Annotation of imach/src/imach.c, revision 1.53
1.53 ! brouard 1: /* $Id: imach.c,v 1.52 2002/07/19 18:49:30 brouard Exp $
! 2: Interpolated Markov Chain
! 3:
! 4: Short summary of the programme:
! 5:
! 6: This program computes Healthy Life Expectancies from
! 7: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
! 8: first survey ("cross") where individuals from different ages are
! 9: interviewed on their health status or degree of disability (in the
! 10: case of a health survey which is our main interest) -2- at least a
! 11: second wave of interviews ("longitudinal") which measure each change
! 12: (if any) in individual health status. Health expectancies are
! 13: computed from the time spent in each health state according to a
! 14: model. More health states you consider, more time is necessary to reach the
! 15: Maximum Likelihood of the parameters involved in the model. The
! 16: simplest model is the multinomial logistic model where pij is the
! 17: probability to be observed in state j at the second wave
! 18: conditional to be observed in state i at the first wave. Therefore
! 19: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
! 20: 'age' is age and 'sex' is a covariate. If you want to have a more
! 21: complex model than "constant and age", you should modify the program
! 22: where the markup *Covariates have to be included here again* invites
! 23: you to do it. More covariates you add, slower the
! 24: convergence.
! 25:
! 26: The advantage of this computer programme, compared to a simple
! 27: multinomial logistic model, is clear when the delay between waves is not
! 28: identical for each individual. Also, if a individual missed an
! 29: intermediate interview, the information is lost, but taken into
! 30: account using an interpolation or extrapolation.
! 31:
! 32: hPijx is the probability to be observed in state i at age x+h
! 33: conditional to the observed state i at age x. The delay 'h' can be
! 34: split into an exact number (nh*stepm) of unobserved intermediate
! 35: states. This elementary transition (by month or quarter trimester,
! 36: semester or year) is model as a multinomial logistic. The hPx
! 37: matrix is simply the matrix product of nh*stepm elementary matrices
! 38: and the contribution of each individual to the likelihood is simply
! 39: hPijx.
! 40:
! 41: Also this programme outputs the covariance matrix of the parameters but also
! 42: of the life expectancies. It also computes the prevalence limits.
! 43:
! 44: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
! 45: Institut national d'études démographiques, Paris.
! 46: This software have been partly granted by Euro-REVES, a concerted action
! 47: from the European Union.
! 48: It is copyrighted identically to a GNU software product, ie programme and
! 49: software can be distributed freely for non commercial use. Latest version
! 50: can be accessed at http://euroreves.ined.fr/imach .
! 51: **********************************************************************/
! 52:
! 53: #include <math.h>
! 54: #include <stdio.h>
! 55: #include <stdlib.h>
! 56: #include <unistd.h>
! 57:
! 58: #define MAXLINE 256
! 59: #define GNUPLOTPROGRAM "gnuplot"
! 60: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
! 61: #define FILENAMELENGTH 80
! 62: /*#define DEBUG*/
! 63: #define unix
! 64: #define GLOCK_ERROR_NOPATH -1 /* empty path */
! 65: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
! 66:
! 67: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
! 68: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
! 69:
! 70: #define NINTERVMAX 8
! 71: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
! 72: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
! 73: #define NCOVMAX 8 /* Maximum number of covariates */
! 74: #define MAXN 20000
! 75: #define YEARM 12. /* Number of months per year */
! 76: #define AGESUP 130
! 77: #define AGEBASE 40
! 78: #ifdef windows
! 79: #define DIRSEPARATOR '\\'
! 80: #define ODIRSEPARATOR '/'
! 81: #else
! 82: #define DIRSEPARATOR '/'
! 83: #define ODIRSEPARATOR '\\'
! 84: #endif
! 85:
! 86: char version[80]="Imach version 0.8j, July 2002, INED-EUROREVES ";
! 87: int erreur; /* Error number */
! 88: int nvar;
! 89: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
! 90: int npar=NPARMAX;
! 91: int nlstate=2; /* Number of live states */
! 92: int ndeath=1; /* Number of dead states */
! 93: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
! 94: int popbased=0;
! 95:
! 96: int *wav; /* Number of waves for this individuual 0 is possible */
! 97: int maxwav; /* Maxim number of waves */
! 98: int jmin, jmax; /* min, max spacing between 2 waves */
! 99: int mle, weightopt;
! 100: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
! 101: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
! 102: double jmean; /* Mean space between 2 waves */
! 103: double **oldm, **newm, **savm; /* Working pointers to matrices */
! 104: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
! 105: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
! 106: FILE *ficlog;
! 107: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
! 108: FILE *ficresprobmorprev;
! 109: FILE *fichtm; /* Html File */
! 110: FILE *ficreseij;
! 111: char filerese[FILENAMELENGTH];
! 112: FILE *ficresvij;
! 113: char fileresv[FILENAMELENGTH];
! 114: FILE *ficresvpl;
! 115: char fileresvpl[FILENAMELENGTH];
! 116: char title[MAXLINE];
! 117: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
! 118: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
! 119:
! 120: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
! 121: char filelog[FILENAMELENGTH]; /* Log file */
! 122: char filerest[FILENAMELENGTH];
! 123: char fileregp[FILENAMELENGTH];
! 124: char popfile[FILENAMELENGTH];
! 125:
! 126: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
! 127:
! 128: #define NR_END 1
! 129: #define FREE_ARG char*
! 130: #define FTOL 1.0e-10
! 131:
! 132: #define NRANSI
! 133: #define ITMAX 200
! 134:
! 135: #define TOL 2.0e-4
! 136:
! 137: #define CGOLD 0.3819660
! 138: #define ZEPS 1.0e-10
! 139: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
! 140:
! 141: #define GOLD 1.618034
! 142: #define GLIMIT 100.0
! 143: #define TINY 1.0e-20
! 144:
! 145: static double maxarg1,maxarg2;
! 146: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
! 147: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
! 148:
! 149: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
! 150: #define rint(a) floor(a+0.5)
! 151:
! 152: static double sqrarg;
! 153: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
! 154: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
! 155:
! 156: int imx;
! 157: int stepm;
! 158: /* Stepm, step in month: minimum step interpolation*/
! 159:
! 160: int estepm;
! 161: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
! 162:
! 163: int m,nb;
! 164: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
! 165: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
! 166: double **pmmij, ***probs, ***mobaverage;
! 167: double dateintmean=0;
! 168:
! 169: double *weight;
! 170: int **s; /* Status */
! 171: double *agedc, **covar, idx;
! 172: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
! 173:
! 174: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
! 175: double ftolhess; /* Tolerance for computing hessian */
! 176:
! 177: /**************** split *************************/
! 178: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
! 179: {
! 180: char *s; /* pointer */
! 181: int l1, l2; /* length counters */
! 182:
! 183: l1 = strlen( path ); /* length of path */
! 184: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
! 185: s= strrchr( path, DIRSEPARATOR ); /* find last / */
! 186: if ( s == NULL ) { /* no directory, so use current */
! 187: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
! 188: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
! 189: #if defined(__bsd__) /* get current working directory */
! 190: extern char *getwd( );
! 191:
! 192: if ( getwd( dirc ) == NULL ) {
! 193: #else
! 194: extern char *getcwd( );
! 195:
! 196: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
! 197: #endif
! 198: return( GLOCK_ERROR_GETCWD );
! 199: }
! 200: strcpy( name, path ); /* we've got it */
! 201: } else { /* strip direcotry from path */
! 202: s++; /* after this, the filename */
! 203: l2 = strlen( s ); /* length of filename */
! 204: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
! 205: strcpy( name, s ); /* save file name */
! 206: strncpy( dirc, path, l1 - l2 ); /* now the directory */
! 207: dirc[l1-l2] = 0; /* add zero */
! 208: }
! 209: l1 = strlen( dirc ); /* length of directory */
! 210: #ifdef windows
! 211: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
! 212: #else
! 213: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
! 214: #endif
! 215: s = strrchr( name, '.' ); /* find last / */
! 216: s++;
! 217: strcpy(ext,s); /* save extension */
! 218: l1= strlen( name);
! 219: l2= strlen( s)+1;
! 220: strncpy( finame, name, l1-l2);
! 221: finame[l1-l2]= 0;
! 222: return( 0 ); /* we're done */
! 223: }
! 224:
! 225:
! 226: /******************************************/
! 227:
! 228: void replace(char *s, char*t)
! 229: {
! 230: int i;
! 231: int lg=20;
! 232: i=0;
! 233: lg=strlen(t);
! 234: for(i=0; i<= lg; i++) {
! 235: (s[i] = t[i]);
! 236: if (t[i]== '\\') s[i]='/';
! 237: }
! 238: }
! 239:
! 240: int nbocc(char *s, char occ)
! 241: {
! 242: int i,j=0;
! 243: int lg=20;
! 244: i=0;
! 245: lg=strlen(s);
! 246: for(i=0; i<= lg; i++) {
! 247: if (s[i] == occ ) j++;
! 248: }
! 249: return j;
! 250: }
! 251:
! 252: void cutv(char *u,char *v, char*t, char occ)
! 253: {
! 254: /* cuts string t into u and v where u is ended by char occ excluding it
! 255: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
! 256: gives u="abcedf" and v="ghi2j" */
! 257: int i,lg,j,p=0;
! 258: i=0;
! 259: for(j=0; j<=strlen(t)-1; j++) {
! 260: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
! 261: }
! 262:
! 263: lg=strlen(t);
! 264: for(j=0; j<p; j++) {
! 265: (u[j] = t[j]);
! 266: }
! 267: u[p]='\0';
! 268:
! 269: for(j=0; j<= lg; j++) {
! 270: if (j>=(p+1))(v[j-p-1] = t[j]);
! 271: }
! 272: }
! 273:
! 274: /********************** nrerror ********************/
! 275:
! 276: void nrerror(char error_text[])
! 277: {
! 278: fprintf(stderr,"ERREUR ...\n");
! 279: fprintf(stderr,"%s\n",error_text);
! 280: exit(1);
! 281: }
! 282: /*********************** vector *******************/
! 283: double *vector(int nl, int nh)
! 284: {
! 285: double *v;
! 286: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
! 287: if (!v) nrerror("allocation failure in vector");
! 288: return v-nl+NR_END;
! 289: }
! 290:
! 291: /************************ free vector ******************/
! 292: void free_vector(double*v, int nl, int nh)
! 293: {
! 294: free((FREE_ARG)(v+nl-NR_END));
! 295: }
! 296:
! 297: /************************ivector *******************************/
! 298: int *ivector(long nl,long nh)
! 299: {
! 300: int *v;
! 301: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
! 302: if (!v) nrerror("allocation failure in ivector");
! 303: return v-nl+NR_END;
! 304: }
! 305:
! 306: /******************free ivector **************************/
! 307: void free_ivector(int *v, long nl, long nh)
! 308: {
! 309: free((FREE_ARG)(v+nl-NR_END));
! 310: }
! 311:
! 312: /******************* imatrix *******************************/
! 313: int **imatrix(long nrl, long nrh, long ncl, long nch)
! 314: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
! 315: {
! 316: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
! 317: int **m;
! 318:
! 319: /* allocate pointers to rows */
! 320: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
! 321: if (!m) nrerror("allocation failure 1 in matrix()");
! 322: m += NR_END;
! 323: m -= nrl;
! 324:
! 325:
! 326: /* allocate rows and set pointers to them */
! 327: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
! 328: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
! 329: m[nrl] += NR_END;
! 330: m[nrl] -= ncl;
! 331:
! 332: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
! 333:
! 334: /* return pointer to array of pointers to rows */
! 335: return m;
! 336: }
! 337:
! 338: /****************** free_imatrix *************************/
! 339: void free_imatrix(m,nrl,nrh,ncl,nch)
! 340: int **m;
! 341: long nch,ncl,nrh,nrl;
! 342: /* free an int matrix allocated by imatrix() */
! 343: {
! 344: free((FREE_ARG) (m[nrl]+ncl-NR_END));
! 345: free((FREE_ARG) (m+nrl-NR_END));
! 346: }
! 347:
! 348: /******************* matrix *******************************/
! 349: double **matrix(long nrl, long nrh, long ncl, long nch)
! 350: {
! 351: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
! 352: double **m;
! 353:
! 354: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
! 355: if (!m) nrerror("allocation failure 1 in matrix()");
! 356: m += NR_END;
! 357: m -= nrl;
! 358:
! 359: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
! 360: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
! 361: m[nrl] += NR_END;
! 362: m[nrl] -= ncl;
! 363:
! 364: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
! 365: return m;
! 366: }
! 367:
! 368: /*************************free matrix ************************/
! 369: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
! 370: {
! 371: free((FREE_ARG)(m[nrl]+ncl-NR_END));
! 372: free((FREE_ARG)(m+nrl-NR_END));
! 373: }
! 374:
! 375: /******************* ma3x *******************************/
! 376: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
! 377: {
! 378: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
! 379: double ***m;
! 380:
! 381: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
! 382: if (!m) nrerror("allocation failure 1 in matrix()");
! 383: m += NR_END;
! 384: m -= nrl;
! 385:
! 386: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
! 387: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
! 388: m[nrl] += NR_END;
! 389: m[nrl] -= ncl;
! 390:
! 391: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
! 392:
! 393: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
! 394: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
! 395: m[nrl][ncl] += NR_END;
! 396: m[nrl][ncl] -= nll;
! 397: for (j=ncl+1; j<=nch; j++)
! 398: m[nrl][j]=m[nrl][j-1]+nlay;
! 399:
! 400: for (i=nrl+1; i<=nrh; i++) {
! 401: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
! 402: for (j=ncl+1; j<=nch; j++)
! 403: m[i][j]=m[i][j-1]+nlay;
! 404: }
! 405: return m;
! 406: }
! 407:
! 408: /*************************free ma3x ************************/
! 409: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
! 410: {
! 411: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
! 412: free((FREE_ARG)(m[nrl]+ncl-NR_END));
! 413: free((FREE_ARG)(m+nrl-NR_END));
! 414: }
! 415:
! 416: /***************** f1dim *************************/
! 417: extern int ncom;
! 418: extern double *pcom,*xicom;
! 419: extern double (*nrfunc)(double []);
! 420:
! 421: double f1dim(double x)
! 422: {
! 423: int j;
! 424: double f;
! 425: double *xt;
! 426:
! 427: xt=vector(1,ncom);
! 428: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
! 429: f=(*nrfunc)(xt);
! 430: free_vector(xt,1,ncom);
! 431: return f;
! 432: }
! 433:
! 434: /*****************brent *************************/
! 435: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
! 436: {
! 437: int iter;
! 438: double a,b,d,etemp;
! 439: double fu,fv,fw,fx;
! 440: double ftemp;
! 441: double p,q,r,tol1,tol2,u,v,w,x,xm;
! 442: double e=0.0;
! 443:
! 444: a=(ax < cx ? ax : cx);
! 445: b=(ax > cx ? ax : cx);
! 446: x=w=v=bx;
! 447: fw=fv=fx=(*f)(x);
! 448: for (iter=1;iter<=ITMAX;iter++) {
! 449: xm=0.5*(a+b);
! 450: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
