![]() ![]() | ![]() |
Moving average of observed prevalence moved
1: /* $Id: imach.c,v 1.53 2002/07/23 23:59:37 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: