Annotation of imach096d/src/imach.c, revision 1.76
1.76 ! brouard 1: /* $Id: imach.c,v 1.75 2003/05/03 01:18:24 brouard Exp $
1.53 brouard 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
1.66 brouard 35: states. This elementary transition (by month, quarter,
36: semester or year) is modelled as a multinomial logistic. The hPx
1.53 brouard 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
1.54 brouard 42: of the life expectancies. It also computes the stable prevalence.
1.53 brouard 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 .
1.74 brouard 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:
1.53 brouard 55: **********************************************************************/
1.74 brouard 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:
1.53 brouard 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*/
1.55 lievre 99: #define windows
1.53 brouard 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:
1.76 ! brouard 122: char version[80]="Imach version 0.95a, May 2003, INED-EUROREVES ";
1.53 brouard 123: int erreur; /* Error number */
124: int nvar;
125: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
126: int npar=NPARMAX;
127: int nlstate=2; /* Number of live states */
128: int ndeath=1; /* Number of dead states */
129: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
130: int popbased=0;
131:
132: int *wav; /* Number of waves for this individuual 0 is possible */
133: int maxwav; /* Maxim number of waves */
134: int jmin, jmax; /* min, max spacing between 2 waves */
135: int mle, weightopt;
136: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
137: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.59 brouard 138: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
139: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.53 brouard 140: double jmean; /* Mean space between 2 waves */
141: double **oldm, **newm, **savm; /* Working pointers to matrices */
142: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
143: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.76 ! brouard 144: FILE *ficlog, *ficrespow;
1.53 brouard 145: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
146: FILE *ficresprobmorprev;
147: FILE *fichtm; /* Html File */
148: FILE *ficreseij;
149: char filerese[FILENAMELENGTH];
150: FILE *ficresvij;
151: char fileresv[FILENAMELENGTH];
152: FILE *ficresvpl;
153: char fileresvpl[FILENAMELENGTH];
154: char title[MAXLINE];
155: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
156: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
157:
158: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
159: char filelog[FILENAMELENGTH]; /* Log file */
160: char filerest[FILENAMELENGTH];
161: char fileregp[FILENAMELENGTH];
162: char popfile[FILENAMELENGTH];
163:
164: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
165:
166: #define NR_END 1
167: #define FREE_ARG char*
168: #define FTOL 1.0e-10
169:
170: #define NRANSI
171: #define ITMAX 200
172:
173: #define TOL 2.0e-4
174:
175: #define CGOLD 0.3819660
176: #define ZEPS 1.0e-10
177: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
178:
179: #define GOLD 1.618034
180: #define GLIMIT 100.0
181: #define TINY 1.0e-20
182:
183: static double maxarg1,maxarg2;
184: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
185: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
186:
187: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
188: #define rint(a) floor(a+0.5)
189:
190: static double sqrarg;
191: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
192: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
193:
194: int imx;
195: int stepm;
196: /* Stepm, step in month: minimum step interpolation*/
197:
198: int estepm;
199: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
200:
201: int m,nb;
202: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
203: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.55 lievre 204: double **pmmij, ***probs;
1.53 brouard 205: double dateintmean=0;
206:
207: double *weight;
208: int **s; /* Status */
209: double *agedc, **covar, idx;
210: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
211:
212: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
213: double ftolhess; /* Tolerance for computing hessian */
214:
215: /**************** split *************************/
216: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
217: {
1.59 brouard 218: char *ss; /* pointer */
219: int l1, l2; /* length counters */
1.53 brouard 220:
1.59 brouard 221: l1 = strlen(path ); /* length of path */
222: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
223: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
224: if ( ss == NULL ) { /* no directory, so use current */
225: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
226: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.74 brouard 227: /* get current working directory */
228: /* extern char* getcwd ( char *buf , int len);*/
1.59 brouard 229: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
230: return( GLOCK_ERROR_GETCWD );
231: }
232: strcpy( name, path ); /* we've got it */
233: } else { /* strip direcotry from path */
234: ss++; /* after this, the filename */
235: l2 = strlen( ss ); /* length of filename */
236: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
237: strcpy( name, ss ); /* save file name */
238: strncpy( dirc, path, l1 - l2 ); /* now the directory */
239: dirc[l1-l2] = 0; /* add zero */
240: }
241: l1 = strlen( dirc ); /* length of directory */
1.53 brouard 242: #ifdef windows
1.59 brouard 243: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
1.53 brouard 244: #else
1.59 brouard 245: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
1.53 brouard 246: #endif
1.59 brouard 247: ss = strrchr( name, '.' ); /* find last / */
248: ss++;
249: strcpy(ext,ss); /* save extension */
250: l1= strlen( name);
251: l2= strlen(ss)+1;
252: strncpy( finame, name, l1-l2);
253: finame[l1-l2]= 0;
254: return( 0 ); /* we're done */
1.53 brouard 255: }
256:
257:
258: /******************************************/
259:
260: void replace(char *s, char*t)
261: {
262: int i;
263: int lg=20;
264: i=0;
265: lg=strlen(t);
266: for(i=0; i<= lg; i++) {
267: (s[i] = t[i]);
268: if (t[i]== '\\') s[i]='/';
269: }
270: }
271:
272: int nbocc(char *s, char occ)
273: {
274: int i,j=0;
275: int lg=20;
276: i=0;
277: lg=strlen(s);
278: for(i=0; i<= lg; i++) {
279: if (s[i] == occ ) j++;
280: }
281: return j;
282: }
283:
284: void cutv(char *u,char *v, char*t, char occ)
285: {
286: /* cuts string t into u and v where u is ended by char occ excluding it
287: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
288: gives u="abcedf" and v="ghi2j" */
289: int i,lg,j,p=0;
290: i=0;
291: for(j=0; j<=strlen(t)-1; j++) {
292: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
293: }
294:
295: lg=strlen(t);
296: for(j=0; j<p; j++) {
297: (u[j] = t[j]);
298: }
299: u[p]='\0';
300:
301: for(j=0; j<= lg; j++) {
302: if (j>=(p+1))(v[j-p-1] = t[j]);
303: }
304: }
305:
306: /********************** nrerror ********************/
307:
308: void nrerror(char error_text[])
309: {
310: fprintf(stderr,"ERREUR ...\n");
311: fprintf(stderr,"%s\n",error_text);
1.59 brouard 312: exit(EXIT_FAILURE);
1.53 brouard 313: }
314: /*********************** vector *******************/
315: double *vector(int nl, int nh)
316: {
317: double *v;
318: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
319: if (!v) nrerror("allocation failure in vector");
320: return v-nl+NR_END;
321: }
322:
323: /************************ free vector ******************/
324: void free_vector(double*v, int nl, int nh)
325: {
326: free((FREE_ARG)(v+nl-NR_END));
327: }
328:
329: /************************ivector *******************************/
1.76 ! brouard 330: char *cvector(long nl,long nh)
! 331: {
! 332: char *v;
! 333: v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
! 334: if (!v) nrerror("allocation failure in cvector");
! 335: return v-nl+NR_END;
! 336: }
! 337:
! 338: /******************free ivector **************************/
! 339: void free_cvector(char *v, long nl, long nh)
! 340: {
! 341: free((FREE_ARG)(v+nl-NR_END));
! 342: }
! 343:
! 344: /************************ivector *******************************/
1.53 brouard 345: int *ivector(long nl,long nh)
346: {
347: int *v;
348: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
349: if (!v) nrerror("allocation failure in ivector");
350: return v-nl+NR_END;
351: }
352:
353: /******************free ivector **************************/
354: void free_ivector(int *v, long nl, long nh)
355: {
356: free((FREE_ARG)(v+nl-NR_END));
357: }
358:
359: /******************* imatrix *******************************/
360: int **imatrix(long nrl, long nrh, long ncl, long nch)
361: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
362: {
363: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
364: int **m;
365:
366: /* allocate pointers to rows */
367: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
368: if (!m) nrerror("allocation failure 1 in matrix()");
369: m += NR_END;
370: m -= nrl;
371:
372:
373: /* allocate rows and set pointers to them */
374: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
375: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
376: m[nrl] += NR_END;
377: m[nrl] -= ncl;
378:
379: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
380:
381: /* return pointer to array of pointers to rows */
382: return m;
383: }
384:
385: /****************** free_imatrix *************************/
386: void free_imatrix(m,nrl,nrh,ncl,nch)
387: int **m;
388: long nch,ncl,nrh,nrl;
389: /* free an int matrix allocated by imatrix() */
390: {
391: free((FREE_ARG) (m[nrl]+ncl-NR_END));
392: free((FREE_ARG) (m+nrl-NR_END));
393: }
394:
395: /******************* matrix *******************************/
396: double **matrix(long nrl, long nrh, long ncl, long nch)
397: {
398: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
399: double **m;
400:
401: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
402: if (!m) nrerror("allocation failure 1 in matrix()");
403: m += NR_END;
404: m -= nrl;
405:
406: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
407: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
408: m[nrl] += NR_END;
409: m[nrl] -= ncl;
410:
411: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
412: return m;
1.74 brouard 413: /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1])
414: */
1.53 brouard 415: }
416:
417: /*************************free matrix ************************/
418: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
419: {
420: free((FREE_ARG)(m[nrl]+ncl-NR_END));
421: free((FREE_ARG)(m+nrl-NR_END));
422: }
423:
424: /******************* ma3x *******************************/
425: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
426: {
427: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
428: double ***m;
429:
430: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
431: if (!m) nrerror("allocation failure 1 in matrix()");
432: m += NR_END;
433: m -= nrl;
434:
435: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
436: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
437: m[nrl] += NR_END;
438: m[nrl] -= ncl;
439:
440: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
441:
442: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
443: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
444: m[nrl][ncl] += NR_END;
445: m[nrl][ncl] -= nll;
446: for (j=ncl+1; j<=nch; j++)
447: m[nrl][j]=m[nrl][j-1]+nlay;
448:
449: for (i=nrl+1; i<=nrh; i++) {
450: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
451: for (j=ncl+1; j<=nch; j++)
452: m[i][j]=m[i][j-1]+nlay;
453: }
1.74 brouard 454: return m;
455: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
456: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
457: */
1.53 brouard 458: }
459:
460: /*************************free ma3x ************************/
461: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
462: {
463: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
464: free((FREE_ARG)(m[nrl]+ncl-NR_END));
465: free((FREE_ARG)(m+nrl-NR_END));
466: }
467:
468: /***************** f1dim *************************/
469: extern int ncom;
470: extern double *pcom,*xicom;
471: extern double (*nrfunc)(double []);
472:
473: double f1dim(double x)
474: {
475: int j;
476: double f;
477: double *xt;
478:
479: xt=vector(1,ncom);
480: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
481: f=(*nrfunc)(xt);
482: free_vector(xt,1,ncom);
483: return f;
484: }
485:
486: /*****************brent *************************/
487: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
488: {
489: int iter;
490: double a,b,d,etemp;
491: double fu,fv,fw,fx;
492: double ftemp;
493: double p,q,r,tol1,tol2,u,v,w,x,xm;
494: double e=0.0;
495:
496: a=(ax < cx ? ax : cx);
497: b=(ax > cx ? ax : cx);
498: x=w=v=bx;
499: fw=fv=fx=(*f)(x);
500: for (iter=1;iter<=ITMAX;iter++) {
501: xm=0.5*(a+b);
502: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
503: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
504: printf(".");fflush(stdout);
505: fprintf(ficlog,".");fflush(ficlog);
506: #ifdef DEBUG
507: 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);
508: 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);
509: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
510: #endif
511: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
512: *xmin=x;
513: return fx;
514: }
515: ftemp=fu;
516: if (fabs(e) > tol1) {
517: r=(x-w)*(fx-fv);
518: q=(x-v)*(fx-fw);
519: p=(x-v)*q-(x-w)*r;
520: q=2.0*(q-r);
521: if (q > 0.0) p = -p;
522: q=fabs(q);
523: etemp=e;
524: e=d;
525: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
526: d=CGOLD*(e=(x >= xm ? a-x : b-x));
527: else {
528: d=p/q;
529: u=x+d;
530: if (u-a < tol2 || b-u < tol2)
531: d=SIGN(tol1,xm-x);
532: }
533: } else {
534: d=CGOLD*(e=(x >= xm ? a-x : b-x));
535: }
536: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
537: fu=(*f)(u);
538: if (fu <= fx) {
539: if (u >= x) a=x; else b=x;
540: SHFT(v,w,x,u)
541: SHFT(fv,fw,fx,fu)
542: } else {
543: if (u < x) a=u; else b=u;
544: if (fu <= fw || w == x) {
545: v=w;
546: w=u;
547: fv=fw;
548: fw=fu;
549: } else if (fu <= fv || v == x || v == w) {
550: v=u;
551: fv=fu;
552: }
553: }
554: }
555: nrerror("Too many iterations in brent");
556: *xmin=x;
557: return fx;
558: }
559:
560: /****************** mnbrak ***********************/
561:
562: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
563: double (*func)(double))
564: {
565: double ulim,u,r,q, dum;
566: double fu;
567:
568: *fa=(*func)(*ax);
569: *fb=(*func)(*bx);
570: if (*fb > *fa) {
571: SHFT(dum,*ax,*bx,dum)
572: SHFT(dum,*fb,*fa,dum)
573: }
574: *cx=(*bx)+GOLD*(*bx-*ax);
575: *fc=(*func)(*cx);
576: while (*fb > *fc) {
577: r=(*bx-*ax)*(*fb-*fc);
578: q=(*bx-*cx)*(*fb-*fa);
579: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
580: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
581: ulim=(*bx)+GLIMIT*(*cx-*bx);
582: if ((*bx-u)*(u-*cx) > 0.0) {
583: fu=(*func)(u);
584: } else if ((*cx-u)*(u-ulim) > 0.0) {
585: fu=(*func)(u);
586: if (fu < *fc) {
587: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
588: SHFT(*fb,*fc,fu,(*func)(u))
589: }
590: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
591: u=ulim;
592: fu=(*func)(u);
593: } else {
594: u=(*cx)+GOLD*(*cx-*bx);
595: fu=(*func)(u);
596: }
597: SHFT(*ax,*bx,*cx,u)
598: SHFT(*fa,*fb,*fc,fu)
599: }
600: }
601:
602: /*************** linmin ************************/
603:
604: int ncom;
605: double *pcom,*xicom;
606: double (*nrfunc)(double []);
607:
608: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
609: {
610: double brent(double ax, double bx, double cx,
611: double (*f)(double), double tol, double *xmin);
612: double f1dim(double x);
613: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
614: double *fc, double (*func)(double));
615: int j;
616: double xx,xmin,bx,ax;
617: double fx,fb,fa;
618:
619: ncom=n;
620: pcom=vector(1,n);
621: xicom=vector(1,n);
622: nrfunc=func;
623: for (j=1;j<=n;j++) {
624: pcom[j]=p[j];
625: xicom[j]=xi[j];
626: }
627: ax=0.0;
628: xx=1.0;
629: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
630: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
631: #ifdef DEBUG
632: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
633: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
634: #endif
635: for (j=1;j<=n;j++) {
636: xi[j] *= xmin;
637: p[j] += xi[j];
638: }
639: free_vector(xicom,1,n);
640: free_vector(pcom,1,n);
641: }
642:
643: /*************** powell ************************/
644: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
645: double (*func)(double []))
646: {
647: void linmin(double p[], double xi[], int n, double *fret,
648: double (*func)(double []));
649: int i,ibig,j;
650: double del,t,*pt,*ptt,*xit;
651: double fp,fptt;
652: double *xits;
653: pt=vector(1,n);
654: ptt=vector(1,n);
655: xit=vector(1,n);
656: xits=vector(1,n);
657: *fret=(*func)(p);
658: for (j=1;j<=n;j++) pt[j]=p[j];
659: for (*iter=1;;++(*iter)) {
660: fp=(*fret);
661: ibig=0;
662: del=0.0;
663: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
664: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
1.76 ! brouard 665: fprintf(ficrespow,"%d %.12f",*iter,*fret);
! 666: for (i=1;i<=n;i++) {
1.53 brouard 667: printf(" %d %.12f",i, p[i]);
1.76 ! brouard 668: fprintf(ficlog," %d %.12lf",i, p[i]);
! 669: fprintf(ficrespow," %.12lf", p[i]);
! 670: }
1.53 brouard 671: printf("\n");
