if (h==(int)(calagedate+12*cpt)){
3214: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3215: /*fprintf(ficrespop," %.3f", kk1);
3216: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3217: }
3218: }
3219: for(i=1; i<=nlstate;i++){
3220: kk1=0.;
3221: for(j=1; j<=nlstate;j++){
3222: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3223: }
3224: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
3225: }
3226:
3227: if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)
3228: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3229: }
3230: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3231: }
3232: }
3233:
3234: /******/
3235:
3236: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3237: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3238: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
3239: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3240: nhstepm = nhstepm/hstepm;
3241:
3242: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3243: oldm=oldms;savm=savms;
3244: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3245: for (h=0; h<=nhstepm; h++){
3246: if (h==(int) (calagedate+YEARM*cpt)) {
3247: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3248: }
3249: for(j=1; j<=nlstate+ndeath;j++) {
3250: kk1=0.;kk2=0;
3251: for(i=1; i<=nlstate;i++) {
3252: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3253: }
3254: if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);
3255: }
3256: }
3257: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3258: }
3259: }
3260: }
3261: }
3262:
3263: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3264:
3265: if (popforecast==1) {
3266: free_ivector(popage,0,AGESUP);
3267: free_vector(popeffectif,0,AGESUP);
3268: free_vector(popcount,0,AGESUP);
3269: }
3270: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3271: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3272: fclose(ficrespop);
3273: }
3274:
3275: /***********************************************/
3276: /**************** Main Program *****************/
3277: /***********************************************/
3278:
3279: int main(int argc, char *argv[])
3280: {
3281: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
3282: int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
3283: double agedeb, agefin,hf;
3284: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3285:
3286: double fret;
3287: double **xi,tmp,delta;
3288:
3289: double dum; /* Dummy variable */
3290: double ***p3mat;
3291: double ***mobaverage;
3292: int *indx;
3293: char line[MAXLINE], linepar[MAXLINE];
3294: char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
3295: int firstobs=1, lastobs=10;
3296: int sdeb, sfin; /* Status at beginning and end */
3297: int c, h , cpt,l;
3298: int ju,jl, mi;
3299: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
3300: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
3301: int mobilav=0,popforecast=0;
3302: int hstepm, nhstepm;
3303: double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
3304:
3305: double bage, fage, age, agelim, agebase;
3306: double ftolpl=FTOL;
3307: double **prlim;
3308: double *severity;
3309: double ***param; /* Matrix of parameters */
3310: double *p;
3311: double **matcov; /* Matrix of covariance */
3312: double ***delti3; /* Scale */
3313: double *delti; /* Scale */
3314: double ***eij, ***vareij;
3315: double **varpl; /* Variances of prevalence limits by age */
3316: double *epj, vepp;
3317: double kk1, kk2;
3318: double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
3319:
3320: char *alph[]={"a","a","b","c","d","e"}, str[4];
3321:
3322:
3323: char z[1]="c", occ;
3324: #include <sys/time.h>
3325: #include <time.h>
3326: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
3327:
3328: /* long total_usecs;
3329: struct timeval start_time, end_time;
3330:
3331: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
3332: getcwd(pathcd, size);
3333:
3334: printf("\n%s",version);
3335: if(argc <=1){
3336: printf("\nEnter the parameter file name: ");
3337: scanf("%s",pathtot);
3338: }
3339: else{
3340: strcpy(pathtot,argv[1]);
3341: }
3342: /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
3343: /*cygwin_split_path(pathtot,path,optionfile);
3344: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3345: /* cutv(path,optionfile,pathtot,'\\');*/
3346:
3347: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
3348: printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3349: chdir(path);
3350: replace(pathc,path);
3351:
3352: /*-------- arguments in the command line --------*/
3353:
3354: /* Log file */
3355: strcat(filelog, optionfilefiname);
3356: strcat(filelog,".log"); /* */