! 451: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
! 452: printf(".");fflush(stdout);
! 453: fprintf(ficlog,".");fflush(ficlog);
! 454: #ifdef DEBUG
! 455: 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);
! 456: 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);
! 457: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
! 458: #endif
! 459: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
! 460: *xmin=x;
! 461: return fx;
! 462: }
! 463: ftemp=fu;
! 464: if (fabs(e) > tol1) {
! 465: r=(x-w)*(fx-fv);
! 466: q=(x-v)*(fx-fw);
! 467: p=(x-v)*q-(x-w)*r;
! 468: q=2.0*(q-r);
! 469: if (q > 0.0) p = -p;
! 470: q=fabs(q);
! 471: etemp=e;
! 472: e=d;
! 473: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
! 474: d=CGOLD*(e=(x >= xm ? a-x : b-x));
! 475: else {
! 476: d=p/q;
! 477: u=x+d;
! 478: if (u-a < tol2 || b-u < tol2)
! 479: d=SIGN(tol1,xm-x);
! 480: }
! 481: } else {
! 482: d=CGOLD*(e=(x >= xm ? a-x : b-x));
! 483: }
! 484: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
! 485: fu=(*f)(u);
! 486: if (fu <= fx) {
! 487: if (u >= x) a=x; else b=x;
! 488: SHFT(v,w,x,u)
! 489: SHFT(fv,fw,fx,fu)
! 490: } else {
! 491: if (u < x) a=u; else b=u;
! 492: if (fu <= fw || w == x) {
! 493: v=w;
! 494: w=u;
! 495: fv=fw;
! 496: fw=fu;
! 497: } else if (fu <= fv || v == x || v == w) {
! 498: v=u;
! 499: fv=fu;
! 500: }
! 501: }
! 502: }
! 503: nrerror("Too many iterations in brent");
! 504: *xmin=x;
! 505: return fx;
! 506: }
! 507:
! 508: /****************** mnbrak ***********************/
! 509:
! 510: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
! 511: double (*func)(double))
! 512: {
! 513: double ulim,u,r,q, dum;
! 514: double fu;
! 515:
! 516: *fa=(*func)(*ax);
! 517: *fb=(*func)(*bx);
! 518: if (*fb > *fa) {
! 519: SHFT(dum,*ax,*bx,dum)
! 520: SHFT(dum,*fb,*fa,dum)
! 521: }
! 522: *cx=(*bx)+GOLD*(*bx-*ax);
! 523: *fc=(*func)(*cx);
! 524: while (*fb > *fc) {
! 525: r=(*bx-*ax)*(*fb-*fc);
! 526: q=(*bx-*cx)*(*fb-*fa);
! 527: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
! 528: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
! 529: ulim=(*bx)+GLIMIT*(*cx-*bx);
! 530: if ((*bx-u)*(u-*cx) > 0.0) {
! 531: fu=(*func)(u);
! 532: } else if ((*cx-u)*(u-ulim) > 0.0) {
! 533: fu=(*func)(u);
! 534: if (fu < *fc) {
! 535: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
! 536: SHFT(*fb,*fc,fu,(*func)(u))
! 537: }
! 538: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
! 539: u=ulim;
! 540: fu=(*func)(u);
! 541: } else {
! 542: u=(*cx)+GOLD*(*cx-*bx);
! 543: fu=(*func)(u);
! 544: }
! 545: SHFT(*ax,*bx,*cx,u)
! 546: SHFT(*fa,*fb,*fc,fu)
! 547: }
! 548: }
! 549:
! 550: /*************** linmin ************************/
! 551:
! 552: int ncom;
! 553: double *pcom,*xicom;
! 554: double (*nrfunc)(double []);
! 555:
! 556: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
! 557: {
! 558: double brent(double ax, double bx, double cx,
! 559: double (*f)(double), double tol, double *xmin);
! 560: double f1dim(double x);
! 561: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
! 562: double *fc, double (*func)(double));
! 563: int j;
! 564: double xx,xmin,bx,ax;
! 565: double fx,fb,fa;
! 566:
! 567: ncom=n;
! 568: pcom=vector(1,n);
! 569: xicom=vector(1,n);
! 570: nrfunc=func;
! 571: for (j=1;j<=n;j++) {
! 572: pcom[j]=p[j];
! 573: xicom[j]=xi[j];
! 574: }
! 575: ax=0.0;
! 576: xx=1.0;
! 577: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
! 578: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
! 579: #ifdef DEBUG
! 580: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
! 581: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
! 582: #endif
! 583: for (j=1;j<=n;j++) {
! 584: xi[j] *= xmin;
! 585: p[j] += xi[j];
! 586: }
! 587: free_vector(xicom,1,n);
! 588: free_vector(pcom,1,n);
! 589: }
! 590:
! 591: /*************** powell ************************/
! 592: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
! 593: double (*func)(double []))
! 594: {
! 595: void linmin(double p[], double xi[], int n, double *fret,
! 596: double (*func)(double []));
! 597: int i,ibig,j;
! 598: double del,t,*pt,*ptt,*xit;
! 599: double fp,fptt;
! 600: double *xits;
! 601: pt=vector(1,n);
! 602: ptt=vector(1,n);
! 603: xit=vector(1,n);
! 604: xits=vector(1,n);
! 605: *fret=(*func)(p);
! 606: for (j=1;j<=n;j++) pt[j]=p[j];
! 607: for (*iter=1;;++(*iter)) {
! 608: fp=(*fret);
! 609: ibig=0;
! 610: del=0.0;
! 611: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
! 612: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
! 613: for (i=1;i<=n;i++)
! 614: printf(" %d %.12f",i, p[i]);
! 615: fprintf(ficlog," %d %.12f",i, p[i]);
! 616: printf("\n");
! 617: fprintf(ficlog,"\n");
! 618: for (i=1;i<=n;i++) {
! 619: for (j=1;j<=n;j++) xit[j]=xi[j][i];
! 620: fptt=(*fret);
! 621: #ifdef DEBUG
! 622: printf("fret=%lf \n",*fret);
! 623: fprintf(ficlog,"fret=%lf \n",*fret);
! 624: #endif
! 625: printf("%d",i);fflush(stdout);
! 626: fprintf(ficlog,"%d",i);fflush(ficlog);
! 627: linmin(p,xit,n,fret,func);
! 628: if (fabs(fptt-(*fret)) > del) {
! 629: del=fabs(fptt-(*fret));
! 630: ibig=i;
! 631: }
! 632: #ifdef DEBUG
! 633: printf("%d %.12e",i,(*fret));
! 634: fprintf(ficlog,"%d %.12e",i,(*fret));
! 635: for (j=1;j<=n;j++) {
! 636: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
! 637: printf(" x(%d)=%.12e",j,xit[j]);
! 638: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
! 639: }
! 640: for(j=1;j<=n;j++) {
! 641: printf(" p=%.12e",p[j]);
! 642: fprintf(ficlog," p=%.12e",p[j]);
! 643: }
! 644: printf("\n");
! 645: fprintf(ficlog,"\n");
! 646: #endif
! 647: }
! 648: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
! 649: #ifdef DEBUG
! 650: int k[2],l;
! 651: k[0]=1;
! 652: k[1]=-1;
! 653: printf("Max: %.12e",(*func)(p));
! 654: fprintf(ficlog,"Max: %.12e",(*func)(p));
! 655: for (j=1;j<=n;j++) {
! 656: printf(" %.12e",p[j]);
! 657: fprintf(ficlog," %.12e",p[j]);
! 658: }
! 659: printf("\n");
! 660: fprintf(ficlog,"\n");
! 661: for(l=0;l<=1;l++) {
! 662: for (j=1;j<=n;j++) {
! 663: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
! 664: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
! 665: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
! 666: }
! 667: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
! 668: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
! 669: }
! 670: #endif
! 671:
! 672:
! 673: free_vector(xit,1,n);
! 674: free_vector(xits,1,n);
! 675: free_vector(ptt,1,n);
! 676: free_vector(pt,1,n);
! 677: return;
! 678: }
! 679: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
! 680: for (j=1;j<=n;j++) {
! 681: ptt[j]=2.0*p[j]-pt[j];
! 682: xit[j]=p[j]-pt[j];
! 683: pt[j]=p[j];
! 684: }
! 685: fptt=(*func)(ptt);
! 686: if (fptt < fp) {
! 687: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
! 688: if (t < 0.0) {
! 689: linmin(p,xit,n,fret,func);
! 690: for (j=1;j<=n;j++) {
! 691: xi[j][ibig]=xi[j][n];
! 692: xi[j][n]=xit[j];
! 693: }
! 694: #ifdef DEBUG
! 695: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
! 696: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
! 697: for(j=1;j<=n;j++){
! 698: printf(" %.12e",xit[j]);
! 699: fprintf(ficlog," %.12e",xit[j]);
! 700: }
! 701: printf("\n");
! 702: fprintf(ficlog,"\n");
! 703: #endif
! 704: }
! 705: }
! 706: }
! 707: }
! 708:
! 709: /**** Prevalence limit ****************/
! 710:
! 711: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
! 712: {
! 713: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
! 714: matrix by transitions matrix until convergence is reached */
! 715:
! 716: int i, ii,j,k;
! 717: double min, max, maxmin, maxmax,sumnew=0.;
! 718: double **matprod2();
! 719: double **out, cov[NCOVMAX], **pmij();
! 720: double **newm;
! 721: double agefin, delaymax=50 ; /* Max number of years to converge */
! 722:
! 723: for (ii=1;ii<=nlstate+ndeath;ii++)
! 724: for (j=1;j<=nlstate+ndeath;j++){
! 725: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 726: }
! 727:
! 728: cov[1]=1.;
! 729:
! 730: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
! 731: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
! 732: newm=savm;
! 733: /* Covariates have to be included here again */
! 734: cov[2]=agefin;
! 735:
! 736: for (k=1; k<=cptcovn;k++) {
! 737: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
! 738: /* 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]]);*/
! 739: }
! 740: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
! 741: for (k=1; k<=cptcovprod;k++)
! 742: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
! 743:
! 744: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
! 745: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
! 746: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
! 747: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
! 748:
! 749: savm=oldm;
! 750: oldm=newm;
! 751: maxmax=0.;
! 752: for(j=1;j<=nlstate;j++){
! 753: min=1.;
! 754: max=0.;
! 755: for(i=1; i<=nlstate; i++) {
! 756: sumnew=0;
! 757: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
! 758: prlim[i][j]= newm[i][j]/(1-sumnew);
! 759: max=FMAX(max,prlim[i][j]);
! 760: min=FMIN(min,prlim[i][j]);
! 761: }
! 762: maxmin=max-min;
! 763: maxmax=FMAX(maxmax,maxmin);
! 764: }
! 765: if(maxmax < ftolpl){
! 766: return prlim;
! 767: }
! 768: }
! 769: }
! 770:
! 771: /*************** transition probabilities ***************/
! 772:
! 773: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
! 774: {
! 775: double s1, s2;
! 776: /*double t34;*/
! 777: int i,j,j1, nc, ii, jj;
! 778:
! 779: for(i=1; i<= nlstate; i++){
! 780: for(j=1; j<i;j++){
! 781: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
! 782: /*s2 += param[i][j][nc]*cov[nc];*/
! 783: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
! 784: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
! 785: }
! 786: ps[i][j]=s2;
! 787: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
! 788: }
! 789: for(j=i+1; j<=nlstate+ndeath;j++){
! 790: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
! 791: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
! 792: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
! 793: }
! 794: ps[i][j]=s2;
! 795: }
! 796: }
! 797: /*ps[3][2]=1;*/
! 798:
! 799: for(i=1; i<= nlstate; i++){
! 800: s1=0;
! 801: for(j=1; j<i; j++)
! 802: s1+=exp(ps[i][j]);
! 803: for(j=i+1; j<=nlstate+ndeath; j++)
! 804: s1+=exp(ps[i][j]);
! 805: ps[i][i]=1./(s1+1.);
! 806: for(j=1; j<i; j++)
! 807: ps[i][j]= exp(ps[i][j])*ps[i][i];
! 808: for(j=i+1; j<=nlstate+ndeath; j++)
! 809: ps[i][j]= exp(ps[i][j])*ps[i][i];
! 810: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
! 811: } /* end i */
! 812:
! 813: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
! 814: for(jj=1; jj<= nlstate+ndeath; jj++){
! 815: ps[ii][jj]=0;
! 816: ps[ii][ii]=1;
! 817: }
! 818: }
! 819:
! 820:
! 821: /* for(ii=1; ii<= nlstate+ndeath; ii++){
! 822: for(jj=1; jj<= nlstate+ndeath; jj++){
! 823: printf("%lf ",ps[ii][jj]);
! 824: }
! 825: printf("\n ");
! 826: }
! 827: printf("\n ");printf("%lf ",cov[2]);*/
! 828: /*
! 829: for(i=1; i<= npar; i++) printf("%f ",x[i]);
! 830: goto end;*/
! 831: return ps;
! 832: }
! 833:
! 834: /**************** Product of 2 matrices ******************/
! 835:
! 836: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
! 837: {
! 838: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
! 839: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
! 840: /* in, b, out are matrice of pointers which should have been initialized
! 841: before: only the contents of out is modified. The function returns
! 842: a pointer to pointers identical to out */
! 843: long i, j, k;
! 844: for(i=nrl; i<= nrh; i++)
! 845: for(k=ncolol; k<=ncoloh; k++)
! 846: for(j=ncl,out[i][k]=0.; j<=nch; j++)
! 847: out[i][k] +=in[i][j]*b[j][k];
! 848:
! 849: return out;
! 850: }
! 851:
! 852:
! 853: /************* Higher Matrix Product ***************/
! 854:
! 855: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
! 856: {
! 857: /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month
! 858: duration (i.e. until
! 859: age (in years) age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.
! 860: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
! 861: (typically every 2 years instead of every month which is too big).
! 862: Model is determined by parameters x and covariates have to be
! 863: included manually here.
! 864:
! 865: */
! 866:
! 867: int i, j, d, h, k;
! 868: double **out, cov[NCOVMAX];
! 869: double **newm;
! 870:
! 871: /* Hstepm could be zero and should return the unit matrix */
! 872: for (i=1;i<=nlstate+ndeath;i++)
! 873: for (j=1;j<=nlstate+ndeath;j++){
! 874: oldm[i][j]=(i==j ? 1.0 : 0.0);
! 875: po[i][j][0]=(i==j ? 1.0 : 0.0);
! 876: }
! 877: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
! 878: for(h=1; h <=nhstepm; h++){
! 879: for(d=1; d <=hstepm; d++){
! 880: newm=savm;
! 881: /* Covariates have to be included here again */
! 882: cov[1]=1.;
! 883: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
! 884: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
! 885: for (k=1; k<=cptcovage;k++)
! 886: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
! 887: for (k=1; k<=cptcovprod;k++)
! 888: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
! 889:
! 890:
! 891: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
! 892: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
! 893: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
! 894: pmij(pmmij,cov,ncovmodel,x,nlstate));
! 895: savm=oldm;
! 896: oldm=newm;
! 897: }
! 898: for(i=1; i<=nlstate+ndeath; i++)
! 899: for(j=1;j<=nlstate+ndeath;j++) {
! 900: po[i][j][h]=newm[i][j];
! 901: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
! 902: */
! 903: }
! 904: } /* end h */
! 905: return po;
! 906: }
! 907:
! 908:
! 909: /*************** log-likelihood *************/
! 910: double func( double *x)
! 911: {
! 912: int i, ii, j, k, mi, d, kk;
! 913: double l, ll[NLSTATEMAX], cov[NCOVMAX];
! 914: double **out;
! 915: double sw; /* Sum of weights */
! 916: double lli; /* Individual log likelihood */
! 917: long ipmx;
! 918: /*extern weight */
! 919: /* We are differentiating ll according to initial status */
! 920: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
! 921: /*for(i=1;i<imx;i++)
! 922: printf(" %d\n",s[4][i]);
! 923: */
! 924: cov[1]=1.;
! 925:
! 926: for(k=1; k<=nlstate; k++) ll[k]=0.;
! 927: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
! 928: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
! 929: for(mi=1; mi<= wav[i]-1; mi++){
! 930: for (ii=1;ii<=nlstate+ndeath;ii++)
! 931: for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 932: for(d=0; d<dh[mi][i]; d++){
! 933: newm=savm;
! 934: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 935: for (kk=1; kk<=cptcovage;kk++) {
! 936: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
! 937: }
! 938:
! 939: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
! 940: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
! 941: savm=oldm;
! 942: oldm=newm;
! 943:
! 944:
! 945: } /* end mult */
! 946:
! 947: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
! 948: /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
! 949: ipmx +=1;
! 950: sw += weight[i];
! 951: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
! 952: } /* end of wave */
! 953: } /* end of individual */
! 954:
! 955: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
! 956: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
! 957: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
! 958: return -l;
! 959: }
! 960:
! 961:
! 962: /*********** Maximum Likelihood Estimation ***************/
! 963:
! 964: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
! 965: {
! 966: int i,j, iter;
! 967: double **xi,*delti;