672: fprintf(ficlog,"\n");
1.76 ! brouard 673: fprintf(ficrespow,"\n");
1.53 brouard 674: for (i=1;i<=n;i++) {
675: for (j=1;j<=n;j++) xit[j]=xi[j][i];
676: fptt=(*fret);
677: #ifdef DEBUG
678: printf("fret=%lf \n",*fret);
679: fprintf(ficlog,"fret=%lf \n",*fret);
680: #endif
681: printf("%d",i);fflush(stdout);
682: fprintf(ficlog,"%d",i);fflush(ficlog);
683: linmin(p,xit,n,fret,func);
684: if (fabs(fptt-(*fret)) > del) {
685: del=fabs(fptt-(*fret));
686: ibig=i;
687: }
688: #ifdef DEBUG
689: printf("%d %.12e",i,(*fret));
690: fprintf(ficlog,"%d %.12e",i,(*fret));
691: for (j=1;j<=n;j++) {
692: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
693: printf(" x(%d)=%.12e",j,xit[j]);
694: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
695: }
696: for(j=1;j<=n;j++) {
697: printf(" p=%.12e",p[j]);
698: fprintf(ficlog," p=%.12e",p[j]);
699: }
700: printf("\n");
701: fprintf(ficlog,"\n");
702: #endif
703: }
704: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
705: #ifdef DEBUG
706: int k[2],l;
707: k[0]=1;
708: k[1]=-1;
709: printf("Max: %.12e",(*func)(p));
710: fprintf(ficlog,"Max: %.12e",(*func)(p));
711: for (j=1;j<=n;j++) {
712: printf(" %.12e",p[j]);
713: fprintf(ficlog," %.12e",p[j]);
714: }
715: printf("\n");
716: fprintf(ficlog,"\n");
717: for(l=0;l<=1;l++) {
718: for (j=1;j<=n;j++) {
719: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
720: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
721: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
722: }
723: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
724: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
725: }
726: #endif
727:
728:
729: free_vector(xit,1,n);
730: free_vector(xits,1,n);
731: free_vector(ptt,1,n);
732: free_vector(pt,1,n);
733: return;
734: }
735: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
736: for (j=1;j<=n;j++) {
737: ptt[j]=2.0*p[j]-pt[j];
738: xit[j]=p[j]-pt[j];
739: pt[j]=p[j];
740: }
741: fptt=(*func)(ptt);
742: if (fptt < fp) {
743: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
744: if (t < 0.0) {
745: linmin(p,xit,n,fret,func);
746: for (j=1;j<=n;j++) {
747: xi[j][ibig]=xi[j][n];
748: xi[j][n]=xit[j];
749: }
750: #ifdef DEBUG
751: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
752: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
753: for(j=1;j<=n;j++){
754: printf(" %.12e",xit[j]);
755: fprintf(ficlog," %.12e",xit[j]);
756: }
757: printf("\n");
758: fprintf(ficlog,"\n");
759: #endif
1.54 brouard 760: }
1.53 brouard 761: }
762: }
763: }
764:
1.54 brouard 765: /**** Prevalence limit (stable prevalence) ****************/
1.53 brouard 766:
767: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
768: {
769: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
770: matrix by transitions matrix until convergence is reached */
771:
772: int i, ii,j,k;
773: double min, max, maxmin, maxmax,sumnew=0.;
774: double **matprod2();
775: double **out, cov[NCOVMAX], **pmij();
776: double **newm;
777: double agefin, delaymax=50 ; /* Max number of years to converge */
778:
779: for (ii=1;ii<=nlstate+ndeath;ii++)
780: for (j=1;j<=nlstate+ndeath;j++){
781: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
782: }
783:
784: cov[1]=1.;
785:
786: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
787: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
788: newm=savm;
789: /* Covariates have to be included here again */
790: cov[2]=agefin;
791:
792: for (k=1; k<=cptcovn;k++) {
793: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
794: /* 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]]);*/
795: }
796: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
797: for (k=1; k<=cptcovprod;k++)
798: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
799:
800: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
801: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
802: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
803: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
804:
805: savm=oldm;
806: oldm=newm;
807: maxmax=0.;
808: for(j=1;j<=nlstate;j++){
809: min=1.;
810: max=0.;
811: for(i=1; i<=nlstate; i++) {
812: sumnew=0;
813: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
814: prlim[i][j]= newm[i][j]/(1-sumnew);
815: max=FMAX(max,prlim[i][j]);
816: min=FMIN(min,prlim[i][j]);
817: }
818: maxmin=max-min;
819: maxmax=FMAX(maxmax,maxmin);
820: }
821: if(maxmax < ftolpl){
822: return prlim;
823: }
824: }
825: }
826:
827: /*************** transition probabilities ***************/
828:
829: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
830: {
831: double s1, s2;
832: /*double t34;*/
833: int i,j,j1, nc, ii, jj;
834:
835: for(i=1; i<= nlstate; i++){
836: for(j=1; j<i;j++){
837: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
838: /*s2 += param[i][j][nc]*cov[nc];*/
839: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
840: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
841: }
842: ps[i][j]=s2;
843: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
844: }
845: for(j=i+1; j<=nlstate+ndeath;j++){
846: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
847: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
848: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
849: }
850: ps[i][j]=s2;
851: }
852: }
853: /*ps[3][2]=1;*/
854:
855: for(i=1; i<= nlstate; i++){
856: s1=0;
857: for(j=1; j<i; j++)
858: s1+=exp(ps[i][j]);
859: for(j=i+1; j<=nlstate+ndeath; j++)
860: s1+=exp(ps[i][j]);
861: ps[i][i]=1./(s1+1.);
862: for(j=1; j<i; j++)
863: ps[i][j]= exp(ps[i][j])*ps[i][i];
864: for(j=i+1; j<=nlstate+ndeath; j++)
865: ps[i][j]= exp(ps[i][j])*ps[i][i];
866: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
867: } /* end i */
868:
869: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
870: for(jj=1; jj<= nlstate+ndeath; jj++){
871: ps[ii][jj]=0;
872: ps[ii][ii]=1;
873: }
874: }
875:
876:
877: /* for(ii=1; ii<= nlstate+ndeath; ii++){
878: for(jj=1; jj<= nlstate+ndeath; jj++){
879: printf("%lf ",ps[ii][jj]);
880: }
881: printf("\n ");
882: }
883: printf("\n ");printf("%lf ",cov[2]);*/
884: /*
885: for(i=1; i<= npar; i++) printf("%f ",x[i]);
886: goto end;*/
887: return ps;
888: }
889:
890: /**************** Product of 2 matrices ******************/
891:
892: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
893: {
894: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
895: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
896: /* in, b, out are matrice of pointers which should have been initialized
897: before: only the contents of out is modified. The function returns
898: a pointer to pointers identical to out */
899: long i, j, k;
900: for(i=nrl; i<= nrh; i++)
901: for(k=ncolol; k<=ncoloh; k++)
902: for(j=ncl,out[i][k]=0.; j<=nch; j++)
903: out[i][k] +=in[i][j]*b[j][k];
904:
905: return out;
906: }
907:
908:
909: /************* Higher Matrix Product ***************/
910:
911: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
912: {
1.66 brouard 913: /* Computes the transition matrix starting at age 'age' over
914: 'nhstepm*hstepm*stepm' months (i.e. until
915: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
916: nhstepm*hstepm matrices.
1.53 brouard 917: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1.66 brouard 918: (typically every 2 years instead of every month which is too big
919: for the memory).
1.53 brouard 920: Model is determined by parameters x and covariates have to be
921: included manually here.
922:
923: */
924:
925: int i, j, d, h, k;
926: double **out, cov[NCOVMAX];
927: double **newm;
928:
929: /* Hstepm could be zero and should return the unit matrix */
930: for (i=1;i<=nlstate+ndeath;i++)
931: for (j=1;j<=nlstate+ndeath;j++){
932: oldm[i][j]=(i==j ? 1.0 : 0.0);
933: po[i][j][0]=(i==j ? 1.0 : 0.0);
934: }
935: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
936: for(h=1; h <=nhstepm; h++){
937: for(d=1; d <=hstepm; d++){
938: newm=savm;
939: /* Covariates have to be included here again */
940: cov[1]=1.;
941: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
942: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
943: for (k=1; k<=cptcovage;k++)
944: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
945: for (k=1; k<=cptcovprod;k++)
946: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
947:
948:
949: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
950: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
951: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
952: pmij(pmmij,cov,ncovmodel,x,nlstate));
953: savm=oldm;
954: oldm=newm;
955: }
956: for(i=1; i<=nlstate+ndeath; i++)
957: for(j=1;j<=nlstate+ndeath;j++) {
958: po[i][j][h]=newm[i][j];
959: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
960: */
961: }
962: } /* end h */
963: return po;
964: }
965:
966:
967: /*************** log-likelihood *************/
968: double func( double *x)
969: {
970: int i, ii, j, k, mi, d, kk;
971: double l, ll[NLSTATEMAX], cov[NCOVMAX];
972: double **out;
973: double sw; /* Sum of weights */
974: double lli; /* Individual log likelihood */
1.59 brouard 975: int s1, s2;
1.68 lievre 976: double bbh, survp;
1.53 brouard 977: long ipmx;
978: /*extern weight */
979: /* We are differentiating ll according to initial status */
980: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
981: /*for(i=1;i<imx;i++)
982: printf(" %d\n",s[4][i]);
983: */
984: cov[1]=1.;
985:
986: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.61 brouard 987:
988: if(mle==1){
989: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
990: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
991: for(mi=1; mi<= wav[i]-1; mi++){
992: for (ii=1;ii<=nlstate+ndeath;ii++)
993: for (j=1;j<=nlstate+ndeath;j++){
994: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
995: savm[ii][j]=(ii==j ? 1.0 : 0.0);
996: }
997: for(d=0; d<dh[mi][i]; d++){
998: newm=savm;
999: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1000: for (kk=1; kk<=cptcovage;kk++) {
1001: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1002: }
1003: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1004: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1005: savm=oldm;
1006: oldm=newm;
1007: } /* end mult */
1.53 brouard 1008:
1.61 brouard 1009: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1010: /* But now since version 0.9 we anticipate for bias and large stepm.
1011: * If stepm is larger than one month (smallest stepm) and if the exact delay
1012: * (in months) between two waves is not a multiple of stepm, we rounded to
1013: * the nearest (and in case of equal distance, to the lowest) interval but now
1014: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1015: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1016: * probability in order to take into account the bias as a fraction of the way
1017: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1018: * -stepm/2 to stepm/2 .
1019: * For stepm=1 the results are the same as for previous versions of Imach.
1020: * For stepm > 1 the results are less biased than in previous versions.
1021: */
1022: s1=s[mw[mi][i]][i];
1023: s2=s[mw[mi+1][i]][i];
1.64 lievre 1024: bbh=(double)bh[mi][i]/(double)stepm;
1025: /* bias is positive if real duration
1026: * is higher than the multiple of stepm and negative otherwise.
1027: */
1028: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1.71 brouard 1029: if( s2 > nlstate){
1030: /* i.e. if s2 is a death state and if the date of death is known then the contribution
1031: to the likelihood is the probability to die between last step unit time and current
1032: step unit time, which is also the differences between probability to die before dh
1033: and probability to die before dh-stepm .
1034: In version up to 0.92 likelihood was computed
1035: as if date of death was unknown. Death was treated as any other
1036: health state: the date of the interview describes the actual state
1037: and not the date of a change in health state. The former idea was
1038: to consider that at each interview the state was recorded
1039: (healthy, disable or death) and IMaCh was corrected; but when we
1040: introduced the exact date of death then we should have modified
1041: the contribution of an exact death to the likelihood. This new
1042: contribution is smaller and very dependent of the step unit
1043: stepm. It is no more the probability to die between last interview
1044: and month of death but the probability to survive from last
1045: interview up to one month before death multiplied by the
1046: probability to die within a month. Thanks to Chris
1047: Jackson for correcting this bug. Former versions increased
1048: mortality artificially. The bad side is that we add another loop
1049: which slows down the processing. The difference can be up to 10%
1050: lower mortality.
1051: */
1052: lli=log(out[s1][s2] - savm[s1][s2]);
1053: }else{
1054: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1055: /* 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 */
1056: }
1.64 lievre 1057: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1058: /*if(lli ==000.0)*/
1059: /*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); */
1.71 brouard 1060: ipmx +=1;
1.64 lievre 1061: sw += weight[i];
1062: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1063: } /* end of wave */
1064: } /* end of individual */
1065: } else if(mle==2){
1066: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1067: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1068: for(mi=1; mi<= wav[i]-1; mi++){
1069: for (ii=1;ii<=nlstate+ndeath;ii++)
1070: for (j=1;j<=nlstate+ndeath;j++){
1071: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1072: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1073: }
1074: for(d=0; d<=dh[mi][i]; d++){
1075: newm=savm;
1076: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1077: for (kk=1; kk<=cptcovage;kk++) {
1078: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1079: }
1080: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1081: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1082: savm=oldm;
1083: oldm=newm;
1084: } /* end mult */
1085:
1086: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1087: /* But now since version 0.9 we anticipate for bias and large stepm.
1088: * If stepm is larger than one month (smallest stepm) and if the exact delay
1089: * (in months) between two waves is not a multiple of stepm, we rounded to
1090: * the nearest (and in case of equal distance, to the lowest) interval but now
1091: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1092: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1093: * probability in order to take into account the bias as a fraction of the way
1094: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1095: * -stepm/2 to stepm/2 .
1096: * For stepm=1 the results are the same as for previous versions of Imach.
1097: * For stepm > 1 the results are less biased than in previous versions.
1098: */
1099: s1=s[mw[mi][i]][i];
1100: s2=s[mw[mi+1][i]][i];
1101: bbh=(double)bh[mi][i]/(double)stepm;
1102: /* bias is positive if real duration
1103: * is higher than the multiple of stepm and negative otherwise.
1104: */
1.63 lievre 1105: 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 */
1.64 lievre 1106: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1107: /*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 */
1108: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1109: /*if(lli ==000.0)*/
1110: /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
1111: ipmx +=1;
1112: sw += weight[i];
1113: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1114: } /* end of wave */
1115: } /* end of individual */
1116: } else if(mle==3){ /* exponential inter-extrapolation */
1117: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1118: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1119: for(mi=1; mi<= wav[i]-1; mi++){
1120: for (ii=1;ii<=nlstate+ndeath;ii++)
1121: for (j=1;j<=nlstate+ndeath;j++){
1122: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1123: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1124: }
1125: for(d=0; d<dh[mi][i]; d++){
1126: newm=savm;
1127: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1128: for (kk=1; kk<=cptcovage;kk++) {
1129: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1130: }
1131: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1132: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1133: savm=oldm;
1134: oldm=newm;
1135: } /* end mult */
1136:
1137: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1138: /* But now since version 0.9 we anticipate for bias and large stepm.
1139: * If stepm is larger than one month (smallest stepm) and if the exact delay
1140: * (in months) between two waves is not a multiple of stepm, we rounded to
1141: * the nearest (and in case of equal distance, to the lowest) interval but now
1142: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1143: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1144: * probability in order to take into account the bias as a fraction of the way
1145: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1146: * -stepm/2 to stepm/2 .
1147: * For stepm=1 the results are the same as for previous versions of Imach.
1148: * For stepm > 1 the results are less biased than in previous versions.
1149: */
1150: s1=s[mw[mi][i]][i];
1151: s2=s[mw[mi+1][i]][i];
1152: bbh=(double)bh[mi][i]/(double)stepm;
1153: /* bias is positive if real duration
1154: * is higher than the multiple of stepm and negative otherwise.
1155: */
1156: /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
1157: lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
1.61 brouard 1158: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1159: /*if(lli ==000.0)*/
1160: /*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); */
1161: ipmx +=1;
1162: sw += weight[i];
1163: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1164: } /* end of wave */
1165: } /* end of individual */
1.64 lievre 1166: }else{ /* ml=4 no inter-extrapolation */
1.61 brouard 1167: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1168: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1169: for(mi=1; mi<= wav[i]-1; mi++){
1170: for (ii=1;ii<=nlstate+ndeath;ii++)
1171: for (j=1;j<=nlstate+ndeath;j++){
1172: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1173: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1174: }
1175: for(d=0; d<dh[mi][i]; d++){
1176: newm=savm;
1177: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1178: for (kk=1; kk<=cptcovage;kk++) {
1179: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1180: }
1181:
1182: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1183: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1184: savm=oldm;
1185: oldm=newm;
1186: } /* end mult */
1187:
1188: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1189: ipmx +=1;
1190: sw += weight[i];
1191: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1192: } /* end of wave */
1193: } /* end of individual */
1194: } /* End of if */
1.53 brouard 1195: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1196: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1197: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1198: return -l;
1199: }
1200:
1201:
1202: /*********** Maximum Likelihood Estimation ***************/
1203:
1204: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1205: {
1206: int i,j, iter;
1.74 brouard 1207: double **xi;
1.53 brouard 1208: double fret;
1.76 ! brouard 1209: char filerespow[FILENAMELENGTH];
1.53 brouard 1210: xi=matrix(1,npar,1,npar);
1211: for (i=1;i<=npar;i++)
1212: for (j=1;j<=npar;j++)
1213: xi[i][j]=(i==j ? 1.0 : 0.0);
1214: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.76 ! brouard 1215: strcpy(filerespow,"pow");
! 1216: strcat(filerespow,fileres);
! 1217: if((ficrespow=fopen(filerespow,"w"))==NULL) {
! 1218: printf("Problem with resultfile: %s\n", filerespow);
! 1219: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
! 1220: }
! 1221: fprintf(ficrespow,"# Powell\n# iter -2*LL");
! 1222: for (i=1;i<=nlstate;i++)
! 1223: for(j=1;j<=nlstate+ndeath;j++)
! 1224: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
! 1225: fprintf(ficrespow,"\n");
1.53 brouard 1226: powell(p,xi,npar,ftol,&iter,&fret,func);
1227:
1.76 ! brouard 1228: fclose(ficrespow);
! 1229: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.65 lievre 1230: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.53 brouard 1231: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1232:
1233: }
1234:
1235: /**** Computes Hessian and covariance matrix ***/
1236: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1237: {
1238: double **a,**y,*x,pd;
1239: double **hess;
1240: int i, j,jk;
1241: int *indx;
1242:
1243: double hessii(double p[], double delta, int theta, double delti[]);
1244: double hessij(double p[], double delti[], int i, int j);
1245: void lubksb(double **a, int npar, int *indx, double b[]) ;
1246: void ludcmp(double **a, int npar, int *indx, double *d) ;
1247:
1248: hess=matrix(1,npar,1,npar);
1249:
1250: printf("\nCalculation of the hessian matrix. Wait...\n");
1251: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1252: for (i=1;i<=npar;i++){
1253: printf("%d",i);fflush(stdout);
1254: fprintf(ficlog,"%d",i);fflush(ficlog);
1255: hess[i][i]=hessii(p,ftolhess,i,delti);
1256: /*printf(" %f ",p[i]);*/
1257: /*printf(" %lf ",hess[i][i]);*/
1258: }
1259:
1260: for (i=1;i<=npar;i++) {
1261: for (j=1;j<=npar;j++) {
1262: if (j>i) {
1263: printf(".%d%d",i,j);fflush(stdout);
1264: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1265: hess[i][j]=hessij(p,delti,i,j);
1266: hess[j][i]=hess[i][j];
1267: /*printf(" %lf ",hess[i][j]);*/
1268: }
1269: }
1270: }
1271: printf("\n");
1272: fprintf(ficlog,"\n");
1273:
1274: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1275: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1276:
1277: a=matrix(1,npar,1,npar);
1278: y=matrix(1,npar,1,npar);
1279: x=vector(1,npar);
1280: indx=ivector(1,npar);
1281: for (i=1;i<=npar;i++)
1282: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1283: ludcmp(a,npar,indx,&pd);
1284:
1285: for (j=1;j<=npar;j++) {
1286: for (i=1;i<=npar;i++) x[i]=0;
1287: x[j]=1;
1288: lubksb(a,npar,indx,x);
1289: for (i=1;i<=npar;i++){
1290: matcov[i][j]=x[i];
1291: }
1292: }
1293:
1294: printf("\n#Hessian matrix#\n");
1295: fprintf(ficlog,"\n#Hessian matrix#\n");
1296: for (i=1;i<=npar;i++) {
1297: for (j=1;j<=npar;j++) {
1298: printf("%.3e ",hess[i][j]);
1299: fprintf(ficlog,"%.3e ",hess[i][j]);
1300: }
1301: printf("\n");
1302: fprintf(ficlog,"\n");
1303: }
1304:
1305: /* Recompute Inverse */
1306: for (i=1;i<=npar;i++)
1307: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1308: ludcmp(a,npar,indx,&pd);
1309:
1310: /* printf("\n#Hessian matrix recomputed#\n");
1311:
1312: for (j=1;j<=npar;j++) {
1313: for (i=1;i<=npar;i++) x[i]=0;
1314: x[j]=1;
1315: lubksb(a,npar,indx,x);
1316: for (i=1;i<=npar;i++){
1317: y[i][j]=x[i];
1318: printf("%.3e ",y[i][j]);
1319: fprintf(ficlog,"%.3e ",y[i][j]);
1320: }
1321: printf("\n");
1322: fprintf(ficlog,"\n");
1323: }
1324: */
1325:
1326: free_matrix(a,1,npar,1,npar);
1327: free_matrix(y,1,npar,1,npar);
1328: free_vector(x,1,npar);
1329: free_ivector(indx,1,npar);
1330: free_matrix(hess,1,npar,1,npar);
1331:
1332:
1333: }
1334:
1335: /*************** hessian matrix ****************/
1336: double hessii( double x[], double delta, int theta, double delti[])
1337: {
1338: int i;
1339: int l=1, lmax=20;
1340: double k1,k2;
1341: double p2[NPARMAX+1];
1342: double res;
1343: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1344: double fx;
1345: int k=0,kmax=10;
1346: double l1;
1347:
1348: fx=func(x);
1349: for (i=1;i<=npar;i++) p2[i]=x[i];
1350: for(l=0 ; l <=lmax; l++){
1351: l1=pow(10,l);
1352: delts=delt;
1353: for(k=1 ; k <kmax; k=k+1){
1354: delt = delta*(l1*k);
1355: p2[theta]=x[theta] +delt;
1356: k1=func(p2)-fx;
1357: p2[theta]=x[theta]-delt;
1358: k2=func(p2)-fx;
1359: /*res= (k1-2.0*fx+k2)/delt/delt; */
1360: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1361:
1362: #ifdef DEBUG
1363: 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);
1364: 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);
1365: #endif
1366: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1367: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1368: k=kmax;
1369: }
1370: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1371: k=kmax; l=lmax*10.;
1372: }
1373: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1374: delts=delt;
1375: }
1376: }
1377: }
1378: delti[theta]=delts;
1379: return res;
1380:
1381: }
1382:
1383: double hessij( double x[], double delti[], int thetai,int thetaj)
1384: {
1385: int i;
1386: int l=1, l1, lmax=20;
1387: double k1,k2,k3,k4,res,fx;
1388: double p2[NPARMAX+1];
1389: int k;
1390:
1391: fx=func(x);
1392: for (k=1; k<=2; k++) {
1393: for (i=1;i<=npar;i++) p2[i]=x[i];
1394: p2[thetai]=x[thetai]+delti[thetai]/k;
1395: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1396: k1=func(p2)-fx;
1397:
1398: p2[thetai]=x[thetai]+delti[thetai]/k;
1399: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1400: k2=func(p2)-fx;
1401:
1402: p2[thetai]=x[thetai]-delti[thetai]/k;
1403: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1404: k3=func(p2)-fx;
1405:
1406: p2[thetai]=x[thetai]-delti[thetai]/k;
1407: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1408: k4=func(p2)-fx;
1409: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1410: #ifdef DEBUG
1411: 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);
1412: 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);
1413: #endif
1414: }
1415: return res;
1416: }
1417:
1418: /************** Inverse of matrix **************/
1419: void ludcmp(double **a, int n, int *indx, double *d)
1420: {
1421: int i,imax,j,k;
1422: double big,dum,sum,temp;
1423: double *vv;
1424:
1425: vv=vector(1,n);
1426: *d=1.0;
1427: for (i=1;i<=n;i++) {
1428: big=0.0;
1429: for (j=1;j<=n;j++)
1430: if ((temp=fabs(a[i][j])) > big) big=temp;
1431: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1432: vv[i]=1.0/big;
1433: }
1434: for (j=1;j<=n;j++) {
1435: for (i=1;i<j;i++) {
1436: sum=a[i][j];
1437: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1438: a[i][j]=sum;
1439: }
1440: big=0.0;
1441: for (i=j;i<=n;i++) {
1442: sum=a[i][j];
1443: for (k=1;k<j;k++)
1444: sum -= a[i][k]*a[k][j];
1445: a[i][j]=sum;
1446: if ( (dum=vv[i]*fabs(sum)) >= big) {
1447: big=dum;
1448: imax=i;
1449: }
1450: }
1451: if (j != imax) {
1452: for (k=1;k<=n;k++) {
1453: dum=a[imax][k];
1454: a[imax][k]=a[j][k];
1455: a[j][k]=dum;
1456: }
1457: *d = -(*d);
1458: vv[imax]=vv[j];
1459: }
1460: indx[j]=imax;
1461: if (a[j][j] == 0.0) a[j][j]=TINY;
1462: if (j != n) {
1463: dum=1.0/(a[j][j]);
1464: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1465: }
1466: }
1467: free_vector(vv,1,n); /* Doesn't work */
1468: ;
1469: }
1470:
1471: void lubksb(double **a, int n, int *indx, double b[])
1472: {
1473: int i,ii=0,ip,j;
1474: double sum;
1475:
1476: for (i=1;i<=n;i++) {
1477: ip=indx[i];
1478: sum=b[ip];
1479: b[ip]=b[i];
1480: if (ii)
1481: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1482: else if (sum) ii=i;
1483: b[i]=sum;
1484: }
1485: for (i=n;i>=1;i--) {
1486: sum=b[i];
1487: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1488: b[i]=sum/a[i][i];
1489: }
1490: }
1491:
1492: /************ Frequencies ********************/
1.74 brouard 1493: 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)
1.53 brouard 1494: { /* Some frequencies */
1495:
1496: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1497: int first;
1498: double ***freq; /* Frequencies */
1.73 lievre 1499: double *pp, **prop;
1500: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.53 brouard 1501: FILE *ficresp;
1502: char fileresp[FILENAMELENGTH];
1503:
1504: pp=vector(1,nlstate);
1.74 brouard 1505: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.53 brouard 1506: strcpy(fileresp,"p");
1507: strcat(fileresp,fileres);
1508: if((ficresp=fopen(fileresp,"w"))==NULL) {
1509: printf("Problem with prevalence resultfile: %s\n", fileresp);
1510: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1511: exit(0);
1512: }
1.74 brouard 1513: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
1.53 brouard 1514: j1=0;
1515:
1516: j=cptcoveff;
1517: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1518:
1519: first=1;
1520:
1521: for(k1=1; k1<=j;k1++){
1522: for(i1=1; i1<=ncodemax[k1];i1++){
1523: j1++;
1524: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1525: scanf("%d", i);*/
1526: for (i=-1; i<=nlstate+ndeath; i++)
1527: for (jk=-1; jk<=nlstate+ndeath; jk++)
1.74 brouard 1528: for(m=iagemin; m <= iagemax+3; m++)
1.53 brouard 1529: freq[i][jk][m]=0;
1.73 lievre 1530:
1531: for (i=1; i<=nlstate; i++)
1.74 brouard 1532: for(m=iagemin; m <= iagemax+3; m++)
1.73 lievre 1533: prop[i][m]=0;
1.53 brouard 1534:
1535: dateintsum=0;
1536: k2cpt=0;
1537: for (i=1; i<=imx; i++) {
1538: bool=1;
1539: if (cptcovn>0) {
1540: for (z1=1; z1<=cptcoveff; z1++)
1541: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1542: bool=0;
1543: }
1.58 lievre 1544: if (bool==1){
1.53 brouard 1545: for(m=firstpass; m<=lastpass; m++){
1546: k2=anint[m][i]+(mint[m][i]/12.);
1547: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1.74 brouard 1548: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1549: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.73 lievre 1550: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1.53 brouard 1551: if (m<lastpass) {
1552: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1.74 brouard 1553: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1.53 brouard 1554: }
1555:
1.74 brouard 1556: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1.53 brouard 1557: dateintsum=dateintsum+k2;
1558: k2cpt++;
1559: }
1560: }
1561: }
1562: }
1563: }
1564:
1565: fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1566:
1567: if (cptcovn>0) {
1568: fprintf(ficresp, "\n#********** Variable ");
1569: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1570: fprintf(ficresp, "**********\n#");
1571: }
1572: for(i=1; i<=nlstate;i++)
1573: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1574: fprintf(ficresp, "\n");
1575:
1.74 brouard 1576: for(i=iagemin; i <= iagemax+3; i++){
1577: if(i==iagemax+3){
1.53 brouard 1578: fprintf(ficlog,"Total");
1579: }else{
1580: if(first==1){
1581: first=0;
1582: printf("See log file for details...\n");
1583: }
1584: fprintf(ficlog,"Age %d", i);
1585: }
1586: for(jk=1; jk <=nlstate ; jk++){
1587: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1588: pp[jk] += freq[jk][m][i];
1589: }
1590: for(jk=1; jk <=nlstate ; jk++){
1591: for(m=-1, pos=0; m <=0 ; m++)
1592: pos += freq[jk][m][i];
1593: if(pp[jk]>=1.e-10){
1594: if(first==1){
1595: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1596: }
1597: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1598: }else{
1599: if(first==1)
1600: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1601: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1602: }
1603: }
1604:
1605: for(jk=1; jk <=nlstate ; jk++){
1606: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1607: pp[jk] += freq[jk][m][i];
1.73 lievre 1608: }
1609: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
1610: pos += pp[jk];
1611: posprop += prop[jk][i];
1.53 brouard 1612: }
1613: for(jk=1; jk <=nlstate ; jk++){
1614: if(pos>=1.e-5){
1615: if(first==1)
1616: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1617: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1618: }else{
1619: if(first==1)
1620: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1621: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1622: }
1.74 brouard 1623: if( i <= iagemax){
1.53 brouard 1624: if(pos>=1.e-5){
1.73 lievre 1625: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.53 brouard 1626: probs[i][jk][j1]= pp[jk]/pos;
1627: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1628: }
1629: else
1.73 lievre 1630: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.53 brouard 1631: }
1632: }
1633:
1.69 brouard 1634: for(jk=-1; jk <=nlstate+ndeath; jk++)
1635: for(m=-1; m <=nlstate+ndeath; m++)
1.53 brouard 1636: if(freq[jk][m][i] !=0 ) {
1637: if(first==1)
1638: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1639: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1640: }
1.74 brouard 1641: if(i <= iagemax)
1.53 brouard 1642: fprintf(ficresp,"\n");
1643: if(first==1)
1644: printf("Others in log...\n");
1645: fprintf(ficlog,"\n");
1646: }
1647: }
1648: }
1649: dateintmean=dateintsum/k2cpt;
1650:
1651: fclose(ficresp);
1.74 brouard 1652: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
1.53 brouard 1653: free_vector(pp,1,nlstate);
1.74 brouard 1654: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1.53 brouard 1655: /* End of Freq */
1656: }
1657:
1658: /************ Prevalence ********************/
1.74 brouard 1659: 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)
1.69 brouard 1660: {
1661: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
1662: in each health status at the date of interview (if between dateprev1 and dateprev2).
1663: We still use firstpass and lastpass as another selection.
1664: */
1.53 brouard 1665:
1666: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1667: double ***freq; /* Frequencies */
1.73 lievre 1668: double *pp, **prop;
1669: double pos,posprop;
1.69 brouard 1670: double y2; /* in fractional years */
1.74 brouard 1671: int iagemin, iagemax;
1.53 brouard 1672:
1.74 brouard 1673: iagemin= (int) agemin;
1674: iagemax= (int) agemax;
1675: /*pp=vector(1,nlstate);*/
1676: prop=matrix(1,nlstate,iagemin,iagemax+3);
1677: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1.53 brouard 1678: j1=0;
1679:
1680: j=cptcoveff;
1681: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1682:
1683: for(k1=1; k1<=j;k1++){
1684: for(i1=1; i1<=ncodemax[k1];i1++){
1685: j1++;
1686:
1.73 lievre 1687: for (i=1; i<=nlstate; i++)
1.74 brouard 1688: for(m=iagemin; m <= iagemax+3; m++)
1689: prop[i][m]=0.0;
1.53 brouard 1690:
1.69 brouard 1691: for (i=1; i<=imx; i++) { /* Each individual */
1.53 brouard 1692: bool=1;
1693: if (cptcovn>0) {
1694: for (z1=1; z1<=cptcoveff; z1++)
1695: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1696: bool=0;
1697: }
1698: if (bool==1) {
1.69 brouard 1699: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
1700: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
1701: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1.74 brouard 1702: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1703: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1704: 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);
1705: if (s[m][i]>0 && s[m][i]<=nlstate) {
1706: /*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]]);*/
1707: prop[s[m][i]][(int)agev[m][i]] += weight[i];
1708: prop[s[m][i]][iagemax+3] += weight[i];
1709: }
1.53 brouard 1710: }
1.69 brouard 1711: } /* end selection of waves */
1.53 brouard 1712: }
1713: }
1.74 brouard 1714: for(i=iagemin; i <= iagemax+3; i++){
1.53 brouard 1715:
1.74 brouard 1716: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
1717: posprop += prop[jk][i];
1718: }
1719:
1720: for(jk=1; jk <=nlstate ; jk++){
1721: if( i <= iagemax){
1722: if(posprop>=1.e-5){
1723: probs[i][jk][j1]= prop[jk][i]/posprop;
1724: }
1725: }
1726: }/* end jk */
1727: }/* end i */
1.53 brouard 1728: } /* end i1 */
1729: } /* end k1 */
1730:
1.74 brouard 1731: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
1732: /*free_vector(pp,1,nlstate);*/
1733: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
1734: } /* End of prevalence */
1.53 brouard 1735:
1736: /************* Waves Concatenation ***************/
1737:
1.59 brouard 1738: 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)
1.53 brouard 1739: {
1740: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1741: Death is a valid wave (if date is known).
1742: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1.59 brouard 1743: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53 brouard 1744: and mw[mi+1][i]. dh depends on stepm.
1745: */
1746:
1747: int i, mi, m;
1748: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1749: double sum=0., jmean=0.;*/
1750: int first;
1751: int j, k=0,jk, ju, jl;
1752: double sum=0.;
1753: first=0;
1754: jmin=1e+5;
1755: jmax=-1;
1756: jmean=0.;
1757: for(i=1; i<=imx; i++){
1758: mi=0;
1759: m=firstpass;
1760: while(s[m][i] <= nlstate){
1.69 brouard 1761: if(s[m][i]>=1)
1.53 brouard 1762: mw[++mi][i]=m;
1763: if(m >=lastpass)
1764: break;
1765: else
1766: m++;
1767: }/* end while */
1768: if (s[m][i] > nlstate){
1769: mi++; /* Death is another wave */
1770: /* if(mi==0) never been interviewed correctly before death */
1771: /* Only death is a correct wave */
1772: mw[mi][i]=m;
1773: }
1774:
1775: wav[i]=mi;
1776: if(mi==0){
1777: if(first==0){
1778: printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
1779: first=1;
1780: }
1781: if(first==1){
1782: fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
1783: }
1784: } /* end mi==0 */
1785: }
1786:
1787: for(i=1; i<=imx; i++){
1788: for(mi=1; mi<wav[i];mi++){
1789: if (stepm <=0)
1790: dh[mi][i]=1;
1791: else{
1792: if (s[mw[mi+1][i]][i] > nlstate) {
1793: if (agedc[i] < 2*AGESUP) {
1794: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1795: if(j==0) j=1; /* Survives at least one month after exam */
1796: k=k+1;
1797: if (j >= jmax) jmax=j;
1798: if (j <= jmin) jmin=j;
1799: sum=sum+j;
1800: /*if (j<0) printf("j=%d num=%d \n",j,i); */
1.68 lievre 1801: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.71 brouard 1802: /*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]);*/
1.53 brouard 1803: }
1804: }
1805: else{
1806: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.68 lievre 1807: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 1808: k=k+1;
1809: if (j >= jmax) jmax=j;
1810: else if (j <= jmin)jmin=j;
1811: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.73 lievre 1812: /*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]);*/
1.53 brouard 1813: sum=sum+j;
1814: }
1815: jk= j/stepm;
1816: jl= j -jk*stepm;
1817: ju= j -(jk+1)*stepm;
1.64 lievre 1818: if(mle <=1){
1819: if(jl==0){
1820: dh[mi][i]=jk;
1821: bh[mi][i]=0;
1822: }else{ /* We want a negative bias in order to only have interpolation ie
1823: * at the price of an extra matrix product in likelihood */
1824: dh[mi][i]=jk+1;
1825: bh[mi][i]=ju;
1826: }
1827: }else{
1828: if(jl <= -ju){
1829: dh[mi][i]=jk;
1830: bh[mi][i]=jl; /* bias is positive if real duration
1831: * is higher than the multiple of stepm and negative otherwise.
1832: */
1833: }
1834: else{
1835: dh[mi][i]=jk+1;
1836: bh[mi][i]=ju;
1837: }
1838: if(dh[mi][i]==0){
1839: dh[mi][i]=1; /* At least one step */
1840: bh[mi][i]=ju; /* At least one step */
1.71 brouard 1841: /* 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);*/
1.64 lievre 1842: }
1.59 brouard 1843: }
1.64 lievre 1844: } /* end if mle */
1845: } /* end wave */
1.53 brouard 1846: }
1847: jmean=sum/k;
1848: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1849: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1850: }
1851:
1852: /*********** Tricode ****************************/
1853: void tricode(int *Tvar, int **nbcode, int imx)
1854: {
1.58 lievre 1855:
1856: int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53 brouard 1857: int cptcode=0;
1858: cptcoveff=0;
1859:
1.58 lievre 1860: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53 brouard 1861: for (k=1; k<=7; k++) ncodemax[k]=0;
1862:
1863: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58 lievre 1864: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
1865: modality*/
1866: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
1867: Ndum[ij]++; /*store the modality */
1.53 brouard 1868: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58 lievre 1869: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
1870: Tvar[j]. If V=sex and male is 0 and
1871: female is 1, then cptcode=1.*/
1.53 brouard 1872: }
1873:
1874: for (i=0; i<=cptcode; i++) {
1.58 lievre 1875: 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 */
1.53 brouard 1876: }
1.58 lievre 1877:
1.53 brouard 1878: ij=1;
1879: for (i=1; i<=ncodemax[j]; i++) {
1.58 lievre 1880: for (k=0; k<= maxncov; k++) {
1.53 brouard 1881: if (Ndum[k] != 0) {
1882: nbcode[Tvar[j]][ij]=k;
1.58 lievre 1883: /* 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; */
1.53 brouard 1884:
1885: ij++;
1886: }
1887: if (ij > ncodemax[j]) break;
1888: }
1889: }
1890: }
1891:
1.58 lievre 1892: for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53 brouard 1893:
1.58 lievre 1894: for (i=1; i<=ncovmodel-2; i++) {
1895: /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
1.53 brouard 1896: ij=Tvar[i];
1.58 lievre 1897: Ndum[ij]++;
1.53 brouard 1898: }
1899:
1900: ij=1;
1.58 lievre 1901: for (i=1; i<= maxncov; i++) {
1.53 brouard 1902: if((Ndum[i]!=0) && (i<=ncovcol)){
1.58 lievre 1903: Tvaraff[ij]=i; /*For printing */
1.53 brouard 1904: ij++;
1905: }
1906: }
1907:
1.58 lievre 1908: cptcoveff=ij-1; /*Number of simple covariates*/
1.53 brouard 1909: }
1910:
1911: /*********** Health Expectancies ****************/
1912:
1913: 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 )
1914:
1915: {
1916: /* Health expectancies */
1917: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
1918: double age, agelim, hf;
1919: double ***p3mat,***varhe;
1920: double **dnewm,**doldm;
1921: double *xp;
1922: double **gp, **gm;
1923: double ***gradg, ***trgradg;
1924: int theta;
1925:
1.74 brouard 1926: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1.53 brouard 1927: xp=vector(1,npar);
1.74 brouard 1928: dnewm=matrix(1,nlstate*nlstate,1,npar);
1929: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1.53 brouard 1930:
1931: fprintf(ficreseij,"# Health expectancies\n");
1932: fprintf(ficreseij,"# Age");
1933: for(i=1; i<=nlstate;i++)
1934: for(j=1; j<=nlstate;j++)
1935: fprintf(ficreseij," %1d-%1d (SE)",i,j);
1936: fprintf(ficreseij,"\n");
1937:
1938: if(estepm < stepm){
1939: printf ("Problem %d lower than %d\n",estepm, stepm);
1940: }
1941: else hstepm=estepm;
1942: /* We compute the life expectancy from trapezoids spaced every estepm months
1943: * This is mainly to measure the difference between two models: for example
1944: * if stepm=24 months pijx are given only every 2 years and by summing them
1945: * we are calculating an estimate of the Life Expectancy assuming a linear
1.66 brouard 1946: * progression in between and thus overestimating or underestimating according
1.53 brouard 1947: * to the curvature of the survival function. If, for the same date, we
1948: * estimate the model with stepm=1 month, we can keep estepm to 24 months
1949: * to compare the new estimate of Life expectancy with the same linear
1950: * hypothesis. A more precise result, taking into account a more precise
1951: * curvature will be obtained if estepm is as small as stepm. */
1952:
1953: /* For example we decided to compute the life expectancy with the smallest unit */
1954: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
1955: nhstepm is the number of hstepm from age to agelim
1956: nstepm is the number of stepm from age to agelin.
1957: Look at hpijx to understand the reason of that which relies in memory size
1958: and note for a fixed period like estepm months */
1959: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
1960: survival function given by stepm (the optimization length). Unfortunately it
1961: means that if the survival funtion is printed only each two years of age and if
1962: you sum them up and add 1 year (area under the trapezoids) you won't get the same
1963: results. So we changed our mind and took the option of the best precision.
1964: */
1965: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
1966:
1967: agelim=AGESUP;
1968: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1969: /* nhstepm age range expressed in number of stepm */
1970: nstepm=(int) rint((agelim-age)*YEARM/stepm);
1971: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
1972: /* if (stepm >= YEARM) hstepm=1;*/
1973: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
1974: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.74 brouard 1975: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
1976: gp=matrix(0,nhstepm,1,nlstate*nlstate);
1977: gm=matrix(0,nhstepm,1,nlstate*nlstate);
1.53 brouard 1978:
1979: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1980: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1981: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1982:
1983:
1984: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1985:
1986: /* Computing Variances of health expectancies */
1987:
1988: for(theta=1; theta <=npar; theta++){
1989: for(i=1; i<=npar; i++){
1990: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1991: }
1992: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1993:
1994: cptj=0;
1995: for(j=1; j<= nlstate; j++){
1996: for(i=1; i<=nlstate; i++){
1997: cptj=cptj+1;
1998: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
1999: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2000: }
2001: }
2002: }
2003:
2004:
2005: for(i=1; i<=npar; i++)
2006: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2007: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2008:
2009: cptj=0;
2010: for(j=1; j<= nlstate; j++){
2011: for(i=1;i<=nlstate;i++){
2012: cptj=cptj+1;
2013: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
2014: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2015: }
2016: }
2017: }
1.74 brouard 2018: for(j=1; j<= nlstate*nlstate; j++)
1.53 brouard 2019: for(h=0; h<=nhstepm-1; h++){
2020: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2021: }
2022: }
2023:
2024: /* End theta */
2025:
1.74 brouard 2026: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2027:
2028: for(h=0; h<=nhstepm-1; h++)
1.74 brouard 2029: for(j=1; j<=nlstate*nlstate;j++)
1.53 brouard 2030: for(theta=1; theta <=npar; theta++)
2031: trgradg[h][j][theta]=gradg[h][theta][j];
2032:
2033:
1.74 brouard 2034: for(i=1;i<=nlstate*nlstate;i++)
2035: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2036: varhe[i][j][(int)age] =0.;
2037:
2038: printf("%d|",(int)age);fflush(stdout);
2039: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2040: for(h=0;h<=nhstepm-1;h++){
2041: for(k=0;k<=nhstepm-1;k++){
1.74 brouard 2042: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2043: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2044: for(i=1;i<=nlstate*nlstate;i++)
2045: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2046: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2047: }
2048: }
2049: /* Computing expectancies */
2050: for(i=1; i<=nlstate;i++)
2051: for(j=1; j<=nlstate;j++)
2052: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2053: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2054:
2055: /* 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]);*/
2056:
2057: }
2058:
2059: fprintf(ficreseij,"%3.0f",age );
2060: cptj=0;
2061: for(i=1; i<=nlstate;i++)
2062: for(j=1; j<=nlstate;j++){
2063: cptj++;
2064: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2065: }
2066: fprintf(ficreseij,"\n");
2067:
1.74 brouard 2068: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2069: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2070: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2071: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2072: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2073: }
2074: printf("\n");
2075: fprintf(ficlog,"\n");
2076:
2077: free_vector(xp,1,npar);
1.74 brouard 2078: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2079: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2080: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
1.53 brouard 2081: }
2082:
2083: /************ Variance ******************/
2084: 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)
2085: {
2086: /* Variance of health expectancies */
2087: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2088: /* double **newm;*/
2089: double **dnewm,**doldm;
2090: double **dnewmp,**doldmp;
2091: int i, j, nhstepm, hstepm, h, nstepm ;
2092: int k, cptcode;
2093: double *xp;
2094: double **gp, **gm; /* for var eij */
2095: double ***gradg, ***trgradg; /*for var eij */
2096: double **gradgp, **trgradgp; /* for var p point j */
2097: double *gpp, *gmp; /* for var p point j */
2098: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2099: double ***p3mat;
2100: double age,agelim, hf;
2101: double ***mobaverage;
2102: int theta;
2103: char digit[4];
1.55 lievre 2104: char digitp[25];
1.53 brouard 2105:
2106: char fileresprobmorprev[FILENAMELENGTH];
2107:
1.55 lievre 2108: if(popbased==1){
1.58 lievre 2109: if(mobilav!=0)
1.55 lievre 2110: strcpy(digitp,"-populbased-mobilav-");
2111: else strcpy(digitp,"-populbased-nomobil-");
2112: }
2113: else
1.53 brouard 2114: strcpy(digitp,"-stablbased-");
1.56 lievre 2115:
1.54 brouard 2116: if (mobilav!=0) {
1.53 brouard 2117: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2118: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2119: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2120: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2121: }
1.53 brouard 2122: }
2123:
2124: strcpy(fileresprobmorprev,"prmorprev");
2125: sprintf(digit,"%-d",ij);
2126: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2127: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2128: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2129: strcat(fileresprobmorprev,fileres);
2130: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2131: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2132: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2133: }
2134: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2135: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.66 brouard 2136: 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);
1.53 brouard 2137: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2138: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2139: fprintf(ficresprobmorprev," p.%-d SE",j);
2140: for(i=1; i<=nlstate;i++)
2141: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2142: }
2143: fprintf(ficresprobmorprev,"\n");
2144: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2145: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2146: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2147: exit(0);
2148: }
2149: else{
2150: fprintf(ficgp,"\n# Routine varevsij");
2151: }
2152: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2153: printf("Problem with html file: %s\n", optionfilehtm);
2154: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2155: exit(0);
2156: }
2157: else{
1.67 brouard 2158: 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");
2159: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
1.53 brouard 2160: }
2161: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2162:
2163: 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");
2164: fprintf(ficresvij,"# Age");
2165: for(i=1; i<=nlstate;i++)
2166: for(j=1; j<=nlstate;j++)
2167: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2168: fprintf(ficresvij,"\n");
2169:
2170: xp=vector(1,npar);
2171: dnewm=matrix(1,nlstate,1,npar);
2172: doldm=matrix(1,nlstate,1,nlstate);
2173: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2174: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2175:
2176: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2177: gpp=vector(nlstate+1,nlstate+ndeath);
2178: gmp=vector(nlstate+1,nlstate+ndeath);
2179: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2180:
2181: if(estepm < stepm){
2182: printf ("Problem %d lower than %d\n",estepm, stepm);
2183: }
2184: else hstepm=estepm;
2185: /* For example we decided to compute the life expectancy with the smallest unit */
2186: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2187: nhstepm is the number of hstepm from age to agelim
2188: nstepm is the number of stepm from age to agelin.
2189: Look at hpijx to understand the reason of that which relies in memory size
2190: and note for a fixed period like k years */
2191: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2192: survival function given by stepm (the optimization length). Unfortunately it
1.66 brouard 2193: means that if the survival funtion is printed every two years of age and if
1.53 brouard 2194: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2195: results. So we changed our mind and took the option of the best precision.
2196: */
2197: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2198: agelim = AGESUP;
2199: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2200: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2201: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2202: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2203: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2204: gp=matrix(0,nhstepm,1,nlstate);
2205: gm=matrix(0,nhstepm,1,nlstate);
2206:
2207:
2208: for(theta=1; theta <=npar; theta++){
1.66 brouard 2209: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
1.53 brouard 2210: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2211: }
2212: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2213: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2214:
2215: if (popbased==1) {
1.54 brouard 2216: if(mobilav ==0){
1.53 brouard 2217: for(i=1; i<=nlstate;i++)
2218: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2219: }else{ /* mobilav */
1.53 brouard 2220: for(i=1; i<=nlstate;i++)
2221: prlim[i][i]=mobaverage[(int)age][i][ij];
2222: }
2223: }
2224:
2225: for(j=1; j<= nlstate; j++){
2226: for(h=0; h<=nhstepm; h++){
2227: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2228: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2229: }
2230: }
1.66 brouard 2231: /* This for computing probability of death (h=1 means
2232: computed over hstepm matrices product = hstepm*stepm months)
2233: as a weighted average of prlim.
2234: */
1.69 brouard 2235: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2236: for(i=1,gpp[j]=0.; i<= nlstate; i++)
1.53 brouard 2237: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2238: }
1.66 brouard 2239: /* end probability of death */
1.53 brouard 2240:
1.66 brouard 2241: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
1.53 brouard 2242: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2243: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2244: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2245:
2246: if (popbased==1) {
1.54 brouard 2247: if(mobilav ==0){
1.53 brouard 2248: for(i=1; i<=nlstate;i++)
2249: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2250: }else{ /* mobilav */
1.53 brouard 2251: for(i=1; i<=nlstate;i++)
2252: prlim[i][i]=mobaverage[(int)age][i][ij];
2253: }
2254: }
2255:
2256: for(j=1; j<= nlstate; j++){
2257: for(h=0; h<=nhstepm; h++){
2258: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2259: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2260: }
2261: }
1.66 brouard 2262: /* This for computing probability of death (h=1 means
2263: computed over hstepm matrices product = hstepm*stepm months)
2264: as a weighted average of prlim.
2265: */
1.69 brouard 2266: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2267: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2268: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.53 brouard 2269: }
1.66 brouard 2270: /* end probability of death */
1.53 brouard 2271:
2272: for(j=1; j<= nlstate; j++) /* vareij */
2273: for(h=0; h<=nhstepm; h++){
2274: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2275: }
1.68 lievre 2276:
1.53 brouard 2277: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2278: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2279: }
2280:
2281: } /* End theta */
2282:
2283: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2284:
2285: for(h=0; h<=nhstepm; h++) /* veij */
2286: for(j=1; j<=nlstate;j++)
2287: for(theta=1; theta <=npar; theta++)
2288: trgradg[h][j][theta]=gradg[h][theta][j];
2289:
2290: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1.69 brouard 2291: for(theta=1; theta <=npar; theta++)
1.53 brouard 2292: trgradgp[j][theta]=gradgp[theta][j];
1.69 brouard 2293:
1.53 brouard 2294:
2295: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2296: for(i=1;i<=nlstate;i++)
2297: for(j=1;j<=nlstate;j++)
2298: vareij[i][j][(int)age] =0.;
2299:
2300: for(h=0;h<=nhstepm;h++){
2301: for(k=0;k<=nhstepm;k++){
2302: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2303: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2304: for(i=1;i<=nlstate;i++)
2305: for(j=1;j<=nlstate;j++)
2306: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2307: }
2308: }
1.70 brouard 2309:
1.53 brouard 2310: /* pptj */
2311: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2312: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
1.70 brouard 2313: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2314: for(i=nlstate+1;i<=nlstate+ndeath;i++)
1.53 brouard 2315: varppt[j][i]=doldmp[j][i];
2316: /* end ppptj */
1.66 brouard 2317: /* x centered again */
1.53 brouard 2318: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2319: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2320:
2321: if (popbased==1) {
1.54 brouard 2322: if(mobilav ==0){
1.53 brouard 2323: for(i=1; i<=nlstate;i++)
2324: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2325: }else{ /* mobilav */
1.53 brouard 2326: for(i=1; i<=nlstate;i++)
2327: prlim[i][i]=mobaverage[(int)age][i][ij];
2328: }
2329: }
1.70 brouard 2330:
1.66 brouard 2331: /* This for computing probability of death (h=1 means
2332: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2333: as a weighted average of prlim.
2334: */
1.68 lievre 2335: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2336: for(i=1,gmp[j]=0.;i<= nlstate; i++)
1.53 brouard 2337: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2338: }
1.66 brouard 2339: /* end probability of death */
1.53 brouard 2340:
2341: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2342: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2343: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2344: for(i=1; i<=nlstate;i++){
2345: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2346: }
2347: }
2348: fprintf(ficresprobmorprev,"\n");
2349:
2350: fprintf(ficresvij,"%.0f ",age );
2351: for(i=1; i<=nlstate;i++)
2352: for(j=1; j<=nlstate;j++){
2353: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2354: }
2355: fprintf(ficresvij,"\n");
2356: free_matrix(gp,0,nhstepm,1,nlstate);
2357: free_matrix(gm,0,nhstepm,1,nlstate);
2358: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2359: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2360: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2361: } /* End age */
2362: free_vector(gpp,nlstate+1,nlstate+ndeath);
2363: free_vector(gmp,nlstate+1,nlstate+ndeath);
2364: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2365: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2366: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2367: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2368: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.67 brouard 2369: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2370: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2371: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
2372: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",fileresprobmorprev);
2373: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
2374: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
1.53 brouard 2375: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
1.71 brouard 2376: 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);
1.53 brouard 2377: /* 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);
2378: */
1.71 brouard 2379: fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
1.53 brouard 2380:
2381: free_vector(xp,1,npar);
2382: free_matrix(doldm,1,nlstate,1,nlstate);
2383: free_matrix(dnewm,1,nlstate,1,npar);
2384: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2385: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2386: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55 lievre 2387: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 2388: fclose(ficresprobmorprev);
2389: fclose(ficgp);
2390: fclose(fichtm);
1.70 brouard 2391: }
1.53 brouard 2392:
2393: /************ Variance of prevlim ******************/
2394: 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)
2395: {
2396: /* Variance of prevalence limit */
1.59 brouard 2397: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53 brouard 2398: double **newm;
2399: double **dnewm,**doldm;
2400: int i, j, nhstepm, hstepm;
2401: int k, cptcode;
2402: double *xp;
2403: double *gp, *gm;
2404: double **gradg, **trgradg;
2405: double age,agelim;
2406: int theta;
2407:
1.54 brouard 2408: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
1.53 brouard 2409: fprintf(ficresvpl,"# Age");
2410: for(i=1; i<=nlstate;i++)
2411: fprintf(ficresvpl," %1d-%1d",i,i);
2412: fprintf(ficresvpl,"\n");
2413:
2414: xp=vector(1,npar);
2415: dnewm=matrix(1,nlstate,1,npar);
2416: doldm=matrix(1,nlstate,1,nlstate);
2417:
2418: hstepm=1*YEARM; /* Every year of age */
2419: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2420: agelim = AGESUP;
2421: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2422: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2423: if (stepm >= YEARM) hstepm=1;
2424: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2425: gradg=matrix(1,npar,1,nlstate);
2426: gp=vector(1,nlstate);
2427: gm=vector(1,nlstate);
2428:
2429: for(theta=1; theta <=npar; theta++){
2430: for(i=1; i<=npar; i++){ /* Computes gradient */
2431: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2432: }
2433: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2434: for(i=1;i<=nlstate;i++)
2435: gp[i] = prlim[i][i];
2436:
2437: for(i=1; i<=npar; i++) /* Computes gradient */
2438: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2439: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2440: for(i=1;i<=nlstate;i++)
2441: gm[i] = prlim[i][i];
2442:
2443: for(i=1;i<=nlstate;i++)
2444: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2445: } /* End theta */
2446:
2447: trgradg =matrix(1,nlstate,1,npar);
2448:
2449: for(j=1; j<=nlstate;j++)
2450: for(theta=1; theta <=npar; theta++)
2451: trgradg[j][theta]=gradg[theta][j];
2452:
2453: for(i=1;i<=nlstate;i++)
2454: varpl[i][(int)age] =0.;
2455: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2456: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2457: for(i=1;i<=nlstate;i++)
2458: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2459:
2460: fprintf(ficresvpl,"%.0f ",age );
2461: for(i=1; i<=nlstate;i++)
2462: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2463: fprintf(ficresvpl,"\n");
2464: free_vector(gp,1,nlstate);
2465: free_vector(gm,1,nlstate);
2466: free_matrix(gradg,1,npar,1,nlstate);
2467: free_matrix(trgradg,1,nlstate,1,npar);
2468: } /* End age */
2469:
2470: free_vector(xp,1,npar);
2471: free_matrix(doldm,1,nlstate,1,npar);
2472: free_matrix(dnewm,1,nlstate,1,nlstate);
2473:
2474: }
2475:
2476: /************ Variance of one-step probabilities ******************/
2477: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2478: {
2479: int i, j=0, i1, k1, l1, t, tj;
2480: int k2, l2, j1, z1;
2481: int k=0,l, cptcode;
2482: int first=1, first1;
2483: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2484: double **dnewm,**doldm;
2485: double *xp;
2486: double *gp, *gm;
2487: double **gradg, **trgradg;
2488: double **mu;
2489: double age,agelim, cov[NCOVMAX];
2490: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2491: int theta;
2492: char fileresprob[FILENAMELENGTH];
2493: char fileresprobcov[FILENAMELENGTH];
2494: char fileresprobcor[FILENAMELENGTH];
2495:
2496: double ***varpij;
2497:
2498: strcpy(fileresprob,"prob");
2499: strcat(fileresprob,fileres);
2500: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2501: printf("Problem with resultfile: %s\n", fileresprob);
2502: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2503: }
2504: strcpy(fileresprobcov,"probcov");
2505: strcat(fileresprobcov,fileres);
2506: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2507: printf("Problem with resultfile: %s\n", fileresprobcov);
2508: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2509: }
2510: strcpy(fileresprobcor,"probcor");
2511: strcat(fileresprobcor,fileres);
2512: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2513: printf("Problem with resultfile: %s\n", fileresprobcor);
2514: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2515: }
2516: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2517: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2518: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2519: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2520: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2521: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2522:
2523: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2524: fprintf(ficresprob,"# Age");
2525: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2526: fprintf(ficresprobcov,"# Age");
2527: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2528: fprintf(ficresprobcov,"# Age");
2529:
2530:
2531: for(i=1; i<=nlstate;i++)
2532: for(j=1; j<=(nlstate+ndeath);j++){
2533: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2534: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2535: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2536: }
1.69 brouard 2537: /* fprintf(ficresprob,"\n");
1.53 brouard 2538: fprintf(ficresprobcov,"\n");
2539: fprintf(ficresprobcor,"\n");
1.69 brouard 2540: */
2541: xp=vector(1,npar);
1.53 brouard 2542: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2543: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2544: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2545: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2546: first=1;
2547: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2548: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2549: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2550: exit(0);
2551: }
2552: else{
2553: fprintf(ficgp,"\n# Routine varprob");
2554: }
2555: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2556: printf("Problem with html file: %s\n", optionfilehtm);
2557: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2558: exit(0);
2559: }
2560: else{
2561: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2562: fprintf(fichtm,"\n");
2563:
2564: fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
2565: 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");
2566: 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");
2567:
2568: }
2569:
2570: cov[1]=1;
2571: tj=cptcoveff;
2572: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2573: j1=0;
2574: for(t=1; t<=tj;t++){
2575: for(i1=1; i1<=ncodemax[t];i1++){
2576: j1++;
2577: if (cptcovn>0) {
2578: fprintf(ficresprob, "\n#********** Variable ");
2579: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2580: fprintf(ficresprob, "**********\n#\n");
1.53 brouard 2581: fprintf(ficresprobcov, "\n#********** Variable ");
2582: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2583: fprintf(ficresprobcov, "**********\n#\n");
1.53 brouard 2584:
2585: fprintf(ficgp, "\n#********** Variable ");
1.69 brouard 2586: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2587: fprintf(ficgp, "**********\n#\n");
1.53 brouard 2588:
2589:
2590: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2591: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2592: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2593:
2594: fprintf(ficresprobcor, "\n#********** Variable ");
2595: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2596: fprintf(ficresprobcor, "**********\n#");
1.53 brouard 2597: }
2598:
2599: for (age=bage; age<=fage; age ++){
2600: cov[2]=age;
2601: for (k=1; k<=cptcovn;k++) {
2602: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2603: }
2604: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2605: for (k=1; k<=cptcovprod;k++)
2606: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2607:
2608: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2609: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2610: gp=vector(1,(nlstate)*(nlstate+ndeath));
2611: gm=vector(1,(nlstate)*(nlstate+ndeath));
2612:
2613: for(theta=1; theta <=npar; theta++){
2614: for(i=1; i<=npar; i++)
1.74 brouard 2615: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.53 brouard 2616:
2617: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2618:
2619: k=0;
2620: for(i=1; i<= (nlstate); i++){
2621: for(j=1; j<=(nlstate+ndeath);j++){
2622: k=k+1;
2623: gp[k]=pmmij[i][j];
2624: }
2625: }
2626:
2627: for(i=1; i<=npar; i++)
1.74 brouard 2628: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.53 brouard 2629:
2630: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2631: k=0;
2632: for(i=1; i<=(nlstate); i++){
2633: for(j=1; j<=(nlstate+ndeath);j++){
2634: k=k+1;
2635: gm[k]=pmmij[i][j];
2636: }
2637: }
2638:
2639: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
1.74 brouard 2640: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
1.53 brouard 2641: }
2642:
2643: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2644: for(theta=1; theta <=npar; theta++)
2645: trgradg[j][theta]=gradg[theta][j];
2646:
2647: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2648: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59 brouard 2649: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2650: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2651: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2652: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2653:
1.53 brouard 2654: pmij(pmmij,cov,ncovmodel,x,nlstate);
2655:
2656: k=0;
2657: for(i=1; i<=(nlstate); i++){
2658: for(j=1; j<=(nlstate+ndeath);j++){
2659: k=k+1;
2660: mu[k][(int) age]=pmmij[i][j];
2661: }
2662: }
2663: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2664: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2665: varpij[i][j][(int)age] = doldm[i][j];
2666:
2667: /*printf("\n%d ",(int)age);
1.59 brouard 2668: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2669: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2670: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2671: }*/
1.53 brouard 2672:
2673: fprintf(ficresprob,"\n%d ",(int)age);
2674: fprintf(ficresprobcov,"\n%d ",(int)age);
2675: fprintf(ficresprobcor,"\n%d ",(int)age);
2676:
2677: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2678: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2679: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2680: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2681: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2682: }
2683: i=0;
2684: for (k=1; k<=(nlstate);k++){
2685: for (l=1; l<=(nlstate+ndeath);l++){
2686: i=i++;
2687: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2688: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2689: for (j=1; j<=i;j++){
2690: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2691: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
2692: }
2693: }
2694: }/* end of loop for state */
2695: } /* end of loop for age */
2696:
2697: /* Confidence intervalle of pij */
2698: /*
1.59 brouard 2699: fprintf(ficgp,"\nset noparametric;unset label");
2700: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
2701: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2702: 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);
2703: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
2704: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
2705: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53 brouard 2706: */
2707:
2708: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
2709: first1=1;
2710: for (k2=1; k2<=(nlstate);k2++){
2711: for (l2=1; l2<=(nlstate+ndeath);l2++){
2712: if(l2==k2) continue;
2713: j=(k2-1)*(nlstate+ndeath)+l2;
2714: for (k1=1; k1<=(nlstate);k1++){
2715: for (l1=1; l1<=(nlstate+ndeath);l1++){
2716: if(l1==k1) continue;
2717: i=(k1-1)*(nlstate+ndeath)+l1;
2718: if(i<=j) continue;
2719: for (age=bage; age<=fage; age ++){
2720: if ((int)age %5==0){
2721: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
2722: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
2723: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
2724: mu1=mu[i][(int) age]/stepm*YEARM ;
2725: mu2=mu[j][(int) age]/stepm*YEARM;
2726: c12=cv12/sqrt(v1*v2);
2727: /* Computing eigen value of matrix of covariance */
2728: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2729: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2730: /* Eigen vectors */
2731: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
2732: /*v21=sqrt(1.-v11*v11); *//* error */
2733: v21=(lc1-v1)/cv12*v11;
2734: v12=-v21;
2735: v22=v11;
2736: tnalp=v21/v11;
2737: if(first1==1){
2738: first1=0;
2739: 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);
2740: }
2741: 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);
2742: /*printf(fignu*/
2743: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
2744: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
2745: if(first==1){
2746: first=0;
2747: fprintf(ficgp,"\nset parametric;unset label");
2748: 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);
2749: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2750: 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);
2751: fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
2752: fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
2753: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
2754: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2755: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2756: 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",\
2757: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2758: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2759: }else{
2760: first=0;
2761: fprintf(fichtm," %d (%.3f),",(int) age, c12);
2762: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2763: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2764: 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",\
2765: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2766: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2767: }/* if first */
2768: } /* age mod 5 */
2769: } /* end loop age */
2770: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
2771: first=1;
2772: } /*l12 */
2773: } /* k12 */
2774: } /*l1 */
2775: }/* k1 */
2776: } /* loop covariates */
2777: }
1.59 brouard 2778: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
2779: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.53 brouard 2780: free_vector(xp,1,npar);
2781: fclose(ficresprob);
2782: fclose(ficresprobcov);
2783: fclose(ficresprobcor);
2784: fclose(ficgp);
2785: fclose(fichtm);
2786: }
2787:
2788:
2789: /******************* Printing html file ***********/
2790: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
2791: int lastpass, int stepm, int weightopt, char model[],\
2792: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
2793: int popforecast, int estepm ,\
2794: double jprev1, double mprev1,double anprev1, \
2795: double jprev2, double mprev2,double anprev2){
2796: int jj1, k1, i1, cpt;
2797: /*char optionfilehtm[FILENAMELENGTH];*/
2798: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2799: printf("Problem with %s \n",optionfilehtm), exit(0);
2800: fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
2801: }
2802:
2803: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
2804: - 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
2805: - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
2806: - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
2807: - Life expectancies by age and initial health status (estepm=%2d months):
2808: <a href=\"e%s\">e%s</a> <br>\n</li>", \
2809: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
2810:
2811: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
2812:
2813: m=cptcoveff;
2814: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2815:
2816: jj1=0;
2817: for(k1=1; k1<=m;k1++){
2818: for(i1=1; i1<=ncodemax[k1];i1++){
2819: jj1++;
2820: if (cptcovn > 0) {
2821: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2822: for (cpt=1; cpt<=cptcoveff;cpt++)
2823: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2824: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2825: }
2826: /* Pij */
1.76 ! brouard 2827: 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>
1.53 brouard 2828: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2829: /* Quasi-incidences */
2830: 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>
2831: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2832: /* Stable prevalence in each health state */
2833: for(cpt=1; cpt<nlstate;cpt++){
2834: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
2835: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2836: }
2837: for(cpt=1; cpt<=nlstate;cpt++) {
2838: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
2839: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2840: }
2841: fprintf(fichtm,"\n<br>- Total life expectancy by age and
2842: health expectancies in states (1) and (2): e%s%d.png<br>
2843: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2844: } /* end i1 */
2845: }/* End k1 */
2846: fprintf(fichtm,"</ul>");
2847:
2848:
2849: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
2850: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
2851: - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
2852: - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
2853: - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
2854: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
2855: - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
2856: - 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);
2857:
1.76 ! brouard 2858: /* if(popforecast==1) fprintf(fichtm,"\n */
! 2859: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
! 2860: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
! 2861: /* <br>",fileres,fileres,fileres,fileres); */
! 2862: /* else */
! 2863: /* 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); */
1.53 brouard 2864: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
2865:
2866: m=cptcoveff;
2867: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2868:
2869: jj1=0;
2870: for(k1=1; k1<=m;k1++){
2871: for(i1=1; i1<=ncodemax[k1];i1++){
2872: jj1++;
2873: if (cptcovn > 0) {
2874: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2875: for (cpt=1; cpt<=cptcoveff;cpt++)
2876: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2877: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2878: }
2879: for(cpt=1; cpt<=nlstate;cpt++) {
1.76 ! brouard 2880: fprintf(fichtm,"<br>- Observed and period prevalence (with confident
1.53 brouard 2881: interval) in state (%d): v%s%d%d.png <br>
2882: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2883: }
2884: } /* end i1 */
2885: }/* End k1 */
2886: fprintf(fichtm,"</ul>");
2887: fclose(fichtm);
2888: }
2889:
2890: /******************* Gnuplot file **************/
2891: void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
2892:
2893: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
2894: int ng;
2895: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2896: printf("Problem with file %s",optionfilegnuplot);
2897: fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
2898: }
2899:
1.54 brouard 2900: /*#ifdef windows */
1.53 brouard 2901: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54 brouard 2902: /*#endif */
1.53 brouard 2903: m=pow(2,cptcoveff);
2904:
2905: /* 1eme*/
2906: for (cpt=1; cpt<= nlstate ; cpt ++) {
2907: for (k1=1; k1<= m ; k1 ++) {
2908: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2909: 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);
2910:
2911: for (i=1; i<= nlstate ; i ++) {
2912: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2913: else fprintf(ficgp," \%%*lf (\%%*lf)");
2914: }
1.69 brouard 2915: 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);
1.53 brouard 2916: for (i=1; i<= nlstate ; i ++) {
2917: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2918: else fprintf(ficgp," \%%*lf (\%%*lf)");
2919: }
1.69 brouard 2920: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
1.53 brouard 2921: for (i=1; i<= nlstate ; i ++) {
2922: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2923: else fprintf(ficgp," \%%*lf (\%%*lf)");
2924: }
2925: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2926: }
2927: }
2928: /*2 eme*/
2929:
2930: for (k1=1; k1<= m ; k1 ++) {
2931: fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
2932: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
2933:
2934: for (i=1; i<= nlstate+1 ; i ++) {
2935: k=2*i;
2936: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2937: for (j=1; j<= nlstate+1 ; j ++) {
2938: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2939: else fprintf(ficgp," \%%*lf (\%%*lf)");
2940: }
2941: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2942: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2943: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2944: for (j=1; j<= nlstate+1 ; j ++) {
2945: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2946: else fprintf(ficgp," \%%*lf (\%%*lf)");
2947: }
2948: fprintf(ficgp,"\" t\"\" w l 0,");
2949: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
2950: for (j=1; j<= nlstate+1 ; j ++) {
2951: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2952: else fprintf(ficgp," \%%*lf (\%%*lf)");
2953: }
2954: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2955: else fprintf(ficgp,"\" t\"\" w l 0,");
2956: }
2957: }
2958:
2959: /*3eme*/
2960:
2961: for (k1=1; k1<= m ; k1 ++) {
2962: for (cpt=1; cpt<= nlstate ; cpt ++) {
2963: k=2+nlstate*(2*cpt-2);
2964: fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2965: fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
2966: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2967: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2968: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2969: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2970: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2971: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2972:
2973: */
2974: for (i=1; i< nlstate ; i ++) {
2975: 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);
2976:
2977: }
2978: }
2979: }
2980:
1.76 ! brouard 2981: /* CV preval stable (period) */
1.53 brouard 2982: for (k1=1; k1<= m ; k1 ++) {
1.76 ! brouard 2983: for (cpt=1; cpt<=nlstate ; cpt ++) {
1.53 brouard 2984: k=3;
2985: fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2986: 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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
2987:
1.76 ! brouard 2988: for (i=1; i<= nlstate ; i ++)
1.53 brouard 2989: fprintf(ficgp,"+$%d",k+i+1);
2990: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
2991:
2992: l=3+(nlstate+ndeath)*cpt;
2993: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
2994: for (i=1; i< nlstate ; i ++) {
2995: l=3+(nlstate+ndeath)*cpt;
2996: fprintf(ficgp,"+$%d",l+i+1);
2997: }
2998: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
2999: }
3000: }
3001:
3002: /* proba elementaires */
3003: for(i=1,jk=1; i <=nlstate; i++){
3004: for(k=1; k <=(nlstate+ndeath); k++){
3005: if (k != i) {
3006: for(j=1; j <=ncovmodel; j++){
3007: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3008: jk++;
3009: fprintf(ficgp,"\n");
3010: }
3011: }
3012: }
3013: }
3014:
3015: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3016: for(jk=1; jk <=m; jk++) {
3017: fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
3018: if (ng==2)
3019: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3020: else
3021: fprintf(ficgp,"\nset title \"Probability\"\n");
3022: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3023: i=1;
3024: for(k2=1; k2<=nlstate; k2++) {
3025: k3=i;
3026: for(k=1; k<=(nlstate+ndeath); k++) {
3027: if (k != k2){
3028: if(ng==2)
3029: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3030: else
3031: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3032: ij=1;
3033: for(j=3; j <=ncovmodel; j++) {
3034: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3035: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3036: ij++;
3037: }
3038: else
3039: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3040: }
3041: fprintf(ficgp,")/(1");
3042:
3043: for(k1=1; k1 <=nlstate; k1++){
3044: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3045: ij=1;
3046: for(j=3; j <=ncovmodel; j++){
3047: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3048: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3049: ij++;
3050: }
3051: else
3052: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3053: }
3054: fprintf(ficgp,")");
3055: }
3056: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3057: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3058: i=i+ncovmodel;
3059: }
3060: } /* end k */
3061: } /* end k2 */
3062: } /* end jk */
3063: } /* end ng */
3064: fclose(ficgp);
3065: } /* end gnuplot */
3066:
3067:
3068: /*************** Moving average **************/
1.54 brouard 3069: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53 brouard 3070:
3071: int i, cpt, cptcod;
1.58 lievre 3072: int modcovmax =1;
1.54 brouard 3073: int mobilavrange, mob;
1.53 brouard 3074: double age;
1.58 lievre 3075:
3076: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3077: a covariate has 2 modalities */
3078: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3079:
1.54 brouard 3080: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3081: if(mobilav==1) mobilavrange=5; /* default */
3082: else mobilavrange=mobilav;
3083: for (age=bage; age<=fage; age++)
3084: for (i=1; i<=nlstate;i++)
1.58 lievre 3085: for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54 brouard 3086: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3087: /* We keep the original values on the extreme ages bage, fage and for
3088: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3089: we use a 5 terms etc. until the borders are no more concerned.
3090: */
3091: for (mob=3;mob <=mobilavrange;mob=mob+2){
3092: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3093: for (i=1; i<=nlstate;i++){
1.58 lievre 3094: for (cptcod=1;cptcod<=modcovmax;cptcod++){
1.54 brouard 3095: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3096: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3097: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3098: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3099: }
3100: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3101: }
1.53 brouard 3102: }
1.54 brouard 3103: }/* end age */
3104: }/* end mob */
3105: }else return -1;
3106: return 0;
3107: }/* End movingaverage */
1.53 brouard 3108:
3109:
3110: /************** Forecasting ******************/
1.70 brouard 3111: 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){
1.69 brouard 3112: /* proj1, year, month, day of starting projection
3113: agemin, agemax range of age
3114: dateprev1 dateprev2 range of dates during which prevalence is computed
1.70 brouard 3115: anproj2 year of en of projection (same day and month as proj1).
1.69 brouard 3116: */
1.73 lievre 3117: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
1.53 brouard 3118: int *popage;
1.70 brouard 3119: double agec; /* generic age */
3120: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.53 brouard 3121: double *popeffectif,*popcount;
3122: double ***p3mat;
1.55 lievre 3123: double ***mobaverage;
1.53 brouard 3124: char fileresf[FILENAMELENGTH];
3125:
1.69 brouard 3126: agelim=AGESUP;
1.70 brouard 3127: prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3128:
3129: strcpy(fileresf,"f");
3130: strcat(fileresf,fileres);
3131: if((ficresf=fopen(fileresf,"w"))==NULL) {
3132: printf("Problem with forecast resultfile: %s\n", fileresf);
3133: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3134: }
3135: printf("Computing forecasting: result on file '%s' \n", fileresf);
3136: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3137:
3138: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3139:
1.54 brouard 3140: if (mobilav!=0) {
1.53 brouard 3141: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3142: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3143: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3144: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3145: }
1.53 brouard 3146: }
3147:
3148: stepsize=(int) (stepm+YEARM-1)/YEARM;
3149: if (stepm<=12) stepsize=1;
1.74 brouard 3150: if(estepm < stepm){
3151: printf ("Problem %d lower than %d\n",estepm, stepm);
3152: }
3153: else hstepm=estepm;
3154:
1.53 brouard 3155: hstepm=hstepm/stepm;
1.69 brouard 3156: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3157: fractional in yp1 */
1.53 brouard 3158: anprojmean=yp;
3159: yp2=modf((yp1*12),&yp);
3160: mprojmean=yp;
3161: yp1=modf((yp2*30.5),&yp);
3162: jprojmean=yp;
3163: if(jprojmean==0) jprojmean=1;
3164: if(mprojmean==0) jprojmean=1;
1.73 lievre 3165:
3166: i1=cptcoveff;
3167: if (cptcovn < 1){i1=1;}
1.53 brouard 3168:
1.70 brouard 3169: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.53 brouard 3170:
1.70 brouard 3171: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.73 lievre 3172:
1.75 brouard 3173: /* if (h==(int)(YEARM*yearp)){ */
1.73 lievre 3174: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
1.53 brouard 3175: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3176: k=k+1;
3177: fprintf(ficresf,"\n#******");
3178: for(j=1;j<=cptcoveff;j++) {
1.70 brouard 3179: 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]]);
1.53 brouard 3180: }
3181: fprintf(ficresf,"******\n");
1.70 brouard 3182: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3183: for(j=1; j<=nlstate+ndeath;j++){
3184: for(i=1; i<=nlstate;i++)
3185: fprintf(ficresf," p%d%d",i,j);
3186: fprintf(ficresf," p.%d",j);
3187: }
1.74 brouard 3188: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.53 brouard 3189: fprintf(ficresf,"\n");
1.70 brouard 3190: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.53 brouard 3191:
1.71 brouard 3192: for (agec=fage; agec>=(ageminpar-1); agec--){
1.70 brouard 3193: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
1.53 brouard 3194: nhstepm = nhstepm/hstepm;
3195: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3196: oldm=oldms;savm=savms;
1.70 brouard 3197: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
1.53 brouard 3198:
3199: for (h=0; h<=nhstepm; h++){
1.75 brouard 3200: if (h*hstepm/YEARM*stepm ==yearp) {
1.69 brouard 3201: fprintf(ficresf,"\n");
3202: for(j=1;j<=cptcoveff;j++)
3203: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.70 brouard 3204: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
1.53 brouard 3205: }
3206: for(j=1; j<=nlstate+ndeath;j++) {
1.70 brouard 3207: ppij=0.;
1.71 brouard 3208: for(i=1; i<=nlstate;i++) {
1.53 brouard 3209: if (mobilav==1)
1.71 brouard 3210: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
1.53 brouard 3211: else {
1.71 brouard 3212: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
1.53 brouard 3213: }
1.75 brouard 3214: if (h*hstepm/YEARM*stepm== yearp) {
1.70 brouard 3215: fprintf(ficresf," %.3f", p3mat[i][j][h]);
1.75 brouard 3216: }
3217: } /* end i */
3218: if (h*hstepm/YEARM*stepm==yearp) {
1.70 brouard 3219: fprintf(ficresf," %.3f", ppij);
1.53 brouard 3220: }
1.75 brouard 3221: }/* end j */
3222: } /* end h */
1.53 brouard 3223: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.75 brouard 3224: } /* end agec */
3225: } /* end yearp */
3226: } /* end cptcod */
3227: } /* end cptcov */
1.53 brouard 3228:
1.54 brouard 3229: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3230:
3231: fclose(ficresf);
3232: }
1.70 brouard 3233:
3234: /************** Forecasting *****not tested NB*************/
1.53 brouard 3235: 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){
3236:
3237: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3238: int *popage;
1.69 brouard 3239: double calagedatem, agelim, kk1, kk2;
1.53 brouard 3240: double *popeffectif,*popcount;
3241: double ***p3mat,***tabpop,***tabpopprev;
1.55 lievre 3242: double ***mobaverage;
1.53 brouard 3243: char filerespop[FILENAMELENGTH];
3244:
3245: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3246: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3247: agelim=AGESUP;
1.69 brouard 3248: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.53 brouard 3249:
1.70 brouard 3250: prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3251:
3252:
3253: strcpy(filerespop,"pop");
3254: strcat(filerespop,fileres);
3255: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3256: printf("Problem with forecast resultfile: %s\n", filerespop);
3257: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3258: }
3259: printf("Computing forecasting: result on file '%s' \n", filerespop);
3260: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3261:
3262: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3263:
1.54 brouard 3264: if (mobilav!=0) {
1.53 brouard 3265: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3266: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3267: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3268: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3269: }
1.53 brouard 3270: }
3271:
3272: stepsize=(int) (stepm+YEARM-1)/YEARM;
3273: if (stepm<=12) stepsize=1;
3274:
3275: agelim=AGESUP;
3276:
3277: hstepm=1;
3278: hstepm=hstepm/stepm;
3279:
3280: if (popforecast==1) {
3281: if((ficpop=fopen(popfile,"r"))==NULL) {
3282: printf("Problem with population file : %s\n",popfile);exit(0);
3283: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3284: }
3285: popage=ivector(0,AGESUP);
3286: popeffectif=vector(0,AGESUP);
3287: popcount=vector(0,AGESUP);
3288:
3289: i=1;
3290: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3291:
3292: imx=i;
3293: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3294: }
3295:
1.69 brouard 3296: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.53 brouard 3297: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3298: k=k+1;
3299: fprintf(ficrespop,"\n#******");
3300: for(j=1;j<=cptcoveff;j++) {
3301: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3302: }
3303: fprintf(ficrespop,"******\n");
3304: fprintf(ficrespop,"# Age");
3305: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3306: if (popforecast==1) fprintf(ficrespop," [Population]");
3307:
3308: for (cpt=0; cpt<=0;cpt++) {
3309: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3310:
1.69 brouard 3311: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3312: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3313: nhstepm = nhstepm/hstepm;
3314:
3315: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3316: oldm=oldms;savm=savms;
3317: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3318:
3319: for (h=0; h<=nhstepm; h++){
1.69 brouard 3320: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3321: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3322: }
3323: for(j=1; j<=nlstate+ndeath;j++) {
3324: kk1=0.;kk2=0;
3325: for(i=1; i<=nlstate;i++) {
3326: if (mobilav==1)
3327: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3328: else {
3329: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3330: }
3331: }
1.69 brouard 3332: if (h==(int)(calagedatem+12*cpt)){
1.53 brouard 3333: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3334: /*fprintf(ficrespop," %.3f", kk1);
3335: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3336: }
3337: }
3338: for(i=1; i<=nlstate;i++){
3339: kk1=0.;
3340: for(j=1; j<=nlstate;j++){
3341: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3342: }
1.69 brouard 3343: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.53 brouard 3344: }
3345:
1.69 brouard 3346: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
1.53 brouard 3347: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3348: }
3349: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3350: }
3351: }
3352:
3353: /******/
3354:
3355: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3356: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.69 brouard 3357: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3358: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3359: nhstepm = nhstepm/hstepm;
3360:
3361: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3362: oldm=oldms;savm=savms;
3363: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3364: for (h=0; h<=nhstepm; h++){
1.69 brouard 3365: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3366: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3367: }
3368: for(j=1; j<=nlstate+ndeath;j++) {
3369: kk1=0.;kk2=0;
3370: for(i=1; i<=nlstate;i++) {
3371: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3372: }
1.69 brouard 3373: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.53 brouard 3374: }
3375: }
3376: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3377: }
3378: }
3379: }
3380: }
3381:
1.54 brouard 3382: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3383:
3384: if (popforecast==1) {
3385: free_ivector(popage,0,AGESUP);
3386: free_vector(popeffectif,0,AGESUP);
3387: free_vector(popcount,0,AGESUP);
3388: }
3389: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3390: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3391: fclose(ficrespop);
3392: }
3393:
3394: /***********************************************/
3395: /**************** Main Program *****************/
3396: /***********************************************/
3397:
3398: int main(int argc, char *argv[])
3399: {
1.61 brouard 3400: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.74 brouard 3401: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
1.53 brouard 3402: double agedeb, agefin,hf;
3403: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3404:
3405: double fret;
3406: double **xi,tmp,delta;
3407:
3408: double dum; /* Dummy variable */
3409: double ***p3mat;
3410: double ***mobaverage;
3411: int *indx;
3412: char line[MAXLINE], linepar[MAXLINE];
3413: char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
3414: int firstobs=1, lastobs=10;
3415: int sdeb, sfin; /* Status at beginning and end */
3416: int c, h , cpt,l;
3417: int ju,jl, mi;
3418: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59 brouard 3419: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
1.69 brouard 3420: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.53 brouard 3421: int mobilav=0,popforecast=0;
3422: int hstepm, nhstepm;
1.74 brouard 3423: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
3424: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
1.53 brouard 3425:
3426: double bage, fage, age, agelim, agebase;
3427: double ftolpl=FTOL;
3428: double **prlim;
3429: double *severity;
3430: double ***param; /* Matrix of parameters */
3431: double *p;
3432: double **matcov; /* Matrix of covariance */
3433: double ***delti3; /* Scale */
3434: double *delti; /* Scale */
3435: double ***eij, ***vareij;
3436: double **varpl; /* Variances of prevalence limits by age */
3437: double *epj, vepp;
3438: double kk1, kk2;
1.74 brouard 3439: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.53 brouard 3440:
3441: char *alph[]={"a","a","b","c","d","e"}, str[4];
3442:
3443:
3444: char z[1]="c", occ;
3445: #include <sys/time.h>
3446: #include <time.h>
3447: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
3448:
3449: /* long total_usecs;
1.59 brouard 3450: struct timeval start_time, end_time;
1.53 brouard 3451:
1.59 brouard 3452: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.53 brouard 3453: getcwd(pathcd, size);
3454:
3455: printf("\n%s",version);
3456: if(argc <=1){
3457: printf("\nEnter the parameter file name: ");
3458: scanf("%s",pathtot);
3459: }
3460: else{
3461: strcpy(pathtot,argv[1]);
3462: }
3463: /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
3464: /*cygwin_split_path(pathtot,path,optionfile);
3465: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3466: /* cutv(path,optionfile,pathtot,'\\');*/
3467:
3468: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.59 brouard 3469: printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.53 brouard 3470: chdir(path);
3471: replace(pathc,path);
3472:
1.59 brouard 3473: /*-------- arguments in the command line --------*/
1.53 brouard 3474:
3475: /* Log file */
3476: strcat(filelog, optionfilefiname);
3477: strcat(filelog,".log"); /* */
3478: if((ficlog=fopen(filelog,"w"))==NULL) {
3479: printf("Problem with logfile %s\n",filelog);
3480: goto end;
3481: }
3482: fprintf(ficlog,"Log filename:%s\n",filelog);
3483: fprintf(ficlog,"\n%s",version);
3484: fprintf(ficlog,"\nEnter the parameter file name: ");
3485: fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3486: fflush(ficlog);
3487:
3488: /* */
3489: strcpy(fileres,"r");
3490: strcat(fileres, optionfilefiname);
3491: strcat(fileres,".txt"); /* Other files have txt extension */
3492:
3493: /*---------arguments file --------*/
3494:
3495: if((ficpar=fopen(optionfile,"r"))==NULL) {
3496: printf("Problem with optionfile %s\n",optionfile);
3497: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
3498: goto end;
3499: }
3500:
3501: strcpy(filereso,"o");
3502: strcat(filereso,fileres);
3503: if((ficparo=fopen(filereso,"w"))==NULL) {
3504: printf("Problem with Output resultfile: %s\n", filereso);
3505: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
3506: goto end;
3507: }
3508:
3509: /* Reads comments: lines beginning with '#' */
3510: while((c=getc(ficpar))=='#' && c!= EOF){
3511: ungetc(c,ficpar);
3512: fgets(line, MAXLINE, ficpar);
3513: puts(line);
3514: fputs(line,ficparo);
3515: }
3516: ungetc(c,ficpar);
3517:
3518: 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);
3519: 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);
3520: 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);
1.59 brouard 3521: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 3522: ungetc(c,ficpar);
3523: fgets(line, MAXLINE, ficpar);
3524: puts(line);
3525: fputs(line,ficparo);
3526: }
3527: ungetc(c,ficpar);
3528:
3529:
3530: covar=matrix(0,NCOVMAX,1,n);
1.58 lievre 3531: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53 brouard 3532: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
3533:
1.58 lievre 3534: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53 brouard 3535: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
3536:
3537: /* Read guess parameters */
3538: /* Reads comments: lines beginning with '#' */
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: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.59 brouard 3548: for(i=1; i <=nlstate; i++)
1.53 brouard 3549: for(j=1; j <=nlstate+ndeath-1; j++){
3550: fscanf(ficpar,"%1d%1d",&i1,&j1);
3551: fprintf(ficparo,"%1d%1d",i1,j1);
3552: if(mle==1)
3553: printf("%1d%1d",i,j);
3554: fprintf(ficlog,"%1d%1d",i,j);
3555: for(k=1; k<=ncovmodel;k++){
3556: fscanf(ficpar," %lf",¶m[i][j][k]);
3557: if(mle==1){
3558: printf(" %lf",param[i][j][k]);
3559: fprintf(ficlog," %lf",param[i][j][k]);
3560: }
3561: else
3562: fprintf(ficlog," %lf",param[i][j][k]);
3563: fprintf(ficparo," %lf",param[i][j][k]);
3564: }
3565: fscanf(ficpar,"\n");
3566: if(mle==1)
3567: printf("\n");
3568: fprintf(ficlog,"\n");
3569: fprintf(ficparo,"\n");
3570: }
3571:
1.59 brouard 3572: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
1.53 brouard 3573:
3574: p=param[1][1];
3575:
3576: /* Reads comments: lines beginning with '#' */
3577: while((c=getc(ficpar))=='#' && c!= EOF){
3578: ungetc(c,ficpar);
