1: /* $Id: imach.c,v 1.81 2003/06/05 15:41:51 brouard Exp $
2: Interpolated Markov Chain
3:
4: Short summary of the programme:
5:
6: This program computes Healthy Life Expectancies from
7: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
8: first survey ("cross") where individuals from different ages are
9: interviewed on their health status or degree of disability (in the
10: case of a health survey which is our main interest) -2- at least a
11: second wave of interviews ("longitudinal") which measure each change
12: (if any) in individual health status. Health expectancies are
13: computed from the time spent in each health state according to a
14: model. More health states you consider, more time is necessary to reach the
15: Maximum Likelihood of the parameters involved in the model. The
16: simplest model is the multinomial logistic model where pij is the
17: probability to be observed in state j at the second wave
18: conditional to be observed in state i at the first wave. Therefore
19: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
20: 'age' is age and 'sex' is a covariate. If you want to have a more
21: complex model than "constant and age", you should modify the program
22: where the markup *Covariates have to be included here again* invites
23: you to do it. More covariates you add, slower the
24: convergence.
25:
26: The advantage of this computer programme, compared to a simple
27: multinomial logistic model, is clear when the delay between waves is not
28: identical for each individual. Also, if a individual missed an
29: intermediate interview, the information is lost, but taken into
30: account using an interpolation or extrapolation.
31:
32: hPijx is the probability to be observed in state i at age x+h
33: conditional to the observed state i at age x. The delay 'h' can be
34: split into an exact number (nh*stepm) of unobserved intermediate
35: states. This elementary transition (by month, quarter,
36: semester or year) is modelled as a multinomial logistic. The hPx
37: matrix is simply the matrix product of nh*stepm elementary matrices
38: and the contribution of each individual to the likelihood is simply
39: hPijx.
40:
41: Also this programme outputs the covariance matrix of the parameters but also
42: of the life expectancies. It also computes the stable prevalence.
43:
44: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
45: Institut national d'études démographiques, Paris.
46: This software have been partly granted by Euro-REVES, a concerted action
47: from the European Union.
48: It is copyrighted identically to a GNU software product, ie programme and
49: software can be distributed freely for non commercial use. Latest version
50: can be accessed at http://euroreves.ined.fr/imach .
51:
52: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
53: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
54:
55: **********************************************************************/
56: /*
57: main
58: read parameterfile
59: read datafile
60: concatwav
61: if (mle >= 1)
62: mlikeli
63: print results files
64: if mle==1
65: computes hessian
66: read end of parameter file: agemin, agemax, bage, fage, estepm
67: begin-prev-date,...
68: open gnuplot file
69: open html file
70: stable prevalence
71: for age prevalim()
72: h Pij x
73: variance of p varprob
74: forecasting if prevfcast==1 prevforecast call prevalence()
75: health expectancies
76: Variance-covariance of DFLE
77: prevalence()
78: movingaverage()
79: varevsij()
80: if popbased==1 varevsij(,popbased)
81: total life expectancies
82: Variance of stable prevalence
83: end
84: */
85:
86:
87:
88:
89: #include <math.h>
90: #include <stdio.h>
91: #include <stdlib.h>
92: #include <unistd.h>
93:
94: #define MAXLINE 256
95: #define GNUPLOTPROGRAM "gnuplot"
96: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
97: #define FILENAMELENGTH 80
98: /*#define DEBUG*/
99: #define windows
100: #define GLOCK_ERROR_NOPATH -1 /* empty path */
101: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
102:
103: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
104: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
105:
106: #define NINTERVMAX 8
107: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
108: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
109: #define NCOVMAX 8 /* Maximum number of covariates */
110: #define MAXN 20000
111: #define YEARM 12. /* Number of months per year */
112: #define AGESUP 130
113: #define AGEBASE 40
114: #ifdef windows
115: #define DIRSEPARATOR '\\'
116: #define ODIRSEPARATOR '/'
117: #else
118: #define DIRSEPARATOR '/'
119: #define ODIRSEPARATOR '\\'
120: #endif
121:
122: /* $Id: imach.c,v 1.81 2003/06/05 15:41:51 brouard Exp $ */
123: /* $Log: imach.c,v $
124: /* Revision 1.81 2003/06/05 15:41:51 brouard
125: /* *** empty log message ***
126: /*
127: /* Revision 1.80 2003/06/05 15:34:14 brouard
128: /* Trying to add the true revision in the program and log
129: /*
130: /* Revision 1.79 2003/06/05 15:17:23 brouard
131: /* *** empty log message ***
132: /* */
133: /* $Revision: 1.81 $ */
134: /* $Date: 2003/06/05 15:41:51 $ */
135: /* $State: Exp $ */
136:
137: char version[80]="Imach version 0.95a1, June 2003, INED-EUROREVES ";
138: char fullversion[]="$Revision: 1.81 $ $Date: 2003/06/05 15:41:51 $";
139: int erreur; /* Error number */
140: int nvar;
141: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
142: int npar=NPARMAX;
143: int nlstate=2; /* Number of live states */
144: int ndeath=1; /* Number of dead states */
145: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
146: int popbased=0;
147:
148: int *wav; /* Number of waves for this individuual 0 is possible */
149: int maxwav; /* Maxim number of waves */
150: int jmin, jmax; /* min, max spacing between 2 waves */
151: int mle, weightopt;
152: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
153: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
154: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
155: * wave mi and wave mi+1 is not an exact multiple of stepm. */
156: double jmean; /* Mean space between 2 waves */
157: double **oldm, **newm, **savm; /* Working pointers to matrices */
158: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
159: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
160: FILE *ficlog, *ficrespow;
161: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
162: FILE *ficresprobmorprev;
163: FILE *fichtm; /* Html File */
164: FILE *ficreseij;
165: char filerese[FILENAMELENGTH];
166: FILE *ficresvij;
167: char fileresv[FILENAMELENGTH];
168: FILE *ficresvpl;
169: char fileresvpl[FILENAMELENGTH];
170: char title[MAXLINE];
171: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
172: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
173:
174: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
175: char filelog[FILENAMELENGTH]; /* Log file */
176: char filerest[FILENAMELENGTH];
177: char fileregp[FILENAMELENGTH];
178: char popfile[FILENAMELENGTH];
179:
180: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
181:
182: #define NR_END 1
183: #define FREE_ARG char*
184: #define FTOL 1.0e-10
185:
186: #define NRANSI
187: #define ITMAX 200
188:
189: #define TOL 2.0e-4
190:
191: #define CGOLD 0.3819660
192: #define ZEPS 1.0e-10
193: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
194:
195: #define GOLD 1.618034
196: #define GLIMIT 100.0
197: #define TINY 1.0e-20
198:
199: static double maxarg1,maxarg2;
200: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
201: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
202:
203: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
204: #define rint(a) floor(a+0.5)
205:
206: static double sqrarg;
207: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
208: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
209:
210: int imx;
211: int stepm;
212: /* Stepm, step in month: minimum step interpolation*/
213:
214: int estepm;
215: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
216:
217: int m,nb;
218: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
219: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
220: double **pmmij, ***probs;
221: double dateintmean=0;
222:
223: double *weight;
224: int **s; /* Status */
225: double *agedc, **covar, idx;
226: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
227:
228: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
229: double ftolhess; /* Tolerance for computing hessian */
230:
231: /**************** split *************************/
232: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
233: {
234: char *ss; /* pointer */
235: int l1, l2; /* length counters */
236:
237: l1 = strlen(path ); /* length of path */
238: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
239: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
240: if ( ss == NULL ) { /* no directory, so use current */
241: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
242: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
243: /* get current working directory */
244: /* extern char* getcwd ( char *buf , int len);*/
245: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
246: return( GLOCK_ERROR_GETCWD );
247: }
248: strcpy( name, path ); /* we've got it */
249: } else { /* strip direcotry from path */
250: ss++; /* after this, the filename */
251: l2 = strlen( ss ); /* length of filename */
252: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
253: strcpy( name, ss ); /* save file name */
254: strncpy( dirc, path, l1 - l2 ); /* now the directory */
255: dirc[l1-l2] = 0; /* add zero */
256: }
257: l1 = strlen( dirc ); /* length of directory */
258: #ifdef windows
259: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
260: #else
261: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
262: #endif
263: ss = strrchr( name, '.' ); /* find last / */
264: ss++;
265: strcpy(ext,ss); /* save extension */
266: l1= strlen( name);
267: l2= strlen(ss)+1;
268: strncpy( finame, name, l1-l2);
269: finame[l1-l2]= 0;
270: return( 0 ); /* we're done */
271: }
272:
273:
274: /******************************************/
275:
276: void replace(char *s, char*t)
277: {
278: int i;
279: int lg=20;
280: i=0;
281: lg=strlen(t);
282: for(i=0; i<= lg; i++) {
283: (s[i] = t[i]);
284: if (t[i]== '\\') s[i]='/';
285: }
286: }
287:
288: int nbocc(char *s, char occ)
289: {
290: int i,j=0;
291: int lg=20;
292: i=0;
293: lg=strlen(s);
294: for(i=0; i<= lg; i++) {
295: if (s[i] == occ ) j++;
296: }
297: return j;
298: }
299:
300: void cutv(char *u,char *v, char*t, char occ)
301: {
302: /* cuts string t into u and v where u is ended by char occ excluding it
303: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
304: gives u="abcedf" and v="ghi2j" */
305: int i,lg,j,p=0;
306: i=0;
307: for(j=0; j<=strlen(t)-1; j++) {
308: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
309: }
310:
311: lg=strlen(t);
312: for(j=0; j<p; j++) {
313: (u[j] = t[j]);
314: }
315: u[p]='\0';
316:
317: for(j=0; j<= lg; j++) {
318: if (j>=(p+1))(v[j-p-1] = t[j]);
319: }
320: }
321:
322: /********************** nrerror ********************/
323:
324: void nrerror(char error_text[])
325: {
326: fprintf(stderr,"ERREUR ...\n");
327: fprintf(stderr,"%s\n",error_text);
328: exit(EXIT_FAILURE);
329: }
330: /*********************** vector *******************/
331: double *vector(int nl, int nh)
332: {
333: double *v;
334: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
335: if (!v) nrerror("allocation failure in vector");
336: return v-nl+NR_END;
337: }
338:
339: /************************ free vector ******************/
340: void free_vector(double*v, int nl, int nh)
341: {
342: free((FREE_ARG)(v+nl-NR_END));
343: }
344:
345: /************************ivector *******************************/
346: char *cvector(long nl,long nh)
347: {
348: char *v;
349: v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
350: if (!v) nrerror("allocation failure in cvector");
351: return v-nl+NR_END;
352: }
353:
354: /******************free ivector **************************/
355: void free_cvector(char *v, long nl, long nh)
356: {
357: free((FREE_ARG)(v+nl-NR_END));
358: }
359:
360: /************************ivector *******************************/
361: int *ivector(long nl,long nh)
362: {
363: int *v;
364: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
365: if (!v) nrerror("allocation failure in ivector");
366: return v-nl+NR_END;
367: }
368:
369: /******************free ivector **************************/
370: void free_ivector(int *v, long nl, long nh)
371: {
372: free((FREE_ARG)(v+nl-NR_END));
373: }
374:
375: /******************* imatrix *******************************/
376: int **imatrix(long nrl, long nrh, long ncl, long nch)
377: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
378: {
379: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
380: int **m;
381:
382: /* allocate pointers to rows */
383: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
384: if (!m) nrerror("allocation failure 1 in matrix()");
385: m += NR_END;
386: m -= nrl;
387:
388:
389: /* allocate rows and set pointers to them */
390: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
391: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
392: m[nrl] += NR_END;
393: m[nrl] -= ncl;
394:
395: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
396:
397: /* return pointer to array of pointers to rows */
398: return m;
399: }
400:
401: /****************** free_imatrix *************************/
402: void free_imatrix(m,nrl,nrh,ncl,nch)
403: int **m;
404: long nch,ncl,nrh,nrl;
405: /* free an int matrix allocated by imatrix() */
406: {
407: free((FREE_ARG) (m[nrl]+ncl-NR_END));
408: free((FREE_ARG) (m+nrl-NR_END));
409: }
410:
411: /******************* matrix *******************************/
412: double **matrix(long nrl, long nrh, long ncl, long nch)
413: {
414: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
415: double **m;
416:
417: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
418: if (!m) nrerror("allocation failure 1 in matrix()");
419: m += NR_END;
420: m -= nrl;
421:
422: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
423: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
424: m[nrl] += NR_END;
425: m[nrl] -= ncl;
426:
427: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
428: return m;
429: /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1])
430: */
431: }
432:
433: /*************************free matrix ************************/
434: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
435: {
436: free((FREE_ARG)(m[nrl]+ncl-NR_END));
437: free((FREE_ARG)(m+nrl-NR_END));
438: }
439:
440: /******************* ma3x *******************************/
441: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
442: {
443: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
444: double ***m;
445:
446: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
447: if (!m) nrerror("allocation failure 1 in matrix()");
448: m += NR_END;
449: m -= nrl;
450:
451: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
452: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
453: m[nrl] += NR_END;
454: m[nrl] -= ncl;
455:
456: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
457:
458: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
459: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
460: m[nrl][ncl] += NR_END;
461: m[nrl][ncl] -= nll;
462: for (j=ncl+1; j<=nch; j++)
463: m[nrl][j]=m[nrl][j-1]+nlay;
464:
465: for (i=nrl+1; i<=nrh; i++) {
466: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
467: for (j=ncl+1; j<=nch; j++)
468: m[i][j]=m[i][j-1]+nlay;
469: }
470: return m;
471: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
472: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
473: */
474: }
475:
476: /*************************free ma3x ************************/
477: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
478: {
479: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
480: free((FREE_ARG)(m[nrl]+ncl-NR_END));
481: free((FREE_ARG)(m+nrl-NR_END));
482: }
483:
484: /***************** f1dim *************************/
485: extern int ncom;
486: extern double *pcom,*xicom;
487: extern double (*nrfunc)(double []);
488:
489: double f1dim(double x)
490: {
491: int j;
492: double f;
493: double *xt;
494:
495: xt=vector(1,ncom);
496: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
497: f=(*nrfunc)(xt);
498: free_vector(xt,1,ncom);
499: return f;
500: }
501:
502: /*****************brent *************************/
503: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
504: {
505: int iter;
506: double a,b,d,etemp;
507: double fu,fv,fw,fx;
508: double ftemp;
509: double p,q,r,tol1,tol2,u,v,w,x,xm;
510: double e=0.0;
511:
512: a=(ax < cx ? ax : cx);
513: b=(ax > cx ? ax : cx);
514: x=w=v=bx;
515: fw=fv=fx=(*f)(x);
516: for (iter=1;iter<=ITMAX;iter++) {
517: xm=0.5*(a+b);
518: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
519: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
520: printf(".");fflush(stdout);
521: fprintf(ficlog,".");fflush(ficlog);
522: #ifdef DEBUG
523: 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);
524: 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);
525: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
526: #endif
527: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
528: *xmin=x;
529: return fx;
530: }
531: ftemp=fu;
532: if (fabs(e) > tol1) {
533: r=(x-w)*(fx-fv);
534: q=(x-v)*(fx-fw);
535: p=(x-v)*q-(x-w)*r;
536: q=2.0*(q-r);
537: if (q > 0.0) p = -p;
538: q=fabs(q);
539: etemp=e;
540: e=d;
541: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
542: d=CGOLD*(e=(x >= xm ? a-x : b-x));
543: else {
544: d=p/q;
545: u=x+d;
546: if (u-a < tol2 || b-u < tol2)
547: d=SIGN(tol1,xm-x);
548: }
549: } else {
550: d=CGOLD*(e=(x >= xm ? a-x : b-x));
551: }
552: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
553: fu=(*f)(u);
554: if (fu <= fx) {
555: if (u >= x) a=x; else b=x;
556: SHFT(v,w,x,u)
557: SHFT(fv,fw,fx,fu)
558: } else {
559: if (u < x) a=u; else b=u;
560: if (fu <= fw || w == x) {
561: v=w;
562: w=u;
563: fv=fw;
564: fw=fu;