3357: if((ficlog=fopen(filelog,"w"))==NULL) {
3358: printf("Problem with logfile %s\n",filelog);
3359: goto end;
3360: }
3361: fprintf(ficlog,"Log filename:%s\n",filelog);
3362: fprintf(ficlog,"\n%s",version);
3363: fprintf(ficlog,"\nEnter the parameter file name: ");
3364: fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3365: fflush(ficlog);
3366:
3367: /* */
3368: strcpy(fileres,"r");
3369: strcat(fileres, optionfilefiname);
3370: strcat(fileres,".txt"); /* Other files have txt extension */
3371:
3372: /*---------arguments file --------*/
3373:
3374: if((ficpar=fopen(optionfile,"r"))==NULL) {
3375: printf("Problem with optionfile %s\n",optionfile);
3376: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
3377: goto end;
3378: }
3379:
3380: strcpy(filereso,"o");
3381: strcat(filereso,fileres);
3382: if((ficparo=fopen(filereso,"w"))==NULL) {
3383: printf("Problem with Output resultfile: %s\n", filereso);
3384: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
3385: goto end;
3386: }
3387:
3388: /* Reads comments: lines beginning with '#' */
3389: while((c=getc(ficpar))=='#' && c!= EOF){
3390: ungetc(c,ficpar);
3391: fgets(line, MAXLINE, ficpar);
3392: puts(line);
3393: fputs(line,ficparo);
3394: }
3395: ungetc(c,ficpar);
3396:
3397: 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);
3398: 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);
3399: 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);
3400: while((c=getc(ficpar))=='#' && c!= EOF){
3401: ungetc(c,ficpar);
3402: fgets(line, MAXLINE, ficpar);
3403: puts(line);
3404: fputs(line,ficparo);
3405: }
3406: ungetc(c,ficpar);
3407:
3408:
3409: covar=matrix(0,NCOVMAX,1,n);
3410: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
3411: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
3412:
3413: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
3414: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
3415:
3416: /* Read guess parameters */
3417: /* Reads comments: lines beginning with '#' */
3418: while((c=getc(ficpar))=='#' && c!= EOF){
3419: ungetc(c,ficpar);
3420: fgets(line, MAXLINE, ficpar);
3421: puts(line);
3422: fputs(line,ficparo);
3423: }
3424: ungetc(c,ficpar);
3425:
3426: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
3427: for(i=1; i <=nlstate; i++)
3428: for(j=1; j <=nlstate+ndeath-1; j++){
3429: fscanf(ficpar,"%1d%1d",&i1,&j1);
3430: fprintf(ficparo,"%1d%1d",i1,j1);
3431: if(mle==1)
3432: printf("%1d%1d",i,j);
3433: fprintf(ficlog,"%1d%1d",i,j);
3434: for(k=1; k<=ncovmodel;k++){
3435: fscanf(ficpar," %lf",¶m[i][j][k]);
3436: if(mle==1){
3437: printf(" %lf",param[i][j][k]);
3438: fprintf(ficlog," %lf",param[i][j][k]);
3439: }
3440: else
3441: fprintf(ficlog," %lf",param[i][j][k]);
3442: fprintf(ficparo," %lf",param[i][j][k]);
3443: }
3444: fscanf(ficpar,"\n");
3445: if(mle==1)
3446: printf("\n");
3447: fprintf(ficlog,"\n");
3448: fprintf(ficparo,"\n");
3449: }
3450:
3451: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
3452:
3453: p=param[1][1];
3454:
3455: /* Reads comments: lines beginning with '#' */
3456: while((c=getc(ficpar))=='#' && c!= EOF){
3457: ungetc(c,ficpar);
3458: fgets(line, MAXLINE, ficpar);
3459: puts(line);
3460: fputs(line,ficparo);
3461: }
3462: ungetc(c,ficpar);
3463:
3464: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
3465: delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
3466: for(i=1; i <=nlstate; i++){
3467: for(j=1; j <=nlstate+ndeath-1; j++){
3468: fscanf(ficpar,"%1d%1d",&i1,&j1);
3469: printf("%1d%1d",i,j);
3470: fprintf(ficparo,"%1d%1d",i1,j1);
3471: for(k=1; k<=ncovmodel;k++){
3472: fscanf(ficpar,"%le",&delti3[i][j][k]);
3473: printf(" %le",delti3[i][j][k]);
3474: fprintf(ficparo," %le",delti3[i][j][k]);
3475: }
3476: fscanf(ficpar,"\n");
3477: printf("\n");
3478: fprintf(ficparo,"\n");
3479: }
3480: }
3481: delti=delti3[1][1];
3482:
3483: /* Reads comments: lines beginning with '#' */
3484: while((c=getc(ficpar))=='#' && c!= EOF){
3485: ungetc(c,ficpar);
3486: fgets(line, MAXLINE, ficpar);
3487: puts(line);
3488: fputs(line,ficparo);
3489: }
3490: ungetc(c,ficpar);
3491:
3492: matcov=matrix(1,npar,1,npar);
3493: for(i=1; i <=npar; i++){
3494: fscanf(ficpar,"%s",&str);
3495: if(mle==1)
3496: printf("%s",str);
3497: fprintf(ficlog,"%s",str);
3498: fprintf(ficparo,"%s",str);
3499: for(j=1; j <=i; j++){
3500: fscanf(ficpar," %le",&matcov[i][j]);
3501: if(mle==1){
3502: printf(" %.5le",matcov[i][j]);
3503: fprintf(ficlog," %.5le",matcov[i][j]);
3504: }
3505: else
3506: fprintf(ficlog," %.5le",matcov[i][j]);
3507: fprintf(ficparo," %.5le",matcov[i][j]);
3508: }
3509: fscanf(ficpar,"\n");
3510: if(mle==1)
3511: printf("\n");
3512: fprintf(ficlog,"\n");
3513: fprintf(ficparo,"\n");
3514: }
3515: for(i=1; i <=npar; i++)
3516: for(j=i+1;j<=npar;j++)
3517: matcov[i][j]=matcov[j][i];
3518:
3519: if(mle==1)
3520: printf("\n");
3521: fprintf(ficlog,"\n");
3522:
3523:
3524: /*-------- Rewriting paramater file ----------*/
3525: strcpy(rfileres,"r"); /* "Rparameterfile */
3526: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
3527: strcat(rfileres,"."); /* */
3528: strcat(rfileres,optionfilext); /* Other files have txt extension */
3529: if((ficres =fopen(rfileres,"w"))==NULL) {
3530: printf("Problem writing new parameter file: %s\n", fileres);goto end;
3531: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
3532: }
3533: fprintf(ficres,"#%s\n",version);
3534:
3535: /*-------- data file ----------*/
3536: if((fic=fopen(datafile,"r"))==NULL) {
3537: printf("Problem with datafile: %s\n", datafile);goto end;
3538: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
3539: }
3540:
3541: n= lastobs;
3542: severity = vector(1,maxwav);
3543: outcome=imatrix(1,maxwav+1,1,n);
3544: num=ivector(1,n);
3545: moisnais=vector(1,n);
3546: annais=vector(1,n);
3547: moisdc=vector(1,n);
3548: andc=vector(1,n);
3549: agedc=vector(1,n);
3550: cod=ivector(1,n);
3551: weight=vector(1,n);
3552: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
3553: mint=matrix(1,maxwav,1,n);
3554: anint=matrix(1,maxwav,1,n);
3555: s=imatrix(1,maxwav+1,1,n);
3556: tab=ivector(1,NCOVMAX);
3557: ncodemax=ivector(1,8);
3558:
3559: i=1;
3560: while (fgets(line, MAXLINE, fic) != NULL) {
3561: if ((i >= firstobs) && (i <=lastobs)) {
3562:
3563: for (j=maxwav;j>=1;j--){
3564: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
3565: strcpy(line,stra);
3566: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3567: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3568: }
3569:
3570: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
3571: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
3572:
3573: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
3574: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
3575:
3576: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
3577: for (j=ncovcol;j>=1;j--){
3578: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3579: }
3580: num[i]=atol(stra);
3581:
3582: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
3583: 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;}*/
3584:
3585: i=i+1;
3586: }
3587: }
3588: /* printf("ii=%d", ij);
3589: scanf("%d",i);*/
3590: imx=i-1; /* Number of individuals */
3591:
3592: /* for (i=1; i<=imx; i++){
3593: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
3594: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
3595: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
3596: }*/
3597: /* for (i=1; i<=imx; i++){
3598: if (s[4][i]==9) s[4][i]=-1;
3599: 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]));}*/
3600:
3601:
3602: /* Calculation of the number of parameter from char model*/
3603: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
3604: Tprod=ivector(1,15);
3605: Tvaraff=ivector(1,15);
3606: Tvard=imatrix(1,15,1,2);
3607: Tage=ivector(1,15);
3608:
3609: if (strlen(model) >1){ /* If there is at least 1 covariate */
3610: j=0, j1=0, k1=1, k2=1;
3611: j=nbocc(model,'+'); /* j=Number of '+' */
3612: j1=nbocc(model,'*'); /* j1=Number of '*' */
3613: cptcovn=j+1;
3614: cptcovprod=j1; /*Number of products */
3615:
3616: strcpy(modelsav,model);
3617: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
3618: printf("Error. Non available option model=%s ",model);
3619: fprintf(ficlog,"Error. Non available option model=%s ",model);
3620: goto end;
3621: }
3622:
3623: /* This loop fills the array Tvar from the string 'model'.*/
3624:
3625: for(i=(j+1); i>=1;i--){
3626: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
3627: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
3628: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
3629: /*scanf("%d",i);*/
3630: if (strchr(strb,'*')) { /* Model includes a product */
3631: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
3632: if (strcmp(strc,"age")==0) { /* Vn*age */
3633: cptcovprod--;
3634: cutv(strb,stre,strd,'V');
3635: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
3636: cptcovage++;
3637: Tage[cptcovage]=i;
3638: /*printf("stre=%s ", stre);*/
3639: }
3640: else if (strcmp(strd,"age")==0) { /* or age*Vn */
3641: cptcovprod--;
3642: cutv(strb,stre,strc,'V');
3643: Tvar[i]=atoi(stre);
3644: cptcovage++;
3645: Tage[cptcovage]=i;
3646: }
3647: else { /* Age is not in the model */
3648: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
3649: Tvar[i]=ncovcol+k1;
3650: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
3651: Tprod[k1]=i;
3652: Tvard[k1][1]=atoi(strc); /* m*/
3653: Tvard[k1][2]=atoi(stre); /* n */
3654: Tvar[cptcovn+k2]=Tvard[k1][1];
3655: Tvar[cptcovn+k2+1]=Tvard[k1][2];
3656: for (k=1; k<=lastobs;k++)
3657: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
3658: k1++;
3659: k2=k2+2;
3660: }
3661: }
3662: else { /* no more sum */
3663: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
3664: /* scanf("%d",i);*/
3665: cutv(strd,strc,strb,'V');
3666: Tvar[i]=atoi(strc);
3667: }
3668: strcpy(modelsav,stra);
3669: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
3670: scanf("%d",i);*/
3671: } /* end of loop + */
3672: } /* end model */
3673:
3674: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
3675: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
3676:
3677: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
3678: printf("cptcovprod=%d ", cptcovprod);
3679: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
3680:
3681: scanf("%d ",i);
3682: fclose(fic);*/
3683:
3684: /* if(mle==1){*/
3685: if (weightopt != 1) { /* Maximisation without weights*/
3686: for(i=1;i<=n;i++) weight[i]=1.0;
3687: }
3688: /*-calculation of age at interview from date of interview and age at death -*/
3689: agev=matrix(1,maxwav,1,imx);
3690:
3691: for (i=1; i<=imx; i++) {
3692: for(m=2; (m<= maxwav); m++) {
3693: if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
3694: anint[m][i]=9999;
3695: s[m][i]=-1;
3696: }
3697: if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
3698: }
3699: }
3700:
3701: for (i=1; i<=imx; i++) {
3702: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
3703: for(m=1; (m<= maxwav); m++){
3704: if(s[m][i] >0){
3705: if (s[m][i] >= nlstate+1) {
3706: if(agedc[i]>0)
3707: if(moisdc[i]!=99 && andc[i]!=9999)
3708: agev[m][i]=agedc[i];
3709: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
3710: else {
3711: if (andc[i]!=9999){
3712: printf("Warning negative age at death: %d line:%d\n",num[i],i);
3713: fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
3714: agev[m][i]=-1;
3715: }
3716: }
3717: }
3718: else if(s[m][i] !=9){ /* Should no more exist */
3719: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
3720: if(mint[m][i]==99 || anint[m][i]==9999)
3721: agev[m][i]=1;
3722: else if(agev[m][i] <agemin){
3723: agemin=agev[m][i];
3724: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
3725: }
3726: else if(agev[m][i] >agemax){
3727: agemax=agev[m][i];
3728: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
3729: }
3730: /*agev[m][i]=anint[m][i]-annais[i];*/
3731: /* agev[m][i] = age[i]+2*m;*/
3732: }
3733: else { /* =9 */
3734: agev[m][i]=1;
3735: s[m][i]=-1;
3736: }
3737: }
3738: else /*= 0 Unknown */
3739: agev[m][i]=1;
3740: }
3741:
3742: }
3743: for (i=1; i<=imx; i++) {
3744: for(m=1; (m<= maxwav); m++){
3745: if (s[m][i] > (nlstate+ndeath)) {
3746: 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);
3747: 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);
3748: goto end;
3749: }
3750: }
3751: }
3752:
3753: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3754: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3755:
3756: free_vector(severity,1,maxwav);
3757: free_imatrix(outcome,1,maxwav+1,1,n);
3758: free_vector(moisnais,1,n);
3759: free_vector(annais,1,n);
3760: /* free_matrix(mint,1,maxwav,1,n);
3761: free_matrix(anint,1,maxwav,1,n);*/
3762: free_vector(moisdc,1,n);
3763: free_vector(andc,1,n);
3764:
3765:
3766: wav=ivector(1,imx);
3767: dh=imatrix(1,lastpass-firstpass+1,1,imx);
3768: bh=imatrix(1,lastpass-firstpass+1,1,imx);
3769: mw=imatrix(1,lastpass-firstpass+1,1,imx);
3770:
3771: /* Concatenates waves */
3772: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
3773:
3774: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
3775:
3776: Tcode=ivector(1,100);
3777: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
3778: ncodemax[1]=1;
3779: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
3780:
3781: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
3782: the estimations*/
3783: h=0;
3784: m=pow(2,cptcoveff);
3785:
3786: for(k=1;k<=cptcoveff; k++){
3787: for(i=1; i <=(m/pow(2,k));i++){
3788: for(j=1; j <= ncodemax[k]; j++){
3789: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
3790: h++;
3791: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
3792: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
3793: }
3794: }
3795: }
3796: }
3797: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
3798: codtab[1][2]=1;codtab[2][2]=2; */
3799: /* for(i=1; i <=m ;i++){
3800: for(k=1; k <=cptcovn; k++){
3801: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
3802: }
3803: printf("\n");
3804: }
3805: scanf("%d",i);*/
3806:
3807: /* Calculates basic frequencies. Computes observed prevalence at single age
3808: and prints on file fileres'p'. */
3809:
3810: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3811: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3812: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3813: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3814: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
3815:
3816:
3817: /* For Powell, parameters are in a vector p[] starting at p[1]
3818: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
3819: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
3820:
3821: if(mle>=1){ /* Could be 1 or 2 */
3822: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
3823: }
3824:
3825: /*--------- results files --------------*/
3826: 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);
3827:
3828:
3829: jk=1;
3830: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3831: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3832: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3833: for(i=1,jk=1; i <=nlstate; i++){
3834: for(k=1; k <=(nlstate+ndeath); k++){
3835: if (k != i)
3836: {
3837: printf("%d%d ",i,k);
3838: fprintf(ficlog,"%d%d ",i,k);
3839: fprintf(ficres,"%1d%1d ",i,k);
3840: for(j=1; j <=ncovmodel; j++){
3841: printf("%f ",p[jk]);
3842: fprintf(ficlog,"%f ",p[jk]);
3843: fprintf(ficres,"%f ",p[jk]);
3844: jk++;
3845: }
3846: printf("\n");
3847: fprintf(ficlog,"\n");
3848: fprintf(ficres,"\n");
3849: }
3850: }
3851: }
3852: if(mle==1){
3853: /* Computing hessian and covariance matrix */
3854: ftolhess=ftol; /* Usually correct */
3855: hesscov(matcov, p, npar, delti, ftolhess, func);
3856: }
3857: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
3858: printf("# Scales (for hessian or gradient estimation)\n");
3859: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
3860: for(i=1,jk=1; i <=nlstate; i++){
3861: for(j=1; j <=nlstate+ndeath; j++){
3862: if (j!=i) {
3863: fprintf(ficres,"%1d%1d",i,j);
3864: printf("%1d%1d",i,j);
3865: fprintf(ficlog,"%1d%1d",i,j);
3866: for(k=1; k<=ncovmodel;k++){
3867: printf(" %.5e",delti[jk]);
3868: fprintf(ficlog," %.5e",delti[jk]);
3869: fprintf(ficres," %.5e",delti[jk]);
3870: jk++;
3871: }
3872: printf("\n");
3873: fprintf(ficlog,"\n");
3874: fprintf(ficres,"\n");
3875: }
3876: }
3877: }
3878:
3879: 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");
3880: if(mle==1)
3881: 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");
3882: 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");
3883: for(i=1,k=1;i<=npar;i++){
3884: /* if (k>nlstate) k=1;
3885: i1=(i-1)/(ncovmodel*nlstate)+1;
3886: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
3887: printf("%s%d%d",alph[k],i1,tab[i]);
3888: */
3889: fprintf(ficres,"%3d",i);
3890: if(mle==1)
3891: printf("%3d",i);
3892: fprintf(ficlog,"%3d",i);
3893: for(j=1; j<=i;j++){
3894: fprintf(ficres," %.5e",matcov[i][j]);
3895: if(mle==1)
3896: printf(" %.5e",matcov[i][j]);
3897: fprintf(ficlog," %.5e",matcov[i][j]);
3898: }
3899: fprintf(ficres,"\n");
3900: if(mle==1)
3901: printf("\n");
3902: fprintf(ficlog,"\n");
3903: k++;
3904: }
3905:
3906: while((c=getc(ficpar))=='#' && c!= EOF){
3907: ungetc(c,ficpar);
3908: fgets(line, MAXLINE, ficpar);
3909: puts(line);
3910: fputs(line,ficparo);
3911: }
3912: ungetc(c,ficpar);
3913:
3914: estepm=0;
3915: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
3916: if (estepm==0 || estepm < stepm) estepm=stepm;
3917: if (fage <= 2) {
3918: bage = ageminpar;
3919: fage = agemaxpar;
3920: }
3921:
3922: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
3923: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
3924: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
3925:
3926: while((c=getc(ficpar))=='#' && c!= EOF){
3927: ungetc(c,ficpar);
3928: fgets(line, MAXLINE, ficpar);
3929: puts(line);
3930: fputs(line,ficparo);
3931: }
3932: ungetc(c,ficpar);
3933:
3934: 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);
3935: 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);
3936: 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);
3937:
3938: while((c=getc(ficpar))=='#' && c!= EOF){
3939: ungetc(c,ficpar);
3940: fgets(line, MAXLINE, ficpar);
3941: puts(line);
3942: fputs(line,ficparo);
3943: }
3944: ungetc(c,ficpar);
3945:
3946:
3947: dateprev1=anprev1+mprev1/12.+jprev1/365.;
3948: dateprev2=anprev2+mprev2/12.+jprev2/365.;
3949:
3950: fscanf(ficpar,"pop_based=%d\n",&popbased);
3951: fprintf(ficparo,"pop_based=%d\n",popbased);
3952: fprintf(ficres,"pop_based=%d\n",popbased);
3953:
3954: while((c=getc(ficpar))=='#' && c!= EOF){
3955: ungetc(c,ficpar);
3956: fgets(line, MAXLINE, ficpar);
3957: puts(line);
3958: fputs(line,ficparo);
3959: }
3960: ungetc(c,ficpar);
3961:
3962: fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
3963: fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
3964: fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
3965:
3966:
3967: while((c=getc(ficpar))=='#' && c!= EOF){
3968: ungetc(c,ficpar);
3969: fgets(line, MAXLINE, ficpar);
3970: puts(line);
3971: fputs(line,ficparo);
3972: }
3973: ungetc(c,ficpar);
3974:
3975: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
3976: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
3977: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
3978:
3979: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
3980:
3981: /*------------ gnuplot -------------*/
3982: strcpy(optionfilegnuplot,optionfilefiname);
3983: strcat(optionfilegnuplot,".gp");
3984: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
3985: printf("Problem with file %s",optionfilegnuplot);
3986: }
3987: else{
3988: fprintf(ficgp,"\n# %s\n", version);
3989: fprintf(ficgp,"# %s\n", optionfilegnuplot);
3990: fprintf(ficgp,"set missing 'NaNq'\n");
3991: }
3992: fclose(ficgp);
3993: printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
3994: /*--------- index.htm --------*/
3995:
3996: strcpy(optionfilehtm,optionfile);
3997: strcat(optionfilehtm,".htm");
3998: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
3999: printf("Problem with %s \n",optionfilehtm), exit(0);
4000: }
4001:
4002: fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
4003: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
4004: \n
4005: Total number of observations=%d <br>\n
4006: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
4007: <hr size=\"2\" color=\"#EC5E5E\">
4008: <ul><li><h4>Parameter files</h4>\n
4009: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
4010: - Log file of the run: <a href=\"%s\">%s</a><br>\n
4011: - 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);
4012: fclose(fichtm);
4013:
4014: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
4015:
4016: /*------------ free_vector -------------*/
4017: chdir(path);
4018:
4019: free_ivector(wav,1,imx);
4020: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
4021: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
4022: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
4023: free_ivector(num,1,n);
4024: free_vector(agedc,1,n);
4025: /*free_matrix(covar,0,NCOVMAX,1,n);*/
4026: /*free_matrix(covar,1,NCOVMAX,1,n);*/
4027: fclose(ficparo);
4028: fclose(ficres);
4029:
4030:
4031: /*--------------- Prevalence limit (stable prevalence) --------------*/
4032:
4033: strcpy(filerespl,"pl");
4034: strcat(filerespl,fileres);
4035: if((ficrespl=fopen(filerespl,"w"))==NULL) {
4036: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4037: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4038: }
4039: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
4040: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
4041: fprintf(ficrespl,"#Stable prevalence \n");
4042: fprintf(ficrespl,"#Age ");
4043: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
4044: fprintf(ficrespl,"\n");
4045:
4046: prlim=matrix(1,nlstate,1,nlstate);
4047:
4048: agebase=ageminpar;
4049: agelim=agemaxpar;
4050: ftolpl=1.e-10;
4051: i1=cptcoveff;
4052: if (cptcovn < 1){i1=1;}
4053:
4054: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4055: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4056: k=k+1;
4057: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
4058: fprintf(ficrespl,"\n#******");
4059: printf("\n#******");
4060: fprintf(ficlog,"\n#******");
4061: for(j=1;j<=cptcoveff;j++) {
4062: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4063: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4064: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4065: }
4066: fprintf(ficrespl,"******\n");
4067: printf("******\n");
4068: fprintf(ficlog,"******\n");
4069:
4070: for (age=agebase; age<=agelim; age++){
4071: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4072: fprintf(ficrespl,"%.0f",age );
4073: for(i=1; i<=nlstate;i++)
4074: fprintf(ficrespl," %.5f", prlim[i][i]);
4075: fprintf(ficrespl,"\n");
4076: }
4077: }
4078: }
4079: fclose(ficrespl);
4080:
4081: /*------------- h Pij x at various ages ------------*/
4082:
4083: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
4084: if((ficrespij=fopen(filerespij,"w"))==NULL) {
4085: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
4086: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
4087: }
4088: printf("Computing pij: result on file '%s' \n", filerespij);
4089: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
4090:
4091: stepsize=(int) (stepm+YEARM-1)/YEARM;