! 968: double fret;
! 969: xi=matrix(1,npar,1,npar);
! 970: for (i=1;i<=npar;i++)
! 971: for (j=1;j<=npar;j++)
! 972: xi[i][j]=(i==j ? 1.0 : 0.0);
! 973: printf("Powell\n"); fprintf(ficlog,"Powell\n");
! 974: powell(p,xi,npar,ftol,&iter,&fret,func);
! 975:
! 976: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
! 977: fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
! 978: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
! 979:
! 980: }
! 981:
! 982: /**** Computes Hessian and covariance matrix ***/
! 983: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
! 984: {
! 985: double **a,**y,*x,pd;
! 986: double **hess;
! 987: int i, j,jk;
! 988: int *indx;
! 989:
! 990: double hessii(double p[], double delta, int theta, double delti[]);
! 991: double hessij(double p[], double delti[], int i, int j);
! 992: void lubksb(double **a, int npar, int *indx, double b[]) ;
! 993: void ludcmp(double **a, int npar, int *indx, double *d) ;
! 994:
! 995: hess=matrix(1,npar,1,npar);
! 996:
! 997: printf("\nCalculation of the hessian matrix. Wait...\n");
! 998: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
! 999: for (i=1;i<=npar;i++){
! 1000: printf("%d",i);fflush(stdout);
! 1001: fprintf(ficlog,"%d",i);fflush(ficlog);
! 1002: hess[i][i]=hessii(p,ftolhess,i,delti);
! 1003: /*printf(" %f ",p[i]);*/
! 1004: /*printf(" %lf ",hess[i][i]);*/
! 1005: }
! 1006:
! 1007: for (i=1;i<=npar;i++) {
! 1008: for (j=1;j<=npar;j++) {
! 1009: if (j>i) {
! 1010: printf(".%d%d",i,j);fflush(stdout);
! 1011: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
! 1012: hess[i][j]=hessij(p,delti,i,j);
! 1013: hess[j][i]=hess[i][j];
! 1014: /*printf(" %lf ",hess[i][j]);*/
! 1015: }
! 1016: }
! 1017: }
! 1018: printf("\n");
! 1019: fprintf(ficlog,"\n");
! 1020:
! 1021: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
! 1022: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
! 1023:
! 1024: a=matrix(1,npar,1,npar);
! 1025: y=matrix(1,npar,1,npar);
! 1026: x=vector(1,npar);
! 1027: indx=ivector(1,npar);
! 1028: for (i=1;i<=npar;i++)
! 1029: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
! 1030: ludcmp(a,npar,indx,&pd);
! 1031:
! 1032: for (j=1;j<=npar;j++) {
! 1033: for (i=1;i<=npar;i++) x[i]=0;
! 1034: x[j]=1;
! 1035: lubksb(a,npar,indx,x);
! 1036: for (i=1;i<=npar;i++){
! 1037: matcov[i][j]=x[i];
! 1038: }
! 1039: }
! 1040:
! 1041: printf("\n#Hessian matrix#\n");
! 1042: fprintf(ficlog,"\n#Hessian matrix#\n");
! 1043: for (i=1;i<=npar;i++) {
! 1044: for (j=1;j<=npar;j++) {
! 1045: printf("%.3e ",hess[i][j]);
! 1046: fprintf(ficlog,"%.3e ",hess[i][j]);
! 1047: }
! 1048: printf("\n");
! 1049: fprintf(ficlog,"\n");
! 1050: }
! 1051:
! 1052: /* Recompute Inverse */
! 1053: for (i=1;i<=npar;i++)
! 1054: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
! 1055: ludcmp(a,npar,indx,&pd);
! 1056:
! 1057: /* printf("\n#Hessian matrix recomputed#\n");
! 1058:
! 1059: for (j=1;j<=npar;j++) {
! 1060: for (i=1;i<=npar;i++) x[i]=0;
! 1061: x[j]=1;
! 1062: lubksb(a,npar,indx,x);
! 1063: for (i=1;i<=npar;i++){
! 1064: y[i][j]=x[i];
! 1065: printf("%.3e ",y[i][j]);
! 1066: fprintf(ficlog,"%.3e ",y[i][j]);
! 1067: }
! 1068: printf("\n");
! 1069: fprintf(ficlog,"\n");
! 1070: }
! 1071: */
! 1072:
! 1073: free_matrix(a,1,npar,1,npar);
! 1074: free_matrix(y,1,npar,1,npar);
! 1075: free_vector(x,1,npar);
! 1076: free_ivector(indx,1,npar);
! 1077: free_matrix(hess,1,npar,1,npar);
! 1078:
! 1079:
! 1080: }
! 1081:
! 1082: /*************** hessian matrix ****************/
! 1083: double hessii( double x[], double delta, int theta, double delti[])
! 1084: {
! 1085: int i;
! 1086: int l=1, lmax=20;
! 1087: double k1,k2;
! 1088: double p2[NPARMAX+1];
! 1089: double res;
! 1090: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
! 1091: double fx;
! 1092: int k=0,kmax=10;
! 1093: double l1;
! 1094:
! 1095: fx=func(x);
! 1096: for (i=1;i<=npar;i++) p2[i]=x[i];
! 1097: for(l=0 ; l <=lmax; l++){
! 1098: l1=pow(10,l);
! 1099: delts=delt;
! 1100: for(k=1 ; k <kmax; k=k+1){
! 1101: delt = delta*(l1*k);
! 1102: p2[theta]=x[theta] +delt;
! 1103: k1=func(p2)-fx;
! 1104: p2[theta]=x[theta]-delt;
! 1105: k2=func(p2)-fx;
! 1106: /*res= (k1-2.0*fx+k2)/delt/delt; */
! 1107: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
! 1108:
! 1109: #ifdef DEBUG
! 1110: 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);
! 1111: 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);
! 1112: #endif
! 1113: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
! 1114: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
! 1115: k=kmax;
! 1116: }
! 1117: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
! 1118: k=kmax; l=lmax*10.;
! 1119: }
! 1120: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
! 1121: delts=delt;
! 1122: }
! 1123: }
! 1124: }
! 1125: delti[theta]=delts;
! 1126: return res;
! 1127:
! 1128: }
! 1129:
! 1130: double hessij( double x[], double delti[], int thetai,int thetaj)
! 1131: {
! 1132: int i;
! 1133: int l=1, l1, lmax=20;
! 1134: double k1,k2,k3,k4,res,fx;
! 1135: double p2[NPARMAX+1];
! 1136: int k;
! 1137:
! 1138: fx=func(x);
! 1139: for (k=1; k<=2; k++) {
! 1140: for (i=1;i<=npar;i++) p2[i]=x[i];
! 1141: p2[thetai]=x[thetai]+delti[thetai]/k;
! 1142: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
! 1143: k1=func(p2)-fx;
! 1144:
! 1145: p2[thetai]=x[thetai]+delti[thetai]/k;
! 1146: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
! 1147: k2=func(p2)-fx;
! 1148:
! 1149: p2[thetai]=x[thetai]-delti[thetai]/k;
! 1150: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
! 1151: k3=func(p2)-fx;
! 1152:
! 1153: p2[thetai]=x[thetai]-delti[thetai]/k;
! 1154: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
! 1155: k4=func(p2)-fx;
! 1156: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
! 1157: #ifdef DEBUG
! 1158: 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);
! 1159: 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);
! 1160: #endif
! 1161: }
! 1162: return res;
! 1163: }
! 1164:
! 1165: /************** Inverse of matrix **************/
! 1166: void ludcmp(double **a, int n, int *indx, double *d)
! 1167: {
! 1168: int i,imax,j,k;
! 1169: double big,dum,sum,temp;
! 1170: double *vv;
! 1171:
! 1172: vv=vector(1,n);
! 1173: *d=1.0;
! 1174: for (i=1;i<=n;i++) {
! 1175: big=0.0;
! 1176: for (j=1;j<=n;j++)
! 1177: if ((temp=fabs(a[i][j])) > big) big=temp;
! 1178: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
! 1179: vv[i]=1.0/big;
! 1180: }
! 1181: for (j=1;j<=n;j++) {
! 1182: for (i=1;i<j;i++) {
! 1183: sum=a[i][j];
! 1184: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
! 1185: a[i][j]=sum;
! 1186: }
! 1187: big=0.0;
! 1188: for (i=j;i<=n;i++) {
! 1189: sum=a[i][j];
! 1190: for (k=1;k<j;k++)
! 1191: sum -= a[i][k]*a[k][j];
! 1192: a[i][j]=sum;
! 1193: if ( (dum=vv[i]*fabs(sum)) >= big) {
! 1194: big=dum;
! 1195: imax=i;
! 1196: }
! 1197: }
! 1198: if (j != imax) {
! 1199: for (k=1;k<=n;k++) {
! 1200: dum=a[imax][k];
! 1201: a[imax][k]=a[j][k];
! 1202: a[j][k]=dum;
! 1203: }
! 1204: *d = -(*d);
! 1205: vv[imax]=vv[j];
! 1206: }
! 1207: indx[j]=imax;
! 1208: if (a[j][j] == 0.0) a[j][j]=TINY;
! 1209: if (j != n) {
! 1210: dum=1.0/(a[j][j]);
! 1211: for (i=j+1;i<=n;i++) a[i][j] *= dum;
! 1212: }
! 1213: }
! 1214: free_vector(vv,1,n); /* Doesn't work */
! 1215: ;
! 1216: }
! 1217:
! 1218: void lubksb(double **a, int n, int *indx, double b[])
! 1219: {
! 1220: int i,ii=0,ip,j;
! 1221: double sum;
! 1222:
! 1223: for (i=1;i<=n;i++) {
! 1224: ip=indx[i];
! 1225: sum=b[ip];
! 1226: b[ip]=b[i];
! 1227: if (ii)
! 1228: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
! 1229: else if (sum) ii=i;
! 1230: b[i]=sum;
! 1231: }
! 1232: for (i=n;i>=1;i--) {
! 1233: sum=b[i];
! 1234: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
! 1235: b[i]=sum/a[i][i];
! 1236: }
! 1237: }
! 1238:
! 1239: /************ Frequencies ********************/
! 1240: void freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
! 1241: { /* Some frequencies */
! 1242:
! 1243: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
! 1244: int first;
! 1245: double ***freq; /* Frequencies */
! 1246: double *pp;
! 1247: double pos, k2, dateintsum=0,k2cpt=0;
! 1248: FILE *ficresp;
! 1249: char fileresp[FILENAMELENGTH];
! 1250:
! 1251: pp=vector(1,nlstate);
! 1252: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 1253: strcpy(fileresp,"p");
! 1254: strcat(fileresp,fileres);
! 1255: if((ficresp=fopen(fileresp,"w"))==NULL) {
! 1256: printf("Problem with prevalence resultfile: %s\n", fileresp);
! 1257: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
! 1258: exit(0);
! 1259: }
! 1260: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
! 1261: j1=0;
! 1262:
! 1263: j=cptcoveff;
! 1264: if (cptcovn<1) {j=1;ncodemax[1]=1;}
! 1265:
! 1266: first=1;
! 1267:
! 1268: for(k1=1; k1<=j;k1++){
! 1269: for(i1=1; i1<=ncodemax[k1];i1++){
! 1270: j1++;
! 1271: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
! 1272: scanf("%d", i);*/
! 1273: for (i=-1; i<=nlstate+ndeath; i++)
! 1274: for (jk=-1; jk<=nlstate+ndeath; jk++)
! 1275: for(m=agemin; m <= agemax+3; m++)
! 1276: freq[i][jk][m]=0;
! 1277:
! 1278: dateintsum=0;
! 1279: k2cpt=0;
! 1280: for (i=1; i<=imx; i++) {
! 1281: bool=1;
! 1282: if (cptcovn>0) {
! 1283: for (z1=1; z1<=cptcoveff; z1++)
! 1284: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
! 1285: bool=0;
! 1286: }
! 1287: if (bool==1) {
! 1288: for(m=firstpass; m<=lastpass; m++){
! 1289: k2=anint[m][i]+(mint[m][i]/12.);
! 1290: if ((k2>=dateprev1) && (k2<=dateprev2)) {
! 1291: if(agev[m][i]==0) agev[m][i]=agemax+1;
! 1292: if(agev[m][i]==1) agev[m][i]=agemax+2;
! 1293: if (m<lastpass) {
! 1294: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
! 1295: freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
! 1296: }
! 1297:
! 1298: if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
! 1299: dateintsum=dateintsum+k2;
! 1300: k2cpt++;
! 1301: }
! 1302: }
! 1303: }
! 1304: }
! 1305: }
! 1306:
! 1307: fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
! 1308:
! 1309: if (cptcovn>0) {
! 1310: fprintf(ficresp, "\n#********** Variable ");
! 1311: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
! 1312: fprintf(ficresp, "**********\n#");
! 1313: }
! 1314: for(i=1; i<=nlstate;i++)
! 1315: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
! 1316: fprintf(ficresp, "\n");
! 1317:
! 1318: for(i=(int)agemin; i <= (int)agemax+3; i++){
! 1319: if(i==(int)agemax+3){
! 1320: fprintf(ficlog,"Total");
! 1321: }else{
! 1322: if(first==1){
! 1323: first=0;
! 1324: printf("See log file for details...\n");
! 1325: }
! 1326: fprintf(ficlog,"Age %d", i);
! 1327: }
! 1328: for(jk=1; jk <=nlstate ; jk++){
! 1329: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
! 1330: pp[jk] += freq[jk][m][i];
! 1331: }
! 1332: for(jk=1; jk <=nlstate ; jk++){
! 1333: for(m=-1, pos=0; m <=0 ; m++)
! 1334: pos += freq[jk][m][i];
! 1335: if(pp[jk]>=1.e-10){
! 1336: if(first==1){
! 1337: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
! 1338: }
! 1339: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
! 1340: }else{
! 1341: if(first==1)
! 1342: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
! 1343: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
! 1344: }
! 1345: }
! 1346:
! 1347: for(jk=1; jk <=nlstate ; jk++){
! 1348: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
! 1349: pp[jk] += freq[jk][m][i];
! 1350: }
! 1351:
! 1352: for(jk=1,pos=0; jk <=nlstate ; jk++)
! 1353: pos += pp[jk];
! 1354: for(jk=1; jk <=nlstate ; jk++){
! 1355: if(pos>=1.e-5){
! 1356: if(first==1)
! 1357: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
! 1358: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
! 1359: }else{
! 1360: if(first==1)
! 1361: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
! 1362: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
! 1363: }
! 1364: if( i <= (int) agemax){
! 1365: if(pos>=1.e-5){
! 1366: fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
! 1367: probs[i][jk][j1]= pp[jk]/pos;
! 1368: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
! 1369: }
! 1370: else
! 1371: fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
! 1372: }
! 1373: }
! 1374:
! 1375: for(jk=-1; jk <=nlstate+ndeath; jk++)
! 1376: for(m=-1; m <=nlstate+ndeath; m++)
! 1377: if(freq[jk][m][i] !=0 ) {
! 1378: if(first==1)
! 1379: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
! 1380: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
! 1381: }
! 1382: if(i <= (int) agemax)
! 1383: fprintf(ficresp,"\n");
! 1384: if(first==1)
! 1385: printf("Others in log...\n");
! 1386: fprintf(ficlog,"\n");
! 1387: }
! 1388: }
! 1389: }
! 1390: dateintmean=dateintsum/k2cpt;
! 1391:
! 1392: fclose(ficresp);
! 1393: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
! 1394: free_vector(pp,1,nlstate);
! 1395:
! 1396: /* End of Freq */
! 1397: }
! 1398:
! 1399: /************ Prevalence ********************/
! 1400: void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
! 1401: { /* Some frequencies */
! 1402:
! 1403: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
! 1404: double ***freq; /* Frequencies */
! 1405: double *pp;
! 1406: double pos, k2;
! 1407:
! 1408: pp=vector(1,nlstate);
! 1409:
! 1410: freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
! 1411: j1=0;
! 1412:
! 1413: j=cptcoveff;
! 1414: if (cptcovn<1) {j=1;ncodemax[1]=1;}
! 1415:
! 1416: for(k1=1; k1<=j;k1++){
! 1417: for(i1=1; i1<=ncodemax[k1];i1++){
! 1418: j1++;
! 1419:
! 1420: for (i=-1; i<=nlstate+ndeath; i++)
! 1421: for (jk=-1; jk<=nlstate+ndeath; jk++)
! 1422: for(m=agemin; m <= agemax+3; m++)
! 1423: freq[i][jk][m]=0;
! 1424:
! 1425: for (i=1; i<=imx; i++) {
! 1426: bool=1;
! 1427: if (cptcovn>0) {
! 1428: for (z1=1; z1<=cptcoveff; z1++)
! 1429: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
! 1430: bool=0;
! 1431: }
! 1432: if (bool==1) {
! 1433: for(m=firstpass; m<=lastpass; m++){
! 1434: k2=anint[m][i]+(mint[m][i]/12.);
! 1435: if ((k2>=dateprev1) && (k2<=dateprev2)) {
! 1436: if(agev[m][i]==0) agev[m][i]=agemax+1;
! 1437: if(agev[m][i]==1) agev[m][i]=agemax+2;
! 1438: if (m<lastpass) {
! 1439: if (calagedate>0)
! 1440: freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
! 1441: else
! 1442: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
! 1443: freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];
! 1444: }
! 1445: }
! 1446: }
! 1447: }
! 1448: }
! 1449: for(i=(int)agemin; i <= (int)agemax+3; i++){
! 1450: for(jk=1; jk <=nlstate ; jk++){
! 1451: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
! 1452: pp[jk] += freq[jk][m][i];
! 1453: }
! 1454: for(jk=1; jk <=nlstate ; jk++){
! 1455: for(m=-1, pos=0; m <=0 ; m++)
! 1456: pos += freq[jk][m][i];
! 1457: }
! 1458:
! 1459: for(jk=1; jk <=nlstate ; jk++){
! 1460: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
! 1461: pp[jk] += freq[jk][m][i];
! 1462: }
! 1463:
! 1464: for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
! 1465:
! 1466: for(jk=1; jk <=nlstate ; jk++){
! 1467: if( i <= (int) agemax){
! 1468: if(pos>=1.e-5){
! 1469: probs[i][jk][j1]= pp[jk]/pos;
! 1470: }
! 1471: }
! 1472: }/* end jk */
! 1473: }/* end i */
! 1474: } /* end i1 */
! 1475: } /* end k1 */
! 1476:
! 1477:
! 1478: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
! 1479: free_vector(pp,1,nlstate);
! 1480:
! 1481: } /* End of Freq */
! 1482:
! 1483: /************* Waves Concatenation ***************/
! 1484:
! 1485: void concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
! 1486: {
! 1487: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
! 1488: Death is a valid wave (if date is known).
! 1489: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
! 1490: dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
! 1491: and mw[mi+1][i]. dh depends on stepm.
! 1492: */
! 1493:
! 1494: int i, mi, m;
! 1495: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
! 1496: double sum=0., jmean=0.;*/
! 1497: int first;
! 1498: int j, k=0,jk, ju, jl;
! 1499: double sum=0.;
! 1500: first=0;
! 1501: jmin=1e+5;
! 1502: jmax=-1;
! 1503: jmean=0.;
! 1504: for(i=1; i<=imx; i++){
! 1505: mi=0;
! 1506: m=firstpass;
! 1507: while(s[m][i] <= nlstate){
! 1508: if(s[m][i]>=1)
! 1509: mw[++mi][i]=m;
! 1510: if(m >=lastpass)
! 1511: break;
! 1512: else
! 1513: m++;
! 1514: }/* end while */
! 1515: if (s[m][i] > nlstate){
! 1516: mi++; /* Death is another wave */
! 1517: /* if(mi==0) never been interviewed correctly before death */
! 1518: /* Only death is a correct wave */
! 1519: mw[mi][i]=m;
! 1520: }
! 1521:
! 1522: wav[i]=mi;
! 1523: if(mi==0){
! 1524: if(first==0){
! 1525: printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
! 1526: first=1;
! 1527: }
! 1528: if(first==1){
! 1529: fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
! 1530: }
! 1531: } /* end mi==0 */
! 1532: }
! 1533:
! 1534: for(i=1; i<=imx; i++){
! 1535: for(mi=1; mi<wav[i];mi++){
! 1536: if (stepm <=0)
! 1537: dh[mi][i]=1;
! 1538: else{
! 1539: if (s[mw[mi+1][i]][i] > nlstate) {
! 1540: if (agedc[i] < 2*AGESUP) {
! 1541: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
! 1542: if(j==0) j=1; /* Survives at least one month after exam */
! 1543: k=k+1;
! 1544: if (j >= jmax) jmax=j;
! 1545: if (j <= jmin) jmin=j;
! 1546: sum=sum+j;
! 1547: /*if (j<0) printf("j=%d num=%d \n",j,i); */
! 1548: }
! 1549: }
! 1550: else{
! 1551: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
! 1552: k=k+1;
! 1553: if (j >= jmax) jmax=j;
! 1554: else if (j <= jmin)jmin=j;
! 1555: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
! 1556: sum=sum+j;
! 1557: }
! 1558: jk= j/stepm;
! 1559: jl= j -jk*stepm;
! 1560: ju= j -(jk+1)*stepm;
! 1561: if(jl <= -ju)
! 1562: dh[mi][i]=jk;
! 1563: else
! 1564: dh[mi][i]=jk+1;
! 1565: if(dh[mi][i]==0)
! 1566: dh[mi][i]=1; /* At least one step */
! 1567: }
! 1568: }
! 1569: }
! 1570: jmean=sum/k;
! 1571: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
! 1572: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
! 1573: }
! 1574:
! 1575: /*********** Tricode ****************************/
! 1576: void tricode(int *Tvar, int **nbcode, int imx)
! 1577: {
! 1578: int Ndum[20],ij=1, k, j, i;
! 1579: int cptcode=0;
! 1580: cptcoveff=0;
! 1581:
! 1582: for (k=0; k<19; k++) Ndum[k]=0;
! 1583: for (k=1; k<=7; k++) ncodemax[k]=0;
! 1584:
! 1585: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
! 1586: for (i=1; i<=imx; i++) {
! 1587: ij=(int)(covar[Tvar[j]][i]);
! 1588: Ndum[ij]++;
! 1589: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
! 1590: if (ij > cptcode) cptcode=ij;
! 1591: }
! 1592:
! 1593: for (i=0; i<=cptcode; i++) {
! 1594: if(Ndum[i]!=0) ncodemax[j]++;
! 1595: }
! 1596: ij=1;
! 1597:
! 1598:
! 1599: for (i=1; i<=ncodemax[j]; i++) {
! 1600: for (k=0; k<=19; k++) {
! 1601: if (Ndum[k] != 0) {
! 1602: nbcode[Tvar[j]][ij]=k;
! 1603:
! 1604: ij++;
! 1605: }
! 1606: if (ij > ncodemax[j]) break;
! 1607: }
! 1608: }
! 1609: }
! 1610:
! 1611: for (k=0; k<19; k++) Ndum[k]=0;
! 1612:
! 1613: for (i=1; i<=ncovmodel-2; i++) {
! 1614: ij=Tvar[i];
! 1615: Ndum[ij]++;
! 1616: }
! 1617:
! 1618: ij=1;
! 1619: for (i=1; i<=10; i++) {
! 1620: if((Ndum[i]!=0) && (i<=ncovcol)){
! 1621: Tvaraff[ij]=i;
! 1622: ij++;
! 1623: }
! 1624: }
! 1625:
! 1626: cptcoveff=ij-1;
! 1627: }
! 1628:
! 1629: /*********** Health Expectancies ****************/
! 1630:
! 1631: 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 )
! 1632:
! 1633: {
! 1634: /* Health expectancies */
! 1635: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
! 1636: double age, agelim, hf;
! 1637: double ***p3mat,***varhe;
! 1638: double **dnewm,**doldm;
! 1639: double *xp;
! 1640: double **gp, **gm;
! 1641: double ***gradg, ***trgradg;
! 1642: int theta;
! 1643:
! 1644: varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
! 1645: xp=vector(1,npar);
! 1646: dnewm=matrix(1,nlstate*2,1,npar);
! 1647: doldm=matrix(1,nlstate*2,1,nlstate*2);
! 1648:
! 1649: fprintf(ficreseij,"# Health expectancies\n");
! 1650: fprintf(ficreseij,"# Age");
! 1651: for(i=1; i<=nlstate;i++)
! 1652: for(j=1; j<=nlstate;j++)
! 1653: fprintf(ficreseij," %1d-%1d (SE)",i,j);
! 1654: fprintf(ficreseij,"\n");
! 1655:
! 1656: if(estepm < stepm){
! 1657: printf ("Problem %d lower than %d\n",estepm, stepm);
! 1658: }
! 1659: else hstepm=estepm;
! 1660: /* We compute the life expectancy from trapezoids spaced every estepm months
! 1661: * This is mainly to measure the difference between two models: for example
! 1662: * if stepm=24 months pijx are given only every 2 years and by summing them
! 1663: * we are calculating an estimate of the Life Expectancy assuming a linear
! 1664: * progression inbetween and thus overestimating or underestimating according
! 1665: * to the curvature of the survival function. If, for the same date, we
! 1666: * estimate the model with stepm=1 month, we can keep estepm to 24 months
! 1667: * to compare the new estimate of Life expectancy with the same linear
! 1668: * hypothesis. A more precise result, taking into account a more precise
! 1669: * curvature will be obtained if estepm is as small as stepm. */
! 1670:
! 1671: /* For example we decided to compute the life expectancy with the smallest unit */
! 1672: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
! 1673: nhstepm is the number of hstepm from age to agelim
! 1674: nstepm is the number of stepm from age to agelin.
! 1675: Look at hpijx to understand the reason of that which relies in memory size
! 1676: and note for a fixed period like estepm months */
! 1677: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
! 1678: survival function given by stepm (the optimization length). Unfortunately it
! 1679: means that if the survival funtion is printed only each two years of age and if
! 1680: you sum them up and add 1 year (area under the trapezoids) you won't get the same
! 1681: results. So we changed our mind and took the option of the best precision.
! 1682: */
! 1683: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
! 1684:
! 1685: agelim=AGESUP;
! 1686: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
! 1687: /* nhstepm age range expressed in number of stepm */
! 1688: nstepm=(int) rint((agelim-age)*YEARM/stepm);
! 1689: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
! 1690: /* if (stepm >= YEARM) hstepm=1;*/
! 1691: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
! 1692: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 1693: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
! 1694: gp=matrix(0,nhstepm,1,nlstate*2);
! 1695: gm=matrix(0,nhstepm,1,nlstate*2);
! 1696:
! 1697: /* Computed by stepm unit matrices, product of hstepm matrices, stored
! 1698: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
! 1699: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
! 1700:
! 1701:
! 1702: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
! 1703:
! 1704: /* Computing Variances of health expectancies */
! 1705:
! 1706: for(theta=1; theta <=npar; theta++){
! 1707: for(i=1; i<=npar; i++){
! 1708: xp[i] = x[i] + (i==theta ?delti[theta]:0);
! 1709: }
! 1710: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
! 1711:
! 1712: cptj=0;
! 1713: for(j=1; j<= nlstate; j++){
! 1714: for(i=1; i<=nlstate; i++){
! 1715: cptj=cptj+1;
! 1716: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
! 1717: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
! 1718: }
! 1719: }
! 1720: }
! 1721:
! 1722:
! 1723: for(i=1; i<=npar; i++)
! 1724: xp[i] = x[i] - (i==theta ?delti[theta]:0);
! 1725: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
! 1726:
! 1727: cptj=0;
! 1728: for(j=1; j<= nlstate; j++){
! 1729: for(i=1;i<=nlstate;i++){
! 1730: cptj=cptj+1;
! 1731: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
! 1732: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
! 1733: }
! 1734: }
! 1735: }
! 1736: for(j=1; j<= nlstate*2; j++)
! 1737: for(h=0; h<=nhstepm-1; h++){
! 1738: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
! 1739: }
! 1740: }
! 1741:
! 1742: /* End theta */
! 1743:
! 1744: trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
! 1745:
! 1746: for(h=0; h<=nhstepm-1; h++)
! 1747: for(j=1; j<=nlstate*2;j++)
! 1748: for(theta=1; theta <=npar; theta++)
! 1749: trgradg[h][j][theta]=gradg[h][theta][j];
! 1750:
! 1751:
! 1752: for(i=1;i<=nlstate*2;i++)
! 1753: for(j=1;j<=nlstate*2;j++)
! 1754: varhe[i][j][(int)age] =0.;
! 1755:
! 1756: printf("%d|",(int)age);fflush(stdout);
! 1757: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
! 1758: for(h=0;h<=nhstepm-1;h++){
! 1759: for(k=0;k<=nhstepm-1;k++){
! 1760: matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
! 1761: matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
! 1762: for(i=1;i<=nlstate*2;i++)
! 1763: for(j=1;j<=nlstate*2;j++)
! 1764: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
! 1765: }
! 1766: }
! 1767: /* Computing expectancies */
! 1768: for(i=1; i<=nlstate;i++)
! 1769: for(j=1; j<=nlstate;j++)
! 1770: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
! 1771: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
! 1772:
! 1773: /* 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]);*/
! 1774:
! 1775: }
! 1776:
! 1777: fprintf(ficreseij,"%3.0f",age );
! 1778: cptj=0;
! 1779: for(i=1; i<=nlstate;i++)
! 1780: for(j=1; j<=nlstate;j++){
! 1781: cptj++;
! 1782: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
! 1783: }
! 1784: fprintf(ficreseij,"\n");
! 1785:
! 1786: free_matrix(gm,0,nhstepm,1,nlstate*2);
! 1787: free_matrix(gp,0,nhstepm,1,nlstate*2);
! 1788: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
! 1789: free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
! 1790: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 1791: }
! 1792: printf("\n");
! 1793: fprintf(ficlog,"\n");
! 1794:
! 1795: free_vector(xp,1,npar);
! 1796: free_matrix(dnewm,1,nlstate*2,1,npar);
! 1797: free_matrix(doldm,1,nlstate*2,1,nlstate*2);
! 1798: free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
! 1799: }
! 1800:
! 1801: /************ Variance ******************/
! 1802: 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)
! 1803: {
! 1804: /* Variance of health expectancies */
! 1805: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
! 1806: /* double **newm;*/
! 1807: double **dnewm,**doldm;
! 1808: double **dnewmp,**doldmp;
! 1809: int i, j, nhstepm, hstepm, h, nstepm ;
! 1810: int k, cptcode;
! 1811: double *xp;
! 1812: double **gp, **gm; /* for var eij */
! 1813: double ***gradg, ***trgradg; /*for var eij */
! 1814: double **gradgp, **trgradgp; /* for var p point j */
! 1815: double *gpp, *gmp; /* for var p point j */
! 1816: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
! 1817: double ***p3mat;
! 1818: double age,agelim, hf;
! 1819: double ***mobaverage;
! 1820: int theta;
! 1821: char digit[4];
! 1822: char digitp[16];
! 1823:
! 1824: char fileresprobmorprev[FILENAMELENGTH];
! 1825:
! 1826: if(popbased==1)
! 1827: strcpy(digitp,"-populbased-");
! 1828: else
! 1829: strcpy(digitp,"-stablbased-");
! 1830: if(mobilav==1)
! 1831: strcat(digitp,"mobilav-");
! 1832: else
! 1833: strcat(digitp,"nomobil-");
! 1834: if (mobilav==1) {
! 1835: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 1836: movingaverage(probs, bage, fage, mobaverage);
! 1837: }
! 1838:
! 1839: strcpy(fileresprobmorprev,"prmorprev");
! 1840: sprintf(digit,"%-d",ij);
! 1841: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
! 1842: strcat(fileresprobmorprev,digit); /* Tvar to be done */
! 1843: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
! 1844: strcat(fileresprobmorprev,fileres);
! 1845: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
! 1846: printf("Problem with resultfile: %s\n", fileresprobmorprev);
! 1847: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
! 1848: }
! 1849: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
! 1850: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
! 1851: fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
! 1852: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
! 1853: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
! 1854: fprintf(ficresprobmorprev," p.%-d SE",j);
! 1855: for(i=1; i<=nlstate;i++)
! 1856: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
! 1857: }
! 1858: fprintf(ficresprobmorprev,"\n");
! 1859: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
! 1860: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
! 1861: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
! 1862: exit(0);
! 1863: }
! 1864: else{
! 1865: fprintf(ficgp,"\n# Routine varevsij");
! 1866: }
! 1867: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
! 1868: printf("Problem with html file: %s\n", optionfilehtm);
! 1869: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
! 1870: exit(0);
! 1871: }
! 1872: else{
! 1873: fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
! 1874: fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
! 1875: }
! 1876: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
! 1877:
! 1878: 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");
! 1879: fprintf(ficresvij,"# Age");
! 1880: for(i=1; i<=nlstate;i++)
! 1881: for(j=1; j<=nlstate;j++)
! 1882: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
! 1883: fprintf(ficresvij,"\n");
! 1884:
! 1885: xp=vector(1,npar);
! 1886: dnewm=matrix(1,nlstate,1,npar);
! 1887: doldm=matrix(1,nlstate,1,nlstate);
! 1888: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
! 1889: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
! 1890:
! 1891: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
! 1892: gpp=vector(nlstate+1,nlstate+ndeath);
! 1893: gmp=vector(nlstate+1,nlstate+ndeath);
! 1894: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
! 1895:
! 1896: if(estepm < stepm){
! 1897: printf ("Problem %d lower than %d\n",estepm, stepm);
! 1898: }
! 1899: else hstepm=estepm;
! 1900: /* For example we decided to compute the life expectancy with the smallest unit */
! 1901: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
! 1902: nhstepm is the number of hstepm from age to agelim
! 1903: nstepm is the number of stepm from age to agelin.
! 1904: Look at hpijx to understand the reason of that which relies in memory size
! 1905: and note for a fixed period like k years */
! 1906: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
! 1907: survival function given by stepm (the optimization length). Unfortunately it
! 1908: means that if the survival funtion is printed only each two years of age and if
! 1909: you sum them up and add 1 year (area under the trapezoids) you won't get the same
! 1910: results. So we changed our mind and took the option of the best precision.
! 1911: */
! 1912: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
! 1913: agelim = AGESUP;
! 1914: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
! 1915: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
! 1916: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
! 1917: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 1918: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
! 1919: gp=matrix(0,nhstepm,1,nlstate);
! 1920: gm=matrix(0,nhstepm,1,nlstate);
! 1921:
! 1922:
! 1923: for(theta=1; theta <=npar; theta++){
! 1924: for(i=1; i<=npar; i++){ /* Computes gradient */
! 1925: xp[i] = x[i] + (i==theta ?delti[theta]:0);
! 1926: }
! 1927: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
! 1928: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
! 1929:
! 1930: if (popbased==1) {
! 1931: if(mobilav !=1){
! 1932: for(i=1; i<=nlstate;i++)
! 1933: prlim[i][i]=probs[(int)age][i][ij];
! 1934: }else{ /* mobilav=1 */
! 1935: for(i=1; i<=nlstate;i++)
! 1936: prlim[i][i]=mobaverage[(int)age][i][ij];
! 1937: }
! 1938: }
! 1939:
! 1940: for(j=1; j<= nlstate; j++){
! 1941: for(h=0; h<=nhstepm; h++){
! 1942: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
! 1943: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
! 1944: }
! 1945: }
! 1946: /* This for computing forces of mortality (h=1)as a weighted average */
! 1947: for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
! 1948: for(i=1; i<= nlstate; i++)
! 1949: gpp[j] += prlim[i][i]*p3mat[i][j][1];
! 1950: }
! 1951: /* end force of mortality */
! 1952:
! 1953: for(i=1; i<=npar; i++) /* Computes gradient */
! 1954: xp[i] = x[i] - (i==theta ?delti[theta]:0);
! 1955: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
! 1956: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
! 1957:
! 1958: if (popbased==1) {
! 1959: if(mobilav !=1){
! 1960: for(i=1; i<=nlstate;i++)
! 1961: prlim[i][i]=probs[(int)age][i][ij];
! 1962: }else{ /* mobilav=1 */
! 1963: for(i=1; i<=nlstate;i++)
! 1964: prlim[i][i]=mobaverage[(int)age][i][ij];
! 1965: }
! 1966: }
! 1967:
! 1968: for(j=1; j<= nlstate; j++){
! 1969: for(h=0; h<=nhstepm; h++){
! 1970: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
! 1971: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
! 1972: }
! 1973: }
! 1974: /* This for computing force of mortality (h=1)as a weighted average */
! 1975: for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
! 1976: for(i=1; i<= nlstate; i++)
! 1977: gmp[j] += prlim[i][i]*p3mat[i][j][1];
! 1978: }
! 1979: /* end force of mortality */
! 1980:
! 1981: for(j=1; j<= nlstate; j++) /* vareij */
! 1982: for(h=0; h<=nhstepm; h++){
! 1983: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
! 1984: }
! 1985: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
! 1986: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
! 1987: }
! 1988:
! 1989: } /* End theta */
! 1990:
! 1991: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
! 1992:
! 1993: for(h=0; h<=nhstepm; h++) /* veij */
! 1994: for(j=1; j<=nlstate;j++)
! 1995: for(theta=1; theta <=npar; theta++)
! 1996: trgradg[h][j][theta]=gradg[h][theta][j];
! 1997:
! 1998: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
! 1999: for(theta=1; theta <=npar; theta++)
! 2000: trgradgp[j][theta]=gradgp[theta][j];
! 2001:
! 2002: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
! 2003: for(i=1;i<=nlstate;i++)
! 2004: for(j=1;j<=nlstate;j++)
! 2005: vareij[i][j][(int)age] =0.;
! 2006:
! 2007: for(h=0;h<=nhstepm;h++){
! 2008: for(k=0;k<=nhstepm;k++){
! 2009: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
! 2010: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
! 2011: for(i=1;i<=nlstate;i++)
! 2012: for(j=1;j<=nlstate;j++)
! 2013: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
! 2014: }
! 2015: }
! 2016:
! 2017: /* pptj */
! 2018: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
! 2019: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
! 2020: for(j=nlstate+1;j<=nlstate+ndeath;j++)
! 2021: for(i=nlstate+1;i<=nlstate+ndeath;i++)
! 2022: varppt[j][i]=doldmp[j][i];
! 2023: /* end ppptj */
! 2024: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
! 2025: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
! 2026:
! 2027: if (popbased==1) {
! 2028: if(mobilav !=1){
! 2029: for(i=1; i<=nlstate;i++)
! 2030: prlim[i][i]=probs[(int)age][i][ij];
! 2031: }else{ /* mobilav=1 */
! 2032: for(i=1; i<=nlstate;i++)
! 2033: prlim[i][i]=mobaverage[(int)age][i][ij];
! 2034: }
! 2035: }
! 2036:
! 2037: /* This for computing force of mortality (h=1)as a weighted average */
! 2038: for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
! 2039: for(i=1; i<= nlstate; i++)
! 2040: gmp[j] += prlim[i][i]*p3mat[i][j][1];
! 2041: }
! 2042: /* end force of mortality */
! 2043:
! 2044: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
! 2045: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
! 2046: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
! 2047: for(i=1; i<=nlstate;i++){
! 2048: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
! 2049: }
! 2050: }
! 2051: fprintf(ficresprobmorprev,"\n");
! 2052:
! 2053: fprintf(ficresvij,"%.0f ",age );
! 2054: for(i=1; i<=nlstate;i++)
! 2055: for(j=1; j<=nlstate;j++){
! 2056: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
! 2057: }
! 2058: fprintf(ficresvij,"\n");
! 2059: free_matrix(gp,0,nhstepm,1,nlstate);
! 2060: free_matrix(gm,0,nhstepm,1,nlstate);
! 2061: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
! 2062: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
! 2063: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 2064: } /* End age */
! 2065: free_vector(gpp,nlstate+1,nlstate+ndeath);
! 2066: free_vector(gmp,nlstate+1,nlstate+ndeath);
! 2067: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
! 2068: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
! 2069: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
! 2070: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
! 2071: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
! 2072: fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);
! 2073: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
! 2074: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
! 2075: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
! 2076: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);
! 2077: /* 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);
! 2078: */
! 2079: fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
! 2080:
! 2081: free_vector(xp,1,npar);
! 2082: free_matrix(doldm,1,nlstate,1,nlstate);
! 2083: free_matrix(dnewm,1,nlstate,1,npar);
! 2084: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
! 2085: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
! 2086: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
! 2087: free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 2088: fclose(ficresprobmorprev);
! 2089: fclose(ficgp);
! 2090: fclose(fichtm);
! 2091:
! 2092: }
! 2093:
! 2094: /************ Variance of prevlim ******************/
! 2095: 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)
! 2096: {
! 2097: /* Variance of prevalence limit */
! 2098: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
! 2099: double **newm;
! 2100: double **dnewm,**doldm;
! 2101: int i, j, nhstepm, hstepm;
! 2102: int k, cptcode;
! 2103: double *xp;
! 2104: double *gp, *gm;
! 2105: double **gradg, **trgradg;
! 2106: double age,agelim;
! 2107: int theta;
! 2108:
! 2109: fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");
! 2110: fprintf(ficresvpl,"# Age");
! 2111: for(i=1; i<=nlstate;i++)
! 2112: fprintf(ficresvpl," %1d-%1d",i,i);
! 2113: fprintf(ficresvpl,"\n");
! 2114:
! 2115: xp=vector(1,npar);
! 2116: dnewm=matrix(1,nlstate,1,npar);
! 2117: doldm=matrix(1,nlstate,1,nlstate);
! 2118:
! 2119: hstepm=1*YEARM; /* Every year of age */
! 2120: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
! 2121: agelim = AGESUP;
! 2122: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
! 2123: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
! 2124: if (stepm >= YEARM) hstepm=1;
! 2125: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
! 2126: gradg=matrix(1,npar,1,nlstate);
! 2127: gp=vector(1,nlstate);
! 2128: gm=vector(1,nlstate);
! 2129:
! 2130: for(theta=1; theta <=npar; theta++){
! 2131: for(i=1; i<=npar; i++){ /* Computes gradient */
! 2132: xp[i] = x[i] + (i==theta ?delti[theta]:0);
! 2133: }
! 2134: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
! 2135: for(i=1;i<=nlstate;i++)
! 2136: gp[i] = prlim[i][i];
! 2137:
! 2138: for(i=1; i<=npar; i++) /* Computes gradient */
! 2139: xp[i] = x[i] - (i==theta ?delti[theta]:0);
! 2140: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
! 2141: for(i=1;i<=nlstate;i++)
! 2142: gm[i] = prlim[i][i];
! 2143:
! 2144: for(i=1;i<=nlstate;i++)
! 2145: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
! 2146: } /* End theta */
! 2147:
! 2148: trgradg =matrix(1,nlstate,1,npar);
! 2149:
! 2150: for(j=1; j<=nlstate;j++)
! 2151: for(theta=1; theta <=npar; theta++)
! 2152: trgradg[j][theta]=gradg[theta][j];
! 2153:
! 2154: for(i=1;i<=nlstate;i++)
! 2155: varpl[i][(int)age] =0.;
! 2156: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
! 2157: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
! 2158: for(i=1;i<=nlstate;i++)
! 2159: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
! 2160:
! 2161: fprintf(ficresvpl,"%.0f ",age );
! 2162: for(i=1; i<=nlstate;i++)
! 2163: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
! 2164: fprintf(ficresvpl,"\n");
! 2165: free_vector(gp,1,nlstate);
! 2166: free_vector(gm,1,nlstate);
! 2167: free_matrix(gradg,1,npar,1,nlstate);
! 2168: free_matrix(trgradg,1,nlstate,1,npar);
! 2169: } /* End age */
! 2170:
! 2171: free_vector(xp,1,npar);
! 2172: free_matrix(doldm,1,nlstate,1,npar);
! 2173: free_matrix(dnewm,1,nlstate,1,nlstate);
! 2174:
! 2175: }
! 2176:
! 2177: /************ Variance of one-step probabilities ******************/
! 2178: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
! 2179: {
! 2180: int i, j=0, i1, k1, l1, t, tj;
! 2181: int k2, l2, j1, z1;
! 2182: int k=0,l, cptcode;
! 2183: int first=1, first1;
! 2184: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
! 2185: double **dnewm,**doldm;
! 2186: double *xp;
! 2187: double *gp, *gm;
! 2188: double **gradg, **trgradg;
! 2189: double **mu;
! 2190: double age,agelim, cov[NCOVMAX];
! 2191: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
! 2192: int theta;
! 2193: char fileresprob[FILENAMELENGTH];
! 2194: char fileresprobcov[FILENAMELENGTH];
! 2195: char fileresprobcor[FILENAMELENGTH];
! 2196:
! 2197: double ***varpij;
! 2198:
! 2199: strcpy(fileresprob,"prob");
! 2200: strcat(fileresprob,fileres);
! 2201: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
! 2202: printf("Problem with resultfile: %s\n", fileresprob);
! 2203: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
! 2204: }
! 2205: strcpy(fileresprobcov,"probcov");
! 2206: strcat(fileresprobcov,fileres);
! 2207: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
! 2208: printf("Problem with resultfile: %s\n", fileresprobcov);
! 2209: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
! 2210: }
! 2211: strcpy(fileresprobcor,"probcor");
! 2212: strcat(fileresprobcor,fileres);
! 2213: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
! 2214: printf("Problem with resultfile: %s\n", fileresprobcor);
! 2215: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
! 2216: }
! 2217: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
! 2218: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
! 2219: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
! 2220: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
! 2221: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
! 2222: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
! 2223:
! 2224: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
! 2225: fprintf(ficresprob,"# Age");
! 2226: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
! 2227: fprintf(ficresprobcov,"# Age");
! 2228: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
! 2229: fprintf(ficresprobcov,"# Age");
! 2230:
! 2231:
! 2232: for(i=1; i<=nlstate;i++)
! 2233: for(j=1; j<=(nlstate+ndeath);j++){
! 2234: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
! 2235: fprintf(ficresprobcov," p%1d-%1d ",i,j);
! 2236: fprintf(ficresprobcor," p%1d-%1d ",i,j);
! 2237: }
! 2238: fprintf(ficresprob,"\n");
! 2239: fprintf(ficresprobcov,"\n");
! 2240: fprintf(ficresprobcor,"\n");
! 2241: xp=vector(1,npar);
! 2242: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
! 2243: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
! 2244: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
! 2245: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
! 2246: first=1;
! 2247: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
! 2248: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
! 2249: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
! 2250: exit(0);
! 2251: }
! 2252: else{
! 2253: fprintf(ficgp,"\n# Routine varprob");
! 2254: }
! 2255: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
! 2256: printf("Problem with html file: %s\n", optionfilehtm);
! 2257: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
! 2258: exit(0);
! 2259: }
! 2260: else{
! 2261: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
! 2262: fprintf(fichtm,"\n");
! 2263:
! 2264: fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
! 2265: 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");
! 2266: 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");
! 2267:
! 2268: }
! 2269:
! 2270:
! 2271: cov[1]=1;
! 2272: tj=cptcoveff;
! 2273: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
! 2274: j1=0;
! 2275: for(t=1; t<=tj;t++){
! 2276: for(i1=1; i1<=ncodemax[t];i1++){
! 2277: j1++;
! 2278:
! 2279: if (cptcovn>0) {
! 2280: fprintf(ficresprob, "\n#********** Variable ");
! 2281: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
! 2282: fprintf(ficresprob, "**********\n#");
! 2283: fprintf(ficresprobcov, "\n#********** Variable ");
! 2284: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
! 2285: fprintf(ficresprobcov, "**********\n#");
! 2286:
! 2287: fprintf(ficgp, "\n#********** Variable ");
! 2288: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
! 2289: fprintf(ficgp, "**********\n#");
! 2290:
! 2291:
! 2292: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
! 2293: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
! 2294: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
! 2295:
! 2296: fprintf(ficresprobcor, "\n#********** Variable ");
! 2297: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
! 2298: fprintf(ficgp, "**********\n#");
! 2299: }
! 2300:
! 2301: for (age=bage; age<=fage; age ++){
! 2302: cov[2]=age;
! 2303: for (k=1; k<=cptcovn;k++) {
! 2304: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
! 2305: }
! 2306: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
! 2307: for (k=1; k<=cptcovprod;k++)
! 2308: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
! 2309:
! 2310: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
! 2311: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
! 2312: gp=vector(1,(nlstate)*(nlstate+ndeath));
! 2313: gm=vector(1,(nlstate)*(nlstate+ndeath));
! 2314:
! 2315: for(theta=1; theta <=npar; theta++){
! 2316: for(i=1; i<=npar; i++)
! 2317: xp[i] = x[i] + (i==theta ?delti[theta]:0);
! 2318:
! 2319: pmij(pmmij,cov,ncovmodel,xp,nlstate);
! 2320:
! 2321: k=0;
! 2322: for(i=1; i<= (nlstate); i++){
! 2323: for(j=1; j<=(nlstate+ndeath);j++){
! 2324: k=k+1;
! 2325: gp[k]=pmmij[i][j];
! 2326: }
! 2327: }
! 2328:
! 2329: for(i=1; i<=npar; i++)
! 2330: xp[i] = x[i] - (i==theta ?delti[theta]:0);
! 2331:
! 2332: pmij(pmmij,cov,ncovmodel,xp,nlstate);
! 2333: k=0;
! 2334: for(i=1; i<=(nlstate); i++){
! 2335: for(j=1; j<=(nlstate+ndeath);j++){
! 2336: k=k+1;
! 2337: gm[k]=pmmij[i][j];
! 2338: }
! 2339: }
! 2340:
! 2341: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
! 2342: gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
! 2343: }
! 2344:
! 2345: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
! 2346: for(theta=1; theta <=npar; theta++)
! 2347: trgradg[j][theta]=gradg[theta][j];
! 2348:
! 2349: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
! 2350: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
! 2351:
! 2352: pmij(pmmij,cov,ncovmodel,x,nlstate);
! 2353:
! 2354: k=0;
! 2355: for(i=1; i<=(nlstate); i++){
! 2356: for(j=1; j<=(nlstate+ndeath);j++){
! 2357: k=k+1;
! 2358: mu[k][(int) age]=pmmij[i][j];
! 2359: }
! 2360: }
! 2361: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
! 2362: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
! 2363: varpij[i][j][(int)age] = doldm[i][j];
! 2364:
! 2365: /*printf("\n%d ",(int)age);
! 2366: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
! 2367: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
! 2368: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
! 2369: }*/
! 2370:
! 2371: fprintf(ficresprob,"\n%d ",(int)age);
! 2372: fprintf(ficresprobcov,"\n%d ",(int)age);
! 2373: fprintf(ficresprobcor,"\n%d ",(int)age);
! 2374:
! 2375: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
! 2376: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
! 2377: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
! 2378: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
! 2379: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
! 2380: }
! 2381: i=0;
! 2382: for (k=1; k<=(nlstate);k++){
! 2383: for (l=1; l<=(nlstate+ndeath);l++){
! 2384: i=i++;
! 2385: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
! 2386: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
! 2387: for (j=1; j<=i;j++){
! 2388: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
! 2389: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
! 2390: }
! 2391: }
! 2392: }/* end of loop for state */
! 2393: } /* end of loop for age */
! 2394:
! 2395: /* Confidence intervalle of pij */
! 2396: /*
! 2397: fprintf(ficgp,"\nset noparametric;unset label");
! 2398: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
! 2399: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
! 2400: 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);
! 2401: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
! 2402: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
! 2403: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
! 2404: */
! 2405:
! 2406: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
! 2407: first1=1;
! 2408: for (k2=1; k2<=(nlstate);k2++){
! 2409: for (l2=1; l2<=(nlstate+ndeath);l2++){
! 2410: if(l2==k2) continue;
! 2411: j=(k2-1)*(nlstate+ndeath)+l2;
! 2412: for (k1=1; k1<=(nlstate);k1++){
! 2413: for (l1=1; l1<=(nlstate+ndeath);l1++){
! 2414: if(l1==k1) continue;
! 2415: i=(k1-1)*(nlstate+ndeath)+l1;
! 2416: if(i<=j) continue;
! 2417: for (age=bage; age<=fage; age ++){
! 2418: if ((int)age %5==0){
! 2419: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
! 2420: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
! 2421: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
! 2422: mu1=mu[i][(int) age]/stepm*YEARM ;
! 2423: mu2=mu[j][(int) age]/stepm*YEARM;
! 2424: c12=cv12/sqrt(v1*v2);
! 2425: /* Computing eigen value of matrix of covariance */
! 2426: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
! 2427: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
! 2428: /* Eigen vectors */
! 2429: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
! 2430: /*v21=sqrt(1.-v11*v11); *//* error */
! 2431: v21=(lc1-v1)/cv12*v11;
! 2432: v12=-v21;
! 2433: v22=v11;
! 2434: tnalp=v21/v11;
! 2435: if(first1==1){
! 2436: first1=0;
! 2437: 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);
! 2438: }
! 2439: 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);
! 2440: /*printf(fignu*/
! 2441: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
! 2442: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
! 2443: if(first==1){
! 2444: first=0;
! 2445: fprintf(ficgp,"\nset parametric;unset label");
! 2446: 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);
! 2447: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
! 2448: 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);
! 2449: fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
! 2450: fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
! 2451: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
! 2452: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
! 2453: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
! 2454: 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",\
! 2455: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
! 2456: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
! 2457: }else{
! 2458: first=0;
! 2459: fprintf(fichtm," %d (%.3f),",(int) age, c12);
! 2460: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
! 2461: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
! 2462: 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",\
! 2463: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
! 2464: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
! 2465: }/* if first */
! 2466: } /* age mod 5 */
! 2467: } /* end loop age */
! 2468: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
! 2469: first=1;
! 2470: } /*l12 */
! 2471: } /* k12 */
! 2472: } /*l1 */
! 2473: }/* k1 */
! 2474: } /* loop covariates */
! 2475: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
! 2476: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
! 2477: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
! 2478: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
! 2479: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
! 2480: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
! 2481: }
! 2482: free_vector(xp,1,npar);
! 2483: fclose(ficresprob);
! 2484: fclose(ficresprobcov);
! 2485: fclose(ficresprobcor);
! 2486: fclose(ficgp);
! 2487: fclose(fichtm);
! 2488: }
! 2489:
! 2490:
! 2491: /******************* Printing html file ***********/
! 2492: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
! 2493: int lastpass, int stepm, int weightopt, char model[],\
! 2494: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
! 2495: int popforecast, int estepm ,\
! 2496: double jprev1, double mprev1,double anprev1, \
! 2497: double jprev2, double mprev2,double anprev2){
! 2498: int jj1, k1, i1, cpt;
! 2499: /*char optionfilehtm[FILENAMELENGTH];*/
! 2500: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
! 2501: printf("Problem with %s \n",optionfilehtm), exit(0);
! 2502: fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
! 2503: }
! 2504:
! 2505: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
! 2506: - 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
! 2507: - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
! 2508: - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
! 2509: - Life expectancies by age and initial health status (estepm=%2d months):
! 2510: <a href=\"e%s\">e%s</a> <br>\n</li>", \
! 2511: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
! 2512:
! 2513: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
! 2514:
! 2515: m=cptcoveff;
! 2516: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
! 2517:
! 2518: jj1=0;
! 2519: for(k1=1; k1<=m;k1++){
! 2520: for(i1=1; i1<=ncodemax[k1];i1++){
! 2521: jj1++;
! 2522: if (cptcovn > 0) {
! 2523: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
! 2524: for (cpt=1; cpt<=cptcoveff;cpt++)
! 2525: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
! 2526: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
! 2527: }
! 2528: /* Pij */
! 2529: 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>
! 2530: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
! 2531: /* Quasi-incidences */
! 2532: 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>
! 2533: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
! 2534: /* Stable prevalence in each health state */
! 2535: for(cpt=1; cpt<nlstate;cpt++){
! 2536: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
! 2537: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
! 2538: }
! 2539: for(cpt=1; cpt<=nlstate;cpt++) {
! 2540: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
! 2541: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
! 2542: }
! 2543: fprintf(fichtm,"\n<br>- Total life expectancy by age and
! 2544: health expectancies in states (1) and (2): e%s%d.png<br>
! 2545: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
! 2546: } /* end i1 */
! 2547: }/* End k1 */
! 2548: fprintf(fichtm,"</ul>");
! 2549:
! 2550:
! 2551: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
! 2552: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
! 2553: - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
! 2554: - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
! 2555: - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
! 2556: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
! 2557: - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
! 2558: - 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);
! 2559:
! 2560: if(popforecast==1) fprintf(fichtm,"\n
! 2561: - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
! 2562: - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
! 2563: <br>",fileres,fileres,fileres,fileres);
! 2564: else
! 2565: 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);
! 2566: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
! 2567:
! 2568: m=cptcoveff;
! 2569: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
! 2570:
! 2571: jj1=0;
! 2572: for(k1=1; k1<=m;k1++){
! 2573: for(i1=1; i1<=ncodemax[k1];i1++){
! 2574: jj1++;
! 2575: if (cptcovn > 0) {
! 2576: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
! 2577: for (cpt=1; cpt<=cptcoveff;cpt++)
! 2578: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
! 2579: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
! 2580: }
! 2581: for(cpt=1; cpt<=nlstate;cpt++) {
! 2582: fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
! 2583: interval) in state (%d): v%s%d%d.png <br>
! 2584: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
! 2585: }
! 2586: } /* end i1 */
! 2587: }/* End k1 */
! 2588: fprintf(fichtm,"</ul>");
! 2589: fclose(fichtm);
! 2590: }
! 2591:
! 2592: /******************* Gnuplot file **************/
! 2593: void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
! 2594:
! 2595: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
! 2596: int ng;
! 2597: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
! 2598: printf("Problem with file %s",optionfilegnuplot);
! 2599: fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
! 2600: }
! 2601:
! 2602: #ifdef windows
! 2603: fprintf(ficgp,"cd \"%s\" \n",pathc);
! 2604: #endif
! 2605: m=pow(2,cptcoveff);
! 2606:
! 2607: /* 1eme*/
! 2608: for (cpt=1; cpt<= nlstate ; cpt ++) {
! 2609: for (k1=1; k1<= m ; k1 ++) {
! 2610: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
! 2611: 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);
! 2612:
! 2613: for (i=1; i<= nlstate ; i ++) {
! 2614: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
! 2615: else fprintf(ficgp," \%%*lf (\%%*lf)");
! 2616: }
! 2617: fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
! 2618: for (i=1; i<= nlstate ; i ++) {
! 2619: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
! 2620: else fprintf(ficgp," \%%*lf (\%%*lf)");
! 2621: }
! 2622: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
! 2623: for (i=1; i<= nlstate ; i ++) {
! 2624: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
! 2625: else fprintf(ficgp," \%%*lf (\%%*lf)");
! 2626: }
! 2627: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
! 2628: }
! 2629: }
! 2630: /*2 eme*/
! 2631:
! 2632: for (k1=1; k1<= m ; k1 ++) {
! 2633: fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
! 2634: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
! 2635:
! 2636: for (i=1; i<= nlstate+1 ; i ++) {
! 2637: k=2*i;
! 2638: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
! 2639: for (j=1; j<= nlstate+1 ; j ++) {
! 2640: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
! 2641: else fprintf(ficgp," \%%*lf (\%%*lf)");
! 2642: }
! 2643: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
! 2644: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
! 2645: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
! 2646: for (j=1; j<= nlstate+1 ; j ++) {
! 2647: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
! 2648: else fprintf(ficgp," \%%*lf (\%%*lf)");
! 2649: }
! 2650: fprintf(ficgp,"\" t\"\" w l 0,");
! 2651: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
! 2652: for (j=1; j<= nlstate+1 ; j ++) {
! 2653: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
! 2654: else fprintf(ficgp," \%%*lf (\%%*lf)");
! 2655: }
! 2656: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
! 2657: else fprintf(ficgp,"\" t\"\" w l 0,");
! 2658: }
! 2659: }
! 2660:
! 2661: /*3eme*/
! 2662:
! 2663: for (k1=1; k1<= m ; k1 ++) {
! 2664: for (cpt=1; cpt<= nlstate ; cpt ++) {
! 2665: k=2+nlstate*(2*cpt-2);
! 2666: fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
! 2667: fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
! 2668: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
! 2669: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
! 2670: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
! 2671: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
! 2672: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
! 2673: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
! 2674:
! 2675: */
! 2676: for (i=1; i< nlstate ; i ++) {
! 2677: 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);
! 2678:
! 2679: }
! 2680: }
! 2681: }
! 2682:
! 2683: /* CV preval stat */
! 2684: for (k1=1; k1<= m ; k1 ++) {
! 2685: for (cpt=1; cpt<nlstate ; cpt ++) {
! 2686: k=3;
! 2687: fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
! 2688: 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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
! 2689:
! 2690: for (i=1; i< nlstate ; i ++)
! 2691: fprintf(ficgp,"+$%d",k+i+1);
! 2692: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
! 2693:
! 2694: l=3+(nlstate+ndeath)*cpt;
! 2695: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
! 2696: for (i=1; i< nlstate ; i ++) {
! 2697: l=3+(nlstate+ndeath)*cpt;
! 2698: fprintf(ficgp,"+$%d",l+i+1);
! 2699: }
! 2700: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
! 2701: }
! 2702: }
! 2703:
! 2704: /* proba elementaires */
! 2705: for(i=1,jk=1; i <=nlstate; i++){
! 2706: for(k=1; k <=(nlstate+ndeath); k++){
! 2707: if (k != i) {
! 2708: for(j=1; j <=ncovmodel; j++){
! 2709: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
! 2710: jk++;
! 2711: fprintf(ficgp,"\n");
! 2712: }
! 2713: }
! 2714: }
! 2715: }
! 2716:
! 2717: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
! 2718: for(jk=1; jk <=m; jk++) {
! 2719: fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
! 2720: if (ng==2)
! 2721: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
! 2722: else
! 2723: fprintf(ficgp,"\nset title \"Probability\"\n");
! 2724: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
! 2725: i=1;
! 2726: for(k2=1; k2<=nlstate; k2++) {
! 2727: k3=i;
! 2728: for(k=1; k<=(nlstate+ndeath); k++) {
! 2729: if (k != k2){
! 2730: if(ng==2)
! 2731: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
! 2732: else
! 2733: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
! 2734: ij=1;
! 2735: for(j=3; j <=ncovmodel; j++) {
! 2736: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
! 2737: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
! 2738: ij++;
! 2739: }
! 2740: else
! 2741: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
! 2742: }
! 2743: fprintf(ficgp,")/(1");
! 2744:
! 2745: for(k1=1; k1 <=nlstate; k1++){
! 2746: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
! 2747: ij=1;
! 2748: for(j=3; j <=ncovmodel; j++){
! 2749: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
! 2750: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
! 2751: ij++;
! 2752: }
! 2753: else
! 2754: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
! 2755: }
! 2756: fprintf(ficgp,")");
! 2757: }
! 2758: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
! 2759: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
! 2760: i=i+ncovmodel;
! 2761: }
! 2762: } /* end k */
! 2763: } /* end k2 */
! 2764: } /* end jk */
! 2765: } /* end ng */
! 2766: fclose(ficgp);
! 2767: } /* end gnuplot */
! 2768:
! 2769:
! 2770: /*************** Moving average **************/
! 2771: void movingaverage(double ***probs, double bage,double fage, double ***mobaverage){
! 2772:
! 2773: int i, cpt, cptcod;
! 2774: double age;
! 2775: for (age=bage; age<=fage; age++)
! 2776: for (i=1; i<=nlstate;i++)
! 2777: for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
! 2778: mobaverage[(int)age][i][cptcod]=0.;
! 2779:
! 2780: for (age=bage+4; age<=fage; age++){
! 2781: for (i=1; i<=nlstate;i++){
! 2782: for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
! 2783: for (cpt=0;cpt<=4;cpt++){
! 2784: mobaverage[(int)age-2][i][cptcod]=mobaverage[(int)age-2][i][cptcod]+probs[(int)age-cpt][i][cptcod];
! 2785: }
! 2786: mobaverage[(int)age-2][i][cptcod]=mobaverage[(int)age-2][i][cptcod]/5;
! 2787: }
! 2788: }
! 2789: }
! 2790:
! 2791: }
! 2792:
! 2793:
! 2794: /************** Forecasting ******************/
! 2795: prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
! 2796:
! 2797: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
! 2798: int *popage;
! 2799: double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
! 2800: double *popeffectif,*popcount;
! 2801: double ***p3mat;
! 2802: char fileresf[FILENAMELENGTH];
! 2803:
! 2804: agelim=AGESUP;
! 2805: calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
! 2806:
! 2807: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
! 2808:
! 2809:
! 2810: strcpy(fileresf,"f");
! 2811: strcat(fileresf,fileres);
! 2812: if((ficresf=fopen(fileresf,"w"))==NULL) {
! 2813: printf("Problem with forecast resultfile: %s\n", fileresf);
! 2814: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
! 2815: }
! 2816: printf("Computing forecasting: result on file '%s' \n", fileresf);
! 2817: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
! 2818:
! 2819: if (cptcoveff==0) ncodemax[cptcoveff]=1;
! 2820:
! 2821: if (mobilav==1) {
! 2822: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 2823: movingaverage(probs, ageminpar,fage, mobaverage);
! 2824: }
! 2825:
! 2826: stepsize=(int) (stepm+YEARM-1)/YEARM;
! 2827: if (stepm<=12) stepsize=1;
! 2828:
! 2829: agelim=AGESUP;
! 2830:
! 2831: hstepm=1;
! 2832: hstepm=hstepm/stepm;
! 2833: yp1=modf(dateintmean,&yp);
! 2834: anprojmean=yp;
! 2835: yp2=modf((yp1*12),&yp);
! 2836: mprojmean=yp;
! 2837: yp1=modf((yp2*30.5),&yp);
! 2838: jprojmean=yp;
! 2839: if(jprojmean==0) jprojmean=1;
! 2840: if(mprojmean==0) jprojmean=1;
! 2841:
! 2842: fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);
! 2843:
! 2844: for(cptcov=1;cptcov<=i2;cptcov++){
! 2845: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
! 2846: k=k+1;
! 2847: fprintf(ficresf,"\n#******");
! 2848: for(j=1;j<=cptcoveff;j++) {
! 2849: fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 2850: }
! 2851: fprintf(ficresf,"******\n");
! 2852: fprintf(ficresf,"# StartingAge FinalAge");
! 2853: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
! 2854:
! 2855:
! 2856: for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {
! 2857: fprintf(ficresf,"\n");
! 2858: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);
! 2859:
! 2860: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
! 2861: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
! 2862: nhstepm = nhstepm/hstepm;
! 2863:
! 2864: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 2865: oldm=oldms;savm=savms;
! 2866: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
! 2867:
! 2868: for (h=0; h<=nhstepm; h++){
! 2869: if (h==(int) (calagedate+YEARM*cpt)) {
! 2870: fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
! 2871: }
! 2872: for(j=1; j<=nlstate+ndeath;j++) {
! 2873: kk1=0.;kk2=0;
! 2874: for(i=1; i<=nlstate;i++) {
! 2875: if (mobilav==1)
! 2876: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
! 2877: else {
! 2878: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
! 2879: }
! 2880:
! 2881: }
! 2882: if (h==(int)(calagedate+12*cpt)){
! 2883: fprintf(ficresf," %.3f", kk1);
! 2884:
! 2885: }
! 2886: }
! 2887: }
! 2888: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 2889: }
! 2890: }
! 2891: }
! 2892: }
! 2893:
! 2894: if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 2895:
! 2896: fclose(ficresf);
! 2897: }
! 2898: /************** Forecasting ******************/
! 2899: 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){
! 2900:
! 2901: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
! 2902: int *popage;
! 2903: double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
! 2904: double *popeffectif,*popcount;
! 2905: double ***p3mat,***tabpop,***tabpopprev;
! 2906: char filerespop[FILENAMELENGTH];
! 2907:
! 2908: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 2909: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 2910: agelim=AGESUP;
! 2911: calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
! 2912:
! 2913: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
! 2914:
! 2915:
! 2916: strcpy(filerespop,"pop");
! 2917: strcat(filerespop,fileres);
! 2918: if((ficrespop=fopen(filerespop,"w"))==NULL) {
! 2919: printf("Problem with forecast resultfile: %s\n", filerespop);
! 2920: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
! 2921: }
! 2922: printf("Computing forecasting: result on file '%s' \n", filerespop);
! 2923: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
! 2924:
! 2925: if (cptcoveff==0) ncodemax[cptcoveff]=1;
! 2926:
! 2927: if (mobilav==1) {
! 2928: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 2929: movingaverage(probs, ageminpar, fage, mobaverage);
! 2930: }
! 2931:
! 2932: stepsize=(int) (stepm+YEARM-1)/YEARM;
! 2933: if (stepm<=12) stepsize=1;
! 2934:
! 2935: agelim=AGESUP;
! 2936:
! 2937: hstepm=1;
! 2938: hstepm=hstepm/stepm;
! 2939:
! 2940: if (popforecast==1) {
! 2941: if((ficpop=fopen(popfile,"r"))==NULL) {
! 2942: printf("Problem with population file : %s\n",popfile);exit(0);
! 2943: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
! 2944: }
! 2945: popage=ivector(0,AGESUP);
! 2946: popeffectif=vector(0,AGESUP);
! 2947: popcount=vector(0,AGESUP);
! 2948:
! 2949: i=1;
! 2950: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
! 2951:
! 2952: imx=i;
! 2953: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
! 2954: }
! 2955:
! 2956: for(cptcov=1;cptcov<=i2;cptcov++){
! 2957: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
! 2958: k=k+1;
! 2959: fprintf(ficrespop,"\n#******");
! 2960: for(j=1;j<=cptcoveff;j++) {
! 2961: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 2962: }
! 2963: fprintf(ficrespop,"******\n");
! 2964: fprintf(ficrespop,"# Age");
! 2965: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
! 2966: if (popforecast==1) fprintf(ficrespop," [Population]");
! 2967:
! 2968: for (cpt=0; cpt<=0;cpt++) {
! 2969: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
! 2970:
! 2971: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
! 2972: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
! 2973: nhstepm = nhstepm/hstepm;
! 2974:
! 2975: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 2976: oldm=oldms;savm=savms;
! 2977: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
! 2978:
! 2979: for (h=0; h<=nhstepm; h++){
! 2980: if (h==(int) (calagedate+YEARM*cpt)) {
! 2981: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
! 2982: }
! 2983: for(j=1; j<=nlstate+ndeath;j++) {
! 2984: kk1=0.;kk2=0;
! 2985: for(i=1; i<=nlstate;i++) {
! 2986: if (mobilav==1)
! 2987: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
! 2988: else {
! 2989: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
! 2990: }
! 2991: }
! 2992: if (h==(int)(calagedate+12*cpt)){
! 2993: tabpop[(int)(agedeb)][j][cptcod]=kk1;
! 2994: /*fprintf(ficrespop," %.3f", kk1);
! 2995: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
! 2996: }
! 2997: }
! 2998: for(i=1; i<=nlstate;i++){
! 2999: kk1=0.;
! 3000: for(j=1; j<=nlstate;j++){
! 3001: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
! 3002: }
! 3003: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
! 3004: }
! 3005:
! 3006: if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)
! 3007: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
! 3008: }
! 3009: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 3010: }
! 3011: }
! 3012:
! 3013: /******/
! 3014:
! 3015: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
! 3016: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
! 3017: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
! 3018: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
! 3019: nhstepm = nhstepm/hstepm;
! 3020:
! 3021: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 3022: oldm=oldms;savm=savms;
! 3023: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
! 3024: for (h=0; h<=nhstepm; h++){
! 3025: if (h==(int) (calagedate+YEARM*cpt)) {
! 3026: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
! 3027: }
! 3028: for(j=1; j<=nlstate+ndeath;j++) {
! 3029: kk1=0.;kk2=0;
! 3030: for(i=1; i<=nlstate;i++) {
! 3031: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
! 3032: }
! 3033: if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);
! 3034: }
! 3035: }
! 3036: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 3037: }
! 3038: }
! 3039: }
! 3040: }
! 3041:
! 3042: if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 3043:
! 3044: if (popforecast==1) {
! 3045: free_ivector(popage,0,AGESUP);
! 3046: free_vector(popeffectif,0,AGESUP);
! 3047: free_vector(popcount,0,AGESUP);
! 3048: }
! 3049: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 3050: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 3051: fclose(ficrespop);
! 3052: }
! 3053:
! 3054: /***********************************************/
! 3055: /**************** Main Program *****************/
! 3056: /***********************************************/
! 3057:
! 3058: int main(int argc, char *argv[])
! 3059: {
! 3060:
! 3061: int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
! 3062: double agedeb, agefin,hf;
! 3063: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
! 3064:
! 3065: double fret;
! 3066: double **xi,tmp,delta;
! 3067:
! 3068: double dum; /* Dummy variable */
! 3069: double ***p3mat;
! 3070: double ***mobaverage;
! 3071: int *indx;
! 3072: char line[MAXLINE], linepar[MAXLINE];
! 3073: char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
! 3074: int firstobs=1, lastobs=10;
! 3075: int sdeb, sfin; /* Status at beginning and end */
! 3076: int c, h , cpt,l;
! 3077: int ju,jl, mi;
! 3078: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
! 3079: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
! 3080: int mobilav=0,popforecast=0;
! 3081: int hstepm, nhstepm;
! 3082: double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
! 3083:
! 3084: double bage, fage, age, agelim, agebase;
! 3085: double ftolpl=FTOL;
! 3086: double **prlim;
! 3087: double *severity;
! 3088: double ***param; /* Matrix of parameters */
! 3089: double *p;
! 3090: double **matcov; /* Matrix of covariance */
! 3091: double ***delti3; /* Scale */
! 3092: double *delti; /* Scale */
! 3093: double ***eij, ***vareij;
! 3094: double **varpl; /* Variances of prevalence limits by age */
! 3095: double *epj, vepp;
! 3096: double kk1, kk2;
! 3097: double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
! 3098:
! 3099:
! 3100: char *alph[]={"a","a","b","c","d","e"}, str[4];
! 3101:
! 3102:
! 3103: char z[1]="c", occ;
! 3104: #include <sys/time.h>
! 3105: #include <time.h>
! 3106: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
! 3107:
! 3108: /* long total_usecs;
! 3109: struct timeval start_time, end_time;
! 3110:
! 3111: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
! 3112: getcwd(pathcd, size);
! 3113:
! 3114: printf("\n%s",version);
! 3115: if(argc <=1){
! 3116: printf("\nEnter the parameter file name: ");
! 3117: scanf("%s",pathtot);
! 3118: }
! 3119: else{
! 3120: strcpy(pathtot,argv[1]);
! 3121: }
! 3122: /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
! 3123: /*cygwin_split_path(pathtot,path,optionfile);
! 3124: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
! 3125: /* cutv(path,optionfile,pathtot,'\\');*/
! 3126:
! 3127: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
! 3128: printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
! 3129: chdir(path);
! 3130: replace(pathc,path);
! 3131:
! 3132: /*-------- arguments in the command line --------*/
! 3133:
! 3134: /* Log file */
! 3135: strcat(filelog, optionfilefiname);
! 3136: strcat(filelog,".log"); /* */
! 3137: if((ficlog=fopen(filelog,"w"))==NULL) {
! 3138: printf("Problem with logfile %s\n",filelog);
! 3139: goto end;
! 3140: }
! 3141: fprintf(ficlog,"Log filename:%s\n",filelog);
! 3142: fprintf(ficlog,"\n%s",version);
! 3143: fprintf(ficlog,"\nEnter the parameter file name: ");
! 3144: fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
! 3145: fflush(ficlog);
! 3146:
! 3147: /* */
! 3148: strcpy(fileres,"r");
! 3149: strcat(fileres, optionfilefiname);
! 3150: strcat(fileres,".txt"); /* Other files have txt extension */
! 3151:
! 3152: /*---------arguments file --------*/
! 3153:
! 3154: if((ficpar=fopen(optionfile,"r"))==NULL) {
! 3155: printf("Problem with optionfile %s\n",optionfile);
! 3156: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
! 3157: goto end;
! 3158: }
! 3159:
! 3160: strcpy(filereso,"o");
! 3161: strcat(filereso,fileres);
! 3162: if((ficparo=fopen(filereso,"w"))==NULL) {
! 3163: printf("Problem with Output resultfile: %s\n", filereso);
! 3164: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
! 3165: goto end;
! 3166: }
! 3167:
! 3168: /* Reads comments: lines beginning with '#' */
! 3169: while((c=getc(ficpar))=='#' && c!= EOF){
! 3170: ungetc(c,ficpar);
! 3171: fgets(line, MAXLINE, ficpar);
! 3172: puts(line);
! 3173: fputs(line,ficparo);
! 3174: }
! 3175: ungetc(c,ficpar);
! 3176:
! 3177: 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);
! 3178: 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);
! 3179: 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);
! 3180: while((c=getc(ficpar))=='#' && c!= EOF){
! 3181: ungetc(c,ficpar);
! 3182: fgets(line, MAXLINE, ficpar);
! 3183: puts(line);
! 3184: fputs(line,ficparo);
! 3185: }
! 3186: ungetc(c,ficpar);
! 3187:
! 3188:
! 3189: covar=matrix(0,NCOVMAX,1,n);
! 3190: cptcovn=0;
! 3191: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
! 3192:
! 3193: ncovmodel=2+cptcovn;
! 3194: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
! 3195:
! 3196: /* Read guess parameters */
! 3197: /* Reads comments: lines beginning with '#' */
! 3198: while((c=getc(ficpar))=='#' && c!= EOF){
! 3199: ungetc(c,ficpar);
! 3200: fgets(line, MAXLINE, ficpar);
! 3201: puts(line);
! 3202: fputs(line,ficparo);
! 3203: }
! 3204: ungetc(c,ficpar);
! 3205:
! 3206: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
! 3207: for(i=1; i <=nlstate; i++)
! 3208: for(j=1; j <=nlstate+ndeath-1; j++){
! 3209: fscanf(ficpar,"%1d%1d",&i1,&j1);
! 3210: fprintf(ficparo,"%1d%1d",i1,j1);
! 3211: if(mle==1)
! 3212: printf("%1d%1d",i,j);
! 3213: fprintf(ficlog,"%1d%1d",i,j);
! 3214: for(k=1; k<=ncovmodel;k++){
! 3215: fscanf(ficpar," %lf",¶m[i][j][k]);
! 3216: if(mle==1){
! 3217: printf(" %lf",param[i][j][k]);
! 3218: fprintf(ficlog," %lf",param[i][j][k]);
! 3219: }
! 3220: else
! 3221: fprintf(ficlog," %lf",param[i][j][k]);
! 3222: fprintf(ficparo," %lf",param[i][j][k]);
! 3223: }
! 3224: fscanf(ficpar,"\n");
! 3225: if(mle==1)
! 3226: printf("\n");
! 3227: fprintf(ficlog,"\n");
! 3228: fprintf(ficparo,"\n");
! 3229: }
! 3230:
! 3231: npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
! 3232:
! 3233: p=param[1][1];
! 3234:
! 3235: /* Reads comments: lines beginning with '#' */
! 3236: while((c=getc(ficpar))=='#' && c!= EOF){
! 3237: ungetc(c,ficpar);
! 3238: fgets(line, MAXLINE, ficpar);
! 3239: puts(line);
! 3240: fputs(line,ficparo);
! 3241: }
! 3242: ungetc(c,ficpar);
! 3243:
! 3244: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
! 3245: delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
! 3246: for(i=1; i <=nlstate; i++){
! 3247: for(j=1; j <=nlstate+ndeath-1; j++){
! 3248: fscanf(ficpar,"%1d%1d",&i1,&j1);
! 3249: printf("%1d%1d",i,j);
! 3250: fprintf(ficparo,"%1d%1d",i1,j1);
! 3251: for(k=1; k<=ncovmodel;k++){
! 3252: fscanf(ficpar,"%le",&delti3[i][j][k]);
! 3253: printf(" %le",delti3[i][j][k]);
! 3254: fprintf(ficparo," %le",delti3[i][j][k]);
! 3255: }
! 3256: fscanf(ficpar,"\n");
! 3257: printf("\n");
! 3258: fprintf(ficparo,"\n");
! 3259: }
! 3260: }
! 3261: delti=delti3[1][1];
! 3262:
! 3263: /* Reads comments: lines beginning with '#' */
! 3264: while((c=getc(ficpar))=='#' && c!= EOF){
! 3265: ungetc(c,ficpar);
! 3266: fgets(line, MAXLINE, ficpar);
! 3267: puts(line);
! 3268: fputs(line,ficparo);
! 3269: }
! 3270: ungetc(c,ficpar);
! 3271:
! 3272: matcov=matrix(1,npar,1,npar);
! 3273: for(i=1; i <=npar; i++){
! 3274: fscanf(ficpar,"%s",&str);
! 3275: if(mle==1)
! 3276: printf("%s",str);
! 3277: fprintf(ficlog,"%s",str);
! 3278: fprintf(ficparo,"%s",str);
! 3279: for(j=1; j <=i; j++){
! 3280: fscanf(ficpar," %le",&matcov[i][j]);
! 3281: if(mle==1){
! 3282: printf(" %.5le",matcov[i][j]);
! 3283: fprintf(ficlog," %.5le",matcov[i][j]);
! 3284: }
! 3285: else
! 3286: fprintf(ficlog," %.5le",matcov[i][j]);
! 3287: fprintf(ficparo," %.5le",matcov[i][j]);
! 3288: }
! 3289: fscanf(ficpar,"\n");
! 3290: if(mle==1)
! 3291: printf("\n");
! 3292: fprintf(ficlog,"\n");
! 3293: fprintf(ficparo,"\n");
! 3294: }
! 3295: for(i=1; i <=npar; i++)
! 3296: for(j=i+1;j<=npar;j++)
! 3297: matcov[i][j]=matcov[j][i];
! 3298:
! 3299: if(mle==1)
! 3300: printf("\n");
! 3301: fprintf(ficlog,"\n");
! 3302:
! 3303:
! 3304: /*-------- Rewriting paramater file ----------*/
! 3305: strcpy(rfileres,"r"); /* "Rparameterfile */
! 3306: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
! 3307: strcat(rfileres,"."); /* */
! 3308: strcat(rfileres,optionfilext); /* Other files have txt extension */
! 3309: if((ficres =fopen(rfileres,"w"))==NULL) {
! 3310: printf("Problem writing new parameter file: %s\n", fileres);goto end;
! 3311: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
! 3312: }
! 3313: fprintf(ficres,"#%s\n",version);
! 3314:
! 3315: /*-------- data file ----------*/
! 3316: if((fic=fopen(datafile,"r"))==NULL) {
! 3317: printf("Problem with datafile: %s\n", datafile);goto end;
! 3318: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
! 3319: }
! 3320:
! 3321: n= lastobs;
! 3322: severity = vector(1,maxwav);
! 3323: outcome=imatrix(1,maxwav+1,1,n);
! 3324: num=ivector(1,n);
! 3325: moisnais=vector(1,n);
! 3326: annais=vector(1,n);
! 3327: moisdc=vector(1,n);
! 3328: andc=vector(1,n);
! 3329: agedc=vector(1,n);
! 3330: cod=ivector(1,n);
! 3331: weight=vector(1,n);
! 3332: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
! 3333: mint=matrix(1,maxwav,1,n);
! 3334: anint=matrix(1,maxwav,1,n);
! 3335: s=imatrix(1,maxwav+1,1,n);
! 3336: adl=imatrix(1,maxwav+1,1,n);
! 3337: tab=ivector(1,NCOVMAX);
! 3338: ncodemax=ivector(1,8);
! 3339:
! 3340: i=1;
! 3341: while (fgets(line, MAXLINE, fic) != NULL) {
! 3342: if ((i >= firstobs) && (i <=lastobs)) {
! 3343:
! 3344: for (j=maxwav;j>=1;j--){
! 3345: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
! 3346: strcpy(line,stra);
! 3347: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
! 3348: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
! 3349: }
! 3350:
! 3351: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
! 3352: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
! 3353:
! 3354: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
! 3355: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
! 3356:
! 3357: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
! 3358: for (j=ncovcol;j>=1;j--){
! 3359: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
! 3360: }
! 3361: num[i]=atol(stra);
! 3362:
! 3363: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
! 3364: 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;}*/
! 3365:
! 3366: i=i+1;
! 3367: }
! 3368: }
! 3369: /* printf("ii=%d", ij);
! 3370: scanf("%d",i);*/
! 3371: imx=i-1; /* Number of individuals */
! 3372:
! 3373: /* for (i=1; i<=imx; i++){
! 3374: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
! 3375: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
! 3376: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
! 3377: }*/
! 3378: /* for (i=1; i<=imx; i++){
! 3379: if (s[4][i]==9) s[4][i]=-1;
! 3380: 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]));}*/
! 3381:
! 3382:
! 3383: /* Calculation of the number of parameter from char model*/
! 3384: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
! 3385: Tprod=ivector(1,15);
! 3386: Tvaraff=ivector(1,15);
! 3387: Tvard=imatrix(1,15,1,2);
! 3388: Tage=ivector(1,15);
! 3389:
! 3390: if (strlen(model) >1){
! 3391: j=0, j1=0, k1=1, k2=1;
! 3392: j=nbocc(model,'+');
! 3393: j1=nbocc(model,'*');
! 3394: cptcovn=j+1;
! 3395: cptcovprod=j1;
! 3396:
! 3397: strcpy(modelsav,model);
! 3398: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
! 3399: printf("Error. Non available option model=%s ",model);
! 3400: fprintf(ficlog,"Error. Non available option model=%s ",model);
! 3401: goto end;
! 3402: }
! 3403:
! 3404: for(i=(j+1); i>=1;i--){
! 3405: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
! 3406: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */
! 3407: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
! 3408: /*scanf("%d",i);*/
! 3409: if (strchr(strb,'*')) { /* Model includes a product */
! 3410: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
! 3411: if (strcmp(strc,"age")==0) { /* Vn*age */
! 3412: cptcovprod--;
! 3413: cutv(strb,stre,strd,'V');
! 3414: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
! 3415: cptcovage++;
! 3416: Tage[cptcovage]=i;
! 3417: /*printf("stre=%s ", stre);*/
! 3418: }
! 3419: else if (strcmp(strd,"age")==0) { /* or age*Vn */
! 3420: cptcovprod--;
! 3421: cutv(strb,stre,strc,'V');
! 3422: Tvar[i]=atoi(stre);
! 3423: cptcovage++;
! 3424: Tage[cptcovage]=i;
! 3425: }
! 3426: else { /* Age is not in the model */
! 3427: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
! 3428: Tvar[i]=ncovcol+k1;
! 3429: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
! 3430: Tprod[k1]=i;
! 3431: Tvard[k1][1]=atoi(strc); /* m*/
! 3432: Tvard[k1][2]=atoi(stre); /* n */
! 3433: Tvar[cptcovn+k2]=Tvard[k1][1];
! 3434: Tvar[cptcovn+k2+1]=Tvard[k1][2];
! 3435: for (k=1; k<=lastobs;k++)
! 3436: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
! 3437: k1++;
! 3438: k2=k2+2;
! 3439: }
! 3440: }
! 3441: else { /* no more sum */
! 3442: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
! 3443: /* scanf("%d",i);*/
! 3444: cutv(strd,strc,strb,'V');
! 3445: Tvar[i]=atoi(strc);
! 3446: }
! 3447: strcpy(modelsav,stra);
! 3448: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
! 3449: scanf("%d",i);*/
! 3450: } /* end of loop + */
! 3451: } /* end model */
! 3452:
! 3453: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
! 3454: printf("cptcovprod=%d ", cptcovprod);
! 3455: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
! 3456: scanf("%d ",i);*/
! 3457: fclose(fic);
! 3458:
! 3459: /* if(mle==1){*/
! 3460: if (weightopt != 1) { /* Maximisation without weights*/
! 3461: for(i=1;i<=n;i++) weight[i]=1.0;
! 3462: }
! 3463: /*-calculation of age at interview from date of interview and age at death -*/
! 3464: agev=matrix(1,maxwav,1,imx);
! 3465:
! 3466: for (i=1; i<=imx; i++) {
! 3467: for(m=2; (m<= maxwav); m++) {
! 3468: if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
! 3469: anint[m][i]=9999;
! 3470: s[m][i]=-1;
! 3471: }
! 3472: if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
! 3473: }
! 3474: }
! 3475:
! 3476: for (i=1; i<=imx; i++) {
! 3477: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
! 3478: for(m=1; (m<= maxwav); m++){
! 3479: if(s[m][i] >0){
! 3480: if (s[m][i] >= nlstate+1) {
! 3481: if(agedc[i]>0)
! 3482: if(moisdc[i]!=99 && andc[i]!=9999)
! 3483: agev[m][i]=agedc[i];
! 3484: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
! 3485: else {
! 3486: if (andc[i]!=9999){
! 3487: printf("Warning negative age at death: %d line:%d\n",num[i],i);
! 3488: fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
! 3489: agev[m][i]=-1;
! 3490: }
! 3491: }
! 3492: }
! 3493: else if(s[m][i] !=9){ /* Should no more exist */
! 3494: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
! 3495: if(mint[m][i]==99 || anint[m][i]==9999)
! 3496: agev[m][i]=1;
! 3497: else if(agev[m][i] <agemin){
! 3498: agemin=agev[m][i];
! 3499: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
! 3500: }
! 3501: else if(agev[m][i] >agemax){
! 3502: agemax=agev[m][i];
! 3503: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
! 3504: }
! 3505: /*agev[m][i]=anint[m][i]-annais[i];*/
! 3506: /* agev[m][i] = age[i]+2*m;*/
! 3507: }
! 3508: else { /* =9 */
! 3509: agev[m][i]=1;
! 3510: s[m][i]=-1;
! 3511: }
! 3512: }
! 3513: else /*= 0 Unknown */
! 3514: agev[m][i]=1;
! 3515: }
! 3516:
! 3517: }
! 3518: for (i=1; i<=imx; i++) {
! 3519: for(m=1; (m<= maxwav); m++){
! 3520: if (s[m][i] > (nlstate+ndeath)) {
! 3521: 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);
! 3522: 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);
! 3523: goto end;
! 3524: }
! 3525: }
! 3526: }
! 3527:
! 3528: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
! 3529: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
! 3530:
! 3531: free_vector(severity,1,maxwav);
! 3532: free_imatrix(outcome,1,maxwav+1,1,n);
! 3533: free_vector(moisnais,1,n);
! 3534: free_vector(annais,1,n);
! 3535: /* free_matrix(mint,1,maxwav,1,n);
! 3536: free_matrix(anint,1,maxwav,1,n);*/
! 3537: free_vector(moisdc,1,n);
! 3538: free_vector(andc,1,n);
! 3539:
! 3540:
! 3541: wav=ivector(1,imx);
! 3542: dh=imatrix(1,lastpass-firstpass+1,1,imx);
! 3543: mw=imatrix(1,lastpass-firstpass+1,1,imx);
! 3544:
! 3545: /* Concatenates waves */
! 3546: concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
! 3547:
! 3548:
! 3549: Tcode=ivector(1,100);
! 3550: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
! 3551: ncodemax[1]=1;
! 3552: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
! 3553:
! 3554: codtab=imatrix(1,100,1,10);
! 3555: h=0;
! 3556: m=pow(2,cptcoveff);
! 3557:
! 3558: for(k=1;k<=cptcoveff; k++){
! 3559: for(i=1; i <=(m/pow(2,k));i++){
! 3560: for(j=1; j <= ncodemax[k]; j++){
! 3561: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
! 3562: h++;
! 3563: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
! 3564: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
! 3565: }
! 3566: }
! 3567: }
! 3568: }
! 3569: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
! 3570: codtab[1][2]=1;codtab[2][2]=2; */
! 3571: /* for(i=1; i <=m ;i++){
! 3572: for(k=1; k <=cptcovn; k++){
! 3573: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
! 3574: }
! 3575: printf("\n");
! 3576: }
! 3577: scanf("%d",i);*/
! 3578:
! 3579: /* Calculates basic frequencies. Computes observed prevalence at single age
! 3580: and prints on file fileres'p'. */
! 3581:
! 3582:
! 3583:
! 3584: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
! 3585: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
! 3586: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
! 3587: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
! 3588: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
! 3589:
! 3590: /* For Powell, parameters are in a vector p[] starting at p[1]
! 3591: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
! 3592: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
! 3593:
! 3594: if(mle==1){
! 3595: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
! 3596: }
! 3597:
! 3598: /*--------- results files --------------*/
! 3599: 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);
! 3600:
! 3601:
! 3602: jk=1;
! 3603: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
! 3604: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
! 3605: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
! 3606: for(i=1,jk=1; i <=nlstate; i++){
! 3607: for(k=1; k <=(nlstate+ndeath); k++){
! 3608: if (k != i)
! 3609: {
! 3610: printf("%d%d ",i,k);
! 3611: fprintf(ficlog,"%d%d ",i,k);
! 3612: fprintf(ficres,"%1d%1d ",i,k);
! 3613: for(j=1; j <=ncovmodel; j++){
! 3614: printf("%f ",p[jk]);
! 3615: fprintf(ficlog,"%f ",p[jk]);
! 3616: fprintf(ficres,"%f ",p[jk]);
! 3617: jk++;
! 3618: }
! 3619: printf("\n");
! 3620: fprintf(ficlog,"\n");
! 3621: fprintf(ficres,"\n");
! 3622: }
! 3623: }
! 3624: }
! 3625: if(mle==1){
! 3626: /* Computing hessian and covariance matrix */
! 3627: ftolhess=ftol; /* Usually correct */
! 3628: hesscov(matcov, p, npar, delti, ftolhess, func);
! 3629: }
! 3630: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
! 3631: printf("# Scales (for hessian or gradient estimation)\n");
! 3632: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
! 3633: for(i=1,jk=1; i <=nlstate; i++){
! 3634: for(j=1; j <=nlstate+ndeath; j++){
! 3635: if (j!=i) {
! 3636: fprintf(ficres,"%1d%1d",i,j);
! 3637: printf("%1d%1d",i,j);
! 3638: fprintf(ficlog,"%1d%1d",i,j);
! 3639: for(k=1; k<=ncovmodel;k++){
! 3640: printf(" %.5e",delti[jk]);
! 3641: fprintf(ficlog," %.5e",delti[jk]);
! 3642: fprintf(ficres," %.5e",delti[jk]);
! 3643: jk++;
! 3644: }
! 3645: printf("\n");
! 3646: fprintf(ficlog,"\n");
! 3647: fprintf(ficres,"\n");
! 3648: }
! 3649: }
! 3650: }
! 3651:
! 3652: k=1;
! 3653: 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");
! 3654: if(mle==1)
! 3655: 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");
! 3656: 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");
! 3657: for(i=1;i<=npar;i++){
! 3658: /* if (k>nlstate) k=1;
! 3659: i1=(i-1)/(ncovmodel*nlstate)+1;
! 3660: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
! 3661: printf("%s%d%d",alph[k],i1,tab[i]);*/
! 3662: fprintf(ficres,"%3d",i);
! 3663: if(mle==1)
! 3664: printf("%3d",i);
! 3665: fprintf(ficlog,"%3d",i);
! 3666: for(j=1; j<=i;j++){
! 3667: fprintf(ficres," %.5e",matcov[i][j]);
! 3668: if(mle==1)
! 3669: printf(" %.5e",matcov[i][j]);
! 3670: fprintf(ficlog," %.5e",matcov[i][j]);
! 3671: }
! 3672: fprintf(ficres,"\n");
! 3673: if(mle==1)
! 3674: printf("\n");
! 3675: fprintf(ficlog,"\n");
! 3676: k++;
! 3677: }
! 3678:
! 3679: while((c=getc(ficpar))=='#' && c!= EOF){
! 3680: ungetc(c,ficpar);
! 3681: fgets(line, MAXLINE, ficpar);
! 3682: puts(line);
! 3683: fputs(line,ficparo);
! 3684: }
! 3685: ungetc(c,ficpar);
! 3686: estepm=0;
! 3687: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
! 3688: if (estepm==0 || estepm < stepm) estepm=stepm;
! 3689: if (fage <= 2) {
! 3690: bage = ageminpar;
! 3691: fage = agemaxpar;
! 3692: }
! 3693:
! 3694: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
! 3695: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
! 3696: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
! 3697:
! 3698: while((c=getc(ficpar))=='#' && c!= EOF){
! 3699: ungetc(c,ficpar);
! 3700: fgets(line, MAXLINE, ficpar);
! 3701: puts(line);
! 3702: fputs(line,ficparo);
! 3703: }
! 3704: ungetc(c,ficpar);
! 3705:
! 3706: 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);
! 3707: 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);
! 3708: 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);
! 3709:
! 3710: while((c=getc(ficpar))=='#' && c!= EOF){
! 3711: ungetc(c,ficpar);
! 3712: fgets(line, MAXLINE, ficpar);
! 3713: puts(line);
! 3714: fputs(line,ficparo);
! 3715: }
! 3716: ungetc(c,ficpar);
! 3717:
! 3718:
! 3719: dateprev1=anprev1+mprev1/12.+jprev1/365.;
! 3720: dateprev2=anprev2+mprev2/12.+jprev2/365.;
! 3721:
! 3722: fscanf(ficpar,"pop_based=%d\n",&popbased);
! 3723: fprintf(ficparo,"pop_based=%d\n",popbased);
! 3724: fprintf(ficres,"pop_based=%d\n",popbased);
! 3725:
! 3726: while((c=getc(ficpar))=='#' && c!= EOF){
! 3727: ungetc(c,ficpar);
! 3728: fgets(line, MAXLINE, ficpar);
! 3729: puts(line);
! 3730: fputs(line,ficparo);
! 3731: }
! 3732: ungetc(c,ficpar);
! 3733:
! 3734: fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
! 3735: fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
! 3736: fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
! 3737:
! 3738:
! 3739: while((c=getc(ficpar))=='#' && c!= EOF){
! 3740: ungetc(c,ficpar);
! 3741: fgets(line, MAXLINE, ficpar);
! 3742: puts(line);
! 3743: fputs(line,ficparo);
! 3744: }
! 3745: ungetc(c,ficpar);
! 3746:
! 3747: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
! 3748: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
! 3749: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
! 3750:
! 3751: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
! 3752: /*------------ gnuplot -------------*/
! 3753: strcpy(optionfilegnuplot,optionfilefiname);
! 3754: strcat(optionfilegnuplot,".gp");
! 3755: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
! 3756: printf("Problem with file %s",optionfilegnuplot);
! 3757: }
! 3758: fclose(ficgp);
! 3759: printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
! 3760: /*--------- index.htm --------*/
! 3761:
! 3762: strcpy(optionfilehtm,optionfile);
! 3763: strcat(optionfilehtm,".htm");
! 3764: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
! 3765: printf("Problem with %s \n",optionfilehtm), exit(0);
! 3766: }
! 3767:
! 3768: fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
! 3769: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
! 3770: \n
! 3771: Total number of observations=%d <br>\n
! 3772: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
! 3773: <hr size=\"2\" color=\"#EC5E5E\">
! 3774: <ul><li><h4>Parameter files</h4>\n
! 3775: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
! 3776: - Log file of the run: <a href=\"%s\">%s</a><br>\n
! 3777: - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
! 3778: fclose(fichtm);
! 3779:
! 3780: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
! 3781:
! 3782: /*------------ free_vector -------------*/
! 3783: chdir(path);
! 3784:
! 3785: free_ivector(wav,1,imx);
! 3786: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
! 3787: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
! 3788: free_ivector(num,1,n);
! 3789: free_vector(agedc,1,n);
! 3790: /*free_matrix(covar,1,NCOVMAX,1,n);*/
! 3791: fclose(ficparo);
! 3792: fclose(ficres);
! 3793:
! 3794:
! 3795: /*--------------- Prevalence limit --------------*/
! 3796:
! 3797: strcpy(filerespl,"pl");
! 3798: strcat(filerespl,fileres);
! 3799: if((ficrespl=fopen(filerespl,"w"))==NULL) {
! 3800: printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
! 3801: fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;
! 3802: }
! 3803: printf("Computing prevalence limit: result on file '%s' \n", filerespl);
! 3804: fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);
! 3805: fprintf(ficrespl,"#Prevalence limit\n");
! 3806: fprintf(ficrespl,"#Age ");
! 3807: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
! 3808: fprintf(ficrespl,"\n");
! 3809:
! 3810: prlim=matrix(1,nlstate,1,nlstate);
! 3811: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
! 3812: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
! 3813: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
! 3814: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
! 3815: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
! 3816: k=0;
! 3817: agebase=ageminpar;
! 3818: agelim=agemaxpar;
! 3819: ftolpl=1.e-10;
! 3820: i1=cptcoveff;
! 3821: if (cptcovn < 1){i1=1;}
! 3822:
! 3823: for(cptcov=1;cptcov<=i1;cptcov++){
! 3824: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
! 3825: k=k+1;
! 3826: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
! 3827: fprintf(ficrespl,"\n#******");
! 3828: printf("\n#******");
! 3829: fprintf(ficlog,"\n#******");
! 3830: for(j=1;j<=cptcoveff;j++) {
! 3831: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 3832: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 3833: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 3834: }
! 3835: fprintf(ficrespl,"******\n");
! 3836: printf("******\n");
! 3837: fprintf(ficlog,"******\n");
! 3838:
! 3839: for (age=agebase; age<=agelim; age++){
! 3840: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
! 3841: fprintf(ficrespl,"%.0f",age );
! 3842: for(i=1; i<=nlstate;i++)
! 3843: fprintf(ficrespl," %.5f", prlim[i][i]);
! 3844: fprintf(ficrespl,"\n");
! 3845: }
! 3846: }
! 3847: }
! 3848: fclose(ficrespl);
! 3849:
! 3850: /*------------- h Pij x at various ages ------------*/
! 3851:
! 3852: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
! 3853: if((ficrespij=fopen(filerespij,"w"))==NULL) {
! 3854: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
! 3855: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
! 3856: }
! 3857: printf("Computing pij: result on file '%s' \n", filerespij);
! 3858: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
! 3859:
! 3860: stepsize=(int) (stepm+YEARM-1)/YEARM;
! 3861: /*if (stepm<=24) stepsize=2;*/
! 3862:
! 3863: agelim=AGESUP;
! 3864: hstepm=stepsize*YEARM; /* Every year of age */
! 3865: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
! 3866:
! 3867: /* hstepm=1; aff par mois*/
! 3868:
! 3869: k=0;
! 3870: for(cptcov=1;cptcov<=i1;cptcov++){
! 3871: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
! 3872: k=k+1;
! 3873: fprintf(ficrespij,"\n#****** ");
! 3874: for(j=1;j<=cptcoveff;j++)
! 3875: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 3876: fprintf(ficrespij,"******\n");
! 3877:
! 3878: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
! 3879: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
! 3880: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
! 3881:
! 3882: /* nhstepm=nhstepm*YEARM; aff par mois*/
! 3883:
! 3884: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 3885: oldm=oldms;savm=savms;
! 3886: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
! 3887: fprintf(ficrespij,"# Age");
! 3888: for(i=1; i<=nlstate;i++)
! 3889: for(j=1; j<=nlstate+ndeath;j++)
! 3890: fprintf(ficrespij," %1d-%1d",i,j);
! 3891: fprintf(ficrespij,"\n");
! 3892: for (h=0; h<=nhstepm; h++){
! 3893: fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
! 3894: for(i=1; i<=nlstate;i++)
! 3895: for(j=1; j<=nlstate+ndeath;j++)
! 3896: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
! 3897: fprintf(ficrespij,"\n");
! 3898: }
! 3899: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 3900: fprintf(ficrespij,"\n");
! 3901: }
! 3902: }
! 3903: }
! 3904:
! 3905: varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
! 3906:
! 3907: fclose(ficrespij);
! 3908:
! 3909:
! 3910: /*---------- Forecasting ------------------*/
! 3911: if((stepm == 1) && (strcmp(model,".")==0)){
! 3912: prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
! 3913: if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
! 3914: }
! 3915: else{
! 3916: erreur=108;
! 3917: 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);
! 3918: 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);
! 3919: }
! 3920:
! 3921:
! 3922: /*---------- Health expectancies and variances ------------*/
! 3923:
! 3924: strcpy(filerest,"t");
! 3925: strcat(filerest,fileres);
! 3926: if((ficrest=fopen(filerest,"w"))==NULL) {
! 3927: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
! 3928: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
! 3929: }
! 3930: printf("Computing Total LEs with variances: file '%s' \n", filerest);
! 3931: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
! 3932:
! 3933:
! 3934: strcpy(filerese,"e");
! 3935: strcat(filerese,fileres);
! 3936: if((ficreseij=fopen(filerese,"w"))==NULL) {
! 3937: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
! 3938: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
! 3939: }
! 3940: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
! 3941: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
! 3942:
! 3943: strcpy(fileresv,"v");
! 3944: strcat(fileresv,fileres);
! 3945: if((ficresvij=fopen(fileresv,"w"))==NULL) {
! 3946: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
! 3947: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
! 3948: }
! 3949: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
! 3950: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
! 3951: calagedate=-1;
! 3952: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
! 3953: if (mobilav==1) {
! 3954: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 3955: movingaverage(probs, ageminpar, fage, mobaverage);
! 3956: }
! 3957:
! 3958: k=0;
! 3959: for(cptcov=1;cptcov<=i1;cptcov++){
! 3960: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
! 3961: k=k+1;
! 3962: fprintf(ficrest,"\n#****** ");
! 3963: for(j=1;j<=cptcoveff;j++)
! 3964: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 3965: fprintf(ficrest,"******\n");
! 3966:
! 3967: fprintf(ficreseij,"\n#****** ");
! 3968: for(j=1;j<=cptcoveff;j++)
! 3969: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 3970: fprintf(ficreseij,"******\n");
! 3971:
! 3972: fprintf(ficresvij,"\n#****** ");
! 3973: for(j=1;j<=cptcoveff;j++)
! 3974: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 3975: fprintf(ficresvij,"******\n");
! 3976:
! 3977: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
! 3978: oldm=oldms;savm=savms;
! 3979: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
! 3980:
! 3981: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
! 3982: oldm=oldms;savm=savms;
! 3983: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
! 3984: if(popbased==1){
! 3985: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
! 3986: }
! 3987:
! 3988:
! 3989: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
! 3990: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
! 3991: fprintf(ficrest,"\n");
! 3992:
! 3993: epj=vector(1,nlstate+1);
! 3994: for(age=bage; age <=fage ;age++){
! 3995: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
! 3996: if (popbased==1) {
! 3997: if(mobilav !=1){
! 3998: for(i=1; i<=nlstate;i++)
! 3999: prlim[i][i]=probs[(int)age][i][k];
! 4000: }else{ /* mobilav=1 */
! 4001: for(i=1; i<=nlstate;i++)
! 4002: prlim[i][i]=mobaverage[(int)age][i][k];
! 4003: }
! 4004: }
! 4005:
! 4006: fprintf(ficrest," %4.0f",age);
! 4007: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
! 4008: for(i=1, epj[j]=0.;i <=nlstate;i++) {
! 4009: epj[j] += prlim[i][i]*eij[i][j][(int)age];
! 4010: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
! 4011: }
! 4012: epj[nlstate+1] +=epj[j];
! 4013: }
! 4014:
! 4015: for(i=1, vepp=0.;i <=nlstate;i++)
! 4016: for(j=1;j <=nlstate;j++)
! 4017: vepp += vareij[i][j][(int)age];
! 4018: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
! 4019: for(j=1;j <=nlstate;j++){
! 4020: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
! 4021: }
! 4022: fprintf(ficrest,"\n");
! 4023: }
! 4024: }
! 4025: }
! 4026: free_matrix(mint,1,maxwav,1,n);
! 4027: free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
! 4028: free_vector(weight,1,n);
! 4029: fclose(ficreseij);
! 4030: fclose(ficresvij);
! 4031: fclose(ficrest);
! 4032: fclose(ficpar);
! 4033: free_vector(epj,1,nlstate+1);
! 4034:
! 4035: /*------- Variance limit prevalence------*/
! 4036:
! 4037: strcpy(fileresvpl,"vpl");
! 4038: strcat(fileresvpl,fileres);
! 4039: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
! 4040: printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
! 4041: exit(0);
! 4042: }
! 4043: printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);
! 4044:
! 4045: k=0;
! 4046: for(cptcov=1;cptcov<=i1;cptcov++){
! 4047: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
! 4048: k=k+1;
! 4049: fprintf(ficresvpl,"\n#****** ");
! 4050: for(j=1;j<=cptcoveff;j++)
! 4051: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 4052: fprintf(ficresvpl,"******\n");
! 4053:
! 4054: varpl=matrix(1,nlstate,(int) bage, (int) fage);
! 4055: oldm=oldms;savm=savms;
! 4056: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
! 4057: }
! 4058: }
! 4059:
! 4060: fclose(ficresvpl);
! 4061:
! 4062: /*---------- End : free ----------------*/
! 4063: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
! 4064:
! 4065: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
! 4066: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
! 4067:
! 4068:
! 4069: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
! 4070: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
! 4071: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
! 4072: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
! 4073:
! 4074: free_matrix(matcov,1,npar,1,npar);
! 4075: free_vector(delti,1,npar);
! 4076: free_matrix(agev,1,maxwav,1,imx);
! 4077: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
! 4078: if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 4079:
! 4080: fprintf(fichtm,"\n</body>");
! 4081: fclose(fichtm);
! 4082: fclose(ficgp);
! 4083:
! 4084:
! 4085: if(erreur >0){
! 4086: printf("End of Imach with error or warning %d\n",erreur);
! 4087: fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
! 4088: }else{
! 4089: printf("End of Imach\n");
! 4090: fprintf(ficlog,"End of Imach\n");
! 4091: }
! 4092: printf("See log file on %s\n",filelog);
! 4093: fclose(ficlog);
! 4094: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
! 4095:
! 4096: /* 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);*/
! 4097: /*printf("Total time was %d uSec.\n", total_usecs);*/
! 4098: /*------ End -----------*/
! 4099:
! 4100:
! 4101: end:
! 4102: #ifdef windows
! 4103: /* chdir(pathcd);*/
! 4104: #endif
! 4105: /*system("wgnuplot graph.plt");*/
! 4106: /*system("../gp37mgw/wgnuplot graph.plt");*/
! 4107: /*system("cd ../gp37mgw");*/
! 4108: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
! 4109: strcpy(plotcmd,GNUPLOTPROGRAM);
! 4110: strcat(plotcmd," ");
! 4111: strcat(plotcmd,optionfilegnuplot);
! 4112: system(plotcmd);
! 4113:
! 4114: #ifdef windows
! 4115: while (z[0] != 'q') {
! 4116: /* chdir(path); */
! 4117: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
! 4118: scanf("%s",z);
! 4119: if (z[0] == 'c') system("./imach");
! 4120: else if (z[0] == 'e') system(optionfilehtm);
! 4121: else if (z[0] == 'g') system(plotcmd);
! 4122: else if (z[0] == 'q') exit(0);
! 4123: }
! 4124: #endif
! 4125: }
! 4126:
! 4127:
FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>
![[BACK]](/icons/small/back.gif){kind=icon}
Return to imach.c CVS log ![[TXT]](/icons/small/text.gif){kind=icon}
![[DIR]](/icons/small/dir.gif){kind=icon}
Up to [Local Repository] / imach / src