3579: fgets(line, MAXLINE, ficpar);
3580: puts(line);
3581: fputs(line,ficparo);
3582: }
3583: ungetc(c,ficpar);
3584:
3585: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.74 brouard 3586: /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
1.53 brouard 3587: for(i=1; i <=nlstate; i++){
3588: for(j=1; j <=nlstate+ndeath-1; j++){
3589: fscanf(ficpar,"%1d%1d",&i1,&j1);
3590: printf("%1d%1d",i,j);
3591: fprintf(ficparo,"%1d%1d",i1,j1);
3592: for(k=1; k<=ncovmodel;k++){
3593: fscanf(ficpar,"%le",&delti3[i][j][k]);
3594: printf(" %le",delti3[i][j][k]);
3595: fprintf(ficparo," %le",delti3[i][j][k]);
3596: }
3597: fscanf(ficpar,"\n");
3598: printf("\n");
3599: fprintf(ficparo,"\n");
3600: }
3601: }
3602: delti=delti3[1][1];
1.74 brouard 3603:
3604:
3605: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
1.53 brouard 3606:
3607: /* Reads comments: lines beginning with '#' */
3608: while((c=getc(ficpar))=='#' && c!= EOF){
3609: ungetc(c,ficpar);
3610: fgets(line, MAXLINE, ficpar);
3611: puts(line);
3612: fputs(line,ficparo);
3613: }
3614: ungetc(c,ficpar);
3615:
3616: matcov=matrix(1,npar,1,npar);
3617: for(i=1; i <=npar; i++){
3618: fscanf(ficpar,"%s",&str);
3619: if(mle==1)
3620: printf("%s",str);
3621: fprintf(ficlog,"%s",str);
3622: fprintf(ficparo,"%s",str);
3623: for(j=1; j <=i; j++){
3624: fscanf(ficpar," %le",&matcov[i][j]);
3625: if(mle==1){
3626: printf(" %.5le",matcov[i][j]);
3627: fprintf(ficlog," %.5le",matcov[i][j]);
3628: }
3629: else
3630: fprintf(ficlog," %.5le",matcov[i][j]);
3631: fprintf(ficparo," %.5le",matcov[i][j]);
3632: }
3633: fscanf(ficpar,"\n");
3634: if(mle==1)
3635: printf("\n");
3636: fprintf(ficlog,"\n");
3637: fprintf(ficparo,"\n");
3638: }
3639: for(i=1; i <=npar; i++)
3640: for(j=i+1;j<=npar;j++)
3641: matcov[i][j]=matcov[j][i];
3642:
3643: if(mle==1)
3644: printf("\n");
3645: fprintf(ficlog,"\n");
3646:
3647:
1.59 brouard 3648: /*-------- Rewriting paramater file ----------*/
3649: strcpy(rfileres,"r"); /* "Rparameterfile */
3650: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
3651: strcat(rfileres,"."); /* */
3652: strcat(rfileres,optionfilext); /* Other files have txt extension */
3653: if((ficres =fopen(rfileres,"w"))==NULL) {
3654: printf("Problem writing new parameter file: %s\n", fileres);goto end;
3655: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
3656: }
3657: fprintf(ficres,"#%s\n",version);
1.53 brouard 3658:
1.59 brouard 3659: /*-------- data file ----------*/
3660: if((fic=fopen(datafile,"r"))==NULL) {
3661: printf("Problem with datafile: %s\n", datafile);goto end;
3662: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
3663: }
3664:
3665: n= lastobs;
3666: severity = vector(1,maxwav);
3667: outcome=imatrix(1,maxwav+1,1,n);
3668: num=ivector(1,n);
3669: moisnais=vector(1,n);
3670: annais=vector(1,n);
3671: moisdc=vector(1,n);
3672: andc=vector(1,n);
3673: agedc=vector(1,n);
3674: cod=ivector(1,n);
3675: weight=vector(1,n);
3676: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
3677: mint=matrix(1,maxwav,1,n);
3678: anint=matrix(1,maxwav,1,n);
3679: s=imatrix(1,maxwav+1,1,n);
3680: tab=ivector(1,NCOVMAX);
3681: ncodemax=ivector(1,8);
3682:
3683: i=1;
3684: while (fgets(line, MAXLINE, fic) != NULL) {
3685: if ((i >= firstobs) && (i <=lastobs)) {
1.53 brouard 3686:
1.59 brouard 3687: for (j=maxwav;j>=1;j--){
3688: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
3689: strcpy(line,stra);
3690: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3691: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3692: }
1.53 brouard 3693:
1.59 brouard 3694: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
3695: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 3696:
1.59 brouard 3697: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
3698: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 3699:
1.59 brouard 3700: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
3701: for (j=ncovcol;j>=1;j--){
3702: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3703: }
3704: num[i]=atol(stra);
1.53 brouard 3705:
1.59 brouard 3706: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
3707: 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;}*/
1.53 brouard 3708:
1.59 brouard 3709: i=i+1;
3710: }
3711: }
3712: /* printf("ii=%d", ij);
3713: scanf("%d",i);*/
1.53 brouard 3714: imx=i-1; /* Number of individuals */
3715:
3716: /* for (i=1; i<=imx; i++){
3717: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
3718: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
3719: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
3720: }*/
3721: /* for (i=1; i<=imx; i++){
3722: if (s[4][i]==9) s[4][i]=-1;
3723: 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]));}*/
3724:
1.71 brouard 3725: for (i=1; i<=imx; i++)
1.53 brouard 3726:
1.71 brouard 3727: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
3728: else weight[i]=1;*/
3729:
1.53 brouard 3730: /* Calculation of the number of parameter from char model*/
3731: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
3732: Tprod=ivector(1,15);
3733: Tvaraff=ivector(1,15);
3734: Tvard=imatrix(1,15,1,2);
3735: Tage=ivector(1,15);
3736:
1.58 lievre 3737: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53 brouard 3738: j=0, j1=0, k1=1, k2=1;
1.58 lievre 3739: j=nbocc(model,'+'); /* j=Number of '+' */
3740: j1=nbocc(model,'*'); /* j1=Number of '*' */
3741: cptcovn=j+1;
3742: cptcovprod=j1; /*Number of products */
1.53 brouard 3743:
3744: strcpy(modelsav,model);
3745: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
3746: printf("Error. Non available option model=%s ",model);
3747: fprintf(ficlog,"Error. Non available option model=%s ",model);
3748: goto end;
3749: }
3750:
1.59 brouard 3751: /* This loop fills the array Tvar from the string 'model'.*/
1.58 lievre 3752:
1.53 brouard 3753: for(i=(j+1); i>=1;i--){
3754: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
1.59 brouard 3755: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53 brouard 3756: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
3757: /*scanf("%d",i);*/
3758: if (strchr(strb,'*')) { /* Model includes a product */
3759: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
3760: if (strcmp(strc,"age")==0) { /* Vn*age */
3761: cptcovprod--;
3762: cutv(strb,stre,strd,'V');
3763: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
3764: cptcovage++;
3765: Tage[cptcovage]=i;
3766: /*printf("stre=%s ", stre);*/
3767: }
3768: else if (strcmp(strd,"age")==0) { /* or age*Vn */
3769: cptcovprod--;
3770: cutv(strb,stre,strc,'V');
3771: Tvar[i]=atoi(stre);
3772: cptcovage++;
3773: Tage[cptcovage]=i;
3774: }
3775: else { /* Age is not in the model */
3776: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
3777: Tvar[i]=ncovcol+k1;
3778: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
3779: Tprod[k1]=i;
3780: Tvard[k1][1]=atoi(strc); /* m*/
3781: Tvard[k1][2]=atoi(stre); /* n */
3782: Tvar[cptcovn+k2]=Tvard[k1][1];
3783: Tvar[cptcovn+k2+1]=Tvard[k1][2];
3784: for (k=1; k<=lastobs;k++)
3785: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
3786: k1++;
3787: k2=k2+2;
3788: }
3789: }
3790: else { /* no more sum */
3791: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
3792: /* scanf("%d",i);*/
3793: cutv(strd,strc,strb,'V');
3794: Tvar[i]=atoi(strc);
3795: }
3796: strcpy(modelsav,stra);
3797: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
3798: scanf("%d",i);*/
3799: } /* end of loop + */
3800: } /* end model */
3801:
1.58 lievre 3802: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
3803: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
3804:
1.53 brouard 3805: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
3806: printf("cptcovprod=%d ", cptcovprod);
3807: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58 lievre 3808:
3809: scanf("%d ",i);
3810: fclose(fic);*/
1.53 brouard 3811:
3812: /* if(mle==1){*/
1.59 brouard 3813: if (weightopt != 1) { /* Maximisation without weights*/
3814: for(i=1;i<=n;i++) weight[i]=1.0;
3815: }
1.53 brouard 3816: /*-calculation of age at interview from date of interview and age at death -*/
1.59 brouard 3817: agev=matrix(1,maxwav,1,imx);
1.53 brouard 3818:
1.59 brouard 3819: for (i=1; i<=imx; i++) {
3820: for(m=2; (m<= maxwav); m++) {
1.76 ! brouard 3821: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
1.59 brouard 3822: anint[m][i]=9999;
3823: s[m][i]=-1;
3824: }
1.76 ! brouard 3825: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
! 3826: printf("Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown %d, set an arbitrary year of death\n",(int)moisdc[i],(int)andc[i],num[i],i);
! 3827: fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown %d, set an arbitrary year of death\n",(int)moisdc[i],(int)andc[i],num[i],i);
! 3828: s[m][i]=-1;
! 3829: }
! 3830: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
! 3831: printf("Warning! Month of death of individual %d on line %d was unknown %2d, we set it to June\n",num[i],i,(int)moisdc[i]);
! 3832: fprintf(ficlog,"Warning! Month of death of individual %d on line %d was unknown %f, we set it to June\n",num[i],i,moisdc[i]);
! 3833: moisdc[i]=6;
! 3834: s[m][i]=-1;
! 3835: }
1.53 brouard 3836: }
1.59 brouard 3837: }
1.53 brouard 3838:
1.59 brouard 3839: for (i=1; i<=imx; i++) {
3840: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1.71 brouard 3841: for(m=firstpass; (m<= lastpass); m++){
1.69 brouard 3842: if(s[m][i] >0){
1.59 brouard 3843: if (s[m][i] >= nlstate+1) {
3844: if(agedc[i]>0)
1.76 ! brouard 3845: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
1.69 brouard 3846: agev[m][i]=agedc[i];
1.59 brouard 3847: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
3848: else {
1.76 ! brouard 3849: if ((int)andc[i]!=9999){
1.59 brouard 3850: printf("Warning negative age at death: %d line:%d\n",num[i],i);
3851: fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
3852: agev[m][i]=-1;
1.53 brouard 3853: }
3854: }
1.70 brouard 3855: }
1.69 brouard 3856: else if(s[m][i] !=9){ /* Standard case, age in fractional
3857: years but with the precision of a
3858: month */
1.59 brouard 3859: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.76 ! brouard 3860: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
1.59 brouard 3861: agev[m][i]=1;
3862: else if(agev[m][i] <agemin){
3863: agemin=agev[m][i];
3864: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53 brouard 3865: }
1.59 brouard 3866: else if(agev[m][i] >agemax){
3867: agemax=agev[m][i];
3868: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53 brouard 3869: }
1.59 brouard 3870: /*agev[m][i]=anint[m][i]-annais[i];*/
3871: /* agev[m][i] = age[i]+2*m;*/
1.53 brouard 3872: }
1.59 brouard 3873: else { /* =9 */
1.53 brouard 3874: agev[m][i]=1;
1.59 brouard 3875: s[m][i]=-1;
3876: }
1.53 brouard 3877: }
1.59 brouard 3878: else /*= 0 Unknown */
3879: agev[m][i]=1;
3880: }
1.53 brouard 3881:
1.59 brouard 3882: }
3883: for (i=1; i<=imx; i++) {
1.71 brouard 3884: for(m=firstpass; (m<=lastpass); m++){
1.59 brouard 3885: if (s[m][i] > (nlstate+ndeath)) {
3886: 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);
3887: 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);
3888: goto end;
1.53 brouard 3889: }
3890: }
1.59 brouard 3891: }
1.53 brouard 3892:
1.71 brouard 3893: /*for (i=1; i<=imx; i++){
3894: for (m=firstpass; (m<lastpass); m++){
3895: printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
3896: }
3897:
3898: }*/
3899:
1.59 brouard 3900: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3901: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3902:
3903: free_vector(severity,1,maxwav);
3904: free_imatrix(outcome,1,maxwav+1,1,n);
3905: free_vector(moisnais,1,n);
3906: free_vector(annais,1,n);
3907: /* free_matrix(mint,1,maxwav,1,n);
3908: free_matrix(anint,1,maxwav,1,n);*/
3909: free_vector(moisdc,1,n);
3910: free_vector(andc,1,n);
1.53 brouard 3911:
3912:
1.59 brouard 3913: wav=ivector(1,imx);
3914: dh=imatrix(1,lastpass-firstpass+1,1,imx);
3915: bh=imatrix(1,lastpass-firstpass+1,1,imx);
3916: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.69 brouard 3917:
1.59 brouard 3918: /* Concatenates waves */
3919: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.53 brouard 3920:
1.59 brouard 3921: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53 brouard 3922:
1.59 brouard 3923: Tcode=ivector(1,100);
3924: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
3925: ncodemax[1]=1;
3926: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53 brouard 3927:
1.59 brouard 3928: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
3929: the estimations*/
3930: h=0;
3931: m=pow(2,cptcoveff);
1.53 brouard 3932:
1.59 brouard 3933: for(k=1;k<=cptcoveff; k++){
3934: for(i=1; i <=(m/pow(2,k));i++){
3935: for(j=1; j <= ncodemax[k]; j++){
3936: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
3937: h++;
3938: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
3939: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
3940: }
3941: }
3942: }
3943: }
3944: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
3945: codtab[1][2]=1;codtab[2][2]=2; */
3946: /* for(i=1; i <=m ;i++){
3947: for(k=1; k <=cptcovn; k++){
3948: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
3949: }
3950: printf("\n");
1.53 brouard 3951: }
1.59 brouard 3952: scanf("%d",i);*/
1.53 brouard 3953:
1.59 brouard 3954: /* Calculates basic frequencies. Computes observed prevalence at single age
3955: and prints on file fileres'p'. */
1.53 brouard 3956:
1.60 brouard 3957: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3958: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3959: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3960: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3961: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.53 brouard 3962:
3963:
1.59 brouard 3964: /* For Powell, parameters are in a vector p[] starting at p[1]
3965: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
3966: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53 brouard 3967:
1.61 brouard 3968: if(mle>=1){ /* Could be 1 or 2 */
1.53 brouard 3969: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59 brouard 3970: }
1.53 brouard 3971:
1.59 brouard 3972: /*--------- results files --------------*/
3973: 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);
1.53 brouard 3974:
3975:
1.59 brouard 3976: jk=1;
3977: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3978: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3979: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3980: for(i=1,jk=1; i <=nlstate; i++){
3981: for(k=1; k <=(nlstate+ndeath); k++){
3982: if (k != i)
3983: {
3984: printf("%d%d ",i,k);
3985: fprintf(ficlog,"%d%d ",i,k);
3986: fprintf(ficres,"%1d%1d ",i,k);
3987: for(j=1; j <=ncovmodel; j++){
3988: printf("%f ",p[jk]);
3989: fprintf(ficlog,"%f ",p[jk]);
3990: fprintf(ficres,"%f ",p[jk]);
3991: jk++;
3992: }
3993: printf("\n");
3994: fprintf(ficlog,"\n");
3995: fprintf(ficres,"\n");
3996: }
3997: }
3998: }
3999: if(mle==1){
4000: /* Computing hessian and covariance matrix */
4001: ftolhess=ftol; /* Usually correct */
4002: hesscov(matcov, p, npar, delti, ftolhess, func);
4003: }
4004: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
4005: printf("# Scales (for hessian or gradient estimation)\n");
4006: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
4007: for(i=1,jk=1; i <=nlstate; i++){
4008: for(j=1; j <=nlstate+ndeath; j++){
4009: if (j!=i) {
4010: fprintf(ficres,"%1d%1d",i,j);
4011: printf("%1d%1d",i,j);
4012: fprintf(ficlog,"%1d%1d",i,j);
4013: for(k=1; k<=ncovmodel;k++){
4014: printf(" %.5e",delti[jk]);
4015: fprintf(ficlog," %.5e",delti[jk]);
4016: fprintf(ficres," %.5e",delti[jk]);
4017: jk++;
4018: }
4019: printf("\n");
4020: fprintf(ficlog,"\n");
4021: fprintf(ficres,"\n");
4022: }
4023: }
4024: }
1.53 brouard 4025:
1.59 brouard 4026: 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");
4027: if(mle==1)
4028: 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");
4029: 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");
4030: for(i=1,k=1;i<=npar;i++){
4031: /* if (k>nlstate) k=1;
4032: i1=(i-1)/(ncovmodel*nlstate)+1;
4033: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
4034: printf("%s%d%d",alph[k],i1,tab[i]);
4035: */
4036: fprintf(ficres,"%3d",i);
4037: if(mle==1)
4038: printf("%3d",i);
4039: fprintf(ficlog,"%3d",i);
4040: for(j=1; j<=i;j++){
4041: fprintf(ficres," %.5e",matcov[i][j]);
4042: if(mle==1)
4043: printf(" %.5e",matcov[i][j]);
4044: fprintf(ficlog," %.5e",matcov[i][j]);
4045: }
4046: fprintf(ficres,"\n");
4047: if(mle==1)
4048: printf("\n");
4049: fprintf(ficlog,"\n");
4050: k++;
4051: }
1.53 brouard 4052:
1.59 brouard 4053: while((c=getc(ficpar))=='#' && c!= EOF){
4054: ungetc(c,ficpar);
4055: fgets(line, MAXLINE, ficpar);
4056: puts(line);
4057: fputs(line,ficparo);
4058: }
4059: ungetc(c,ficpar);
4060:
4061: estepm=0;
4062: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
4063: if (estepm==0 || estepm < stepm) estepm=stepm;
4064: if (fage <= 2) {
4065: bage = ageminpar;
4066: fage = agemaxpar;
4067: }
1.53 brouard 4068:
1.59 brouard 4069: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
4070: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
4071: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.53 brouard 4072:
1.59 brouard 4073: while((c=getc(ficpar))=='#' && c!= EOF){
4074: ungetc(c,ficpar);
4075: fgets(line, MAXLINE, ficpar);
4076: puts(line);
4077: fputs(line,ficparo);
4078: }
4079: ungetc(c,ficpar);