565: } else if (fu <= fv || v == x || v == w) {
566: v=u;
567: fv=fu;
568: }
569: }
570: }
571: nrerror("Too many iterations in brent");
572: *xmin=x;
573: return fx;
574: }
575:
576: /****************** mnbrak ***********************/
577:
578: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
579: double (*func)(double))
580: {
581: double ulim,u,r,q, dum;
582: double fu;
583:
584: *fa=(*func)(*ax);
585: *fb=(*func)(*bx);
586: if (*fb > *fa) {
587: SHFT(dum,*ax,*bx,dum)
588: SHFT(dum,*fb,*fa,dum)
589: }
590: *cx=(*bx)+GOLD*(*bx-*ax);
591: *fc=(*func)(*cx);
592: while (*fb > *fc) {
593: r=(*bx-*ax)*(*fb-*fc);
594: q=(*bx-*cx)*(*fb-*fa);
595: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
596: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
597: ulim=(*bx)+GLIMIT*(*cx-*bx);
598: if ((*bx-u)*(u-*cx) > 0.0) {
599: fu=(*func)(u);
600: } else if ((*cx-u)*(u-ulim) > 0.0) {
601: fu=(*func)(u);
602: if (fu < *fc) {
603: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
604: SHFT(*fb,*fc,fu,(*func)(u))
605: }
606: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
607: u=ulim;
608: fu=(*func)(u);
609: } else {
610: u=(*cx)+GOLD*(*cx-*bx);
611: fu=(*func)(u);
612: }
613: SHFT(*ax,*bx,*cx,u)
614: SHFT(*fa,*fb,*fc,fu)
615: }
616: }
617:
618: /*************** linmin ************************/
619:
620: int ncom;
621: double *pcom,*xicom;
622: double (*nrfunc)(double []);
623:
624: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
625: {
626: double brent(double ax, double bx, double cx,
627: double (*f)(double), double tol, double *xmin);
628: double f1dim(double x);
629: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
630: double *fc, double (*func)(double));
631: int j;
632: double xx,xmin,bx,ax;
633: double fx,fb,fa;
634:
635: ncom=n;
636: pcom=vector(1,n);
637: xicom=vector(1,n);
638: nrfunc=func;
639: for (j=1;j<=n;j++) {
640: pcom[j]=p[j];
641: xicom[j]=xi[j];
642: }
643: ax=0.0;
644: xx=1.0;
645: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
646: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
647: #ifdef DEBUG
648: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
649: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
650: #endif
651: for (j=1;j<=n;j++) {
652: xi[j] *= xmin;
653: p[j] += xi[j];
654: }
655: free_vector(xicom,1,n);
656: free_vector(pcom,1,n);
657: }
658:
659: /*************** powell ************************/
660: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
661: double (*func)(double []))
662: {
663: void linmin(double p[], double xi[], int n, double *fret,
664: double (*func)(double []));
665: int i,ibig,j;
666: double del,t,*pt,*ptt,*xit;
667: double fp,fptt;
668: double *xits;
669: pt=vector(1,n);
670: ptt=vector(1,n);
671: xit=vector(1,n);
672: xits=vector(1,n);
673: *fret=(*func)(p);
674: for (j=1;j<=n;j++) pt[j]=p[j];
675: for (*iter=1;;++(*iter)) {
676: fp=(*fret);
677: ibig=0;
678: del=0.0;
679: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
680: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
681: fprintf(ficrespow,"%d %.12f",*iter,*fret);
682: for (i=1;i<=n;i++) {
683: printf(" %d %.12f",i, p[i]);
684: fprintf(ficlog," %d %.12lf",i, p[i]);
685: fprintf(ficrespow," %.12lf", p[i]);
686: }
687: printf("\n");
688: fprintf(ficlog,"\n");
689: fprintf(ficrespow,"\n");
690: for (i=1;i<=n;i++) {
691: for (j=1;j<=n;j++) xit[j]=xi[j][i];
692: fptt=(*fret);
693: #ifdef DEBUG
694: printf("fret=%lf \n",*fret);
695: fprintf(ficlog,"fret=%lf \n",*fret);
696: #endif
697: printf("%d",i);fflush(stdout);
698: fprintf(ficlog,"%d",i);fflush(ficlog);
699: linmin(p,xit,n,fret,func);
700: if (fabs(fptt-(*fret)) > del) {
701: del=fabs(fptt-(*fret));
702: ibig=i;
703: }
704: #ifdef DEBUG
705: printf("%d %.12e",i,(*fret));
706: fprintf(ficlog,"%d %.12e",i,(*fret));
707: for (j=1;j<=n;j++) {
708: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
709: printf(" x(%d)=%.12e",j,xit[j]);
710: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
711: }
712: for(j=1;j<=n;j++) {
713: printf(" p=%.12e",p[j]);
714: fprintf(ficlog," p=%.12e",p[j]);
715: }
716: printf("\n");
717: fprintf(ficlog,"\n");
718: #endif
719: }
720: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
721: #ifdef DEBUG
722: int k[2],l;
723: k[0]=1;
724: k[1]=-1;
725: printf("Max: %.12e",(*func)(p));
726: fprintf(ficlog,"Max: %.12e",(*func)(p));
727: for (j=1;j<=n;j++) {
728: printf(" %.12e",p[j]);
729: fprintf(ficlog," %.12e",p[j]);
730: }
731: printf("\n");
732: fprintf(ficlog,"\n");
733: for(l=0;l<=1;l++) {
734: for (j=1;j<=n;j++) {
735: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
736: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
737: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
738: }
739: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
740: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
741: }
742: #endif
743:
744:
745: free_vector(xit,1,n);
746: free_vector(xits,1,n);
747: free_vector(ptt,1,n);
748: free_vector(pt,1,n);
749: return;
750: }
751: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
752: for (j=1;j<=n;j++) {
753: ptt[j]=2.0*p[j]-pt[j];
754: xit[j]=p[j]-pt[j];
755: pt[j]=p[j];
756: }
757: fptt=(*func)(ptt);
758: if (fptt < fp) {
759: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
760: if (t < 0.0) {
761: linmin(p,xit,n,fret,func);
762: for (j=1;j<=n;j++) {
763: xi[j][ibig]=xi[j][n];
764: xi[j][n]=xit[j];
765: }
766: #ifdef DEBUG
767: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
768: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
769: for(j=1;j<=n;j++){
770: printf(" %.12e",xit[j]);
771: fprintf(ficlog," %.12e",xit[j]);
772: }
773: printf("\n");
774: fprintf(ficlog,"\n");
775: #endif
776: }
777: }
778: }
779: }
780:
781: /**** Prevalence limit (stable prevalence) ****************/
782:
783: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
784: {
785: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
786: matrix by transitions matrix until convergence is reached */
787:
788: int i, ii,j,k;
789: double min, max, maxmin, maxmax,sumnew=0.;
790: double **matprod2();
791: double **out, cov[NCOVMAX], **pmij();
792: double **newm;
793: double agefin, delaymax=50 ; /* Max number of years to converge */
794:
795: for (ii=1;ii<=nlstate+ndeath;ii++)
796: for (j=1;j<=nlstate+ndeath;j++){
797: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
798: }
799:
800: cov[1]=1.;
801:
802: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
803: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
804: newm=savm;
805: /* Covariates have to be included here again */
806: cov[2]=agefin;
807:
808: for (k=1; k<=cptcovn;k++) {
809: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
810: /* 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]]);*/
811: }
812: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
813: for (k=1; k<=cptcovprod;k++)
814: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
815:
816: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
817: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
818: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
819: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
820:
821: savm=oldm;
822: oldm=newm;
823: maxmax=0.;
824: for(j=1;j<=nlstate;j++){
825: min=1.;
826: max=0.;
827: for(i=1; i<=nlstate; i++) {
828: sumnew=0;
829: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
830: prlim[i][j]= newm[i][j]/(1-sumnew);
831: max=FMAX(max,prlim[i][j]);
832: min=FMIN(min,prlim[i][j]);
833: }
834: maxmin=max-min;
835: maxmax=FMAX(maxmax,maxmin);
836: }
837: if(maxmax < ftolpl){
838: return prlim;
839: }
840: }
841: }
842:
843: /*************** transition probabilities ***************/
844:
845: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
846: {
847: double s1, s2;
848: /*double t34;*/
849: int i,j,j1, nc, ii, jj;
850:
851: for(i=1; i<= nlstate; i++){
852: for(j=1; j<i;j++){
853: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
854: /*s2 += param[i][j][nc]*cov[nc];*/
855: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
856: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
857: }
858: ps[i][j]=s2;
859: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
860: }
861: for(j=i+1; j<=nlstate+ndeath;j++){
862: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
863: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
864: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
865: }
866: ps[i][j]=s2;
867: }
868: }
869: /*ps[3][2]=1;*/
870:
871: for(i=1; i<= nlstate; i++){
872: s1=0;
873: for(j=1; j<i; j++)
874: s1+=exp(ps[i][j]);
875: for(j=i+1; j<=nlstate+ndeath; j++)
876: s1+=exp(ps[i][j]);
877: ps[i][i]=1./(s1+1.);
878: for(j=1; j<i; j++)
879: ps[i][j]= exp(ps[i][j])*ps[i][i];
880: for(j=i+1; j<=nlstate+ndeath; j++)
881: ps[i][j]= exp(ps[i][j])*ps[i][i];
882: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
883: } /* end i */
884:
885: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
886: for(jj=1; jj<= nlstate+ndeath; jj++){
887: ps[ii][jj]=0;
888: ps[ii][ii]=1;
889: }
890: }
891:
892:
893: /* for(ii=1; ii<= nlstate+ndeath; ii++){
894: for(jj=1; jj<= nlstate+ndeath; jj++){
895: printf("%lf ",ps[ii][jj]);
896: }
897: printf("\n ");
898: }
899: printf("\n ");printf("%lf ",cov[2]);*/
900: /*
901: for(i=1; i<= npar; i++) printf("%f ",x[i]);
902: goto end;*/
903: return ps;
904: }
905:
906: /**************** Product of 2 matrices ******************/
907:
908: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
909: {
910: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
911: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
912: /* in, b, out are matrice of pointers which should have been initialized
913: before: only the contents of out is modified. The function returns
914: a pointer to pointers identical to out */
915: long i, j, k;
916: for(i=nrl; i<= nrh; i++)
917: for(k=ncolol; k<=ncoloh; k++)
918: for(j=ncl,out[i][k]=0.; j<=nch; j++)
919: out[i][k] +=in[i][j]*b[j][k];
920:
921: return out;
922: }
923:
924:
925: /************* Higher Matrix Product ***************/
926:
927: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
928: {
929: /* Computes the transition matrix starting at age 'age' over
930: 'nhstepm*hstepm*stepm' months (i.e. until
931: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
932: nhstepm*hstepm matrices.
933: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
934: (typically every 2 years instead of every month which is too big
935: for the memory).
936: Model is determined by parameters x and covariates have to be
937: included manually here.
938:
939: */
940:
941: int i, j, d, h, k;
942: double **out, cov[NCOVMAX];
943: double **newm;
944:
945: /* Hstepm could be zero and should return the unit matrix */
946: for (i=1;i<=nlstate+ndeath;i++)
947: for (j=1;j<=nlstate+ndeath;j++){
948: oldm[i][j]=(i==j ? 1.0 : 0.0);
949: po[i][j][0]=(i==j ? 1.0 : 0.0);
950: }
951: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
952: for(h=1; h <=nhstepm; h++){
953: for(d=1; d <=hstepm; d++){
954: newm=savm;
955: /* Covariates have to be included here again */
956: cov[1]=1.;
957: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
958: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
959: for (k=1; k<=cptcovage;k++)
960: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
961: for (k=1; k<=cptcovprod;k++)
962: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
963:
964:
965: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
966: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
967: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
968: pmij(pmmij,cov,ncovmodel,x,nlstate));
969: savm=oldm;
970: oldm=newm;
971: }
972: for(i=1; i<=nlstate+ndeath; i++)
973: for(j=1;j<=nlstate+ndeath;j++) {
974: po[i][j][h]=newm[i][j];
975: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
976: */
977: }
978: } /* end h */
979: return po;
980: }
981:
982:
983: /*************** log-likelihood *************/
984: double func( double *x)
985: {
986: int i, ii, j, k, mi, d, kk;
987: double l, ll[NLSTATEMAX], cov[NCOVMAX];
988: double **out;
989: double sw; /* Sum of weights */
990: double lli; /* Individual log likelihood */
991: int s1, s2;
992: double bbh, survp;
993: long ipmx;
994: /*extern weight */
995: /* We are differentiating ll according to initial status */
996: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
997: /*for(i=1;i<imx;i++)
998: printf(" %d\n",s[4][i]);
999: */
1000: cov[1]=1.;
1001:
1002: for(k=1; k<=nlstate; k++) ll[k]=0.;
1003:
1004: if(mle==1){
1005: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1006: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1007: for(mi=1; mi<= wav[i]-1; mi++){
1008: for (ii=1;ii<=nlstate+ndeath;ii++)
1009: for (j=1;j<=nlstate+ndeath;j++){
1010: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1011: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1012: }
1013: for(d=0; d<dh[mi][i]; d++){
1014: newm=savm;
1015: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1016: for (kk=1; kk<=cptcovage;kk++) {
1017: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1018: }
1019: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1020: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1021: savm=oldm;
1022: oldm=newm;
1023: } /* end mult */
1024:
1025: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1026: /* But now since version 0.9 we anticipate for bias and large stepm.
1027: * If stepm is larger than one month (smallest stepm) and if the exact delay
1028: * (in months) between two waves is not a multiple of stepm, we rounded to
1029: * the nearest (and in case of equal distance, to the lowest) interval but now
1030: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1031: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1032: * probability in order to take into account the bias as a fraction of the way
1033: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1034: * -stepm/2 to stepm/2 .
1035: * For stepm=1 the results are the same as for previous versions of Imach.
1036: * For stepm > 1 the results are less biased than in previous versions.
1037: */
1038: s1=s[mw[mi][i]][i];
1039: s2=s[mw[mi+1][i]][i];
1040: bbh=(double)bh[mi][i]/(double)stepm;
1041: /* bias is positive if real duration
1042: * is higher than the multiple of stepm and negative otherwise.
1043: */
1044: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1045: if( s2 > nlstate){
1046: /* i.e. if s2 is a death state and if the date of death is known then the contribution
1047: to the likelihood is the probability to die between last step unit time and current
1048: step unit time, which is also the differences between probability to die before dh
1049: and probability to die before dh-stepm .
1050: In version up to 0.92 likelihood was computed
1051: as if date of death was unknown. Death was treated as any other
1052: health state: the date of the interview describes the actual state
1053: and not the date of a change in health state. The former idea was
1054: to consider that at each interview the state was recorded
1055: (healthy, disable or death) and IMaCh was corrected; but when we
1056: introduced the exact date of death then we should have modified
1057: the contribution of an exact death to the likelihood. This new
1058: contribution is smaller and very dependent of the step unit
1059: stepm. It is no more the probability to die between last interview
1060: and month of death but the probability to survive from last
1061: interview up to one month before death multiplied by the
1062: probability to die within a month. Thanks to Chris
1063: Jackson for correcting this bug. Former versions increased
1064: mortality artificially. The bad side is that we add another loop
1065: which slows down the processing. The difference can be up to 10%
1066: lower mortality.
1067: */
1068: lli=log(out[s1][s2] - savm[s1][s2]);
1069: }else{
1070: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1071: /* 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 */
1072: }
1073: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1074: /*if(lli ==000.0)*/
1075: /*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); */
1076: ipmx +=1;
1077: sw += weight[i];
1078: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1079: } /* end of wave */
1080: } /* end of individual */
1081: } else if(mle==2){
1082: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1083: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1084: for(mi=1; mi<= wav[i]-1; mi++){
1085: for (ii=1;ii<=nlstate+ndeath;ii++)
1086: for (j=1;j<=nlstate+ndeath;j++){
1087: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1088: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1089: }
1090: for(d=0; d<=dh[mi][i]; d++){
1091: newm=savm;
1092: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1093: for (kk=1; kk<=cptcovage;kk++) {
1094: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1095: }
1096: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1097: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1098: savm=oldm;
1099: oldm=newm;
1100: } /* end mult */
1101:
1102: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1103: /* But now since version 0.9 we anticipate for bias and large stepm.
1104: * If stepm is larger than one month (smallest stepm) and if the exact delay
1105: * (in months) between two waves is not a multiple of stepm, we rounded to
1106: * the nearest (and in case of equal distance, to the lowest) interval but now
1107: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1108: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1109: * probability in order to take into account the bias as a fraction of the way
1110: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1111: * -stepm/2 to stepm/2 .
1112: * For stepm=1 the results are the same as for previous versions of Imach.
1113: * For stepm > 1 the results are less biased than in previous versions.
1114: */
1115: s1=s[mw[mi][i]][i];
1116: s2=s[mw[mi+1][i]][i];
1117: bbh=(double)bh[mi][i]/(double)stepm;
1118: /* bias is positive if real duration
1119: * is higher than the multiple of stepm and negative otherwise.
1120: */
1121: 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 */
1122: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1123: /*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 */
1124: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1125: /*if(lli ==000.0)*/
1126: /*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); */
1127: ipmx +=1;
1128: sw += weight[i];
1129: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1130: } /* end of wave */
1131: } /* end of individual */
1132: } else if(mle==3){ /* exponential inter-extrapolation */
1133: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1134: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1135: for(mi=1; mi<= wav[i]-1; mi++){
1136: for (ii=1;ii<=nlstate+ndeath;ii++)
1137: for (j=1;j<=nlstate+ndeath;j++){
1138: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1139: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1140: }
1141: for(d=0; d<dh[mi][i]; d++){
1142: newm=savm;
1143: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1144: for (kk=1; kk<=cptcovage;kk++) {
1145: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1146: }
1147: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1148: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1149: savm=oldm;
1150: oldm=newm;
1151: } /* end mult */
1152:
1153: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1154: /* But now since version 0.9 we anticipate for bias and large stepm.
1155: * If stepm is larger than one month (smallest stepm) and if the exact delay
1156: * (in months) between two waves is not a multiple of stepm, we rounded to
1157: * the nearest (and in case of equal distance, to the lowest) interval but now
1158: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1159: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1160: * probability in order to take into account the bias as a fraction of the way
1161: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1162: * -stepm/2 to stepm/2 .
1163: * For stepm=1 the results are the same as for previous versions of Imach.
1164: * For stepm > 1 the results are less biased than in previous versions.
1165: */
1166: s1=s[mw[mi][i]][i];
1167: s2=s[mw[mi+1][i]][i];
1168: bbh=(double)bh[mi][i]/(double)stepm;
1169: /* bias is positive if real duration
1170: * is higher than the multiple of stepm and negative otherwise.
1171: */
1172: /* 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 */
1173: 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 */
1174: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1175: /*if(lli ==000.0)*/
1176: /*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); */
1177: ipmx +=1;
1178: sw += weight[i];
1179: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1180: } /* end of wave */
1181: } /* end of individual */
1182: }else{ /* ml=4 no inter-extrapolation */
1183: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1184: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1185: for(mi=1; mi<= wav[i]-1; mi++){
1186: for (ii=1;ii<=nlstate+ndeath;ii++)
1187: for (j=1;j<=nlstate+ndeath;j++){
1188: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1189: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1190: }
1191: for(d=0; d<dh[mi][i]; d++){
1192: newm=savm;
1193: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1194: for (kk=1; kk<=cptcovage;kk++) {
1195: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1196: }
1197:
1198: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1199: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1200: savm=oldm;
1201: oldm=newm;
1202: } /* end mult */
1203:
1204: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1205: ipmx +=1;
1206: sw += weight[i];
1207: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1208: } /* end of wave */
1209: } /* end of individual */
1210: } /* End of if */
1211: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1212: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1213: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1214: return -l;
1215: }
1216:
1217:
1218: /*********** Maximum Likelihood Estimation ***************/
1219:
1220: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1221: {
1222: int i,j, iter;
1223: double **xi;
1224: double fret;
1225: char filerespow[FILENAMELENGTH];
1226: xi=matrix(1,npar,1,npar);
1227: for (i=1;i<=npar;i++)
1228: for (j=1;j<=npar;j++)
1229: xi[i][j]=(i==j ? 1.0 : 0.0);
1230: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1231: strcpy(filerespow,"pow");
1232: strcat(filerespow,fileres);
1233: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1234: printf("Problem with resultfile: %s\n", filerespow);
1235: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1236: }
1237: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1238: for (i=1;i<=nlstate;i++)
1239: for(j=1;j<=nlstate+ndeath;j++)
1240: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1241: fprintf(ficrespow,"\n");
1242: powell(p,xi,npar,ftol,&iter,&fret,func);
1243:
1244: fclose(ficrespow);
1245: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1246: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1247: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1248:
1249: }
1250:
1251: /**** Computes Hessian and covariance matrix ***/
1252: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1253: {
1254: double **a,**y,*x,pd;
1255: double **hess;
1256: int i, j,jk;
1257: int *indx;
1258:
1259: double hessii(double p[], double delta, int theta, double delti[]);
1260: double hessij(double p[], double delti[], int i, int j);
1261: void lubksb(double **a, int npar, int *indx, double b[]) ;
1262: void ludcmp(double **a, int npar, int *indx, double *d) ;
1263:
1264: hess=matrix(1,npar,1,npar);
1265:
1266: printf("\nCalculation of the hessian matrix. Wait...\n");
1267: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1268: for (i=1;i<=npar;i++){
1269: printf("%d",i);fflush(stdout);
1270: fprintf(ficlog,"%d",i);fflush(ficlog);
1271: hess[i][i]=hessii(p,ftolhess,i,delti);
1272: /*printf(" %f ",p[i]);*/
1273: /*printf(" %lf ",hess[i][i]);*/
1274: }
1275:
1276: for (i=1;i<=npar;i++) {
1277: for (j=1;j<=npar;j++) {
1278: if (j>i) {
1279: printf(".%d%d",i,j);fflush(stdout);
1280: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1281: hess[i][j]=hessij(p,delti,i,j);
1282: hess[j][i]=hess[i][j];
1283: /*printf(" %lf ",hess[i][j]);*/
1284: }
1285: }
1286: }
1287: printf("\n");
1288: fprintf(ficlog,"\n");
1289:
1290: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1291: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1292:
1293: a=matrix(1,npar,1,npar);
1294: y=matrix(1,npar,1,npar);
1295: x=vector(1,npar);
1296: indx=ivector(1,npar);
1297: for (i=1;i<=npar;i++)
1298: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1299: ludcmp(a,npar,indx,&pd);
1300:
1301: for (j=1;j<=npar;j++) {
1302: for (i=1;i<=npar;i++) x[i]=0;
1303: x[j]=1;
1304: lubksb(a,npar,indx,x);
1305: for (i=1;i<=npar;i++){
1306: matcov[i][j]=x[i];
1307: }
1308: }
1309:
1310: printf("\n#Hessian matrix#\n");
1311: fprintf(ficlog,"\n#Hessian matrix#\n");
1312: for (i=1;i<=npar;i++) {
1313: for (j=1;j<=npar;j++) {
1314: printf("%.3e ",hess[i][j]);
1315: fprintf(ficlog,"%.3e ",hess[i][j]);
1316: }
1317: printf("\n");
1318: fprintf(ficlog,"\n");
1319: }
1320:
1321: /* Recompute Inverse */
1322: for (i=1;i<=npar;i++)
1323: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1324: ludcmp(a,npar,indx,&pd);
1325:
1326: /* printf("\n#Hessian matrix recomputed#\n");
1327:
1328: for (j=1;j<=npar;j++) {
1329: for (i=1;i<=npar;i++) x[i]=0;
1330: x[j]=1;
1331: lubksb(a,npar,indx,x);
1332: for (i=1;i<=npar;i++){
1333: y[i][j]=x[i];
1334: printf("%.3e ",y[i][j]);
1335: fprintf(ficlog,"%.3e ",y[i][j]);
1336: }
1337: printf("\n");
1338: fprintf(ficlog,"\n");
1339: }
1340: */
1341:
1342: free_matrix(a,1,npar,1,npar);
1343: free_matrix(y,1,npar,1,npar);
1344: free_vector(x,1,npar);
1345: free_ivector(indx,1,npar);
1346: free_matrix(hess,1,npar,1,npar);
1347:
1348:
1349: }
1350:
1351: /*************** hessian matrix ****************/
1352: double hessii( double x[], double delta, int theta, double delti[])
1353: {
1354: int i;
1355: int l=1, lmax=20;
1356: double k1,k2;
1357: double p2[NPARMAX+1];
1358: double res;
1359: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1360: double fx;
1361: int k=0,kmax=10;
1362: double l1;
1363:
1364: fx=func(x);
1365: for (i=1;i<=npar;i++) p2[i]=x[i];
1366: for(l=0 ; l <=lmax; l++){
1367: l1=pow(10,l);
1368: delts=delt;
1369: for(k=1 ; k <kmax; k=k+1){
1370: delt = delta*(l1*k);
1371: p2[theta]=x[theta] +delt;
1372: k1=func(p2)-fx;
1373: p2[theta]=x[theta]-delt;
1374: k2=func(p2)-fx;
1375: /*res= (k1-2.0*fx+k2)/delt/delt; */
1376: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1377:
1378: #ifdef DEBUG
1379: 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);
1380: 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);
1381: #endif
1382: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1383: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1384: k=kmax;
1385: }
1386: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1387: k=kmax; l=lmax*10.;
1388: }
1389: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1390: delts=delt;
1391: }
1392: }
1393: }
1394: delti[theta]=delts;
1395: return res;
1396:
1397: }
1398:
1399: double hessij( double x[], double delti[], int thetai,int thetaj)
1400: {
1401: int i;
1402: int l=1, l1, lmax=20;
1403: double k1,k2,k3,k4,res,fx;
1404: double p2[NPARMAX+1];
1405: int k;
1406:
1407: fx=func(x);
1408: for (k=1; k<=2; k++) {
1409: for (i=1;i<=npar;i++) p2[i]=x[i];
1410: p2[thetai]=x[thetai]+delti[thetai]/k;
1411: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1412: k1=func(p2)-fx;
1413:
1414: p2[thetai]=x[thetai]+delti[thetai]/k;
1415: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1416: k2=func(p2)-fx;
1417:
1418: p2[thetai]=x[thetai]-delti[thetai]/k;
1419: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1420: k3=func(p2)-fx;
1421:
1422: p2[thetai]=x[thetai]-delti[thetai]/k;
1423: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1424: k4=func(p2)-fx;
1425: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1426: #ifdef DEBUG
1427: 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);
1428: 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);
1429: #endif
1430: }
1431: return res;
1432: }
1433:
1434: /************** Inverse of matrix **************/
1435: void ludcmp(double **a, int n, int *indx, double *d)
1436: {
1437: int i,imax,j,k;
1438: double big,dum,sum,temp;
1439: double *vv;
1440:
1441: vv=vector(1,n);
1442: *d=1.0;
1443: for (i=1;i<=n;i++) {
1444: big=0.0;
1445: for (j=1;j<=n;j++)
1446: if ((temp=fabs(a[i][j])) > big) big=temp;
1447: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1448: vv[i]=1.0/big;
1449: }
1450: for (j=1;j<=n;j++) {
1451: for (i=1;i<j;i++) {
1452: sum=a[i][j];
1453: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1454: a[i][j]=sum;
1455: }
1456: big=0.0;
1457: for (i=j;i<=n;i++) {
1458: sum=a[i][j];
1459: for (k=1;k<j;k++)
1460: sum -= a[i][k]*a[k][j];
1461: a[i][j]=sum;
1462: if ( (dum=vv[i]*fabs(sum)) >= big) {
1463: big=dum;
1464: imax=i;
1465: }
1466: }
1467: if (j != imax) {
1468: for (k=1;k<=n;k++) {
1469: dum=a[imax][k];
1470: a[imax][k]=a[j][k];
1471: a[j][k]=dum;
1472: }
1473: *d = -(*d);
1474: vv[imax]=vv[j];
1475: }
1476: indx[j]=imax;
1477: if (a[j][j] == 0.0) a[j][j]=TINY;
1478: if (j != n) {
1479: dum=1.0/(a[j][j]);
1480: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1481: }
1482: }
1483: free_vector(vv,1,n); /* Doesn't work */
1484: ;
1485: }
1486:
1487: void lubksb(double **a, int n, int *indx, double b[])
1488: {
1489: int i,ii=0,ip,j;
1490: double sum;
1491:
1492: for (i=1;i<=n;i++) {
1493: ip=indx[i];
1494: sum=b[ip];
1495: b[ip]=b[i];
1496: if (ii)
1497: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1498: else if (sum) ii=i;
1499: b[i]=sum;
1500: }
1501: for (i=n;i>=1;i--) {
1502: sum=b[i];
1503: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1504: b[i]=sum/a[i][i];
1505: }
1506: }
1507:
1508: /************ Frequencies ********************/
1509: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
1510: { /* Some frequencies */
1511:
1512: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1513: int first;
1514: double ***freq; /* Frequencies */
1515: double *pp, **prop;
1516: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1517: FILE *ficresp;
1518: char fileresp[FILENAMELENGTH];
1519:
1520: pp=vector(1,nlstate);
1521: prop=matrix(1,nlstate,iagemin,iagemax+3);
1522: strcpy(fileresp,"p");
1523: strcat(fileresp,fileres);
1524: if((ficresp=fopen(fileresp,"w"))==NULL) {
1525: printf("Problem with prevalence resultfile: %s\n", fileresp);
1526: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1527: exit(0);
1528: }
1529: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
1530: j1=0;
1531:
1532: j=cptcoveff;
1533: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1534:
1535: first=1;
1536:
1537: for(k1=1; k1<=j;k1++){
1538: for(i1=1; i1<=ncodemax[k1];i1++){
1539: j1++;
1540: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1541: scanf("%d", i);*/
1542: for (i=-1; i<=nlstate+ndeath; i++)
1543: for (jk=-1; jk<=nlstate+ndeath; jk++)
1544: for(m=iagemin; m <= iagemax+3; m++)
1545: freq[i][jk][m]=0;
1546:
1547: for (i=1; i<=nlstate; i++)
1548: for(m=iagemin; m <= iagemax+3; m++)
1549: prop[i][m]=0;
1550:
1551: dateintsum=0;
1552: k2cpt=0;
1553: for (i=1; i<=imx; i++) {
1554: bool=1;
1555: if (cptcovn>0) {
1556: for (z1=1; z1<=cptcoveff; z1++)
1557: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1558: bool=0;
1559: }
1560: if (bool==1){
1561: for(m=firstpass; m<=lastpass; m++){
1562: k2=anint[m][i]+(mint[m][i]/12.);
1563: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1564: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1565: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1566: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1567: if (m<lastpass) {
1568: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1569: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1570: }
1571:
1572: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1573: dateintsum=dateintsum+k2;
1574: k2cpt++;
1575: }
1576: }
1577: }
1578: }
1579: }
1580:
1581: fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1582:
1583: if (cptcovn>0) {
1584: fprintf(ficresp, "\n#********** Variable ");
1585: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1586: fprintf(ficresp, "**********\n#");
1587: }
1588: for(i=1; i<=nlstate;i++)
1589: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1590: fprintf(ficresp, "\n");
1591:
1592: for(i=iagemin; i <= iagemax+3; i++){
1593: if(i==iagemax+3){
1594: fprintf(ficlog,"Total");
1595: }else{
1596: if(first==1){
1597: first=0;
1598: printf("See log file for details...\n");
1599: }
1600: fprintf(ficlog,"Age %d", i);
1601: }
1602: for(jk=1; jk <=nlstate ; jk++){
1603: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1604: pp[jk] += freq[jk][m][i];
1605: }
1606: for(jk=1; jk <=nlstate ; jk++){
1607: for(m=-1, pos=0; m <=0 ; m++)
1608: pos += freq[jk][m][i];
1609: if(pp[jk]>=1.e-10){
1610: if(first==1){
1611: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1612: }
1613: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1614: }else{
1615: if(first==1)
1616: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1617: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1618: }
1619: }
1620:
1621: for(jk=1; jk <=nlstate ; jk++){
1622: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1623: pp[jk] += freq[jk][m][i];
1624: }
1625: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
1626: pos += pp[jk];
1627: posprop += prop[jk][i];
1628: }
1629: for(jk=1; jk <=nlstate ; jk++){
1630: if(pos>=1.e-5){
1631: if(first==1)
1632: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1633: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1634: }else{
1635: if(first==1)
1636: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1637: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1638: }
1639: if( i <= iagemax){
1640: if(pos>=1.e-5){
1641: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1642: probs[i][jk][j1]= pp[jk]/pos;
1643: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1644: }
1645: else
1646: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1647: }
1648: }
1649:
1650: for(jk=-1; jk <=nlstate+ndeath; jk++)
1651: for(m=-1; m <=nlstate+ndeath; m++)
1652: if(freq[jk][m][i] !=0 ) {
1653: if(first==1)
1654: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1655: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1656: }
1657: if(i <= iagemax)
1658: fprintf(ficresp,"\n");
1659: if(first==1)
1660: printf("Others in log...\n");
1661: fprintf(ficlog,"\n");
1662: }
1663: }
1664: }
1665: dateintmean=dateintsum/k2cpt;
1666:
1667: fclose(ficresp);
1668: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
1669: free_vector(pp,1,nlstate);
1670: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1671: /* End of Freq */
1672: }
1673:
1674: /************ Prevalence ********************/
1675: void prevalence(double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
1676: {
1677: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
1678: in each health status at the date of interview (if between dateprev1 and dateprev2).
1679: We still use firstpass and lastpass as another selection.
1680: */
1681:
1682: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1683: double ***freq; /* Frequencies */
1684: double *pp, **prop;
1685: double pos,posprop;
1686: double y2; /* in fractional years */
1687: int iagemin, iagemax;
1688:
1689: iagemin= (int) agemin;
1690: iagemax= (int) agemax;
1691: /*pp=vector(1,nlstate);*/
1692: prop=matrix(1,nlstate,iagemin,iagemax+3);
1693: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1694: j1=0;
1695:
1696: j=cptcoveff;
1697: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1698:
1699: for(k1=1; k1<=j;k1++){
1700: for(i1=1; i1<=ncodemax[k1];i1++){
1701: j1++;
1702:
1703: for (i=1; i<=nlstate; i++)
1704: for(m=iagemin; m <= iagemax+3; m++)
1705: prop[i][m]=0.0;
1706:
1707: for (i=1; i<=imx; i++) { /* Each individual */
1708: bool=1;
1709: if (cptcovn>0) {
1710: for (z1=1; z1<=cptcoveff; z1++)
1711: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1712: bool=0;
1713: }
1714: if (bool==1) {
1715: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
1716: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
1717: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1718: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1719: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1720: if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
1721: if (s[m][i]>0 && s[m][i]<=nlstate) {
1722: /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
1723: prop[s[m][i]][(int)agev[m][i]] += weight[i];
1724: prop[s[m][i]][iagemax+3] += weight[i];
1725: }
1726: }
1727: } /* end selection of waves */
1728: }
1729: }
1730: for(i=iagemin; i <= iagemax+3; i++){
1731:
1732: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
1733: posprop += prop[jk][i];
1734: }
1735:
1736: for(jk=1; jk <=nlstate ; jk++){
1737: if( i <= iagemax){
1738: if(posprop>=1.e-5){
1739: probs[i][jk][j1]= prop[jk][i]/posprop;
1740: }
1741: }
1742: }/* end jk */
1743: }/* end i */
1744: } /* end i1 */
1745: } /* end k1 */
1746:
1747: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
1748: /*free_vector(pp,1,nlstate);*/
1749: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
1750: } /* End of prevalence */
1751:
1752: /************* Waves Concatenation ***************/
1753:
1754: 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)
1755: {
1756: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1757: Death is a valid wave (if date is known).
1758: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1759: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1760: and mw[mi+1][i]. dh depends on stepm.
1761: */
1762:
1763: int i, mi, m;
1764: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1765: double sum=0., jmean=0.;*/
1766: int first;
1767: int j, k=0,jk, ju, jl;
1768: double sum=0.;
1769: first=0;
1770: jmin=1e+5;
1771: jmax=-1;
1772: jmean=0.;
1773: for(i=1; i<=imx; i++){
1774: mi=0;
1775: m=firstpass;
1776: while(s[m][i] <= nlstate){
1777: if(s[m][i]>=1)
1778: mw[++mi][i]=m;
1779: if(m >=lastpass)
1780: break;
1781: else
1782: m++;
1783: }/* end while */
1784: if (s[m][i] > nlstate){
1785: mi++; /* Death is another wave */
1786: /* if(mi==0) never been interviewed correctly before death */
1787: /* Only death is a correct wave */
1788: mw[mi][i]=m;
1789: }
1790:
1791: wav[i]=mi;
1792: if(mi==0){
1793: if(first==0){
1794: printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
1795: first=1;
1796: }
1797: if(first==1){
1798: fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
1799: }
1800: } /* end mi==0 */
1801: } /* End individuals */
1802:
1803: for(i=1; i<=imx; i++){
1804: for(mi=1; mi<wav[i];mi++){
1805: if (stepm <=0)
1806: dh[mi][i]=1;
1807: else{
1808: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
1809: if (agedc[i] < 2*AGESUP) {
1810: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1811: if(j==0) j=1; /* Survives at least one month after exam */
1812: k=k+1;
1813: if (j >= jmax) jmax=j;
1814: if (j <= jmin) jmin=j;
1815: sum=sum+j;
1816: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
1817: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1818: if(j<0)printf("Error! Negative delay (%d to death) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
1819: }
1820: }
1821: else{
1822: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1823: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1824: k=k+1;
1825: if (j >= jmax) jmax=j;
1826: else if (j <= jmin)jmin=j;
1827: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1828: /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
1829: if(j<0)printf("Error! Negative delay (%d) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
1830: sum=sum+j;
1831: }
1832: jk= j/stepm;
1833: jl= j -jk*stepm;
1834: ju= j -(jk+1)*stepm;
1835: if(mle <=1){
1836: if(jl==0){
1837: dh[mi][i]=jk;
1838: bh[mi][i]=0;
1839: }else{ /* We want a negative bias in order to only have interpolation ie
1840: * at the price of an extra matrix product in likelihood */
1841: dh[mi][i]=jk+1;
1842: bh[mi][i]=ju;
1843: }
1844: }else{
1845: if(jl <= -ju){
1846: dh[mi][i]=jk;
1847: bh[mi][i]=jl; /* bias is positive if real duration
1848: * is higher than the multiple of stepm and negative otherwise.
1849: */
1850: }
1851: else{
1852: dh[mi][i]=jk+1;
1853: bh[mi][i]=ju;
1854: }
1855: if(dh[mi][i]==0){
1856: dh[mi][i]=1; /* At least one step */
1857: bh[mi][i]=ju; /* At least one step */
1858: /* 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);*/
1859: }
1860: }
1861: } /* end if mle */
1862: } /* end wave */
1863: }
1864: jmean=sum/k;
1865: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1866: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1867: }
1868:
1869: /*********** Tricode ****************************/
1870: void tricode(int *Tvar, int **nbcode, int imx)
1871: {
1872:
1873: int Ndum[20],ij=1, k, j, i, maxncov=19;
1874: int cptcode=0;
1875: cptcoveff=0;
1876:
1877: for (k=0; k<maxncov; k++) Ndum[k]=0;
1878: for (k=1; k<=7; k++) ncodemax[k]=0;
1879:
1880: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1881: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
1882: modality*/
1883: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
1884: Ndum[ij]++; /*store the modality */
1885: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1886: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
1887: Tvar[j]. If V=sex and male is 0 and
1888: female is 1, then cptcode=1.*/
1889: }
1890:
1891: for (i=0; i<=cptcode; i++) {
1892: 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 */
1893: }
1894:
1895: ij=1;
1896: for (i=1; i<=ncodemax[j]; i++) {
1897: for (k=0; k<= maxncov; k++) {
1898: if (Ndum[k] != 0) {
1899: nbcode[Tvar[j]][ij]=k;
1900: /* 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; */
1901:
1902: ij++;
1903: }
1904: if (ij > ncodemax[j]) break;
1905: }
1906: }
1907: }
1908:
1909: for (k=0; k< maxncov; k++) Ndum[k]=0;
1910:
1911: for (i=1; i<=ncovmodel-2; i++) {
1912: /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
1913: ij=Tvar[i];
1914: Ndum[ij]++;
1915: }
1916:
1917: ij=1;
1918: for (i=1; i<= maxncov; i++) {
1919: if((Ndum[i]!=0) && (i<=ncovcol)){
1920: Tvaraff[ij]=i; /*For printing */
1921: ij++;
1922: }
1923: }
1924:
1925: cptcoveff=ij-1; /*Number of simple covariates*/
1926: }
1927:
1928: /*********** Health Expectancies ****************/
1929:
1930: 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 )
1931:
1932: {
1933: /* Health expectancies */
1934: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
1935: double age, agelim, hf;
1936: double ***p3mat,***varhe;
1937: double **dnewm,**doldm;
1938: double *xp;
1939: double **gp, **gm;
1940: double ***gradg, ***trgradg;
1941: int theta;
1942:
1943: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1944: xp=vector(1,npar);
1945: dnewm=matrix(1,nlstate*nlstate,1,npar);
1946: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1947:
1948: fprintf(ficreseij,"# Health expectancies\n");
1949: fprintf(ficreseij,"# Age");
1950: for(i=1; i<=nlstate;i++)
1951: for(j=1; j<=nlstate;j++)
1952: fprintf(ficreseij," %1d-%1d (SE)",i,j);
1953: fprintf(ficreseij,"\n");
1954:
1955: if(estepm < stepm){
1956: printf ("Problem %d lower than %d\n",estepm, stepm);
1957: }
1958: else hstepm=estepm;
1959: /* We compute the life expectancy from trapezoids spaced every estepm months
1960: * This is mainly to measure the difference between two models: for example
1961: * if stepm=24 months pijx are given only every 2 years and by summing them
1962: * we are calculating an estimate of the Life Expectancy assuming a linear
1963: * progression in between and thus overestimating or underestimating according
1964: * to the curvature of the survival function. If, for the same date, we
1965: * estimate the model with stepm=1 month, we can keep estepm to 24 months
1966: * to compare the new estimate of Life expectancy with the same linear
1967: * hypothesis. A more precise result, taking into account a more precise
1968: * curvature will be obtained if estepm is as small as stepm. */
1969:
1970: /* For example we decided to compute the life expectancy with the smallest unit */
1971: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
1972: nhstepm is the number of hstepm from age to agelim
1973: nstepm is the number of stepm from age to agelin.
1974: Look at hpijx to understand the reason of that which relies in memory size
1975: and note for a fixed period like estepm months */
1976: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
1977: survival function given by stepm (the optimization length). Unfortunately it
1978: means that if the survival funtion is printed only each two years of age and if
1979: you sum them up and add 1 year (area under the trapezoids) you won't get the same
1980: results. So we changed our mind and took the option of the best precision.
1981: */
1982: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
1983:
1984: agelim=AGESUP;
1985: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1986: /* nhstepm age range expressed in number of stepm */
1987: nstepm=(int) rint((agelim-age)*YEARM/stepm);
1988: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
1989: /* if (stepm >= YEARM) hstepm=1;*/
1990: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
1991: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1992: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
1993: gp=matrix(0,nhstepm,1,nlstate*nlstate);
1994: gm=matrix(0,nhstepm,1,nlstate*nlstate);
1995:
1996: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1997: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1998: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1999:
2000:
2001: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2002:
2003: /* Computing Variances of health expectancies */
2004:
2005: for(theta=1; theta <=npar; theta++){
2006: for(i=1; i<=npar; i++){
2007: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2008: }
2009: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2010:
2011: cptj=0;
2012: for(j=1; j<= nlstate; j++){
2013: for(i=1; i<=nlstate; i++){
2014: cptj=cptj+1;
2015: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2016: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2017: }
2018: }
2019: }
2020:
2021:
2022: for(i=1; i<=npar; i++)
2023: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2024: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2025:
2026: cptj=0;
2027: for(j=1; j<= nlstate; j++){
2028: for(i=1;i<=nlstate;i++){
2029: cptj=cptj+1;
2030: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
2031:
2032: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2033: }
2034: }
2035: }
2036: for(j=1; j<= nlstate*nlstate; j++)
2037: for(h=0; h<=nhstepm-1; h++){
2038: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2039: }
2040: }
2041:
2042: /* End theta */
2043:
2044: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2045:
2046: for(h=0; h<=nhstepm-1; h++)
2047: for(j=1; j<=nlstate*nlstate;j++)
2048: for(theta=1; theta <=npar; theta++)
2049: trgradg[h][j][theta]=gradg[h][theta][j];
2050:
2051:
2052: for(i=1;i<=nlstate*nlstate;i++)
2053: for(j=1;j<=nlstate*nlstate;j++)
2054: varhe[i][j][(int)age] =0.;
2055:
2056: printf("%d|",(int)age);fflush(stdout);
2057: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2058: for(h=0;h<=nhstepm-1;h++){
2059: for(k=0;k<=nhstepm-1;k++){
2060: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2061: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2062: for(i=1;i<=nlstate*nlstate;i++)
2063: for(j=1;j<=nlstate*nlstate;j++)
2064: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2065: }
2066: }
2067: /* Computing expectancies */
2068: for(i=1; i<=nlstate;i++)
2069: for(j=1; j<=nlstate;j++)
2070: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2071: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2072:
2073: /* 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]);*/
2074:
2075: }
2076:
2077: fprintf(ficreseij,"%3.0f",age );
2078: cptj=0;
2079: for(i=1; i<=nlstate;i++)
2080: for(j=1; j<=nlstate;j++){
2081: cptj++;
2082: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2083: }
2084: fprintf(ficreseij,"\n");
2085:
2086: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2087: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2088: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2089: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2090: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2091: }
2092: printf("\n");
2093: fprintf(ficlog,"\n");
2094:
2095: free_vector(xp,1,npar);
2096: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2097: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2098: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2099: }
2100:
2101: /************ Variance ******************/
2102: 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)
2103: {
2104: /* Variance of health expectancies */
2105: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2106: /* double **newm;*/
2107: double **dnewm,**doldm;
2108: double **dnewmp,**doldmp;
2109: int i, j, nhstepm, hstepm, h, nstepm ;
2110: int k, cptcode;
2111: double *xp;
2112: double **gp, **gm; /* for var eij */
2113: double ***gradg, ***trgradg; /*for var eij */
2114: double **gradgp, **trgradgp; /* for var p point j */
2115: double *gpp, *gmp; /* for var p point j */
2116: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2117: double ***p3mat;
2118: double age,agelim, hf;
2119: double ***mobaverage;
2120: int theta;
2121: char digit[4];
2122: char digitp[25];
2123:
2124: char fileresprobmorprev[FILENAMELENGTH];
2125:
2126: if(popbased==1){
2127: if(mobilav!=0)
2128: strcpy(digitp,"-populbased-mobilav-");
2129: else strcpy(digitp,"-populbased-nomobil-");
2130: }
2131: else
2132: strcpy(digitp,"-stablbased-");
2133:
2134: if (mobilav!=0) {
2135: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2136: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2137: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2138: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2139: }
2140: }
2141:
2142: strcpy(fileresprobmorprev,"prmorprev");
2143: sprintf(digit,"%-d",ij);
2144: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2145: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2146: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2147: strcat(fileresprobmorprev,fileres);
2148: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2149: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2150: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2151: }
2152: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2153: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2154: 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);
2155: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2156: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2157: fprintf(ficresprobmorprev," p.%-d SE",j);
2158: for(i=1; i<=nlstate;i++)
2159: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2160: }
2161: fprintf(ficresprobmorprev,"\n");
2162: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2163: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2164: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2165: exit(0);
2166: }
2167: else{
2168: fprintf(ficgp,"\n# Routine varevsij");
2169: }
2170: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2171: printf("Problem with html file: %s\n", optionfilehtm);
2172: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2173: exit(0);
2174: }
2175: else{
2176: fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
2177: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2178: }
2179: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2180:
2181: 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");
2182: fprintf(ficresvij,"# Age");
2183: for(i=1; i<=nlstate;i++)
2184: for(j=1; j<=nlstate;j++)
2185: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2186: fprintf(ficresvij,"\n");
2187:
2188: xp=vector(1,npar);
2189: dnewm=matrix(1,nlstate,1,npar);
2190: doldm=matrix(1,nlstate,1,nlstate);
2191: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2192: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2193:
2194: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2195: gpp=vector(nlstate+1,nlstate+ndeath);
2196: gmp=vector(nlstate+1,nlstate+ndeath);
2197: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2198:
2199: if(estepm < stepm){
2200: printf ("Problem %d lower than %d\n",estepm, stepm);
2201: }
2202: else hstepm=estepm;
2203: /* For example we decided to compute the life expectancy with the smallest unit */
2204: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2205: nhstepm is the number of hstepm from age to agelim
2206: nstepm is the number of stepm from age to agelin.
2207: Look at hpijx to understand the reason of that which relies in memory size
2208: and note for a fixed period like k years */
2209: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2210: survival function given by stepm (the optimization length). Unfortunately it
2211: means that if the survival funtion is printed every two years of age and if
2212: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2213: results. So we changed our mind and took the option of the best precision.
2214: */
2215: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2216: agelim = AGESUP;
2217: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2218: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2219: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2220: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2221: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2222: gp=matrix(0,nhstepm,1,nlstate);
2223: gm=matrix(0,nhstepm,1,nlstate);
2224:
2225:
2226: for(theta=1; theta <=npar; theta++){
2227: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2228: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2229: }
2230: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2231: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2232:
2233: if (popbased==1) {
2234: if(mobilav ==0){
2235: for(i=1; i<=nlstate;i++)
2236: prlim[i][i]=probs[(int)age][i][ij];
2237: }else{ /* mobilav */
2238: for(i=1; i<=nlstate;i++)
2239: prlim[i][i]=mobaverage[(int)age][i][ij];
2240: }
2241: }
2242:
2243: for(j=1; j<= nlstate; j++){
2244: for(h=0; h<=nhstepm; h++){
2245: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2246: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2247: }
2248: }
2249: /* This for computing probability of death (h=1 means
2250: computed over hstepm matrices product = hstepm*stepm months)
2251: as a weighted average of prlim.
2252: */
2253: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2254: for(i=1,gpp[j]=0.; i<= nlstate; i++)
2255: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2256: }
2257: /* end probability of death */
2258:
2259: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
2260: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2261: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2262: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2263:
2264: if (popbased==1) {
2265: if(mobilav ==0){
2266: for(i=1; i<=nlstate;i++)
2267: prlim[i][i]=probs[(int)age][i][ij];
2268: }else{ /* mobilav */
2269: for(i=1; i<=nlstate;i++)
2270: prlim[i][i]=mobaverage[(int)age][i][ij];
2271: }
2272: }
2273:
2274: for(j=1; j<= nlstate; j++){
2275: for(h=0; h<=nhstepm; h++){
2276: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2277: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2278: }
2279: }
2280: /* This for computing probability of death (h=1 means
2281: computed over hstepm matrices product = hstepm*stepm months)
2282: as a weighted average of prlim.
2283: */
2284: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2285: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2286: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2287: }
2288: /* end probability of death */
2289:
2290: for(j=1; j<= nlstate; j++) /* vareij */
2291: for(h=0; h<=nhstepm; h++){
2292: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2293: }
2294:
2295: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2296: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2297: }
2298:
2299: } /* End theta */
2300:
2301: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2302:
2303: for(h=0; h<=nhstepm; h++) /* veij */
2304: for(j=1; j<=nlstate;j++)
2305: for(theta=1; theta <=npar; theta++)
2306: trgradg[h][j][theta]=gradg[h][theta][j];
2307:
2308: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
2309: for(theta=1; theta <=npar; theta++)
2310: trgradgp[j][theta]=gradgp[theta][j];
2311:
2312:
2313: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2314: for(i=1;i<=nlstate;i++)
2315: for(j=1;j<=nlstate;j++)
2316: vareij[i][j][(int)age] =0.;
2317:
2318: for(h=0;h<=nhstepm;h++){
2319: for(k=0;k<=nhstepm;k++){
2320: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2321: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2322: for(i=1;i<=nlstate;i++)
2323: for(j=1;j<=nlstate;j++)
2324: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2325: }
2326: }
2327:
2328: /* pptj */
2329: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2330: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
2331: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2332: for(i=nlstate+1;i<=nlstate+ndeath;i++)
2333: varppt[j][i]=doldmp[j][i];
2334: /* end ppptj */
2335: /* x centered again */
2336: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2337: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2338:
2339: if (popbased==1) {
2340: if(mobilav ==0){
2341: for(i=1; i<=nlstate;i++)
2342: prlim[i][i]=probs[(int)age][i][ij];
2343: }else{ /* mobilav */
2344: for(i=1; i<=nlstate;i++)
2345: prlim[i][i]=mobaverage[(int)age][i][ij];
2346: }
2347: }
2348:
2349: /* This for computing probability of death (h=1 means
2350: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2351: as a weighted average of prlim.
2352: */
2353: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2354: for(i=1,gmp[j]=0.;i<= nlstate; i++)
2355: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2356: }
2357: /* end probability of death */
2358:
2359: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2360: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2361: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2362: for(i=1; i<=nlstate;i++){
2363: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2364: }
2365: }
2366: fprintf(ficresprobmorprev,"\n");
2367:
2368: fprintf(ficresvij,"%.0f ",age );
2369: for(i=1; i<=nlstate;i++)
2370: for(j=1; j<=nlstate;j++){
2371: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2372: }
2373: fprintf(ficresvij,"\n");
2374: free_matrix(gp,0,nhstepm,1,nlstate);
2375: free_matrix(gm,0,nhstepm,1,nlstate);
2376: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2377: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2378: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2379: } /* End age */
2380: free_vector(gpp,nlstate+1,nlstate+ndeath);
2381: free_vector(gmp,nlstate+1,nlstate+ndeath);
2382: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2383: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2384: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2385: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2386: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
2387: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2388: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2389: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
2390: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",fileresprobmorprev);
2391: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
2392: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
2393: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
2394: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
2395: /* 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);
2396: */
2397: fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
2398:
2399: free_vector(xp,1,npar);
2400: free_matrix(doldm,1,nlstate,1,nlstate);
2401: free_matrix(dnewm,1,nlstate,1,npar);
2402: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2403: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2404: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2405: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2406: fclose(ficresprobmorprev);
2407: fclose(ficgp);
2408: fclose(fichtm);
2409: }
2410:
2411: /************ Variance of prevlim ******************/
2412: 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)
2413: {
2414: /* Variance of prevalence limit */
2415: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
2416: double **newm;
2417: double **dnewm,**doldm;
2418: int i, j, nhstepm, hstepm;
2419: int k, cptcode;
2420: double *xp;
2421: double *gp, *gm;
2422: double **gradg, **trgradg;
2423: double age,agelim;
2424: int theta;
2425:
2426: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
2427: fprintf(ficresvpl,"# Age");
2428: for(i=1; i<=nlstate;i++)
2429: fprintf(ficresvpl," %1d-%1d",i,i);
2430: fprintf(ficresvpl,"\n");
2431:
2432: xp=vector(1,npar);
2433: dnewm=matrix(1,nlstate,1,npar);
2434: doldm=matrix(1,nlstate,1,nlstate);
2435:
2436: hstepm=1*YEARM; /* Every year of age */
2437: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2438: agelim = AGESUP;
2439: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2440: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2441: if (stepm >= YEARM) hstepm=1;
2442: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2443: gradg=matrix(1,npar,1,nlstate);
2444: gp=vector(1,nlstate);
2445: gm=vector(1,nlstate);
2446:
2447: for(theta=1; theta <=npar; theta++){
2448: for(i=1; i<=npar; i++){ /* Computes gradient */
2449: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2450: }
2451: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2452: for(i=1;i<=nlstate;i++)
2453: gp[i] = prlim[i][i];
2454:
2455: for(i=1; i<=npar; i++) /* Computes gradient */
2456: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2457: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2458: for(i=1;i<=nlstate;i++)
2459: gm[i] = prlim[i][i];
2460:
2461: for(i=1;i<=nlstate;i++)
2462: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2463: } /* End theta */
2464:
2465: trgradg =matrix(1,nlstate,1,npar);
2466:
2467: for(j=1; j<=nlstate;j++)
2468: for(theta=1; theta <=npar; theta++)
2469: trgradg[j][theta]=gradg[theta][j];
2470:
2471: for(i=1;i<=nlstate;i++)
2472: varpl[i][(int)age] =0.;
2473: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2474: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2475: for(i=1;i<=nlstate;i++)
2476: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2477:
2478: fprintf(ficresvpl,"%.0f ",age );
2479: for(i=1; i<=nlstate;i++)
2480: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2481: fprintf(ficresvpl,"\n");
2482: free_vector(gp,1,nlstate);
2483: free_vector(gm,1,nlstate);
2484: free_matrix(gradg,1,npar,1,nlstate);
2485: free_matrix(trgradg,1,nlstate,1,npar);
2486: } /* End age */
2487:
2488: free_vector(xp,1,npar);
2489: free_matrix(doldm,1,nlstate,1,npar);
2490: free_matrix(dnewm,1,nlstate,1,nlstate);
2491:
2492: }
2493:
2494: /************ Variance of one-step probabilities ******************/
2495: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2496: {
2497: int i, j=0, i1, k1, l1, t, tj;
2498: int k2, l2, j1, z1;
2499: int k=0,l, cptcode;
2500: int first=1, first1;
2501: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2502: double **dnewm,**doldm;
2503: double *xp;
2504: double *gp, *gm;
2505: double **gradg, **trgradg;
2506: double **mu;
2507: double age,agelim, cov[NCOVMAX];
2508: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2509: int theta;
2510: char fileresprob[FILENAMELENGTH];
2511: char fileresprobcov[FILENAMELENGTH];
2512: char fileresprobcor[FILENAMELENGTH];
2513:
2514: double ***varpij;
2515:
2516: strcpy(fileresprob,"prob");
2517: strcat(fileresprob,fileres);
2518: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2519: printf("Problem with resultfile: %s\n", fileresprob);
2520: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2521: }
2522: strcpy(fileresprobcov,"probcov");
2523: strcat(fileresprobcov,fileres);
2524: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2525: printf("Problem with resultfile: %s\n", fileresprobcov);
2526: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2527: }
2528: strcpy(fileresprobcor,"probcor");
2529: strcat(fileresprobcor,fileres);
2530: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2531: printf("Problem with resultfile: %s\n", fileresprobcor);
2532: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2533: }
2534: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2535: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2536: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2537: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2538: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2539: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2540:
2541: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2542: fprintf(ficresprob,"# Age");
2543: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2544: fprintf(ficresprobcov,"# Age");
2545: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2546: fprintf(ficresprobcov,"# Age");
2547:
2548:
2549: for(i=1; i<=nlstate;i++)
2550: for(j=1; j<=(nlstate+ndeath);j++){
2551: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2552: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2553: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2554: }
2555: /* fprintf(ficresprob,"\n");
2556: fprintf(ficresprobcov,"\n");
2557: fprintf(ficresprobcor,"\n");
2558: */
2559: xp=vector(1,npar);
2560: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2561: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2562: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2563: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2564: first=1;
2565: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2566: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2567: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2568: exit(0);
2569: }
2570: else{
2571: fprintf(ficgp,"\n# Routine varprob");
2572: }
2573: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2574: printf("Problem with html file: %s\n", optionfilehtm);
2575: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2576: exit(0);
2577: }
2578: else{
2579: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2580: fprintf(fichtm,"\n");
2581:
2582: fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
2583: 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");
2584: 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");
2585:
2586: }
2587:
2588: cov[1]=1;
2589: tj=cptcoveff;
2590: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2591: j1=0;
2592: for(t=1; t<=tj;t++){
2593: for(i1=1; i1<=ncodemax[t];i1++){
2594: j1++;
2595: if (cptcovn>0) {
2596: fprintf(ficresprob, "\n#********** Variable ");
2597: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2598: fprintf(ficresprob, "**********\n#\n");
2599: fprintf(ficresprobcov, "\n#********** Variable ");
2600: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2601: fprintf(ficresprobcov, "**********\n#\n");
2602:
2603: fprintf(ficgp, "\n#********** Variable ");
2604: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2605: fprintf(ficgp, "**********\n#\n");
2606:
2607:
2608: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2609: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2610: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2611:
2612: fprintf(ficresprobcor, "\n#********** Variable ");
2613: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2614: fprintf(ficresprobcor, "**********\n#");
2615: }
2616:
2617: for (age=bage; age<=fage; age ++){
2618: cov[2]=age;
2619: for (k=1; k<=cptcovn;k++) {
2620: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2621: }
2622: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2623: for (k=1; k<=cptcovprod;k++)
2624: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2625:
2626: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2627: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2628: gp=vector(1,(nlstate)*(nlstate+ndeath));
2629: gm=vector(1,(nlstate)*(nlstate+ndeath));
2630:
2631: for(theta=1; theta <=npar; theta++){
2632: for(i=1; i<=npar; i++)
2633: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
2634:
2635: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2636:
2637: k=0;
2638: for(i=1; i<= (nlstate); i++){
2639: for(j=1; j<=(nlstate+ndeath);j++){
2640: k=k+1;
2641: gp[k]=pmmij[i][j];
2642: }
2643: }
2644:
2645: for(i=1; i<=npar; i++)
2646: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
2647:
2648: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2649: k=0;
2650: for(i=1; i<=(nlstate); i++){
2651: for(j=1; j<=(nlstate+ndeath);j++){
2652: k=k+1;
2653: gm[k]=pmmij[i][j];
2654: }
2655: }
2656:
2657: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
2658: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
2659: }
2660:
2661: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2662: for(theta=1; theta <=npar; theta++)
2663: trgradg[j][theta]=gradg[theta][j];
2664:
2665: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2666: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
2667: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2668: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2669: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2670: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2671:
2672: pmij(pmmij,cov,ncovmodel,x,nlstate);
2673:
2674: k=0;
2675: for(i=1; i<=(nlstate); i++){
2676: for(j=1; j<=(nlstate+ndeath);j++){
2677: k=k+1;
2678: mu[k][(int) age]=pmmij[i][j];
2679: }
2680: }
2681: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2682: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2683: varpij[i][j][(int)age] = doldm[i][j];
2684:
2685: /*printf("\n%d ",(int)age);
2686: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2687: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2688: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2689: }*/
2690:
2691: fprintf(ficresprob,"\n%d ",(int)age);
2692: fprintf(ficresprobcov,"\n%d ",(int)age);
2693: fprintf(ficresprobcor,"\n%d ",(int)age);
2694:
2695: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2696: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2697: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2698: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2699: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2700: }
2701: i=0;
2702: for (k=1; k<=(nlstate);k++){
2703: for (l=1; l<=(nlstate+ndeath);l++){
2704: i=i++;
2705: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2706: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2707: for (j=1; j<=i;j++){
2708: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2709: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
2710: }
2711: }
2712: }/* end of loop for state */
2713: } /* end of loop for age */
2714:
2715: /* Confidence intervalle of pij */
2716: /*
2717: fprintf(ficgp,"\nset noparametric;unset label");
2718: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
2719: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2720: 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);
2721: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
2722: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
2723: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
2724: */
2725:
2726: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
2727: first1=1;
2728: for (k2=1; k2<=(nlstate);k2++){
2729: for (l2=1; l2<=(nlstate+ndeath);l2++){
2730: if(l2==k2) continue;
2731: j=(k2-1)*(nlstate+ndeath)+l2;
2732: for (k1=1; k1<=(nlstate);k1++){
2733: for (l1=1; l1<=(nlstate+ndeath);l1++){
2734: if(l1==k1) continue;
2735: i=(k1-1)*(nlstate+ndeath)+l1;
2736: if(i<=j) continue;
2737: for (age=bage; age<=fage; age ++){
2738: if ((int)age %5==0){
2739: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
2740: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
2741: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
2742: mu1=mu[i][(int) age]/stepm*YEARM ;
2743: mu2=mu[j][(int) age]/stepm*YEARM;
2744: c12=cv12/sqrt(v1*v2);
2745: /* Computing eigen value of matrix of covariance */
2746: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2747: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2748: /* Eigen vectors */
2749: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
2750: /*v21=sqrt(1.-v11*v11); *//* error */
2751: v21=(lc1-v1)/cv12*v11;
2752: v12=-v21;
2753: v22=v11;
2754: tnalp=v21/v11;
2755: if(first1==1){
2756: first1=0;
2757: 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);
2758: }
2759: 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);
2760: /*printf(fignu*/
2761: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
2762: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
2763: if(first==1){
2764: first=0;
2765: fprintf(ficgp,"\nset parametric;unset label");
2766: 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);
2767: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2768: 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);
2769: fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
2770: fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
2771: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
2772: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2773: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2774: 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",\
2775: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2776: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2777: }else{
2778: first=0;
2779: fprintf(fichtm," %d (%.3f),",(int) age, c12);
2780: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2781: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2782: 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",\
2783: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2784: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2785: }/* if first */
2786: } /* age mod 5 */
2787: } /* end loop age */
2788: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
2789: first=1;
2790: } /*l12 */
2791: } /* k12 */
2792: } /*l1 */
2793: }/* k1 */
2794: } /* loop covariates */
2795: }
2796: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
2797: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
2798: free_vector(xp,1,npar);
2799: fclose(ficresprob);
2800: fclose(ficresprobcov);
2801: fclose(ficresprobcor);
2802: fclose(ficgp);
2803: fclose(fichtm);
2804: }
2805:
2806:
2807: /******************* Printing html file ***********/
2808: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
2809: int lastpass, int stepm, int weightopt, char model[],\
2810: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
2811: int popforecast, int estepm ,\
2812: double jprev1, double mprev1,double anprev1, \
2813: double jprev2, double mprev2,double anprev2){
2814: int jj1, k1, i1, cpt;
2815: /*char optionfilehtm[FILENAMELENGTH];*/
2816: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2817: printf("Problem with %s \n",optionfilehtm), exit(0);
2818: fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
2819: }
2820:
2821: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
2822: - 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
2823: - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
2824: - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
2825: - Life expectancies by age and initial health status (estepm=%2d months):
2826: <a href=\"e%s\">e%s</a> <br>\n</li>", \
2827: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
2828:
2829: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
2830:
2831: m=cptcoveff;
2832: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2833:
2834: jj1=0;
2835: for(k1=1; k1<=m;k1++){
2836: for(i1=1; i1<=ncodemax[k1];i1++){
2837: jj1++;
2838: if (cptcovn > 0) {
2839: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2840: for (cpt=1; cpt<=cptcoveff;cpt++)
2841: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2842: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2843: }
2844: /* Pij */
2845: 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>
2846: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2847: /* Quasi-incidences */
2848: 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>
2849: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2850: /* Stable prevalence in each health state */
2851: for(cpt=1; cpt<nlstate;cpt++){
2852: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
2853: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2854: }
2855: for(cpt=1; cpt<=nlstate;cpt++) {
2856: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
2857: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2858: }
2859: fprintf(fichtm,"\n<br>- Total life expectancy by age and
2860: health expectancies in states (1) and (2): e%s%d.png<br>
2861: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2862: } /* end i1 */
2863: }/* End k1 */
2864: fprintf(fichtm,"</ul>");
2865:
2866:
2867: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
2868: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
2869: - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
2870: - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
2871: - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
2872: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
2873: - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
2874: - 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);
2875:
2876: /* if(popforecast==1) fprintf(fichtm,"\n */
2877: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
2878: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
2879: /* <br>",fileres,fileres,fileres,fileres); */
2880: /* else */
2881: /* 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); */
2882: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
2883:
2884: m=cptcoveff;
2885: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2886:
2887: jj1=0;
2888: for(k1=1; k1<=m;k1++){
2889: for(i1=1; i1<=ncodemax[k1];i1++){
2890: jj1++;
2891: if (cptcovn > 0) {
2892: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2893: for (cpt=1; cpt<=cptcoveff;cpt++)
2894: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2895: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2896: }
2897: for(cpt=1; cpt<=nlstate;cpt++) {
2898: fprintf(fichtm,"<br>- Observed and period prevalence (with confident
2899: interval) in state (%d): v%s%d%d.png <br>
2900: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2901: }
2902: } /* end i1 */
2903: }/* End k1 */
2904: fprintf(fichtm,"</ul>");
2905: fclose(fichtm);
2906: }
2907:
2908: /******************* Gnuplot file **************/
2909: void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
2910:
2911: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
2912: int ng;
2913: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2914: printf("Problem with file %s",optionfilegnuplot);
2915: fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
2916: }
2917:
2918: /*#ifdef windows */
2919: fprintf(ficgp,"cd \"%s\" \n",pathc);
2920: /*#endif */
2921: m=pow(2,cptcoveff);
2922:
2923: /* 1eme*/
2924: for (cpt=1; cpt<= nlstate ; cpt ++) {
2925: for (k1=1; k1<= m ; k1 ++) {
2926: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2927: 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);
2928:
2929: for (i=1; i<= nlstate ; i ++) {
2930: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2931: else fprintf(ficgp," \%%*lf (\%%*lf)");
2932: }
2933: fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
2934: for (i=1; i<= nlstate ; i ++) {
2935: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2936: else fprintf(ficgp," \%%*lf (\%%*lf)");
2937: }
2938: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
2939: for (i=1; i<= nlstate ; i ++) {
2940: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2941: else fprintf(ficgp," \%%*lf (\%%*lf)");
2942: }
2943: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2944: }
2945: }
2946: /*2 eme*/
2947:
2948: for (k1=1; k1<= m ; k1 ++) {
2949: fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
2950: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
2951:
2952: for (i=1; i<= nlstate+1 ; i ++) {
2953: k=2*i;
2954: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2955: for (j=1; j<= nlstate+1 ; j ++) {
2956: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2957: else fprintf(ficgp," \%%*lf (\%%*lf)");
2958: }
2959: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2960: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2961: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2962: for (j=1; j<= nlstate+1 ; j ++) {
2963: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2964: else fprintf(ficgp," \%%*lf (\%%*lf)");
2965: }
2966: fprintf(ficgp,"\" t\"\" w l 0,");
2967: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
2968: for (j=1; j<= nlstate+1 ; j ++) {
2969: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2970: else fprintf(ficgp," \%%*lf (\%%*lf)");
2971: }
2972: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2973: else fprintf(ficgp,"\" t\"\" w l 0,");
2974: }
2975: }
2976:
2977: /*3eme*/
2978:
2979: for (k1=1; k1<= m ; k1 ++) {
2980: for (cpt=1; cpt<= nlstate ; cpt ++) {
2981: k=2+nlstate*(2*cpt-2);
2982: fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2983: fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
2984: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2985: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2986: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2987: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2988: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2989: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2990:
2991: */
2992: for (i=1; i< nlstate ; i ++) {
2993: 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);
2994:
2995: }
2996: }
2997: }
2998:
2999: /* CV preval stable (period) */
3000: for (k1=1; k1<= m ; k1 ++) {
3001: for (cpt=1; cpt<=nlstate ; cpt ++) {
3002: k=3;
3003: fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
3004: 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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
3005:
3006: for (i=1; i<= nlstate ; i ++)
3007: fprintf(ficgp,"+$%d",k+i+1);
3008: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3009:
3010: l=3+(nlstate+ndeath)*cpt;
3011: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
3012: for (i=1; i< nlstate ; i ++) {
3013: l=3+(nlstate+ndeath)*cpt;
3014: fprintf(ficgp,"+$%d",l+i+1);
3015: }
3016: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3017: }
3018: }
3019:
3020: /* proba elementaires */
3021: for(i=1,jk=1; i <=nlstate; i++){
3022: for(k=1; k <=(nlstate+ndeath); k++){
3023: if (k != i) {
3024: for(j=1; j <=ncovmodel; j++){
3025: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3026: jk++;
3027: fprintf(ficgp,"\n");
3028: }
3029: }
3030: }
3031: }
3032:
3033: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3034: for(jk=1; jk <=m; jk++) {
3035: fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
3036: if (ng==2)
3037: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3038: else
3039: fprintf(ficgp,"\nset title \"Probability\"\n");
3040: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3041: i=1;
3042: for(k2=1; k2<=nlstate; k2++) {
3043: k3=i;
3044: for(k=1; k<=(nlstate+ndeath); k++) {
3045: if (k != k2){
3046: if(ng==2)
3047: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3048: else
3049: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3050: ij=1;
3051: for(j=3; j <=ncovmodel; j++) {
3052: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3053: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3054: ij++;
3055: }
3056: else
3057: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3058: }
3059: fprintf(ficgp,")/(1");
3060:
3061: for(k1=1; k1 <=nlstate; k1++){
3062: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3063: ij=1;
3064: for(j=3; j <=ncovmodel; j++){
3065: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3066: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3067: ij++;
3068: }
3069: else
3070: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3071: }
3072: fprintf(ficgp,")");
3073: }
3074: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3075: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3076: i=i+ncovmodel;
3077: }
3078: } /* end k */
3079: } /* end k2 */
3080: } /* end jk */
3081: } /* end ng */
3082: fclose(ficgp);
3083: } /* end gnuplot */
3084:
3085:
3086: /*************** Moving average **************/
3087: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3088:
3089: int i, cpt, cptcod;
3090: int modcovmax =1;
3091: int mobilavrange, mob;
3092: double age;
3093:
3094: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3095: a covariate has 2 modalities */
3096: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3097:
3098: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3099: if(mobilav==1) mobilavrange=5; /* default */
3100: else mobilavrange=mobilav;
3101: for (age=bage; age<=fage; age++)
3102: for (i=1; i<=nlstate;i++)
3103: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3104: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3105: /* We keep the original values on the extreme ages bage, fage and for
3106: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3107: we use a 5 terms etc. until the borders are no more concerned.
3108: */
3109: for (mob=3;mob <=mobilavrange;mob=mob+2){
3110: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3111: for (i=1; i<=nlstate;i++){
3112: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3113: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3114: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3115: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3116: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3117: }
3118: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3119: }
3120: }
3121: }/* end age */
3122: }/* end mob */
3123: }else return -1;
3124: return 0;
3125: }/* End movingaverage */
3126:
3127:
3128: /************** Forecasting ******************/
3129: prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
3130: /* proj1, year, month, day of starting projection
3131: agemin, agemax range of age
3132: dateprev1 dateprev2 range of dates during which prevalence is computed
3133: anproj2 year of en of projection (same day and month as proj1).
3134: */
3135: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
3136: int *popage;
3137: double agec; /* generic age */
3138: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3139: double *popeffectif,*popcount;
3140: double ***p3mat;
3141: double ***mobaverage;
3142: char fileresf[FILENAMELENGTH];
3143:
3144: agelim=AGESUP;
3145: prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3146:
3147: strcpy(fileresf,"f");
3148: strcat(fileresf,fileres);
3149: if((ficresf=fopen(fileresf,"w"))==NULL) {
3150: printf("Problem with forecast resultfile: %s\n", fileresf);
3151: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3152: }
3153: printf("Computing forecasting: result on file '%s' \n", fileresf);
3154: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3155:
3156: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3157:
3158: if (mobilav!=0) {
3159: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3160: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3161: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3162: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3163: }
3164: }
3165:
3166: stepsize=(int) (stepm+YEARM-1)/YEARM;
3167: if (stepm<=12) stepsize=1;
3168: if(estepm < stepm){
3169: printf ("Problem %d lower than %d\n",estepm, stepm);
3170: }
3171: else hstepm=estepm;
3172:
3173: hstepm=hstepm/stepm;
3174: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3175: fractional in yp1 */
3176: anprojmean=yp;
3177: yp2=modf((yp1*12),&yp);
3178: mprojmean=yp;
3179: yp1=modf((yp2*30.5),&yp);
3180: jprojmean=yp;
3181: if(jprojmean==0) jprojmean=1;
3182: if(mprojmean==0) jprojmean=1;
3183:
3184: i1=cptcoveff;
3185: if (cptcovn < 1){i1=1;}
3186:
3187: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
3188:
3189: fprintf(ficresf,"#****** Routine prevforecast **\n");
3190:
3191: /* if (h==(int)(YEARM*yearp)){ */
3192: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
3193: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3194: k=k+1;
3195: fprintf(ficresf,"\n#******");
3196: for(j=1;j<=cptcoveff;j++) {
3197: fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3198: }
3199: fprintf(ficresf,"******\n");
3200: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3201: for(j=1; j<=nlstate+ndeath;j++){
3202: for(i=1; i<=nlstate;i++)
3203: fprintf(ficresf," p%d%d",i,j);
3204: fprintf(ficresf," p.%d",j);
3205: }
3206: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
3207: fprintf(ficresf,"\n");
3208: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
3209:
3210: for (agec=fage; agec>=(ageminpar-1); agec--){
3211: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
3212: nhstepm = nhstepm/hstepm;
3213: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3214: oldm=oldms;savm=savms;
3215: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
3216:
3217: for (h=0; h<=nhstepm; h++){
3218: if (h*hstepm/YEARM*stepm ==yearp) {
3219: fprintf(ficresf,"\n");
3220: for(j=1;j<=cptcoveff;j++)
3221: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3222: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
3223: }
3224: for(j=1; j<=nlstate+ndeath;j++) {
3225: ppij=0.;
3226: for(i=1; i<=nlstate;i++) {
3227: if (mobilav==1)
3228: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
3229: else {
3230: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
3231: }
3232: if (h*hstepm/YEARM*stepm== yearp) {
3233: fprintf(ficresf," %.3f", p3mat[i][j][h]);
3234: }
3235: } /* end i */
3236: if (h*hstepm/YEARM*stepm==yearp) {
3237: fprintf(ficresf," %.3f", ppij);
3238: }
3239: }/* end j */
3240: } /* end h */
3241: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3242: } /* end agec */
3243: } /* end yearp */
3244: } /* end cptcod */
3245: } /* end cptcov */
3246:
3247: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3248:
3249: fclose(ficresf);
3250: }
3251:
3252: /************** Forecasting *****not tested NB*************/
3253: 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){
3254:
3255: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3256: int *popage;
3257: double calagedatem, agelim, kk1, kk2;
3258: double *popeffectif,*popcount;
3259: double ***p3mat,***tabpop,***tabpopprev;
3260: double ***mobaverage;
3261: char filerespop[FILENAMELENGTH];
3262:
3263: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3264: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3265: agelim=AGESUP;
3266: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
3267:
3268: prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3269:
3270:
3271: strcpy(filerespop,"pop");
3272: strcat(filerespop,fileres);
3273: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3274: printf("Problem with forecast resultfile: %s\n", filerespop);
3275: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3276: }
3277: printf("Computing forecasting: result on file '%s' \n", filerespop);
3278: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3279:
3280: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3281:
3282: if (mobilav!=0) {
3283: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3284: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3285: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3286: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3287: }
3288: }
3289:
3290: stepsize=(int) (stepm+YEARM-1)/YEARM;
3291: if (stepm<=12) stepsize=1;
3292:
3293: agelim=AGESUP;
3294:
3295: hstepm=1;
3296: hstepm=hstepm/stepm;
3297:
3298: if (popforecast==1) {
3299: if((ficpop=fopen(popfile,"r"))==NULL) {
3300: printf("Problem with population file : %s\n",popfile);exit(0);
3301: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3302: }
3303: popage=ivector(0,AGESUP);
3304: popeffectif=vector(0,AGESUP);
3305: popcount=vector(0,AGESUP);
3306:
3307: i=1;
3308: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3309:
3310: imx=i;
3311: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3312: }
3313:
3314: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
3315: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3316: k=k+1;
3317: fprintf(ficrespop,"\n#******");
3318: for(j=1;j<=cptcoveff;j++) {
3319: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3320: }
3321: fprintf(ficrespop,"******\n");
3322: fprintf(ficrespop,"# Age");
3323: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3324: if (popforecast==1) fprintf(ficrespop," [Population]");
3325:
3326: for (cpt=0; cpt<=0;cpt++) {
3327: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3328:
3329: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3330: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3331: nhstepm = nhstepm/hstepm;
3332:
3333: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3334: oldm=oldms;savm=savms;
3335: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3336:
3337: for (h=0; h<=nhstepm; h++){
3338: if (h==(int) (calagedatem+YEARM*cpt)) {
3339: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3340: }
3341: for(j=1; j<=nlstate+ndeath;j++) {
3342: kk1=0.;kk2=0;
3343: for(i=1; i<=nlstate;i++) {
3344: if (mobilav==1)
3345: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3346: else {
3347: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3348: }
3349: }
3350: if (h==(int)(calagedatem+12*cpt)){
3351: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3352: /*fprintf(ficrespop," %.3f", kk1);
3353: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3354: }