4092: /*if (stepm<=24) stepsize=2;*/
4093:
4094: agelim=AGESUP;
4095: hstepm=stepsize*YEARM; /* Every year of age */
4096: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
4097:
4098: /* hstepm=1; aff par mois*/
4099:
4100: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4101: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4102: k=k+1;
4103: fprintf(ficrespij,"\n#****** ");
4104: for(j=1;j<=cptcoveff;j++)
4105: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4106: fprintf(ficrespij,"******\n");
4107:
4108: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
4109: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4110: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4111:
4112: /* nhstepm=nhstepm*YEARM; aff par mois*/
4113:
4114: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4115: oldm=oldms;savm=savms;
4116: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4117: fprintf(ficrespij,"# Age");
4118: for(i=1; i<=nlstate;i++)
4119: for(j=1; j<=nlstate+ndeath;j++)
4120: fprintf(ficrespij," %1d-%1d",i,j);
4121: fprintf(ficrespij,"\n");
4122: for (h=0; h<=nhstepm; h++){
4123: fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
4124: for(i=1; i<=nlstate;i++)
4125: for(j=1; j<=nlstate+ndeath;j++)
4126: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
4127: fprintf(ficrespij,"\n");
4128: }
4129: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4130: fprintf(ficrespij,"\n");
4131: }
4132: }
4133: }
4134:
4135: varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
4136:
4137: fclose(ficrespij);
4138:
4139:
4140: /*---------- Forecasting ------------------*/
4141: if((stepm == 1) && (strcmp(model,".")==0)){
4142: prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
4143: if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
4144: }
4145: else{
4146: erreur=108;
4147: 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);
4148: 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);
4149: }
4150:
4151:
4152: /*---------- Health expectancies and variances ------------*/
4153:
4154: strcpy(filerest,"t");
4155: strcat(filerest,fileres);
4156: if((ficrest=fopen(filerest,"w"))==NULL) {
4157: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
4158: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
4159: }
4160: printf("Computing Total LEs with variances: file '%s' \n", filerest);
4161: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
4162:
4163:
4164: strcpy(filerese,"e");
4165: strcat(filerese,fileres);
4166: if((ficreseij=fopen(filerese,"w"))==NULL) {
4167: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4168: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4169: }
4170: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
4171: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
4172:
4173: strcpy(fileresv,"v");
4174: strcat(fileresv,fileres);
4175: if((ficresvij=fopen(fileresv,"w"))==NULL) {
4176: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
4177: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
4178: }
4179: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4180: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4181:
4182: calagedate=-1;
4183:
4184: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
4185:
4186: if (mobilav!=0) {
4187: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4188: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4189: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4190: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4191: }
4192: }
4193:
4194: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4195: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4196: k=k+1;
4197: fprintf(ficrest,"\n#****** ");
4198: for(j=1;j<=cptcoveff;j++)
4199: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4200: fprintf(ficrest,"******\n");
4201:
4202: fprintf(ficreseij,"\n#****** ");
4203: for(j=1;j<=cptcoveff;j++)
4204: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4205: fprintf(ficreseij,"******\n");
4206:
4207: fprintf(ficresvij,"\n#****** ");
4208: for(j=1;j<=cptcoveff;j++)
4209: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4210: fprintf(ficresvij,"******\n");
4211:
4212: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4213: oldm=oldms;savm=savms;
4214: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
4215:
4216: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4217: oldm=oldms;savm=savms;
4218: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
4219: if(popbased==1){
4220: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
4221: }
4222:
4223:
4224: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
4225: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