1.53 brouard 4080:
1.59 brouard 4081: 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);
4082: 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);
4083: 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);
1.69 brouard 4084: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
4085: 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);
1.53 brouard 4086:
1.59 brouard 4087: while((c=getc(ficpar))=='#' && c!= EOF){
4088: ungetc(c,ficpar);
4089: fgets(line, MAXLINE, ficpar);
4090: puts(line);
4091: fputs(line,ficparo);
4092: }
4093: ungetc(c,ficpar);
1.53 brouard 4094:
4095:
1.70 brouard 4096: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
4097: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
1.53 brouard 4098:
4099: fscanf(ficpar,"pop_based=%d\n",&popbased);
4100: fprintf(ficparo,"pop_based=%d\n",popbased);
4101: fprintf(ficres,"pop_based=%d\n",popbased);
4102:
4103: while((c=getc(ficpar))=='#' && c!= EOF){
4104: ungetc(c,ficpar);
4105: fgets(line, MAXLINE, ficpar);
4106: puts(line);
4107: fputs(line,ficparo);
4108: }
4109: ungetc(c,ficpar);
4110:
1.69 brouard 4111: 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);
1.70 brouard 4112: 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);
1.71 brouard 4113: 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);
4114: 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);
4115: 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);
1.69 brouard 4116: /* day and month of proj2 are not used but only year anproj2.*/
1.53 brouard 4117:
1.59 brouard 4118: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 4119: ungetc(c,ficpar);
4120: fgets(line, MAXLINE, ficpar);
4121: puts(line);
4122: fputs(line,ficparo);
4123: }
4124: ungetc(c,ficpar);
4125:
4126: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
4127: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4128: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4129:
1.74 brouard 4130: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.59 brouard 4131: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1.58 lievre 4132:
1.59 brouard 4133: /*------------ gnuplot -------------*/
4134: strcpy(optionfilegnuplot,optionfilefiname);
4135: strcat(optionfilegnuplot,".gp");
4136: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4137: printf("Problem with file %s",optionfilegnuplot);
4138: }
4139: else{
4140: fprintf(ficgp,"\n# %s\n", version);
4141: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4142: fprintf(ficgp,"set missing 'NaNq'\n");
4143: }
4144: fclose(ficgp);
4145: printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
4146: /*--------- index.htm --------*/
1.53 brouard 4147:
4148: strcpy(optionfilehtm,optionfile);
4149: strcat(optionfilehtm,".htm");
4150: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4151: printf("Problem with %s \n",optionfilehtm), exit(0);
4152: }
4153:
4154: fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
4155: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
4156: \n
4157: Total number of observations=%d <br>\n
1.76 ! brouard 4158: Youngest age at first pass %.2f, oldest age %.2f<br>\n
1.53 brouard 4159: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
4160: <hr size=\"2\" color=\"#EC5E5E\">
4161: <ul><li><h4>Parameter files</h4>\n
4162: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
4163: - Log file of the run: <a href=\"%s\">%s</a><br>\n
1.76 ! brouard 4164: - 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);
1.74 brouard 4165: fclose(fichtm);
1.53 brouard 4166:
1.59 brouard 4167: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
1.53 brouard 4168:
1.59 brouard 4169: /*------------ free_vector -------------*/
4170: chdir(path);
1.53 brouard 4171:
1.59 brouard 4172: free_ivector(wav,1,imx);
4173: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
4174: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
4175: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
4176: free_ivector(num,1,n);
4177: free_vector(agedc,1,n);
1.65 lievre 4178: /*free_matrix(covar,0,NCOVMAX,1,n);*/
1.59 brouard 4179: /*free_matrix(covar,1,NCOVMAX,1,n);*/
4180: fclose(ficparo);
4181: fclose(ficres);
1.53 brouard 4182:
4183:
1.54 brouard 4184: /*--------------- Prevalence limit (stable prevalence) --------------*/
1.53 brouard 4185:
4186: strcpy(filerespl,"pl");
4187: strcat(filerespl,fileres);
4188: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.54 brouard 4189: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4190: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
1.53 brouard 4191: }
1.54 brouard 4192: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
4193: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
4194: fprintf(ficrespl,"#Stable prevalence \n");
1.53 brouard 4195: fprintf(ficrespl,"#Age ");
4196: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
4197: fprintf(ficrespl,"\n");
4198:
4199: prlim=matrix(1,nlstate,1,nlstate);
1.59 brouard 4200:
1.53 brouard 4201: agebase=ageminpar;
4202: agelim=agemaxpar;
4203: ftolpl=1.e-10;
4204: i1=cptcoveff;
4205: if (cptcovn < 1){i1=1;}
4206:
1.59 brouard 4207: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4208: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.59 brouard 4209: k=k+1;
4210: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
4211: fprintf(ficrespl,"\n#******");
4212: printf("\n#******");
4213: fprintf(ficlog,"\n#******");
4214: for(j=1;j<=cptcoveff;j++) {
4215: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4216: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4217: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4218: }
4219: fprintf(ficrespl,"******\n");
4220: printf("******\n");
4221: fprintf(ficlog,"******\n");
1.53 brouard 4222:
1.59 brouard 4223: for (age=agebase; age<=agelim; age++){
4224: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
1.69 brouard 4225: fprintf(ficrespl,"%.0f ",age );
4226: for(j=1;j<=cptcoveff;j++)
4227: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.59 brouard 4228: for(i=1; i<=nlstate;i++)
1.53 brouard 4229: fprintf(ficrespl," %.5f", prlim[i][i]);
1.59 brouard 4230: fprintf(ficrespl,"\n");
1.53 brouard 4231: }
4232: }
1.59 brouard 4233: }
1.53 brouard 4234: fclose(ficrespl);
4235:
4236: /*------------- h Pij x at various ages ------------*/
4237:
4238: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
4239: if((ficrespij=fopen(filerespij,"w"))==NULL) {
4240: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
4241: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
4242: }
4243: printf("Computing pij: result on file '%s' \n", filerespij);
4244: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
4245:
4246: stepsize=(int) (stepm+YEARM-1)/YEARM;
4247: /*if (stepm<=24) stepsize=2;*/
4248:
4249: agelim=AGESUP;
4250: hstepm=stepsize*YEARM; /* Every year of age */
4251: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
4252:
4253: /* hstepm=1; aff par mois*/
4254:
1.70 brouard 4255: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.59 brouard 4256: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4257: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4258: k=k+1;
1.59 brouard 4259: fprintf(ficrespij,"\n#****** ");
4260: for(j=1;j<=cptcoveff;j++)
4261: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4262: fprintf(ficrespij,"******\n");
1.53 brouard 4263:
1.59 brouard 4264: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
4265: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4266: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4267:
4268: /* nhstepm=nhstepm*YEARM; aff par mois*/
4269:
4270: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4271: oldm=oldms;savm=savms;
4272: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.70 brouard 4273: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
1.59 brouard 4274: for(i=1; i<=nlstate;i++)
4275: for(j=1; j<=nlstate+ndeath;j++)
4276: fprintf(ficrespij," %1d-%1d",i,j);
4277: fprintf(ficrespij,"\n");
4278: for (h=0; h<=nhstepm; h++){
1.70 brouard 4279: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
1.53 brouard 4280: for(i=1; i<=nlstate;i++)
4281: for(j=1; j<=nlstate+ndeath;j++)
1.59 brouard 4282: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.53 brouard 4283: fprintf(ficrespij,"\n");
4284: }
1.59 brouard 4285: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4286: fprintf(ficrespij,"\n");
4287: }
1.53 brouard 4288: }
4289: }
4290:
1.74 brouard 4291: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
1.53 brouard 4292:
4293: fclose(ficrespij);
4294:
4295:
4296: /*---------- Forecasting ------------------*/
1.69 brouard 4297: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
4298: if(prevfcast==1){
1.74 brouard 4299: /* if(stepm ==1){*/
1.70 brouard 4300: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.74 brouard 4301: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
4302: /* } */
4303: /* else{ */
4304: /* erreur=108; */
4305: /* 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); */
4306: /* 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); */
4307: /* } */
1.69 brouard 4308: }
1.53 brouard 4309:
4310:
4311: /*---------- Health expectancies and variances ------------*/
4312:
4313: strcpy(filerest,"t");
4314: strcat(filerest,fileres);
4315: if((ficrest=fopen(filerest,"w"))==NULL) {
4316: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
4317: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
4318: }
4319: printf("Computing Total LEs with variances: file '%s' \n", filerest);
4320: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
4321:
4322:
4323: strcpy(filerese,"e");
4324: strcat(filerese,fileres);
4325: if((ficreseij=fopen(filerese,"w"))==NULL) {
4326: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4327: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4328: }
4329: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
4330: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.68 lievre 4331:
1.53 brouard 4332: strcpy(fileresv,"v");
4333: strcat(fileresv,fileres);
4334: if((ficresvij=fopen(fileresv,"w"))==NULL) {
4335: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
4336: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
4337: }
4338: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4339: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58 lievre 4340:
1.74 brouard 4341: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
4342: prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4343: /* 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",\
4344: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
4345: */
1.58 lievre 4346:
1.54 brouard 4347: if (mobilav!=0) {
1.53 brouard 4348: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 4349: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4350: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4351: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4352: }
1.53 brouard 4353: }
4354:
1.59 brouard 4355: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4356: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4357: k=k+1;
4358: fprintf(ficrest,"\n#****** ");
4359: for(j=1;j<=cptcoveff;j++)
4360: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4361: fprintf(ficrest,"******\n");
4362:
4363: fprintf(ficreseij,"\n#****** ");
4364: for(j=1;j<=cptcoveff;j++)
4365: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4366: fprintf(ficreseij,"******\n");
4367:
4368: fprintf(ficresvij,"\n#****** ");
4369: for(j=1;j<=cptcoveff;j++)
4370: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4371: fprintf(ficresvij,"******\n");
4372:
4373: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4374: oldm=oldms;savm=savms;
4375: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
4376:
4377: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4378: oldm=oldms;savm=savms;
4379: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
4380: if(popbased==1){
4381: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
1.59 brouard 4382: }
1.53 brouard 4383:
4384:
4385: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
4386: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
4387: fprintf(ficrest,"\n");
4388:
4389: epj=vector(1,nlstate+1);
4390: for(age=bage; age <=fage ;age++){
4391: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4392: if (popbased==1) {
1.54 brouard 4393: if(mobilav ==0){
1.53 brouard 4394: for(i=1; i<=nlstate;i++)
4395: prlim[i][i]=probs[(int)age][i][k];
1.54 brouard 4396: }else{ /* mobilav */
1.53 brouard 4397: for(i=1; i<=nlstate;i++)
4398: prlim[i][i]=mobaverage[(int)age][i][k];
4399: }
4400: }
4401:
4402: fprintf(ficrest," %4.0f",age);
4403: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
4404: for(i=1, epj[j]=0.;i <=nlstate;i++) {
4405: epj[j] += prlim[i][i]*eij[i][j][(int)age];
4406: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
4407: }
4408: epj[nlstate+1] +=epj[j];
4409: }
4410:
4411: for(i=1, vepp=0.;i <=nlstate;i++)
4412: for(j=1;j <=nlstate;j++)
4413: vepp += vareij[i][j][(int)age];
4414: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
4415: for(j=1;j <=nlstate;j++){
4416: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
4417: }
4418: fprintf(ficrest,"\n");
4419: }
1.59 brouard 4420: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4421: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4422: free_vector(epj,1,nlstate+1);
1.53 brouard 4423: }
4424: }
1.59 brouard 4425: free_vector(weight,1,n);
4426: free_imatrix(Tvard,1,15,1,2);
4427: free_imatrix(s,1,maxwav+1,1,n);
4428: free_matrix(anint,1,maxwav,1,n);
4429: free_matrix(mint,1,maxwav,1,n);
4430: free_ivector(cod,1,n);
4431: free_ivector(tab,1,NCOVMAX);
1.53 brouard 4432: fclose(ficreseij);
4433: fclose(ficresvij);
4434: fclose(ficrest);
4435: fclose(ficpar);
4436:
1.54 brouard 4437: /*------- Variance of stable prevalence------*/
1.53 brouard 4438:
4439: strcpy(fileresvpl,"vpl");
4440: strcat(fileresvpl,fileres);
4441: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.54 brouard 4442: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
1.53 brouard 4443: exit(0);
4444: }
1.54 brouard 4445: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
1.53 brouard 4446:
1.59 brouard 4447: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4448: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4449: k=k+1;
4450: fprintf(ficresvpl,"\n#****** ");
4451: for(j=1;j<=cptcoveff;j++)
4452: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4453: fprintf(ficresvpl,"******\n");
4454:
4455: varpl=matrix(1,nlstate,(int) bage, (int) fage);
4456: oldm=oldms;savm=savms;
1.59 brouard 4457: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
4458: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53 brouard 4459: }
1.59 brouard 4460: }
1.53 brouard 4461:
4462: fclose(ficresvpl);
4463:
4464: /*---------- End : free ----------------*/
4465: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
4466: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
4467: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
4468: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.65 lievre 4469:
4470: free_matrix(covar,0,NCOVMAX,1,n);
1.53 brouard 4471: free_matrix(matcov,1,npar,1,npar);
1.74 brouard 4472: /*free_vector(delti,1,npar);*/
4473: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.53 brouard 4474: free_matrix(agev,1,maxwav,1,imx);
4475: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.54 brouard 4476: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.74 brouard 4477: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
4478:
1.59 brouard 4479: free_ivector(ncodemax,1,8);
4480: free_ivector(Tvar,1,15);
4481: free_ivector(Tprod,1,15);
4482: free_ivector(Tvaraff,1,15);
4483: free_ivector(Tage,1,15);
4484: free_ivector(Tcode,1,100);
1.53 brouard 4485:
1.74 brouard 4486: /* fclose(fichtm);*/
4487: /* fclose(ficgp);*/ /* ALready done */
1.53 brouard 4488:
4489:
4490: if(erreur >0){
4491: printf("End of Imach with error or warning %d\n",erreur);
4492: fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
4493: }else{
4494: printf("End of Imach\n");
4495: fprintf(ficlog,"End of Imach\n");
4496: }
4497: printf("See log file on %s\n",filelog);
4498: fclose(ficlog);
4499: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
4500:
4501: /* 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);*/
4502: /*printf("Total time was %d uSec.\n", total_usecs);*/
4503: /*------ End -----------*/
4504:
1.59 brouard 4505: end:
1.53 brouard 4506: #ifdef windows
4507: /* chdir(pathcd);*/
4508: #endif
4509: /*system("wgnuplot graph.plt");*/
4510: /*system("../gp37mgw/wgnuplot graph.plt");*/
4511: /*system("cd ../gp37mgw");*/
4512: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
1.59 brouard 4513: strcpy(plotcmd,GNUPLOTPROGRAM);
4514: strcat(plotcmd," ");
4515: strcat(plotcmd,optionfilegnuplot);
1.75 brouard 4516: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
1.59 brouard 4517: system(plotcmd);
1.75 brouard 4518: printf(" Wait...");
1.53 brouard 4519:
1.54 brouard 4520: /*#ifdef windows*/
1.53 brouard 4521: while (z[0] != 'q') {
4522: /* chdir(path); */
4523: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
4524: scanf("%s",z);
4525: if (z[0] == 'c') system("./imach");
4526: else if (z[0] == 'e') system(optionfilehtm);
4527: else if (z[0] == 'g') system(plotcmd);
4528: else if (z[0] == 'q') exit(0);
4529: }
1.54 brouard 4530: /*#endif */
1.53 brouard 4531: }
4532:
4533:
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