3355: }
3356: for(i=1; i<=nlstate;i++){
3357: kk1=0.;
3358: for(j=1; j<=nlstate;j++){
3359: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3360: }
3361: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
3362: }
3363:
3364: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
3365: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3366: }
3367: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3368: }
3369: }
3370:
3371: /******/
3372:
3373: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3374: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3375: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3376: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3377: nhstepm = nhstepm/hstepm;
3378:
3379: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3380: oldm=oldms;savm=savms;
3381: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3382: for (h=0; h<=nhstepm; h++){
3383: if (h==(int) (calagedatem+YEARM*cpt)) {
3384: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3385: }
3386: for(j=1; j<=nlstate+ndeath;j++) {
3387: kk1=0.;kk2=0;
3388: for(i=1; i<=nlstate;i++) {
3389: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3390: }
3391: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
3392: }
3393: }
3394: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3395: }
3396: }
3397: }
3398: }
3399:
3400: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3401:
3402: if (popforecast==1) {
3403: free_ivector(popage,0,AGESUP);
3404: free_vector(popeffectif,0,AGESUP);
3405: free_vector(popcount,0,AGESUP);
3406: }
3407: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3408: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3409: fclose(ficrespop);
3410: }
3411:
3412: /***********************************************/
3413: /**************** Main Program *****************/
3414: /***********************************************/
3415:
3416: int main(int argc, char *argv[])
3417: {
3418: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
3419: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
3420: double agedeb, agefin,hf;
3421: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3422:
3423: double fret;
3424: double **xi,tmp,delta;
3425:
3426: double dum; /* Dummy variable */
3427: double ***p3mat;
3428: double ***mobaverage;
3429: int *indx;
3430: char line[MAXLINE], linepar[MAXLINE];
3431: char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
3432: int firstobs=1, lastobs=10;
3433: int sdeb, sfin; /* Status at beginning and end */
3434: int c, h , cpt,l;
3435: int ju,jl, mi;
3436: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
3437: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
3438: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
3439: int mobilav=0,popforecast=0;
3440: int hstepm, nhstepm;
3441: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
3442: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
3443:
3444: double bage, fage, age, agelim, agebase;
3445: double ftolpl=FTOL;
3446: double **prlim;
3447: double *severity;
3448: double ***param; /* Matrix of parameters */
3449: double *p;
3450: double **matcov; /* Matrix of covariance */
3451: double ***delti3; /* Scale */
3452: double *delti; /* Scale */
3453: double ***eij, ***vareij;
3454: double **varpl; /* Variances of prevalence limits by age */
3455: double *epj, vepp;
3456: double kk1, kk2;
3457: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
3458:
3459: char *alph[]={"a","a","b","c","d","e"}, str[4];
3460:
3461:
3462: char z[1]="c", occ;
3463: #include <sys/time.h>
3464: #include <time.h>
3465: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
3466:
3467: /* long total_usecs;
3468: struct timeval start_time, end_time;
3469:
3470: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
3471: getcwd(pathcd, size);
3472:
3473: printf("\n%s\n%s",version,fullversion);
3474: if(argc <=1){
3475: printf("\nEnter the parameter file name: ");
3476: scanf("%s",pathtot);
3477: }
3478: else{
3479: strcpy(pathtot,argv[1]);
3480: }
3481: /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
3482: /*cygwin_split_path(pathtot,path,optionfile);
3483: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3484: /* cutv(path,optionfile,pathtot,'\\');*/
3485:
3486: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
3487: printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3488: chdir(path);
3489: replace(pathc,path);
3490:
3491: /*-------- arguments in the command line --------*/
3492:
3493: /* Log file */
3494: strcat(filelog, optionfilefiname);
3495: strcat(filelog,".log"); /* */
3496: if((ficlog=fopen(filelog,"w"))==NULL) {
3497: printf("Problem with logfile %s\n",filelog);
3498: goto end;
3499: }
3500: fprintf(ficlog,"Log filename:%s\n",filelog);
3501: fprintf(ficlog,"\n%s",version);
3502: fprintf(ficlog,"\nEnter the parameter file name: ");
3503: fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3504: fflush(ficlog);
3505:
3506: /* */
3507: strcpy(fileres,"r");
3508: strcat(fileres, optionfilefiname);
3509: strcat(fileres,".txt"); /* Other files have txt extension */
3510:
3511: /*---------arguments file --------*/
3512:
3513: if((ficpar=fopen(optionfile,"r"))==NULL) {
3514: printf("Problem with optionfile %s\n",optionfile);
3515: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
3516: goto end;
3517: }
3518:
3519: strcpy(filereso,"o");
3520: strcat(filereso,fileres);
3521: if((ficparo=fopen(filereso,"w"))==NULL) {
3522: printf("Problem with Output resultfile: %s\n", filereso);
3523: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
3524: goto end;
3525: }
3526:
3527: /* Reads comments: lines beginning with '#' */
3528: while((c=getc(ficpar))=='#' && c!= EOF){
3529: ungetc(c,ficpar);
3530: fgets(line, MAXLINE, ficpar);
3531: puts(line);
3532: fputs(line,ficparo);
3533: }
3534: ungetc(c,ficpar);
3535:
3536: 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);
3537: 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);
3538: 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);
3539: while((c=getc(ficpar))=='#' && c!= EOF){
3540: ungetc(c,ficpar);
3541: fgets(line, MAXLINE, ficpar);
3542: puts(line);
3543: fputs(line,ficparo);
3544: }
3545: ungetc(c,ficpar);
3546:
3547:
3548: covar=matrix(0,NCOVMAX,1,n);
3549: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
3550: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
3551:
3552: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
3553: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
3554:
3555: /* Read guess parameters */
3556: /* Reads comments: lines beginning with '#' */
3557: while((c=getc(ficpar))=='#' && c!= EOF){
3558: ungetc(c,ficpar);
3559: fgets(line, MAXLINE, ficpar);
3560: puts(line);
3561: fputs(line,ficparo);
3562: }
3563: ungetc(c,ficpar);
3564:
3565: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
3566: for(i=1; i <=nlstate; i++)
3567: for(j=1; j <=nlstate+ndeath-1; j++){
3568: fscanf(ficpar,"%1d%1d",&i1,&j1);
3569: fprintf(ficparo,"%1d%1d",i1,j1);
3570: if(mle==1)
3571: printf("%1d%1d",i,j);
3572: fprintf(ficlog,"%1d%1d",i,j);
3573: for(k=1; k<=ncovmodel;k++){
3574: fscanf(ficpar," %lf",¶m[i][j][k]);
3575: if(mle==1){
3576: printf(" %lf",param[i][j][k]);
3577: fprintf(ficlog," %lf",param[i][j][k]);
3578: }
3579: else
3580: fprintf(ficlog," %lf",param[i][j][k]);
3581: fprintf(ficparo," %lf",param[i][j][k]);
3582: }
3583: fscanf(ficpar,"\n");
3584: if(mle==1)
3585: printf("\n");
3586: fprintf(ficlog,"\n");
3587: fprintf(ficparo,"\n");
3588: }
3589:
3590: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
3591:
3592: p=param[1][1];
3593:
3594: /* Reads comments: lines beginning with '#' */
3595: while((c=getc(ficpar))=='#' && c!= EOF){
3596: ungetc(c,ficpar);
3597: fgets(line, MAXLINE, ficpar);
3598: puts(line);
3599: fputs(line,ficparo);
3600: }
3601: ungetc(c,ficpar);
3602:
3603: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
3604: /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
3605: for(i=1; i <=nlstate; i++){
3606: for(j=1; j <=nlstate+ndeath-1; j++){
3607: fscanf(ficpar,"%1d%1d",&i1,&j1);
3608: printf("%1d%1d",i,j);
3609: fprintf(ficparo,"%1d%1d",i1,j1);
3610: for(k=1; k<=ncovmodel;k++){
3611: fscanf(ficpar,"%le",&delti3[i][j][k]);
3612: printf(" %le",delti3[i][j][k]);
3613: fprintf(ficparo," %le",delti3[i][j][k]);
3614: }
3615: fscanf(ficpar,"\n");
3616: printf("\n");
3617: fprintf(ficparo,"\n");
3618: }
3619: }
3620: delti=delti3[1][1];
3621:
3622:
3623: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
3624:
3625: /* Reads comments: lines beginning with '#' */
3626: while((c=getc(ficpar))=='#' && c!= EOF){
3627: ungetc(c,ficpar);
3628: fgets(line, MAXLINE, ficpar);
3629: puts(line);
3630: fputs(line,ficparo);
3631: }
3632: ungetc(c,ficpar);
3633:
3634: matcov=matrix(1,npar,1,npar);
3635: for(i=1; i <=npar; i++){
3636: fscanf(ficpar,"%s",&str);
3637: if(mle==1)
3638: printf("%s",str);
3639: fprintf(ficlog,"%s",str);
3640: fprintf(ficparo,"%s",str);
3641: for(j=1; j <=i; j++){
3642: fscanf(ficpar," %le",&matcov[i][j]);
3643: if(mle==1){
3644: printf(" %.5le",matcov[i][j]);
3645: fprintf(ficlog," %.5le",matcov[i][j]);
3646: }
3647: else
3648: fprintf(ficlog," %.5le",matcov[i][j]);
3649: fprintf(ficparo," %.5le",matcov[i][j]);
3650: }
3651: fscanf(ficpar,"\n");
3652: if(mle==1)
3653: printf("\n");
3654: fprintf(ficlog,"\n");
3655: fprintf(ficparo,"\n");
3656: }
3657: for(i=1; i <=npar; i++)
3658: for(j=i+1;j<=npar;j++)
3659: matcov[i][j]=matcov[j][i];
3660:
3661: if(mle==1)
3662: printf("\n");
3663: fprintf(ficlog,"\n");
3664:
3665:
3666: /*-------- Rewriting paramater file ----------*/
3667: strcpy(rfileres,"r"); /* "Rparameterfile */
3668: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
3669: strcat(rfileres,"."); /* */
3670: strcat(rfileres,optionfilext); /* Other files have txt extension */
3671: if((ficres =fopen(rfileres,"w"))==NULL) {
3672: printf("Problem writing new parameter file: %s\n", fileres);goto end;
3673: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
3674: }
3675: fprintf(ficres,"#%s\n",version);
3676:
3677: /*-------- data file ----------*/
3678: if((fic=fopen(datafile,"r"))==NULL) {
3679: printf("Problem with datafile: %s\n", datafile);goto end;
3680: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
3681: }
3682:
3683: n= lastobs;
3684: severity = vector(1,maxwav);
3685: outcome=imatrix(1,maxwav+1,1,n);
3686: num=ivector(1,n);
3687: moisnais=vector(1,n);
3688: annais=vector(1,n);
3689: moisdc=vector(1,n);
3690: andc=vector(1,n);
3691: agedc=vector(1,n);
3692: cod=ivector(1,n);
3693: weight=vector(1,n);
3694: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
3695: mint=matrix(1,maxwav,1,n);
3696: anint=matrix(1,maxwav,1,n);
3697: s=imatrix(1,maxwav+1,1,n);
3698: tab=ivector(1,NCOVMAX);
3699: ncodemax=ivector(1,8);
3700:
3701: i=1;
3702: while (fgets(line, MAXLINE, fic) != NULL) {
3703: if ((i >= firstobs) && (i <=lastobs)) {
3704:
3705: for (j=maxwav;j>=1;j--){
3706: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
3707: strcpy(line,stra);
3708: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3709: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3710: }
3711:
3712: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
3713: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
3714:
3715: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
3716: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
3717:
3718: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
3719: for (j=ncovcol;j>=1;j--){
3720: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3721: }
3722: num[i]=atol(stra);
3723:
3724: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
3725: 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;}*/
3726:
3727: i=i+1;
3728: }
3729: }
3730: /* printf("ii=%d", ij);
3731: scanf("%d",i);*/
3732: imx=i-1; /* Number of individuals */
3733:
3734: /* for (i=1; i<=imx; i++){
3735: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
3736: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
3737: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
3738: }*/
3739: /* for (i=1; i<=imx; i++){
3740: if (s[4][i]==9) s[4][i]=-1;
3741: 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]));}*/
3742:
3743: for (i=1; i<=imx; i++)
3744:
3745: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
3746: else weight[i]=1;*/
3747:
3748: /* Calculation of the number of parameter from char model*/
3749: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
3750: Tprod=ivector(1,15);
3751: Tvaraff=ivector(1,15);
3752: Tvard=imatrix(1,15,1,2);
3753: Tage=ivector(1,15);
3754:
3755: if (strlen(model) >1){ /* If there is at least 1 covariate */
3756: j=0, j1=0, k1=1, k2=1;
3757: j=nbocc(model,'+'); /* j=Number of '+' */
3758: j1=nbocc(model,'*'); /* j1=Number of '*' */
3759: cptcovn=j+1;
3760: cptcovprod=j1; /*Number of products */
3761:
3762: strcpy(modelsav,model);
3763: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
3764: printf("Error. Non available option model=%s ",model);
3765: fprintf(ficlog,"Error. Non available option model=%s ",model);
3766: goto end;
3767: }
3768:
3769: /* This loop fills the array Tvar from the string 'model'.*/
3770:
3771: for(i=(j+1); i>=1;i--){
3772: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
3773: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
3774: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
3775: /*scanf("%d",i);*/
3776: if (strchr(strb,'*')) { /* Model includes a product */
3777: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
3778: if (strcmp(strc,"age")==0) { /* Vn*age */
3779: cptcovprod--;
3780: cutv(strb,stre,strd,'V');
3781: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
3782: cptcovage++;
3783: Tage[cptcovage]=i;
3784: /*printf("stre=%s ", stre);*/
3785: }
3786: else if (strcmp(strd,"age")==0) { /* or age*Vn */
3787: cptcovprod--;
3788: cutv(strb,stre,strc,'V');
3789: Tvar[i]=atoi(stre);
3790: cptcovage++;
3791: Tage[cptcovage]=i;
3792: }
3793: else { /* Age is not in the model */
3794: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
3795: Tvar[i]=ncovcol+k1;
3796: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
3797: Tprod[k1]=i;
3798: Tvard[k1][1]=atoi(strc); /* m*/
3799: Tvard[k1][2]=atoi(stre); /* n */
3800: Tvar[cptcovn+k2]=Tvard[k1][1];
3801: Tvar[cptcovn+k2+1]=Tvard[k1][2];
3802: for (k=1; k<=lastobs;k++)
3803: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
3804: k1++;
3805: k2=k2+2;
3806: }
3807: }
3808: else { /* no more sum */
3809: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
3810: /* scanf("%d",i);*/
3811: cutv(strd,strc,strb,'V');
3812: Tvar[i]=atoi(strc);
3813: }
3814: strcpy(modelsav,stra);
3815: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
3816: scanf("%d",i);*/
3817: } /* end of loop + */
3818: } /* end model */
3819:
3820: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
3821: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
3822:
3823: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
3824: printf("cptcovprod=%d ", cptcovprod);
3825: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
3826:
3827: scanf("%d ",i);
3828: fclose(fic);*/
3829:
3830: /* if(mle==1){*/
3831: if (weightopt != 1) { /* Maximisation without weights*/
3832: for(i=1;i<=n;i++) weight[i]=1.0;
3833: }
3834: /*-calculation of age at interview from date of interview and age at death -*/
3835: agev=matrix(1,maxwav,1,imx);
3836:
3837: for (i=1; i<=imx; i++) {
3838: for(m=2; (m<= maxwav); m++) {
3839: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
3840: anint[m][i]=9999;
3841: s[m][i]=-1;
3842: }
3843: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
3844: printf("Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
3845: fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
3846: s[m][i]=-1;
3847: }
3848: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
3849: printf("Error! Month of death of individual %d on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
3850: fprintf(ficlog,"Error! Month of death of individual %d on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
3851: s[m][i]=-1;
3852: }
3853: }
3854: }
3855:
3856: for (i=1; i<=imx; i++) {
3857: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
3858: for(m=firstpass; (m<= lastpass); m++){
3859: if(s[m][i] >0){
3860: if (s[m][i] >= nlstate+1) {
3861: if(agedc[i]>0)
3862: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
3863: agev[m][i]=agedc[i];
3864: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
3865: else {
3866: if ((int)andc[i]!=9999){
3867: printf("Warning negative age at death: %d line:%d\n",num[i],i);
3868: fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
3869: agev[m][i]=-1;
3870: }
3871: }
3872: }
3873: else if(s[m][i] !=9){ /* Standard case, age in fractional
3874: years but with the precision of a
3875: month */
3876: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
3877: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
3878: agev[m][i]=1;
3879: else if(agev[m][i] <agemin){
3880: agemin=agev[m][i];
3881: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
3882: }
3883: else if(agev[m][i] >agemax){
3884: agemax=agev[m][i];
3885: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
3886: }
3887: /*agev[m][i]=anint[m][i]-annais[i];*/
3888: /* agev[m][i] = age[i]+2*m;*/
3889: }
3890: else { /* =9 */
3891: agev[m][i]=1;
3892: s[m][i]=-1;
3893: }
3894: }
3895: else /*= 0 Unknown */
3896: agev[m][i]=1;
3897: }
3898:
3899: }
3900: for (i=1; i<=imx; i++) {
3901: for(m=firstpass; (m<=lastpass); m++){
3902: if (s[m][i] > (nlstate+ndeath)) {
3903: 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);
3904: 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);
3905: goto end;
3906: }
3907: }
3908: }
3909:
3910: /*for (i=1; i<=imx; i++){
3911: for (m=firstpass; (m<lastpass); m++){
3912: printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
3913: }
3914:
3915: }*/
3916:
3917: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3918: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3919:
3920: free_vector(severity,1,maxwav);
3921: free_imatrix(outcome,1,maxwav+1,1,n);
3922: free_vector(moisnais,1,n);
3923: free_vector(annais,1,n);
3924: /* free_matrix(mint,1,maxwav,1,n);
3925: free_matrix(anint,1,maxwav,1,n);*/
3926: free_vector(moisdc,1,n);
3927: free_vector(andc,1,n);
3928:
3929:
3930: wav=ivector(1,imx);
3931: dh=imatrix(1,lastpass-firstpass+1,1,imx);
3932: bh=imatrix(1,lastpass-firstpass+1,1,imx);
3933: mw=imatrix(1,lastpass-firstpass+1,1,imx);
3934:
3935: /* Concatenates waves */
3936: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
3937:
3938: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
3939:
3940: Tcode=ivector(1,100);
3941: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
3942: ncodemax[1]=1;
3943: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
3944:
3945: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
3946: the estimations*/
3947: h=0;
3948: m=pow(2,cptcoveff);
3949:
3950: for(k=1;k<=cptcoveff; k++){
3951: for(i=1; i <=(m/pow(2,k));i++){
3952: for(j=1; j <= ncodemax[k]; j++){
3953: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
3954: h++;
3955: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
3956: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
3957: }
3958: }
3959: }
3960: }
3961: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
3962: codtab[1][2]=1;codtab[2][2]=2; */
3963: /* for(i=1; i <=m ;i++){
3964: for(k=1; k <=cptcovn; k++){
3965: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
3966: }
3967: printf("\n");
3968: }
3969: scanf("%d",i);*/
3970:
3971: /* Calculates basic frequencies. Computes observed prevalence at single age
3972: and prints on file fileres'p'. */