4226: fprintf(ficrest,"\n");
4227:
4228: epj=vector(1,nlstate+1);
4229: for(age=bage; age <=fage ;age++){
4230: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4231: if (popbased==1) {
4232: if(mobilav ==0){
4233: for(i=1; i<=nlstate;i++)
4234: prlim[i][i]=probs[(int)age][i][k];
4235: }else{ /* mobilav */
4236: for(i=1; i<=nlstate;i++)
4237: prlim[i][i]=mobaverage[(int)age][i][k];
4238: }
4239: }
4240:
4241: fprintf(ficrest," %4.0f",age);
4242: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
4243: for(i=1, epj[j]=0.;i <=nlstate;i++) {
4244: epj[j] += prlim[i][i]*eij[i][j][(int)age];
4245: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
4246: }
4247: epj[nlstate+1] +=epj[j];
4248: }
4249:
4250: for(i=1, vepp=0.;i <=nlstate;i++)
4251: for(j=1;j <=nlstate;j++)
4252: vepp += vareij[i][j][(int)age];
4253: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
4254: for(j=1;j <=nlstate;j++){
4255: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
4256: }
4257: fprintf(ficrest,"\n");
4258: }
4259: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4260: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4261: free_vector(epj,1,nlstate+1);
4262: }
4263: }
4264: free_vector(weight,1,n);
4265: free_imatrix(Tvard,1,15,1,2);
4266: free_imatrix(s,1,maxwav+1,1,n);
4267: free_matrix(anint,1,maxwav,1,n);
4268: free_matrix(mint,1,maxwav,1,n);
4269: free_ivector(cod,1,n);
4270: free_ivector(tab,1,NCOVMAX);
4271: fclose(ficreseij);
4272: fclose(ficresvij);
4273: fclose(ficrest);
4274: fclose(ficpar);
4275:
4276: /*------- Variance of stable prevalence------*/
4277:
4278: strcpy(fileresvpl,"vpl");
4279: strcat(fileresvpl,fileres);
4280: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
4281: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
4282: exit(0);
4283: }
4284: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
4285:
4286: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4287: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4288: k=k+1;
4289: fprintf(ficresvpl,"\n#****** ");
4290: for(j=1;j<=cptcoveff;j++)
4291: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4292: fprintf(ficresvpl,"******\n");
4293:
4294: varpl=matrix(1,nlstate,(int) bage, (int) fage);
4295: oldm=oldms;savm=savms;
4296: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
4297: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
4298: }
4299: }
4300:
4301: fclose(ficresvpl);
4302:
4303: /*---------- End : free ----------------*/
4304: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
4305: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
4306: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
4307: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
4308:
4309: free_matrix(covar,0,NCOVMAX,1,n);
4310: free_matrix(matcov,1,npar,1,npar);
4311: free_vector(delti,1,npar);
4312: free_matrix(agev,1,maxwav,1,imx);
4313: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4314: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4315: free_ivector(ncodemax,1,8);
4316: free_ivector(Tvar,1,15);
4317: free_ivector(Tprod,1,15);
4318: free_ivector(Tvaraff,1,15);
4319: free_ivector(Tage,1,15);
4320: free_ivector(Tcode,1,100);
4321:
4322: fprintf(fichtm,"\n</body>");
4323: fclose(fichtm);
4324: fclose(ficgp);
4325:
4326:
4327: if(erreur >0){
4328: printf("End of Imach with error or warning %d\n",erreur);
4329: fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
4330: }else{
4331: printf("End of Imach\n");
4332: fprintf(ficlog,"End of Imach\n");
4333: }
4334: printf("See log file on %s\n",filelog);
4335: fclose(ficlog);
4336: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
4337:
4338: /* 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);*/
4339: /*printf("Total time was %d uSec.\n", total_usecs);*/
4340: /*------ End -----------*/
4341:
4342: end:
4343: #ifdef windows
4344: /* chdir(pathcd);*/
4345: #endif
4346: /*system("wgnuplot graph.plt");*/
4347: /*system("../gp37mgw/wgnuplot graph.plt");*/
4348: /*system("cd ../gp37mgw");*/
4349: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
4350: strcpy(plotcmd,GNUPLOTPROGRAM);
4351: strcat(plotcmd," ");
4352: strcat(plotcmd,optionfilegnuplot);
4353: printf("Starting: %s\n",plotcmd);fflush(stdout);
4354: system(plotcmd);
4355:
4356: /*#ifdef windows*/
4357: while (z[0] != 'q') {
4358: /* chdir(path); */
4359: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
4360: scanf("%s",z);
4361: if (z[0] == 'c') system("./imach");
4362: else if (z[0] == 'e') system(optionfilehtm);
4363: else if (z[0] == 'g') system(plotcmd);
4364: else if (z[0] == 'q') exit(0);
4365: }
4366: /*#endif */
4367: }
4368:
4369:
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