3973:
3974: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3975: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3976: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3977: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3978: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
3979:
3980:
3981: /* For Powell, parameters are in a vector p[] starting at p[1]
3982: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
3983: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
3984:
3985: if(mle>=1){ /* Could be 1 or 2 */
3986: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
3987: }
3988:
3989: /*--------- results files --------------*/
3990: 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);
3991:
3992:
3993: jk=1;
3994: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3995: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3996: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3997: for(i=1,jk=1; i <=nlstate; i++){
3998: for(k=1; k <=(nlstate+ndeath); k++){
3999: if (k != i)
4000: {
4001: printf("%d%d ",i,k);
4002: fprintf(ficlog,"%d%d ",i,k);
4003: fprintf(ficres,"%1d%1d ",i,k);
4004: for(j=1; j <=ncovmodel; j++){
4005: printf("%f ",p[jk]);
4006: fprintf(ficlog,"%f ",p[jk]);
4007: fprintf(ficres,"%f ",p[jk]);
4008: jk++;
4009: }
4010: printf("\n");
4011: fprintf(ficlog,"\n");
4012: fprintf(ficres,"\n");
4013: }
4014: }
4015: }
4016: if(mle==1){
4017: /* Computing hessian and covariance matrix */
4018: ftolhess=ftol; /* Usually correct */
4019: hesscov(matcov, p, npar, delti, ftolhess, func);
4020: }
4021: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
4022: printf("# Scales (for hessian or gradient estimation)\n");
4023: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
4024: for(i=1,jk=1; i <=nlstate; i++){
4025: for(j=1; j <=nlstate+ndeath; j++){
4026: if (j!=i) {
4027: fprintf(ficres,"%1d%1d",i,j);
4028: printf("%1d%1d",i,j);
4029: fprintf(ficlog,"%1d%1d",i,j);
4030: for(k=1; k<=ncovmodel;k++){
4031: printf(" %.5e",delti[jk]);
4032: fprintf(ficlog," %.5e",delti[jk]);
4033: fprintf(ficres," %.5e",delti[jk]);
4034: jk++;
4035: }
4036: printf("\n");
4037: fprintf(ficlog,"\n");
4038: fprintf(ficres,"\n");
4039: }
4040: }
4041: }
4042:
4043: 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");
4044: if(mle==1)
4045: 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");
4046: 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");
4047: for(i=1,k=1;i<=npar;i++){
4048: /* if (k>nlstate) k=1;
4049: i1=(i-1)/(ncovmodel*nlstate)+1;
4050: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
4051: printf("%s%d%d",alph[k],i1,tab[i]);
4052: */
4053: fprintf(ficres,"%3d",i);
4054: if(mle==1)
4055: printf("%3d",i);
4056: fprintf(ficlog,"%3d",i);
4057: for(j=1; j<=i;j++){
4058: fprintf(ficres," %.5e",matcov[i][j]);
4059: if(mle==1)
4060: printf(" %.5e",matcov[i][j]);
4061: fprintf(ficlog," %.5e",matcov[i][j]);
4062: }
4063: fprintf(ficres,"\n");
4064: if(mle==1)
4065: printf("\n");
4066: fprintf(ficlog,"\n");
4067: k++;
4068: }
4069:
4070: while((c=getc(ficpar))=='#' && c!= EOF){
4071: ungetc(c,ficpar);
4072: fgets(line, MAXLINE, ficpar);
4073: puts(line);
4074: fputs(line,ficparo);
4075: }
4076: ungetc(c,ficpar);
4077:
4078: estepm=0;
4079: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
4080: if (estepm==0 || estepm < stepm) estepm=stepm;
4081: if (fage <= 2) {
4082: bage = ageminpar;
4083: fage = agemaxpar;
4084: }
4085:
4086: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
4087: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
4088: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
4089:
4090: while((c=getc(ficpar))=='#' && c!= EOF){
4091: ungetc(c,ficpar);
4092: fgets(line, MAXLINE, ficpar);
4093: puts(line);
4094: fputs(line,ficparo);
4095: }
4096: ungetc(c,ficpar);
4097:
4098: 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);
4099: 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);
4100: 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);
4101: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
4102: fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
4103:
4104: while((c=getc(ficpar))=='#' && c!= EOF){
4105: ungetc(c,ficpar);
4106: fgets(line, MAXLINE, ficpar);
4107: puts(line);
4108: fputs(line,ficparo);
4109: }
4110: ungetc(c,ficpar);
4111:
4112:
4113: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
4114: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
4115:
4116: fscanf(ficpar,"pop_based=%d\n",&popbased);
4117: fprintf(ficparo,"pop_based=%d\n",popbased);
4118: fprintf(ficres,"pop_based=%d\n",popbased);
4119:
4120: while((c=getc(ficpar))=='#' && c!= EOF){
4121: ungetc(c,ficpar);
4122: fgets(line, MAXLINE, ficpar);
4123: puts(line);
4124: fputs(line,ficparo);
4125: }
4126: ungetc(c,ficpar);
4127:
4128: fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
4129: fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
4130: printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
4131: fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
4132: fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
4133: /* day and month of proj2 are not used but only year anproj2.*/
4134:
4135: while((c=getc(ficpar))=='#' && c!= EOF){
4136: ungetc(c,ficpar);
4137: fgets(line, MAXLINE, ficpar);
4138: puts(line);
4139: fputs(line,ficparo);
4140: }
4141: ungetc(c,ficpar);
4142:
4143: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
4144: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4145: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4146:
4147: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
4148: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
4149:
4150: /*------------ gnuplot -------------*/
4151: strcpy(optionfilegnuplot,optionfilefiname);
4152: strcat(optionfilegnuplot,".gp");
4153: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4154: printf("Problem with file %s",optionfilegnuplot);
4155: }
4156: else{
4157: fprintf(ficgp,"\n# %s\n", version);
4158: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4159: fprintf(ficgp,"set missing 'NaNq'\n");
4160: }
4161: fclose(ficgp);
4162: printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
4163: /*--------- index.htm --------*/
4164:
4165: strcpy(optionfilehtm,optionfile);
4166: strcat(optionfilehtm,".htm");
4167: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4168: printf("Problem with %s \n",optionfilehtm), exit(0);
4169: }
4170:
4171: fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
4172: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
4173: \n
4174: Total number of observations=%d <br>\n
4175: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n
4176: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
4177: <hr size=\"2\" color=\"#EC5E5E\">
4178: <ul><li><h4>Parameter files</h4>\n
4179: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
4180: - Log file of the run: <a href=\"%s\">%s</a><br>\n
4181: - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
4182: fclose(fichtm);
4183:
4184: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
4185:
4186: /*------------ free_vector -------------*/
4187: chdir(path);
4188:
4189: free_ivector(wav,1,imx);
4190: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
4191: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
4192: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
4193: free_ivector(num,1,n);
4194: free_vector(agedc,1,n);
4195: /*free_matrix(covar,0,NCOVMAX,1,n);*/
4196: /*free_matrix(covar,1,NCOVMAX,1,n);*/
4197: fclose(ficparo);
4198: fclose(ficres);
4199:
4200:
4201: /*--------------- Prevalence limit (stable prevalence) --------------*/
4202:
4203: strcpy(filerespl,"pl");
4204: strcat(filerespl,fileres);
4205: if((ficrespl=fopen(filerespl,"w"))==NULL) {
4206: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4207: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4208: }
4209: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
4210: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
4211: fprintf(ficrespl,"#Stable prevalence \n");
4212: fprintf(ficrespl,"#Age ");
4213: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
4214: fprintf(ficrespl,"\n");
4215:
4216: prlim=matrix(1,nlstate,1,nlstate);
4217:
4218: agebase=ageminpar;
4219: agelim=agemaxpar;
4220: ftolpl=1.e-10;
4221: i1=cptcoveff;
4222: if (cptcovn < 1){i1=1;}
4223:
4224: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4225: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4226: k=k+1;
4227: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
4228: fprintf(ficrespl,"\n#******");
4229: printf("\n#******");
4230: fprintf(ficlog,"\n#******");
4231: for(j=1;j<=cptcoveff;j++) {
4232: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4233: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4234: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4235: }
4236: fprintf(ficrespl,"******\n");
4237: printf("******\n");
4238: fprintf(ficlog,"******\n");
4239:
4240: for (age=agebase; age<=agelim; age++){
4241: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4242: fprintf(ficrespl,"%.0f ",age );
4243: for(j=1;j<=cptcoveff;j++)
4244: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4245: for(i=1; i<=nlstate;i++)
4246: fprintf(ficrespl," %.5f", prlim[i][i]);
4247: fprintf(ficrespl,"\n");
4248: }
4249: }
4250: }
4251: fclose(ficrespl);
4252:
4253: /*------------- h Pij x at various ages ------------*/
4254:
4255: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
4256: if((ficrespij=fopen(filerespij,"w"))==NULL) {
4257: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
4258: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
4259: }
4260: printf("Computing pij: result on file '%s' \n", filerespij);
4261: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
4262:
4263: stepsize=(int) (stepm+YEARM-1)/YEARM;
4264: /*if (stepm<=24) stepsize=2;*/
4265:
4266: agelim=AGESUP;
4267: hstepm=stepsize*YEARM; /* Every year of age */
4268: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
4269:
4270: /* hstepm=1; aff par mois*/
4271:
4272: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
4273: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4274: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4275: k=k+1;
4276: fprintf(ficrespij,"\n#****** ");
4277: for(j=1;j<=cptcoveff;j++)
4278: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4279: fprintf(ficrespij,"******\n");
4280:
4281: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
4282: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4283: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4284:
4285: /* nhstepm=nhstepm*YEARM; aff par mois*/
4286:
4287: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4288: oldm=oldms;savm=savms;
4289: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4290: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
4291: for(i=1; i<=nlstate;i++)
4292: for(j=1; j<=nlstate+ndeath;j++)
4293: fprintf(ficrespij," %1d-%1d",i,j);
4294: fprintf(ficrespij,"\n");
4295: for (h=0; h<=nhstepm; h++){
4296: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
4297: for(i=1; i<=nlstate;i++)
4298: for(j=1; j<=nlstate+ndeath;j++)
4299: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
4300: fprintf(ficrespij,"\n");
4301: }
4302: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4303: fprintf(ficrespij,"\n");
4304: }
4305: }
4306: }
4307:
4308: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
4309:
4310: fclose(ficrespij);
4311:
4312:
4313: /*---------- Forecasting ------------------*/
4314: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
4315: if(prevfcast==1){
4316: /* if(stepm ==1){*/
4317: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
4318: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
4319: /* } */
4320: /* else{ */
4321: /* erreur=108; */
4322: /* 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); */
4323: /* 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); */
4324: /* } */
4325: }
4326:
4327:
4328: /*---------- Health expectancies and variances ------------*/
4329:
4330: strcpy(filerest,"t");
4331: strcat(filerest,fileres);
4332: if((ficrest=fopen(filerest,"w"))==NULL) {
4333: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
4334: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
4335: }
4336: printf("Computing Total LEs with variances: file '%s' \n", filerest);
4337: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
4338:
4339:
4340: strcpy(filerese,"e");
4341: strcat(filerese,fileres);
4342: if((ficreseij=fopen(filerese,"w"))==NULL) {
4343: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4344: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4345: }
4346: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
4347: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
4348:
4349: strcpy(fileresv,"v");
4350: strcat(fileresv,fileres);
4351: if((ficresvij=fopen(fileresv,"w"))==NULL) {
4352: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
4353: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
4354: }
4355: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4356: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4357:
4358: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
4359: prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4360: /* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
4361: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
4362: */
4363:
4364: if (mobilav!=0) {
4365: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4366: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4367: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4368: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4369: }
4370: }
4371:
4372: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4373: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4374: k=k+1;
4375: fprintf(ficrest,"\n#****** ");
4376: for(j=1;j<=cptcoveff;j++)
4377: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4378: fprintf(ficrest,"******\n");
4379:
4380: fprintf(ficreseij,"\n#****** ");
4381: for(j=1;j<=cptcoveff;j++)
4382: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4383: fprintf(ficreseij,"******\n");
4384:
4385: fprintf(ficresvij,"\n#****** ");
4386: for(j=1;j<=cptcoveff;j++)
4387: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4388: fprintf(ficresvij,"******\n");
4389:
4390: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4391: oldm=oldms;savm=savms;
4392: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
4393:
4394: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4395: oldm=oldms;savm=savms;
4396: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
4397: if(popbased==1){
4398: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
4399: }
4400:
4401:
4402: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
4403: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
4404: fprintf(ficrest,"\n");
4405:
4406: epj=vector(1,nlstate+1);
4407: for(age=bage; age <=fage ;age++){
4408: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4409: if (popbased==1) {
4410: if(mobilav ==0){
4411: for(i=1; i<=nlstate;i++)
4412: prlim[i][i]=probs[(int)age][i][k];
4413: }else{ /* mobilav */
4414: for(i=1; i<=nlstate;i++)
4415: prlim[i][i]=mobaverage[(int)age][i][k];
4416: }
4417: }
4418:
4419: fprintf(ficrest," %4.0f",age);
4420: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
4421: for(i=1, epj[j]=0.;i <=nlstate;i++) {
4422: epj[j] += prlim[i][i]*eij[i][j][(int)age];
4423: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
4424: }
4425: epj[nlstate+1] +=epj[j];
4426: }
4427:
4428: for(i=1, vepp=0.;i <=nlstate;i++)
4429: for(j=1;j <=nlstate;j++)
4430: vepp += vareij[i][j][(int)age];
4431: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
4432: for(j=1;j <=nlstate;j++){
4433: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
4434: }
4435: fprintf(ficrest,"\n");
4436: }
4437: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4438: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4439: free_vector(epj,1,nlstate+1);
4440: }
4441: }
4442: free_vector(weight,1,n);
4443: free_imatrix(Tvard,1,15,1,2);
4444: free_imatrix(s,1,maxwav+1,1,n);
4445: free_matrix(anint,1,maxwav,1,n);
4446: free_matrix(mint,1,maxwav,1,n);
4447: free_ivector(cod,1,n);
4448: free_ivector(tab,1,NCOVMAX);
4449: fclose(ficreseij);
4450: fclose(ficresvij);
4451: fclose(ficrest);
4452: fclose(ficpar);
4453:
4454: /*------- Variance of stable prevalence------*/
4455:
4456: strcpy(fileresvpl,"vpl");
4457: strcat(fileresvpl,fileres);
4458: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
4459: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
4460: exit(0);
4461: }
4462: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
4463:
4464: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4465: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4466: k=k+1;
4467: fprintf(ficresvpl,"\n#****** ");
4468: for(j=1;j<=cptcoveff;j++)
4469: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4470: fprintf(ficresvpl,"******\n");
4471:
4472: varpl=matrix(1,nlstate,(int) bage, (int) fage);
4473: oldm=oldms;savm=savms;
4474: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
4475: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
4476: }
4477: }
4478:
4479: fclose(ficresvpl);
4480:
4481: /*---------- End : free ----------------*/
4482: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
4483: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
4484: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
4485: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
4486:
4487: free_matrix(covar,0,NCOVMAX,1,n);
4488: free_matrix(matcov,1,npar,1,npar);
4489: /*free_vector(delti,1,npar);*/
4490: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4491: free_matrix(agev,1,maxwav,1,imx);
4492: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4493: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4494: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
4495:
4496: free_ivector(ncodemax,1,8);
4497: free_ivector(Tvar,1,15);
4498: free_ivector(Tprod,1,15);
4499: free_ivector(Tvaraff,1,15);
4500: free_ivector(Tage,1,15);
4501: free_ivector(Tcode,1,100);
4502:
4503: /* fclose(fichtm);*/
4504: /* fclose(ficgp);*/ /* ALready done */
4505:
4506:
4507: if(erreur >0){
4508: printf("End of Imach with error or warning %d\n",erreur);
4509: fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
4510: }else{
4511: printf("End of Imach\n");
4512: fprintf(ficlog,"End of Imach\n");
4513: }
4514: printf("See log file on %s\n",filelog);
4515: fclose(ficlog);
4516: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
4517:
4518: /* 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);*/
4519: /*printf("Total time was %d uSec.\n", total_usecs);*/
4520: /*------ End -----------*/
4521:
4522: end:
4523: #ifdef windows
4524: /* chdir(pathcd);*/
4525: #endif
4526: /*system("wgnuplot graph.plt");*/
4527: /*system("../gp37mgw/wgnuplot graph.plt");*/
4528: /*system("cd ../gp37mgw");*/
4529: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
4530: strcpy(plotcmd,GNUPLOTPROGRAM);
4531: strcat(plotcmd," ");
4532: strcat(plotcmd,optionfilegnuplot);
4533: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
4534: system(plotcmd);
4535: printf(" Wait...");
4536:
4537: /*#ifdef windows*/
4538: while (z[0] != 'q') {
4539: /* chdir(path); */
4540: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
4541: scanf("%s",z);
4542: if (z[0] == 'c') system("./imach");
4543: else if (z[0] == 'e') system(optionfilehtm);
4544: else if (z[0] == 'g') system(plotcmd);
4545: else if (z[0] == 'q') exit(0);
4546: }
4547: /*#endif */
4548: }
4549:
4550:
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